My primary research area is coastal water quality, and recently I have expanded my research to include activities on sanitation more broadly. The work on coastal water quality is focused on understanding the sources, transformation, transport, and ecology of biocolloids - specifically fecal indicator organisms, pathogens, and phytoplankton, as well as sources and fate of nitrogen and phosphorus. This knowledge is crucial to directing new policies, and management and engineering practices that protect human and ecosystem health along the coastal margin. The work on sanitation aims to develop microbial risk assessment models to gain a better understanding of how pathogens are transmitted to humans through their contact with water, feces, and contaminated surfaces. Research is focused on key problems in developed and developing countries. The goal is to design and test effective interventions and technologies for reducing the burden of infectious disease.

Academic Appointments

Administrative Appointments

  • Faculty Fellow, Center for Innovation in Global Health (2015 - Present)

Honors & Awards

  • Huber Prize, ASCE (2016)
  • Participant in National Academy of Engineers' Frontiers of Engineering Symposium, National Academy of Engineers (2008)
  • CAREER Award, National Science Foundation (2007)
  • Visiting Scholar, Pacific Rim Center for Oceans and Human Health (2007)
  • Excellence in Teaching Award, UC Irvine (2001)
  • Faculty Fellow Award, UC Irvine (2000-2002)
  • Chair of West Coast Panel on Ocean Acidification and Hypoxia, States of California, Oregon, Washington, Province of British Colombia (2013-2016)

Professional Education

  • BS, California Institute of Technology, Engineering & Applied Science (1996)
  • MS, UC Irvine, Environmental Engineering (1997)
  • PhD, UC Irvine (2000)

Community and International Work

  • Pathogen contamination in household environments, Bangladesh



    Ongoing Project


    Opportunities for Student Involvement



  • Microbial Source Tracking in Developing Countries, Stanford University




    • Amy Pickering, Dr. , Stanford University
  • Coastal Water Quality - Citizen science



2018-19 Courses

Stanford Advisees

All Publications

  • Photoinactivation of uncultured, indigenous enterococci. Environmental science. Processes & impacts McClary, J. S., Ramos, N. A., Boehm, A. B. 2018


    Enterococci are used to monitor recreational water quality worldwide, so understanding their fate and transport in the environment is essential to the protection of human health. As such, researchers have documented enterococci inactivation under various exposure conditions and in diverse water matrices. However, the majority of studies have been performed using lab-cultured bacteria, which are distinct from indigenous, uncultured bacteria found in the environment. Here we investigate the photoinactivation of indigenous, uncultured enterococci from a range of sources, including wastewater treatment plants (WWTPs), marine beaches, urban streams, and a wastewater-influenced pond. We concentrated indigenous enterococci from their sources using filtration and centrifugation, placed them in a clear buffer solution, and then exposed them to simulated sunlight to measure their photoinactivation rates. First order decay rate constants (k) of indigenous, uncultured enterococci spanned an order of magnitude, from 0.3 to 2.3 m2 kJUVB-1. k values of indigenous enterococci from WWTPs tended to be larger than those from surface waters. The k value of lab-cultured Enterococcus faecalis was larger than those of indigenous, uncultured enterococci from most sources. Negative associations between the fraction of pigmented enterococci and sunlight susceptibility were observed. This work suggests that caution should be taken when extending results on bacterial photoinactivation obtained using lab-cultured bacteria to environmental bacteria, and that enterococci pigmentation may be a useful metric for estimating photoinactivation rate constants.

    View details for DOI 10.1039/c8em00443a

    View details for PubMedID 30525134

  • Role of microbial cell properties on bacterial pathogen and coliphage removal in biochar-modified stormwater biofilters ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY Afrooz, A., Pitol, A. K., Kitt, D., Boehm, A. B. 2018; 4 (12): 2160–69

    View details for DOI 10.1039/c8ew00297e

    View details for Web of Science ID 000451072500025

  • Transfer of Enteric Viruses Adenovirus and Coxsackievirus and Bacteriophage MS2 from Liquid to Human Skin APPLIED AND ENVIRONMENTAL MICROBIOLOGY Pitol, A. K., Bischel, H. N., Boehm, A. B., Kohn, T., Julian, T. R. 2018; 84 (22)


    Indirect exposure to waterborne viruses increases the risk of infection, especially among children with frequent hand-to-mouth contacts. Here, we quantified the transfer of one bacteriophage (MS2) and two enteric viruses (adenovirus and coxsackievirus) from liquid to skin. MS2, a commonly used enteric virus surrogate, was used to compare virus transfer rates in a volunteer trial to those obtained using human cadaver skin and synthetic skin. MS2 transfer to volunteer skin was similar to transfer to cadaver skin but significantly different from transfer to synthetic skin. The transfer of MS2, adenovirus, and coxsackievirus to cadaver skin was modeled using measurements for viruses attaching to the skin (adsorbed) and viruses in liquid residual on skin (unadsorbed). We find virus transfer per surface area is a function of the concentration of virus in the liquid and the film thickness of liquid retained on the skin and is estimable using a linear model. Notably, the amount of MS2 adsorbed on the skin was on average 5 times higher than the amount of adenovirus and 4 times higher than the amount of coxsackievirus. Quantification of pathogenic virus retention to skin would thus be overestimated using MS2 adsorption data. This study provides models of virus transfer useful for risk assessments of water-related activities, demonstrates significant differences in the transfer of pathogenic virus and MS2, and suggests cadaver skin as an alternative testing system for studying interactions between viruses and skin.IMPORTANCE Enteric viruses (viruses that infect the gastrointestinal tract) are responsible for most water-transmitted diseases. They are shed in high concentrations in the feces of infected individuals, persist for an extended period of time in water, and are highly infective. Exposure to contaminated water directly (through ingestion) or indirectly (for example, through hand-water contacts followed by hand-to-mouth contacts) increases the risk of virus transmission. The work described herein provides a quantitative model for estimating human-pathogenic virus retention on skin following contact with contaminated water. The work will be important in refining the contribution of indirect transmission of virus to risks associated with water-related activities.

    View details for DOI 10.1128/AEM.01809-18

    View details for Web of Science ID 000448811300015

    View details for PubMedID 30217840

  • Implementation of an automated beach water quality nowcast system at ten California oceanic beaches JOURNAL OF ENVIRONMENTAL MANAGEMENT Searcy, R. T., Taggart, M., Gold, M., Boehm, A. B. 2018; 223: 633–43


    Fecal indicator bacteria like Escherichia coli and entercococci are monitored at beaches around the world to reduce incidence of recreational waterborne illness. Measurements are usually made weekly, but FIB concentrations can exhibit extreme variability, fluctuating at shorter periods. The result is that water quality has likely changed by the time data are provided to beachgoers. Here, we present an automated water quality prediction system (called the nowcast system) that is capable of providing daily predictions of water quality for numerous beaches. We created nowcast models for 10 California beaches using weather, oceanographic, and other environmental variables as input to tuned regression models to predict if FIB concentrations were above single sample water quality standards. Rainfall was used as a variable in nearly every model. The models were calibrated and validated using historical data. Subsequently, models were implemented during the 2017 swim season in collaboration with local beach managers. During the 2017 swim season, the median sensitivity of the nowcast models was 0.5 compared to 0 for the current method of using day-to-week old measurements to make beach posting decisions. Model specificity was also high (median of 0.87). During the implementation phase, nowcast models provided an average of 140 additional days per beach of updated water quality information to managers when water quality measurements were not made. The work presented herein emphasizes that a one-size-fits all approach to nowcast modeling, even when beaches are in close proximity, is infeasible. Flexibility in modeling approaches and adaptive responses to modeling and data challenges are required when implementing nowcast models for beach management.

    View details for DOI 10.1016/j.jenvman.2018.06.058

    View details for Web of Science ID 000442057500062

    View details for PubMedID 29975890

  • Can We Swim Yet? Systematic Review, Meta-Analysis, and Risk Assessment of Aging Sewage in Surface Waters. Environmental science & technology Boehm, A. B., Graham, K. E., Jennings, W. C. 2018


    This study investigated the risk of gastrointestinal illness associated with swimming in surface waters with aged sewage contamination. First, a systematic review compiled 333 first order decay rate constants ( k) for human norovirus and its surrogates feline calicivirus and murine norovirus, Salmonella, Campylobacter, Escherichia coli O157:H7, Giardia, and Cryptosporidium, and human-associated indicators in surface water. A meta-analysis investigated effects of sunlight, temperature, and water matrix on k. There was a relatively large number of k for bacterial pathogens and some human-associated indicators ( n > 40), fewer for protozoans ( n = 14-22), and few for human norovirus and its Caliciviridae surrogates ( n = 2-4). Average k ranked: Campylobacter > human-associated markers > Salmonella> E. coli O157:H7 > norovirus and its surrogates > Giardia > Cryptosporidium. Compiled k values were used in a quantitative microbial risk assessment (QMRA) to simulate gastrointestinal illness risk associated with swimming in water with aged sewage contamination. The QMRA used human-associated fecal indicator HF183 as an index for the amount of sewage present and thereby provided insight into how risk relates to HF183 concentrations in surface water. Because exposure to norovirus contributed the majority of risk, and HF183 k is greater than norovirus k, the risk associated with exposure to a fixed HF183 concentration increases with the age of contamination. Swimmer exposure to sewage after it has aged 3 days results in median risks less than 30/1000. A risk-based water quality threshold for HF183 in surface waters that takes into account uncertainty in contamination age is derived to be 4100 copies/100 mL.

    View details for DOI 10.1021/acs.est.8b01948

    View details for PubMedID 30080397

  • Sunlight-mediated inactivation of health-relevant microorganisms in water: a review of mechanisms and modeling approaches ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS Nelson, K. L., Boehm, A. B., Davies-Colley, R. J., Dodd, M. C., Kohn, T., Linden, K. G., Liu, Y., Maraccini, P. A., McNeill, K., Mitch, W. A., Nguyen, T. H., Parker, K. M., Rodriguez, R. A., Sassoubre, L. M., Silverman, A. I., Wigginton, K. R., Zepp, R. G. 2018; 20 (8): 1089–1122


    Health-relevant microorganisms present in natural surface waters and engineered treatment systems that are exposed to sunlight can be inactivated by a complex set of interacting mechanisms. The net impact of sunlight depends on the solar spectral irradiance, the susceptibility of the specific microorganism to each mechanism, and the water quality; inactivation rates can vary by orders of magnitude depending on the organism and environmental conditions. Natural organic matter (NOM) has a large influence, as it can attenuate radiation and thus decrease inactivation by endogenous mechanisms. Simultaneously NOM sensitizes the formation of reactive intermediates that can damage microorganisms via exogenous mechanisms. To accurately predict inactivation and design engineered systems that enhance solar inactivation, it is necessary to model these processes, although some details are not yet sufficiently well understood. In this critical review, we summarize the photo-physics, -chemistry, and -biology that underpin sunlight-mediated inactivation, as well as the targets of damage and cellular responses to sunlight exposure. Viruses that are not susceptible to exogenous inactivation are only inactivated if UVB wavelengths (280-320 nm) are present, such as in very clear, open waters or in containers that are transparent to UVB. Bacteria are susceptible to slightly longer wavelengths. Some viruses and bacteria (especially Gram-positive) are susceptible to exogenous inactivation, which can be initiated by visible as well as UV wavelengths. We review approaches to model sunlight-mediated inactivation and illustrate how the environmental conditions can dramatically shift the inactivation rate of organisms. The implications of this mechanistic understanding of solar inactivation are discussed for a range of applications, including recreational water quality, natural treatment systems, solar disinfection of drinking water (SODIS), and enhanced inactivation via the use of sensitizers and photocatalysts. Finally, priorities for future research are identified that will further our understanding of the key role that sunlight disinfection plays in natural systems and the potential to enhance this process in engineered systems.

    View details for DOI 10.1039/c8em00047f

    View details for Web of Science ID 000441765000001

    View details for PubMedID 30047962

  • Sewage loading and microbial risk in urban waters of the Great Lakes ELEMENTA-SCIENCE OF THE ANTHROPOCENE McLellan, S. L., Sauer, E. P., Corsi, S. R., Bootsma, M. J., Boehm, A. B., Spencer, S. K., Borchardt, M. A. 2018; 6
  • Multiple Pathways to Bacterial Load Reduction by Stormwater Best Management Practices: Trade-Offs in Performance, Volume, and Treated Area ENVIRONMENTAL SCIENCE & TECHNOLOGY Wolfand, J. M., Bell, C. D., Boehm, A. B., Hogue, T. S., Luthy, R. G. 2018; 52 (11): 6370–79


    Stormwater best management practices (BMPs) are implemented to reduce microbial pollution in runoff, but their removal efficiencies differ. Enhanced BMPs, such as those with media amendments, can increase removal of fecal indicator bacteria (FIB) in runoff from 0.25-log10 to above 3-log10; however, their implications for watershed-scale management are poorly understood. In this work, a computational model was developed to simulate watershed-scale bacteria loading and BMP performance using the Ballona Creek Watershed (Los Angeles County, CA) as a case study. Over 1400 scenarios with varying BMP performance, percent watershed area treated, BMP treatment volume, and infiltrative capabilities were simulated. Incremental improvement of BMP performance by 0.25-log10, while keeping other scenario variables constant, reduces annual bacterial load at the outlet by a range of 0-29%. In addition, various simulated scenarios provide the same FIB load reduction; for example, 75% load reduction is achieved by diverting runoff from either 95% of the watershed area to 25 000 infiltrating BMPs with 0.5-log10 removal or 75% of the watershed area to 75 000 infiltrating BMPs with 1.5-log10 removal. Lastly, simulated infiltrating BMPs provide greater FIB reduction than noninfiltrating BMPs at the watershed scale. Results provide new insight on the trade-offs between BMP treatment volume, performance, and distribution.

    View details for DOI 10.1021/acs.est.8600408

    View details for Web of Science ID 000434892900032

    View details for PubMedID 29676892

  • Microbial community structure of sea spray aerosols at three California beaches. FEMS microbiology ecology Graham, K. E., Prussin, A. J., Marr, L. C., Sassoubre, L. M., Boehm, A. B. 2018; 94 (3)


    We characterized the microbial communities in sea spray aerosols (SSA), water and sand of three beaches in central California (Cowell Beach, Baker Beach and Lovers Point) by sequencing the V4 region of the 16S rRNA gene. Average concentrations of 16S rRNA genes in SSA ranged from 2.4 * 104 to 1.4 * 105 gene copies per m3 of air. A total of 9781 distinct OTUs were identified in SSA and of these, 1042 OTUs were found in SSA of all beaches. SSA microbial communities included marine taxa, as well as some associated with the terrestrial environment. SSA taxa included organisms that play important roles in biogeochemical cycling of elements such as Planctomyces and Synechococcus, as well as those representing potential pathogens and fecal indicator bacteria including Staphylococcus epidermidis and Enterococcus spp. There were a large number of shared OTUs among SSA and water, and there was relatively high similarity between SSA and water communities. Results are consistent with a conceptual model where SSA is generated by breaking waves and bubble bursting in marine waters and that enables the transport of microorganisms from the sea to sand or other environments.

    View details for DOI 10.1093/femsec/fiy005

    View details for PubMedID 29346534

  • Frequent detection of a human fecal indicator in the urban ocean: environmental drivers and covariation with enterococci ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS Jennings, W. C., Chern, E. C., O'Donohue, D., Kellogg, M. G., Boehm, A. B. 2018; 20 (3): 480–92


    Fecal pollution of surface waters presents a global human health threat. New molecular indicators of fecal pollution have been developed to address shortcomings of traditional culturable fecal indicators. However, there is still little information on their fate and transport in the environment. The present study uses spatially and temporally extensive data on traditional (culturable enterococci, cENT) and molecular (qPCR-enterococci, qENT and human-associated marker, HF183/BacR287) indicator concentrations in marine water surrounding highly-urbanized San Francisco, California, USA to investigate environmental and anthropogenic processes that impact fecal pollution. We constructed multivariable regression models for fecal indicator bacteria at 14 sampling stations. The human marker was detected more frequently in our study than in many other published studies, with detection frequency at some stations as high as 97%. The odds of cENT, qENT, and HF183/BacR287 exceeding health-relevant thresholds were statistically elevated immediately following discharges of partially treated combined sewage, and cENT levels dissipated after approximately 1 day. However, combined sewer discharges were not important predictors of indicator levels typically measured in weekly monitoring samples. Instead, precipitation and solar insolation were important predictors of cENT in weekly samples, while precipitation and water temperature were important predictors of HF183/BacR287 and qENT. The importance of precipitation highlights the significance of untreated storm water as a source of fecal pollution to the urban ocean, even for a city served by a combined sewage system. Sunlight and water temperature likely control persistence of the indicators via photoinactivation and dark decay processes, respectively.

    View details for DOI 10.1039/c7em00594f

    View details for Web of Science ID 000428988500005

    View details for PubMedID 29404550

  • Transcriptional Response of Staphylococcus aureus to Sunlight in Oxic and Anoxic Conditions FRONTIERS IN MICROBIOLOGY McClary, J. S., Boehm, A. B. 2018; 9: 249


    The transcriptional response of Staphylococcus aureus strain Newman to sunlight exposure was investigated under both oxic and anoxic conditions using RNA sequencing to gain insight into potential mechanisms of inactivation. S. aureus is a pathogenic bacterium detected at recreational beaches which can cause gastrointestinal illness and skin infections, and is of increasing public health concern. To investigate the S. aureus photostress response in oligotrophic seawater, S. aureus cultures were suspended in seawater and exposed to full spectrum simulated sunlight. Experiments were performed under oxic or anoxic conditions to gain insight into the effects of oxygen-mediated and non-oxygen-mediated inactivation mechanisms. Transcript abundance was measured after 6 h of sunlight exposure using RNA sequencing and was compared to transcript abundance in paired dark control experiments. Culturable S. aureus decayed following biphasic inactivation kinetics with initial decay rate constants of 0.1 and 0.03 m2 kJ-1 in oxic and anoxic conditions, respectively. RNA sequencing revealed that 71 genes had different transcript abundance in the oxic sunlit experiments compared to dark controls, and 18 genes had different transcript abundance in the anoxic sunlit experiments compared to dark controls. The majority of genes showed reduced transcript abundance in the sunlit experiments under both conditions. Three genes (ebpS, NWMN_0867, and NWMN_1608) were found to have the same transcriptional response to sunlight between both oxic and anoxic conditions. In the oxic condition, transcripts associated with porphyrin metabolism, nitrate metabolism, and membrane transport functions were increased in abundance during sunlight exposure. Results suggest that S. aureus responds differently to oxygen-dependent and oxygen-independent photostress, and that endogenous photosensitizers play an important role during oxygen-dependent indirect photoinactivation.

    View details for DOI 10.3389/fmicb.2018.00249

    View details for Web of Science ID 000425948000001

    View details for PubMedID 29599752

    View details for PubMedCentralID PMC5863498

  • A human fecal contamination score for ranking recreational sites using the HF183/BacR287 quantitative real-time PCR method WATER RESEARCH Cao, Y., Sivaganesan, M., Kelty, C. A., Wang, D., Boehm, A. B., Griffith, J. F., Weisberg, S. B., Shanks, O. C. 2018; 128: 148–56


    Human fecal pollution of recreational waters remains a public health concern worldwide. As a result, there is a growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality research and management. However, there are currently no standardized approaches for field implementation and interpretation of qPCR data. In this study, a standardized HF183/BacR287 qPCR method was combined with a water sampling strategy and a novel Bayesian weighted average approach to establish a human fecal contamination score (HFS) that can be used to prioritize sampling sites for remediation based on measured human waste levels. The HFS was then used to investigate 975 study design scenarios utilizing different combinations of sites with varying sampling intensities (daily to once per week) and number of qPCR replicates per sample (2-14 replicates). Findings demonstrate that site prioritization with HFS is feasible and that both sampling intensity and number of qPCR replicates influence reliability of HFS estimates. The novel data analysis strategy presented here provides a prescribed approach for the implementation and interpretation of human-associated HF183/BacR287 qPCR data with the goal of site prioritization based on human fecal pollution levels. In addition, information is provided for future users to customize study designs for optimal HFS performance.

    View details for DOI 10.1016/j.watres.2017.10.071

    View details for Web of Science ID 000418464500015

    View details for PubMedID 29101858

  • Fecal Contamination on Produce from Wholesale and Retail Food Markets in Dhaka, Bangladesh AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Harris, A. R., Islam, M., Unicomb, L., Boehm, A. B., Luby, S., Davis, J., Pickering, A. J. 2018; 98 (1): 287–94


    Fresh produce items can become contaminated with enteric pathogens along the supply chain at the preharvest (e.g., irrigation water, soil, fertilizer) or postharvest (e.g., vendor handling or consumer handling) stages. This study assesses the concentrations of fecal indicator bacteria Escherichia coli, enterococci (ENT), and Bacteriodales on surfaces of carrots, eggplants, red amaranth leaves, and tomatoes obtained from both a wholesale market (recently harvested) and neighborhood retail markets in Dhaka, Bangladesh. We detected E. coli in 100% of carrot and red amaranth rinses, 92% of eggplant rinses, and 46% of tomato rinses. Using a molecular microbial source tracking assay, we found that 32% of produce samples were positive for ruminant fecal contamination. Fecal indicator bacteria were more likely to be detected on produce collected in retail markets compared with that in the wholesale market; retail market produce were 1.25 times more likely to have E. coli detected (P = 0.03) and 1.24 times more likely to have ENT detected (P = 0.03) as compared with wholesale market produce. Bacteriodales was detected in higher concentrations in retail market produce samples compared with wholesale market produce samples (0.40 log10 gene copies per 100 cm2 higher, P = 0.03). Our results suggest that ruminant and general fecal contamination of produce in markets in Dhaka is common, and suggest that unsanitary conditions in markets are an important source of produce fecal contamination postharvest.

    View details for DOI 10.4269/ajtmh.17-0255

    View details for Web of Science ID 000430950900054

    View details for PubMedID 29165214

    View details for PubMedCentralID PMC5928698

  • Estimating the probability of illness due to swimming in recreational water with a mixture of human- and gull-associated microbial source tracking markers ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS Brown, K. I., Graham, K. E., Soller, J. A., Boehm, A. B. 2017; 19 (12): 1528–41


    Beaches often receive fecal contamination from more than one source. Human sources include untreated sewage as well as treated wastewater effluent, and animal sources include wildlife such as gulls. Different contamination sources are expected to pose different health risks to swimmers. Genetic microbial source tracking (MST) markers can be used to detect bacteria that are associated with different animal sources, but the health risks associated with a mixture of MST markers are unknown. This study presents a method for predicting these health risks, using human- and gull-associated markers as an example. Quantitative Microbial Risk Assessment (QMRA) is conducted with MST markers as indicators. We find that risks associated with exposure to a specific concentration of a human-associated MST marker (HF) are greater if the HF source is untreated sewage rather than treated wastewater effluent. We also provide a risk-based threshold of HF from untreated sewage at a beach, to stay below a predicted illness risk of 3 per 100 swimmers, that is a function of gull-associated MST marker (CAT) concentration.

    View details for DOI 10.1039/c7em00316a

    View details for Web of Science ID 000418094400007

    View details for PubMedID 29114693

  • Persistence of marine fish environmental DNA and the influence of sunlight PLOS ONE Andruszkiewicz, E. A., Sassoubre, L. M., Boehm, A. B. 2017; 12 (9): e0185043


    Harnessing information encoded in environmental DNA (eDNA) in marine waters has the potential to revolutionize marine biomonitoring. Whether using organism-specific quantitative PCR assays or metabarcoding in conjunction with amplicon sequencing, scientists have illustrated that realistic organism censuses can be inferred from eDNA. The next step is establishing ways to link information obtained from eDNA analyses to actual organism abundance. This is only possible by understanding the processes that control eDNA concentrations. The present study uses mesocosm experiments to study the persistence of eDNA in marine waters and explore the role of sunlight in modulating eDNA persistence. We seeded solute-permeable dialysis bags with water containing indigenous eDNA and suspended them in a large tank containing seawater. Bags were subjected to two treatments: half the bags were suspended near the water surface where they received high doses of sunlight, and half at depth where they received lower doses of sunlight. Bags were destructively sampled over the course of 87 hours. eDNA was extracted from water samples and used as template for a Scomber japonicus qPCR assay and a marine fish-specific 12S rRNA PCR assay. The latter was subsequently sequenced using a metabarcoding approach. S. japonicus eDNA, as measured by qPCR, exhibited first order decay with a rate constant ~0.01 hr -1 with no difference in decay rate constants between the two experimental treatments. eDNA metabarcoding identified 190 organizational taxonomic units (OTUs) assigned to varying taxonomic ranks. There was no difference in marine fish communities as measured by eDNA metabarcoding between the two experimental treatments, but there was an effect of time. Given the differences in UVA and UVB fluence received by the two experimental treatments, we conclude that sunlight is not the main driver of fish eDNA decay in the experiments. However, there are clearly temporal effects that need to be considered when interpreting information obtained using eDNA approaches.

    View details for DOI 10.1371/journal.pone.0185043

    View details for Web of Science ID 000410861600030

    View details for PubMedID 28915253

    View details for PubMedCentralID PMC5600408

  • Staphylococcus aureus Strain Newman Photoinactivation and Cellular Response to Sunlight Exposure APPLIED AND ENVIRONMENTAL MICROBIOLOGY McClary, J. S., Sassoubre, L. M., Boehm, A. B. 2017; 83 (17)


    Sunlight influences microbial water quality of surface waters. Previous studies have investigated photoinactivation mechanisms and cellular photostress responses of fecal indicator bacteria (FIB), including Escherichia coli and enterococci, but further work is needed to characterize photostress responses of bacterial pathogens. Here we investigate the photoinactivation of Staphylococcus aureus (strain Newman), a pigmented, waterborne pathogen of emerging concern. We measured photodecay using standard culture-based assays and cellular membrane integrity and investigated photostress response by measuring the relative number of mRNA transcripts of select oxidative stress, DNA repair, and metabolism genes. Photoinactivation experiments were performed in both oxic and anoxic systems to further investigate the role of oxygen-mediated and non-oxygen-mediated photoinactivation mechanisms. S. aureus lost culturability much faster in oxic systems than in anoxic systems, indicating an important role for oxygen in photodecay mechanisms. S. aureus cell membranes were damaged by sunlight exposure in anoxic systems but not in oxic systems, as measured by cell membrane permeability to propidium iodide. After sunlight exposure, S. aureus increased expression of a gene coding for methionine sulfoxide reductase after 12 h of sunlight exposure in the oxic system and after 6 h of sunlight exposure in the anoxic system, suggesting that methionine sulfoxide reductase is an important enzyme for defense against both oxygen-dependent and oxygen-independent photostresses. This research highlights the importance of oxygen in bacterial photoinactivation in environmentally relevant systems and the complexity of the bacterial photostress response with respect to cell structure and transcriptional regulation.IMPORTANCEStaphylococcus aureus is a pathogenic bacterium that causes gastrointestinal, respiratory, and skin infections. In severe cases, S. aureus infection can lead to life-threatening diseases, including pneumonia and sepsis. Cases of community-acquired S. aureus infection have been increasing in recent years, pointing to the importance of considering S. aureus transmission pathways outside the hospital environment. Associations have been observed between recreational water contact and staphylococcal skin infections, suggesting that recreational waters may be an important environmental transmission pathway for S. aureus However, prediction of human health risk in recreational waters is hindered by incomplete knowledge of pathogen sources, fate, and transport in this environment. This study is an in-depth investigation of the inactivation of a representative strain of S. aureus by sunlight exposure, one of the most important factors controlling the fate of microbial contaminants in clear waters, which will improve our ability to predict water quality changes and human health risk in recreational waters.

    View details for DOI 10.1128/AEM.01052-17

    View details for Web of Science ID 000408259000021

    View details for PubMedID 28646114

    View details for PubMedCentralID PMC5561283

  • Environmental spread of NDM-1-producing multi-drug resistant bacteria in Dhaka, Bangladesh. Applied and environmental microbiology Islam, M. A., Islam, M., Hasan, R., Hossain, M. I., Nabi, A., Rahman, M., Goessens, W. H., Endtz, H. P., Boehm, A. B., Faruque, S. M. 2017


    Resistance to carbapenem antibiotics through the production of New Delhi Metallo-β-lactamase-1 (NDM-1) constitutes an emerging challenge in the treatment of bacterial infections. To monitor possible source of spread of these organisms in Dhaka, Bangladesh, we conducted comparative analysis of waste water samples from hospital adjacent areas (HAR) and from community areas (COM) as well as public tap water samples for the occurrence and characteristics of NDM-1 producing bacteria. Of 72 HAR samples tested 51 (71%) were positive for NDM-1-producing bacteria as evidenced by phenotypic tests and the presence of blaNDM-1 gene, compared to 5 of 41 (12.1%) from COM samples (P<0⋅001). All tap water samples were negative for NDM-1-producing bacteria. Klebsiella pneumoniae (44%) was the predominant bacterial species among blaNDM-1 positive isolates followed by E. coli (29%), Acinetobacter sp., (15%) and Enterobacter spp. (9%). These bacteria were also positive for one or more other antibiotic resistance genes including blaCTX-M-1 (80%),blaCTX-M-15 (63%), blaTEM (76%), blaSHV (33%), blaCMY-2 (16%), blaOXA-48-like (2%), blaOXA-1 (53%) and blaOXA-47-like (60%). Around 40% of the isolates contained qnr gene while 50% had 16s-rRNA methylase genes. The majority of isolates hosted multiple plasmids, and plasmids of 30-50 MDa carrying blaNDM-1 were self-transmissible. Our results highlight a number of issues related to the characteristics and source of spread of multiple drug resistant bacteria as a potential public health threat. In view of existing practice of discharging untreated liquid wastes into the environment, hospitals in Dhaka city contribute to potential dissemination of NDM-1-producing bacteria into the community.IMPORTANCE. Infections caused by carbapenemase-producing Enterobacteriaceae are extremely difficult to manage due to their marked resistance to a wide range of antibiotics. NDM-1 is the most recently-described carbapenemase, and the blaNDM-1 gene encoding NDM-1 is located on self-transmissible plasmids that also carry a considerable number of other antibiotic resistance genes. The present study shows high prevalence of NDM-1-producing organisms in the wastewater samples from hospital adjacent areas as a potential source for spread of these organisms to community areas in Dhaka, Bangladesh. The study also examines characteristics of the isolates and their potential to horizontally transmit the resistance determinants. The significance of our research is in identifying the mode of spread of multiple antibiotic resistant organisms, which will allow the development of containment measures, leading to broader impacts in reducing their spread to the community.

    View details for DOI 10.1128/AEM.00793-17

    View details for PubMedID 28526792

  • Effects of submerged zone, media aging, and antecedent dry period on the performance of biochar-amended biofilters in removing fecal indicators and nutrients from natural stormwater ECOLOGICAL ENGINEERING Afrooz, A. R., Boehm, A. B. 2017; 102: 320-330
  • Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding PLOS ONE Andruszkiewicz, E. A., Starks, H. A., Chavez, F. P., Sassoubre, L. M., Block, B. A., Boehm, A. B. 2017; 12 (4)


    Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies to marine waters. Further, there is limited understanding of the spatial distribution of vertebrate eDNA in marine waters. Here, we use an eDNA metabarcoding approach to target and amplify a hypervariable region of the mitochondrial 12S rRNA gene to characterize vertebrate communities at 10 oceanographic stations spanning 45 km within the Monterey Bay National Marine Sanctuary (MBNMS). In this study, we collected three biological replicates of small volume water samples (1 L) at 2 depths at each of the 10 stations. We amplified fish mitochondrial DNA using a universal primer set. We obtained 5,644,299 high quality Illumina sequence reads from the environmental samples. The sequence reads were annotated to the lowest taxonomic assignment using a bioinformatics pipeline. The eDNA survey identified, to the lowest taxonomic rank, 7 families, 3 subfamilies, 10 genera, and 72 species of vertebrates at the study sites. These 92 distinct taxa come from 33 unique marine vertebrate families. We observed significantly different vertebrate community composition between sampling depths (0 m and 20/40 m deep) across all stations and significantly different communities at stations located on the continental shelf (<200 m bottom depth) versus in the deeper waters of the canyons of Monterey Bay (>200 m bottom depth). All but 1 family identified using eDNA metabarcoding is known to occur in MBNMS. The study informs the implementation of eDNA metabarcoding for vertebrate biomonitoring.

    View details for DOI 10.1371/journal.pone.0176343

    View details for Web of Science ID 000400308800048

    View details for PubMedID 28441466

  • Detecting and enumerating soil-transmitted helminth eggs in soil: New method development and results from field testing in Kenya and Bangladesh. PLoS neglected tropical diseases Steinbaum, L., Kwong, L. H., Ercumen, A., Negash, M. S., Lovely, A. J., Njenga, S. M., Boehm, A. B., Pickering, A. J., Nelson, K. L. 2017; 11 (4)


    Globally, about 1.5 billion people are infected with at least one species of soil-transmitted helminth (STH). Soil is a critical environmental reservoir of STH, yet there is no standard method for detecting STH eggs in soil. We developed a field method for enumerating STH eggs in soil and tested the method in Bangladesh and Kenya. The US Environmental Protection Agency (EPA) method for enumerating Ascaris eggs in biosolids was modified through a series of recovery efficiency experiments; we seeded soil samples with a known number of Ascaris suum eggs and assessed the effect of protocol modifications on egg recovery. We found the use of 1% 7X as a surfactant compared to 0.1% Tween 80 significantly improved recovery efficiency (two-sided t-test, t = 5.03, p = 0.007) while other protocol modifications-including different agitation and flotation methods-did not have a significant impact. Soil texture affected the egg recovery efficiency; sandy samples resulted in higher recovery compared to loamy samples processed using the same method (two-sided t-test, t = 2.56, p = 0.083). We documented a recovery efficiency of 73% for the final improved method using loamy soil in the lab. To field test the improved method, we processed soil samples from 100 households in Bangladesh and 100 households in Kenya from June to November 2015. The prevalence of any STH (Ascaris, Trichuris or hookworm) egg in soil was 78% in Bangladesh and 37% in Kenya. The median concentration of STH eggs in soil in positive samples was 0.59 eggs/g dry soil in Bangladesh and 0.15 eggs/g dry soil in Kenya. The prevalence of STH eggs in soil was significantly higher in Bangladesh than Kenya (chi-square, χ2 = 34.39, p < 0.001) as was the concentration (Mann-Whitney, z = 7.10, p < 0.001). This new method allows for detecting STH eggs in soil in low-resource settings and could be used for standardizing soil STH detection globally.

    View details for DOI 10.1371/journal.pntd.0005522

    View details for PubMedID 28379956

  • Occurrence of norovirus in raw sewage - A systematic literature review and meta-analysis. Water research Eftim, S. E., Hong, T., Soller, J., Boehm, A., Warren, I., Ichida, A., Nappier, S. P. 2017; 111: 366-374


    Human noroviruses (NoV) are a leading cause of recreational waterborne illnesses and responsible for the majority of viral-associated gastrointestinal illnesses nationwide. We conducted a systematic literature review of published peer-reviewed publications to identify NoV density data in wastewater influent, and provided an approach for developing pathogen density distributions, using the NoV data. Literature review inclusion criteria included scope, study quality, and data availability. A non-parametric bootstrap statistical model was used to estimate the NoV distribution in wastewater influent. The approach used accounts for heterogeneity in study-specific distribution curves, sampling locations, and sampling season and provides a comprehensive representation of the data. Study results illustrate that pooling all of the available NoV data together in a meta-analysis provides a more comprehensive understanding of the technical literature than what could be appreciated from individual studies. The studies included in this analysis indicate a high density of NoV in wastewater influent (overall mean = 4.6 log10 genome copies (GC)/liter (L)), with a higher density of NoV genogroup (G) II (overall mean = 4.9 log10 GC/L) than for GI (overall mean = 4.4 log10 GC/L for GI). The bootstrapping approach was also used to account for differences in seasonal and geographical occurrences of NoV GI and GII. The methods presented are reproducible and can be used to develop QMRA-ready density distributions for other viral pathogens in wastewater influent, effluent, and ambient waters. To our knowledge, our results are the first to quantitatively characterize seasonal and geographic differences, which could be particularly useful for future risk assessments.

    View details for DOI 10.1016/j.watres.2017.01.017

    View details for PubMedID 28110140

  • Risk-Based Threshold of Gull-Associated Fecal Marker Concentrations for Recreational Water ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Brown, K. I., Graham, K. E., Boehm, A. B. 2017; 4 (2): 44-48
  • Oceans in Peril: Grand Challenges in Applied Water Quality Research for the 21st Century ENVIRONMENTAL ENGINEERING SCIENCE Boehm, A. B., Ismail, N. S., Sassoubre, L. M., Andruszkiewicz, E. A. 2017; 34 (1): 3-15
  • Decay of sewage-sourced microbial source tracking markers and fecal indicator bacteria in marine waters WATER RESEARCH Mattioli, M. C., Sassoubre, L. M., Russell, T. L., Boehm, A. B. 2017; 108: 106-114


    The decay of sewage-sourced enterococci, Escherichia coli, three human-associated microbial source tracking (MST) markers, Salmonella, Campylobacter, and norovirus GII was measured in situ in coastal, marine waters. Experiments examined the effects of sunlight intensity and season on decay. Seawater was seeded with untreated sewage, placed into permeable dialysis bags, and deployed in the coastal ocean near the water surface, and at 18 cm, and 99 cm depths, to vary solar intensity, during winter and summer seasons. Microbial decay was modeled using a log-linear or shoulder log-linear decay model. Pathogen levels were too low in sewage to obtain kinetic parameters. Human-associated MST markers all decayed with approximately the same rate constant (k ∼ 1.5 d(-1)) in all experimental treatments, suggesting markers could be detectable up to ∼6 days after a raw sewage spill. E. coli and enterococci (culturable and molecular marker) k significantly varied with season and depth; enterococci decayed faster at shallow depths and during the summer, while E. coli decayed faster at shallow depths and during the winter. Rate constants for MST markers and culturable FIB diverged except at the deepest depth in the water column potentially complicating the use of MST marker concentrations to allocate sources of FIB contamination.

    View details for DOI 10.1016/j.watres.2016.10.066

    View details for Web of Science ID 000390181600011

    View details for PubMedID 27855952

  • Transport of Fecal Indicators from Beach Sand to the Surf Zone by Recirculating Seawater: Laboratory Experiments and Numerical Modeling ENVIRONMENTAL SCIENCE & TECHNOLOGY Brown, K. I., Boehm, A. B. 2016; 50 (23): 12840-12847


    Recirculating seawater is an important component of submarine groundwater discharge, yet its role in transporting microbial contaminants from beach sand to coastal water is unknown. This study investigated the extent to which recirculating seawater carries fecal indicators, Enterococcus and bird-associated Catellicoccus, through the beach subsurface. Laboratory experiments and numerical modeling were performed to characterize the transport of fecal indicators suspended in seawater through medium-grained beach sand under transient and saturated flow conditions. Enterococcus was measured both by culture (cENT) and DNA assay (tENT), and Catellicoccus (CAT) by DNA assay. There were differences between transport of tENT and CAT compared to cENT through laboratory columns containing beach sands. Under transient flow conditions, first-order attachment rate coefficients (katt) of DNA markers were greater (∼10 h(-1)) than katt of cENT (∼1 h(-1)), although under saturated conditions katt values were similar (∼1 h(-1)). First-order detachment rate coefficients, kdet, of DNA markers were greater (∼1 h(-1)) than kdet of cENT (∼0.1h(-1)) under both types of flow conditions. Incorporating the rate coefficients into field-scale subsurface transport simulations showed that, in this sand type, the contribution of recirculating seawater to surf zone contamination is likely to be minimal unless bird feces are deposited close to the land-sea interface.

    View details for DOI 10.1021/acs.est.6b02534

    View details for Web of Science ID 000389557100036

    View details for PubMedID 27783485

  • Rapid water disinfection using vertically aligned MoS2 nanofilms and visible light NATURE NANOTECHNOLOGY Liu, C., Kong, D., Hsu, P., Yuan, H., Lee, H., Liu, Y., Wang, H., Wang, S., Yan, K., Lin, D., Maraccini, P. A., Parker, K. M., Boehm, A. B., Cui, Y. 2016; 11 (12): 1098-1104


    Solar energy is readily available in most climates and can be used for water purification. However, solar disinfection of drinking water mostly relies on ultraviolet light, which represents only 4% of the total solar energy, and this leads to a slow treatment speed. Therefore, the development of new materials that can harvest visible light for water disinfection, and so speed up solar water purification, is highly desirable. Here we show that few-layered vertically aligned MoS2 (FLV-MoS2) films can be used to harvest the whole spectrum of visible light (∼50% of solar energy) and achieve highly efficient water disinfection. The bandgap of MoS2 was increased from 1.3 to 1.55 eV by decreasing the domain size, which allowed the FLV-MoS2 to generate reactive oxygen species (ROS) for bacterial inactivation in the water. The FLV-MoS2 showed a ∼15 times better log inactivation efficiency of the indicator bacteria compared with that of bulk MoS2, and a much faster inactivation of bacteria under both visible light and sunlight illumination compared with the widely used TiO2. Moreover, by using a 5 nm copper film on top of the FLV-MoS2 as a catalyst to facilitate electron-hole pair separation and promote the generation of ROS, the disinfection rate was increased a further sixfold. With our approach, we achieved water disinfection of >99.999% inactivation of bacteria in 20 min with a small amount of material (1.6 mg l(-1)) under simulated visible light.

    View details for DOI 10.1038/NNANO.2016.138

    View details for Web of Science ID 000389962500021

  • Escherichia coli Removal in Biochar-Modified Biofilters: Effects of Biofilm PLOS ONE Afrooz, A. R., Boehm, A. B. 2016; 11 (12)


    The presence of microbial contaminants in urban stormwater is a significant concern for public health; however, their removal by traditional stormwater biofilters has been reported as inconsistent and inadequate. Recent work has explored the use of biochar to improve performance of stormwater biofilters under simplified conditions that do not consider potential effects of biofilm development on filter media. The present study investigates the role of biofilm on microbial contaminant removal performance of stormwater biofilters. Pseudomonas aeruginosa biofilms were formed in laboratory-scale sand and biochar-modified sand packed columns, which were then challenged with Escherichia coli laden synthetic stormwater containing natural organic matter. Results suggests that the presence of biofilm influences the removal of E. coli. However, the nature of the influence depends on the specific surface area and the relative hydrophobicity of filter media. The distribution of attached bacteria within the columns indicates that removal by filter media varies along the length of the column: the inlet was the primary removal zone regardless of experimental conditions. Findings from this research inform the design of field-scale biofilters for better and consistent performance in removing microbial contaminants from urban stormwater.

    View details for DOI 10.1371/journal.pone.0167489

    View details for Web of Science ID 000389482700168

    View details for PubMedID 27907127

    View details for PubMedCentralID PMC5132165

  • Occurrence of Host-Associated Fecal Markers on Child Hands, Household Soil, and Drinking Water in Rural Bangladeshi Households ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Boehm, A. B., Wang, D., Ercumen, A., Shea, M., Harris, A. R., Shanks, O. C., Kelty, C., Ahmed, A., Mahmud, Z. H., Arnold, B. F., Chase, C., Kullmann, C., Colford, J. M., Luby, S. P., Pickering, A. J. 2016; 3 (11): 393-398
  • Escherichia coli Reduction by Bivalves in an Impaired River Impacted by Agricultural Land Use. Environmental science & technology Ismail, N. S., Tommerdahl, J. P., Boehm, A. B., Luthy, R. G. 2016; 50 (20): 11025-11033


    Fecal indicator bacteria (FIB) are leading causes of impaired surface waters. Innovative and environmentally appropriate best management practices are needed to reduce FIB concentrations and associated risk. This study examines the ability of the native freshwater mussel Anodonta californiensis and an invasive freshwater clam Corbicula fluminea to reduce concentrations of the FIB Escherichia coli in natural waters. Laboratory batch experiments were used to show bivalve species-specific E. coli removal capabilities and to develop a relationship between bivalve size and clearance rates. A field survey within an impaired coastal river containing both species of bivalves in an agricultural- and grazing-dominated area of the central coast of California showed a significant inverse correlation between E. coli concentration and bivalve density. An in situ field spiking and sampling study showed filtration by freshwater bivalves resulting in 1-1.5 log10 reduction of E. coli over 24 h, and calculated clearance rates ranged from 1.2 to 7.4 L hr(-1) bivalve(-1). Results of this study show the importance of freshwater bivalves for improving water quality through the removal of E. coli. While both native and invasive bivalves can reduce E. coli levels, the use of native bivalves through integration into best management practices is recommended as a way to improve water quality and protect and encourage re-establishment of native bivalve species that are in decline.

    View details for PubMedID 27616202

  • Quantification of Environmental DNA (eDNA) Shedding and Decay Rates for Three Marine Fish ENVIRONMENTAL SCIENCE & TECHNOLOGY Sassoubre, L. M., Yamahara, K. M., Gardner, L. D., Block, B. A., Boehm, A. B. 2016; 50 (19): 10456-10464


    Analysis of environmental DNA (eDNA) to identify macroorganisms and biodiversity has the potential to significantly augment spatial and temporal biological monitoring in aquatic ecosystems. Current monitoring methods relying on the physical identification of organisms can be time consuming, expensive, and invasive. Measuring eDNA shed from organisms provides detailed information on the presence and abundance of communities of organisms. However, little is known about eDNA shedding and decay in aquatic environments. In the present study, we designed novel Taqman qPCR assays for three ecologically and economically important marine fish-Engraulis mordax (Northern Anchovy), Sardinops sagax (Pacific Sardine), and Scomber japonicas (Pacific Chub Mackerel). We subsequently measured fish eDNA shedding and decay rates in seawater mesocosms. eDNA shedding rates ranged from 165 to 3368 pg of DNA per hour per gram of biomass. First-order decay rate constants ranged from 0.055 to 0.101 per hour. We also examined the size fractionation of eDNA and concluded eDNA is both intra- and extracellular. Finally, we derived a simple mass-balance model to estimate fish abundance from eDNA concentration. The mesocosm-derived shedding and decay rates inform the interpretation of eDNA concentrations measured in environmental samples and future use of eDNA as a monitoring tool.

    View details for DOI 10.1021/acs.est.6b03114

    View details for Web of Science ID 000384841900019

    View details for PubMedID 27580258

  • Rapid water disinfection using vertically aligned MoS2 nanofilms and visible light. Nature nanotechnology Liu, C., Kong, D., Hsu, P., Yuan, H., Lee, H., Liu, Y., Wang, H., Wang, S., Yan, K., Lin, D., Maraccini, P. A., Parker, K. M., Boehm, A. B., Cui, Y. 2016


    Solar energy is readily available in most climates and can be used for water purification. However, solar disinfection of drinking water mostly relies on ultraviolet light, which represents only 4% of the total solar energy, and this leads to a slow treatment speed. Therefore, the development of new materials that can harvest visible light for water disinfection, and so speed up solar water purification, is highly desirable. Here we show that few-layered vertically aligned MoS2 (FLV-MoS2) films can be used to harvest the whole spectrum of visible light (∼50% of solar energy) and achieve highly efficient water disinfection. The bandgap of MoS2 was increased from 1.3 to 1.55 eV by decreasing the domain size, which allowed the FLV-MoS2 to generate reactive oxygen species (ROS) for bacterial inactivation in the water. The FLV-MoS2 showed a ∼15 times better log inactivation efficiency of the indicator bacteria compared with that of bulk MoS2, and a much faster inactivation of bacteria under both visible light and sunlight illumination compared with the widely used TiO2. Moreover, by using a 5 nm copper film on top of the FLV-MoS2 as a catalyst to facilitate electron-hole pair separation and promote the generation of ROS, the disinfection rate was increased a further sixfold. With our approach, we achieved water disinfection of >99.999% inactivation of bacteria in 20 min with a small amount of material (1.6 mg l(-1)) under simulated visible light.

    View details for DOI 10.1038/nnano.2016.138

    View details for PubMedID 27525474

  • Exogenous indirect photoinactivation of bacterial pathogens and indicators in water with natural and synthetic photosensitizers in simulated sunlight with reduced UVB. Journal of applied microbiology Maraccini, P. A., Wenk, J., Boehm, A. B. 2016; 121 (2): 587-597


    To investigate the UVB-independent and exogenous indirect photoinactivation of eight human health-relevant bacterial species in the presence of photosensitizers.Eight bacterial species were exposed to simulated sunlight with greatly reduced UVB light intensity in the presence of three synthetic photosensitizers and two natural photosensitizers. Inactivation curves were fit with shoulder log-linear or first-order kinetic models, from which the presence of a shoulder and magnitude of inactivation rate constants were compared. Eighty-four percent reduction in the UVB light intensity roughly matched a 72-95% reduction in the overall bacterial photoinactivation rate constants in sensitizer-free water. With the UVB light mostly reduced, the exogenous indirect mechanism contribution was evident for most bacteria and photosensitizers tested, although most prominently with the Gram-positive bacteria.Results confirm the importance of UVB light in bacterial photoinactivation and, with the reduction of the UVB light intensity, that the Gram-positive bacteria are more vulnerable to the exogenous indirect mechanism than Gram-negative bacteria.UVB is the most important range of the sunlight spectrum for bacterial photoinactivation. In aquatic environments where photosensitizers are present and there is high UVB light attenuation, UVA and visible wavelengths can contribute to exogenous indirect photoinactivation.

    View details for DOI 10.1111/jam.13183

    View details for PubMedID 27207818

  • Soil-Transmitted Helminth Eggs Are Present in Soil at Multiple Locations within Households in Rural Kenya PLOS ONE Steinbaum, L., Njenga, S. M., Kihara, J., Boehm, A. B., Davis, J., Null, C., Pickering, A. J. 2016; 11 (6)


    Almost one-quarter of the world's population is infected with soil-transmitted helminths (STH). We conducted a study to determine the prevalence and location of STH-Ascaris, Trichuris, and hookworm spp.-egg contamination in soil within rural household plots in Kenya. Field staff collected soil samples from July to September 2014 from the house entrance and the latrine entrance of households in Kakamega County; additional spatial sampling was conducted at a subset of households (N = 22 samples from 3 households). We analyzed soil samples using a modified version of the US Environmental Protection Agency (EPA) method for enumerating Ascaris in biosolids. We found 26.8% of households had one or more species of STH eggs present in the soil in at least one household location (n = 18 out of 67 households), and Ascaris was the most commonly detected STH (19.4%, n = 13 out of 67 households). Prevalence of STH eggs in soil was equally likely at the house entrance (19.4%, N = 67) as at the latrine entrance (11.3%, N = 62) (p = 0.41). We also detected STH eggs at bathing and food preparation areas in the three houses revisited for additional spatial sampling, indicating STH exposure can occur at multiple sites within a household plot, not just near the latrine. The highest concentration of eggs in one house occurred in the child's play area. Our findings suggest interventions to limit child exposure to household soil could complement other STH control strategies.

    View details for DOI 10.1371/journal.pone.0157780

    View details for Web of Science ID 000378393600017

    View details for PubMedID 27341102

    View details for PubMedCentralID PMC4920396

  • Water quality criteria for an acidifying ocean: Challenges and opportunities for improvement OCEAN & COASTAL MANAGEMENT Weisberg, S. B., Bednarsek, N., Feely, R. A., Chan, F., Boehm, A. B., Sutula, M., Ruesink, J. L., Hales, B., Largier, J. L., Newton, J. A. 2016; 126: 31-41
  • Photoinactivation of Eight Health-Relevant Bacterial Species: Determining the Importance of the Exogenous Indirect Mechanism ENVIRONMENTAL SCIENCE & TECHNOLOGY Maraccini, P. A., Wenk, J., Boehm, A. B. 2016; 50 (10): 5050-5059


    It is presently unknown to what extent the endogenous direct, endogenous indirect, and exogenous indirect mechanisms contribute to bacterial photoinactivation in natural surface waters. In this study, we investigated the importance of the exogenous indirect mechanism by conducting photoinactivation experiments with eight health-relevant bacterial species (Bacteroides thetaiotaomicron, Campylobacter jejuni, Enterococcus faecalis, Escherichia coli K12, E. coli O157:H7, Salmonella enterica serovar Typhimurium LT2, Staphylococcus aureus, and Streptococcus bovis). We used three synthetic photosensitizers (methylene blue, rose bengal, and nitrite) and two model natural photosensitizers (Suwannee River natural organic matter and dissolved organic matter isolated from a wastewater treatment wetland) that generated singlet oxygen and hydroxyl radical. B. thetaiotaomicron had larger first order rate constants than all other organisms under all conditions tested. The presence of the synthetic photosensitizers generally enhanced photoinactivation of Gram-positive facultative anaerobes (Ent. faecalis, Staph. aureus, and Strep. bovis). Among Gram-negative bacteria, only methylene blue with E. coli K12 and rose bengal with C. jejuni showed an enhancing effect. The presence of model natural photosensitizers either reduced or did not affect photoinactivation rate constants. Our findings highlight the importance of the cellular membrane and photosensitizer properties in modulating the contribution of the exogenous indirect mechanism to the overall bacterial photoinactivation.

    View details for DOI 10.1021/acs.est.6b00074

    View details for Web of Science ID 000376331500018

    View details for PubMedID 27121126

  • Solar Inactivation of Enterococci and Escherichia coli in Natural Waters: Effects of Water Absorbance and Depth ENVIRONMENTAL SCIENCE & TECHNOLOGY Maraccini, P. A., Mattioli, M. C., Sassoubre, L. M., Cao, Y., Griffith, J. F., Ervin, J. S., Van De Werfhorst, L. C., Boehm, A. B. 2016; 50 (10): 5068-5076


    The decay of sewage-sourced Escherichia coli and enterococci was measured at multiple depths in a freshwater marsh, a brackish water lagoon, and a marine site, all located in California. The marine site had very clear water, while the waters from the marsh and lagoon contained colored dissolved organic matter that not only blocked light but also produced reactive oxygen species. First order decay rate constants of both enterococci and E. coli were between 1 and 2 d(-1) under low light conditions and as high as 6 d(-1) under high light conditions. First order decay rate constants were well correlated to the daily average UVB light intensity corrected for light screening incorporating water absorbance and depth, suggesting endogenous photoinactivation is a major pathway for bacterial decay. Additional laboratory experiments demonstrated the presence of colored dissolved organic matter in marsh water enhanced photoinactivation of a laboratory strain of Enterococcus faecalis, but depressed photoinactivation of sewage-sourced enterococci and E. coli after correcting for UVB light screening, suggesting that although the exogenous indirect photoinactivation mechanism may be active against Ent. faecalis, it is not for the sewage-source organisms. A simple linear regression model based on UVB light intensity appears to be a useful tool for predicting inactivation rate constants in natural waters of any depth and absorbance.

    View details for DOI 10.1021/acs.est.6b00505

    View details for Web of Science ID 000376331500020

    View details for PubMedID 27119980

  • Ruminants Contribute Fecal Contamination to the Urban Household Environment in Dhaka, Bangladesh ENVIRONMENTAL SCIENCE & TECHNOLOGY Harris, A. R., Pickering, A. J., Harris, M., Doza, S., Islam, M. S., Unicomb, L., Luby, S., Davis, J., Boehm, A. B. 2016; 50 (9): 4642-4649


    In Dhaka, Bangladesh, the sensitivity and specificity of three human, three ruminant, and one avian source-associated QPCR microbial source tracking assays were evaluated using fecal samples collected on site. Ruminant-associated assays performed well, whereas the avian and human assays exhibited unacceptable cross-reactions with feces from other hosts. Subsequently, child hand rinses (n = 44) and floor sponge samples (n = 44) from low-income-households in Dhaka were assayed for fecal indicator bacteria (enterococci, Bacteroidales, and Escherichia coli) and a ruminant-associated bacterial target (BacR). Mean enterococci concentrations were of 100 most probable number (MPN)/2 hands and 1000 MPN/225 cm(2) floor. Mean concentrations of Bacteroidales were 10(6) copies/2 hands and 10(5) copies/225 cm(2) floor. E. coli were detected in a quarter of hand rinse and floor samples. BacR was detected in 18% of hand rinse and 27% of floor samples. Results suggest that effective household fecal management should account not only for human sources of contamination but also for animal sources. The poor performance of the human-associated assays in the study area calls into the question the feasibility of developing a human-associated marker in urban slum environments, where domestic animals are exposed to human feces that have been disposed in pits and open drains.

    View details for DOI 10.1021/acs.est.5b06282

    View details for Web of Science ID 000375521400007

    View details for PubMedID 27045990

  • Absolute Quantification of Enterococcal 23S rRNA Gene Using Digital PCR ENVIRONMENTAL SCIENCE & TECHNOLOGY Wang, D., Yamahara, K. M., Cao, Y., Boehm, A. B. 2016; 50 (7): 3399-3408


    We evaluated the ability of chip-based digital PCR (dPCR) to quantify enterococci, the fecal indicator recommended by the United States Environmental Protection Agency (USEPA) for water-quality monitoring. dPCR uses Poisson statistics to estimate the number of DNA fragments in a sample with a specific sequence. Underestimation may occur when a gene is redundantly encoded in the genome and multiple copies of that gene are on one DNA fragment. When genomic DNA (gDNA) was extracted using two commercial DNA extraction kits, we confirmed that dPCR could discern individual copies of the redundant 23s rRNA gene in the enterococcal genome. dPCR quantification was accurate when compared to the nominal concentration inferred from fluorometer measurements (linear regression slope = 0.98, intercept = 0.03, R(2) = 0.99, and p value <0.0001). dPCR quantification was also consistent with quantitative PCR (qPCR) measurements as well as cell counts for BioBall reference standard and 24 environmental water samples. qPCR and dPCR quantification of enterococci in the 24 environmental samples were significantly correlated (linear regression slope =1.08, R(2) of 0.96, and p value <0.0001); the group mean of the qPCR measurements was 0.19 log units higher than that of the dPCR measurements. At environmentally relevant concentrations, dPCR quantification was more precise (i.e., had narrower 95% confidence intervals than qPCR quantification). We observed that humic acid caused a similar level of inhibition in both dPCR and qPCR, but calcium inhibited dPCR to a lesser degree than qPCR. Inhibition of dPCR was partially relieved when the number of thermal cycles was increased. Based on these results, we conclude that dPCR is a viable option for enumerating enterococci in ambient water.

    View details for DOI 10.1021/acs.est.5b05747

    View details for Web of Science ID 000373655800013

    View details for PubMedID 26903207

  • Transport of enterococci and F+ coliphage through the saturated zone of the beach aquifer. Journal of water and health de Sieyes, N. R., Russell, T. L., Brown, K. I., Mohanty, S. K., Boehm, A. B. 2016; 14 (1): 26-38


    Coastal groundwater has been implicated as a source of microbial pollution to recreational beaches. However, there is little work investigating the transport of fecal microbes through beach aquifers where waters of variable salinity are present. In this study, the potential for fecal indicator organisms enterococci (ENT) and F+ coliphage to be transported through marine beach aquifers was investigated. Native sediment and groundwaters were collected from the fresh and saline sections of the subterranean estuary at three beaches along the California coast where coastal communities utilize septic systems for wastewater treatment. Groundwaters were seeded with sewage and removal of F+ coliphage and ENT by the sediments during saturated flow was tested in laboratory column experiments. Removal varied significantly between beach and organism. F+ coliphage was removed to a greater extent than ENT, and removal was greater in saline sediments and groundwater than fresh. At one of the three beaches, a field experiment was conducted to investigate the attenuation of F+ coliphage and ENT down gradient of a septic leach field. ENT were detected up to 24 m from the leach field. The column study and field observations together suggest ENT can be mobile within native aquifer sediments and groundwater under certain conditions.

    View details for DOI 10.2166/wh.2015.290

    View details for PubMedID 26837827

  • Effect of weathering on mobilization of biochar particles and bacterial removal in a stormwater biofilter. Water research Mohanty, S. K., Boehm, A. B. 2015; 85: 208-215

    View details for DOI 10.1016/j.watres.2015.08.026

    View details for PubMedID 26320722

  • Sunlight inactivation of fecal indicator bacteria in open-water unit process treatment wetlands: Modeling endogenous and exogenous inactivation rates WATER RESEARCH Nguyen, M. T., Jasper, J. T., Boehm, A. B., Nelson, K. L. 2015; 83: 282-292


    A pilot-scale open-water unit process wetland was monitored for one year and found to be effective in enhancing sunlight inactivation of fecal indicator bacteria (FIB). The removal of Escherichia coli and enterococci in the open-water wetland receiving non-disinfected secondary municipal wastewater reached 3 logs and 2 logs in summer time, respectively. Pigmented enterococci were shown to be significantly more resistant to sunlight inactivation than non-pigmented enterococci. A model was developed to predict the inactivation of E. coli, and pigmented and non-pigmented enterococci that accounts for endogenous and exogenous sunlight inactivation mechanisms and dark processes. Endogenous inactivation rates were modeled using the sum of UVA and UVB irradiance. Exogenous inactivation was only significant for enterococci, and was modeled as a function of steady-state singlet oxygen concentration. The rate constants were determined from lab experiments and an empirical correction factor was used to account for differences between lab and field conditions. The model was used to predict removal rate constants for FIB in the pilot-scale wetland; considering the variability of the monitoring data, there was general agreement between the modeled values and those determined from measurements. Using the model, we estimate that open-water wetlands at 40° latitude with practical sizes can achieve 3-log (99.9%) removal of E. coli and non-pigmented enterococci throughout the year [5.5 ha and 7.0 ha per million gallons of wastewater effluent per day (MGD), respectively]. Differences in sunlight inactivation rates observed between pigmented and non-pigmented enterococci, as well as between lab-cultured and indigenous wastewater bacteria highlight the challenges of using FIB as model organisms for actual pathogens in natural sunlit environments.

    View details for DOI 10.1016/j.watres.2015.06.043

    View details for Web of Science ID 000360418000028

  • Comparative decay of Catellicoccus marimmalium and enterococci in beach sand and seawater WATER RESEARCH Brown, K. I., Boehm, A. B. 2015; 83: 377-384
  • Sunlight inactivation of fecal indicator bacteria in open-water unit process treatment wetlands: Modeling endogenous and exogenous inactivation rates. Water research Nguyen, M. T., Jasper, J. T., Boehm, A. B., Nelson, K. L. 2015; 83: 282-292


    A pilot-scale open-water unit process wetland was monitored for one year and found to be effective in enhancing sunlight inactivation of fecal indicator bacteria (FIB). The removal of Escherichia coli and enterococci in the open-water wetland receiving non-disinfected secondary municipal wastewater reached 3 logs and 2 logs in summer time, respectively. Pigmented enterococci were shown to be significantly more resistant to sunlight inactivation than non-pigmented enterococci. A model was developed to predict the inactivation of E. coli, and pigmented and non-pigmented enterococci that accounts for endogenous and exogenous sunlight inactivation mechanisms and dark processes. Endogenous inactivation rates were modeled using the sum of UVA and UVB irradiance. Exogenous inactivation was only significant for enterococci, and was modeled as a function of steady-state singlet oxygen concentration. The rate constants were determined from lab experiments and an empirical correction factor was used to account for differences between lab and field conditions. The model was used to predict removal rate constants for FIB in the pilot-scale wetland; considering the variability of the monitoring data, there was general agreement between the modeled values and those determined from measurements. Using the model, we estimate that open-water wetlands at 40° latitude with practical sizes can achieve 3-log (99.9%) removal of E. coli and non-pigmented enterococci throughout the year [5.5 ha and 7.0 ha per million gallons of wastewater effluent per day (MGD), respectively]. Differences in sunlight inactivation rates observed between pigmented and non-pigmented enterococci, as well as between lab-cultured and indigenous wastewater bacteria highlight the challenges of using FIB as model organisms for actual pathogens in natural sunlit environments.

    View details for DOI 10.1016/j.watres.2015.06.043

    View details for PubMedID 26164800

  • Human-Associated Fecal Quantitative Polymerase Chain Reaction Measurements and Simulated Risk of Gastrointestinal Illness in Recreational Waters Contaminated with Raw Sewage ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Boehm, A. B., Soller, J. A., Shanks, O. C. 2015; 2 (10): 270-275
  • Quantification of Human Norovirus GII on Hands of Mothers with Children Under the Age of Five Years in Bagamoyo, Tanzania. The American journal of tropical medicine and hygiene Mattioli, M. C., Davis, J., Mrisho, M., Boehm, A. B. 2015; 93 (3): 478-484


    Human noroviruses are the most common cause of viral gastroenteritis worldwide and one of the leading causes of viral diarrhea in children under the age of 5 years. Hands have been shown to play an important role in norovirus transmission. Norovirus outbreaks tend to exhibit strong seasonality, most often occurring during cold, dry months, but recently have also been documented during hot, dry winter months in the southern hemisphere. Other research suggests that rainfall is an important factor in norovirus outbreaks. This study examines the prevalence and concentration of human norovirus GII on the hands of mothers in Bagamoyo, Tanzania, during the rainy and dry seasons. Norovirus GII was detected in approximately 5% of hand rinse samples during both the rainy and dry seasons. Fecal indicator bacteria levels, Escherichia coli and enterococci, in hand rinse samples were not associated with norovirus hand contamination. Turbidity of the hand rinses was found to be associated with norovirus presence on mothers' hands; however, this relationship was only observed during the rainy season. The results suggest mothers' hands serve as a source of norovirus exposure for young children in Tanzanian households, and further work is needed to determine better indicators of norovirus contamination in these environments.

    View details for DOI 10.4269/ajtmh.14-0778

    View details for PubMedID 26149861

    View details for PubMedCentralID PMC4559683

  • Simultaneous monitoring of faecal indicators and harmful algae using an in-situ autonomous sensor. Letters in applied microbiology Yamahara, K. M., Demir-Hilton, E., Preston, C. M., Marin, R., Pargett, D., Roman, B., JENSEN, S., Birch, J. M., Boehm, A. B., Scholin, C. A. 2015; 61 (2): 130-138


    Faecal indicator bacteria (FIB) and harmful algal blooms (HABs) threaten the health and the economy of coastal communities worldwide. Emerging automated sampling technologies combined with molecular analytical techniques could enable rapid detection of micro-organisms in-situ, thereby improving resource management and public health decision-making. We evaluated this concept using a robotic device, the Environmental Sample Processor (ESP). The ESP automates in-situ sample collection, nucleic acid extraction and molecular analyses. Here, the ESP measured and reported concentrations of FIB (Enterococcus spp.), a microbial source-tracking marker (human-specific Bacteriodales) and a HAB species (Psuedo-nitzschia spp.) over a 45-day deployment on the Santa Cruz Municipal Wharf (Santa Cruz, CA, USA). Both FIB and HABs were enumerated from single in-situ collected water samples. The in-situ qPCR efficiencies ranged from 86% to 105%, while the limit of quantifications during the deployment was 10 copies reaction(-1) . No differences were observed in the concentrations of enterococci, the human-specific marker in Bacteroidales spp., and P. australis between in-situ collected sample and traditional hand sampling methods (P > 0·05). Analytical results were Internet-accessible within hours of sample collection, demonstrating the feasibility of same-day public notification of current water quality conditions.This study presents the first report of in-situ qPCR enumeration of both faecal indicators and harmful algal species in coastal marine waters. We utilize a robotic device for in-situ quantification of enterococci, the human-specific marker in Bacteriodales and Pseudo-nitzschia spp. from the same water samples collected and processed in-situ. The results demonstrate that rapid, in-situ monitoring can be utilized to identify and quantify multiple health-relevant micro-organisms important in water quality monitoring and that this monitoring can be used to inform same-day notifications.

    View details for DOI 10.1111/lam.12432

    View details for PubMedID 25900660

  • Ocean Acidification Science Needs for Natural Resource Managers of the North American West Coast OCEANOGRAPHY Boehm, A. B., Jacobson, M. Z., O'Donnell, M. J., Sutula, M., Wakefield, W. W., Weisberg, S. B., Whiteman, E. 2015; 28 (2): 170-181
  • Growth-dependent photoinactivation kinetics of Enterococcus faecalis JOURNAL OF APPLIED MICROBIOLOGY Maraccini, P. A., Wang, D., McClary, J. S., Boehm, A. B. 2015; 118 (5): 1226-1237


    To investigate how the growth stage of Enterococcus faecalis affects its photoinactivation in clear water.Enterococcus faecalis were grown in batch cultures to four different growth stages or grown in chemostats set at four different dilution rates, then harvested and exposed to full spectrum or UVB-blocked simulated sunlight. Experiments were conducted in triplicate in clear water with no added sensitizers. Decay curves were shoulder-log linear and were generally not statistically different in experiments conducted under full spectrum light. Shoulders were longer and first order inactivation rates smaller when experiments were seeded with cells grown to stationary as compared to exponential phase, and for slower growing cells when experiments were done under UVB-blocked light. Chemostat-sourced bacteria generally showed less variability among replicates than batch-sourced cells.The physiological state of cells and the method via which they are being generated may affect the photoinactivation experimental results.Photoinactivation experiments conducted with exponential phase cells may overestimate the photoinactivation kinetics in the environment, particular if UVB-independent mechanisms predominate. Chemostat-sourced cells are likely to provide more consistent experimental results than batch-sourced cells.

    View details for DOI 10.1111/jam.12773

    View details for Web of Science ID 000352577000015

    View details for PubMedID 25688992

  • Temporal stability of the microbial community in sewage-polluted seawater exposed to natural sunlight cycles and marine microbiota. Applied and environmental microbiology Sassoubre, L. M., Yamahara, K. M., Boehm, A. B. 2015; 81 (6): 2107-2116


    Billions of gallons of untreated wastewater enter the coastal ocean each year. Once sewage microorganisms are in the marine environment, they are exposed to environmental stressors, such as sunlight and predation. Previous research has investigated the fate of individual sewage microorganisms in seawater but not the entire sewage microbial community. The present study used next-generation sequencing (NGS) to examine how the microbial community in sewage-impacted seawater changes over 48 h when exposed to natural sunlight cycles and marine microbiota. We compared the results from microcosms composed of unfiltered seawater (containing naturally occurring marine microbiota) and filtered seawater (containing no marine microbiota) to investigate the effect of marine microbiota. We also compared the results from microcosms that were exposed to natural sunlight cycles with those from microcosms kept in the dark to investigate the effect of sunlight. The microbial community composition and the relative abundance of operational taxonomic units (OTUs) changed over 48 h in all microcosms. Exposure to sunlight had a significant effect on both community composition and OTU abundance. The effect of marine microbiota, however, was minimal. The proportion of sewage-derived microorganisms present in the microcosms decreased rapidly within 48 h, and the decrease was the most pronounced in the presence of both sunlight and marine microbiota, where the proportion decreased from 85% to 3% of the total microbial community. The results from this study demonstrate the strong effect that sunlight has on microbial community composition, as measured by NGS, and the importance of considering temporal effects in future applications of NGS to identify microbial pollution sources.

    View details for DOI 10.1128/AEM.03950-14

    View details for PubMedID 25576619

  • Improvement of Urban Lake Water Quality by Removal of Escherichia coli through the Action of the Bivalve Anodonta californiensis. Environmental science & technology Ismail, N. S., Dodd, H., Sassoubre, L. M., Horne, A. J., Boehm, A. B., Luthy, R. G. 2015; 49 (3): 1664-1672


    High levels of fecal indicator bacteria, such as Escherichia coli, can be indicative of poor water quality. The use of shellfish to reduce eutrophication has been proposed, but application of bivalves to reduce bacterial levels has not been extensively reported. Removal of E. coli by the native freshwater mussel Anodonta californiensis was studied using laboratory batch systems and field-based flow-through systems. Batch systems were utilized to determine the fate and inactivation of E. coli after uptake by the mussel. Batch experiments demonstrated that uptake patterns followed first order kinetics and E. coli was inactivated with less than 5% of the initial colonies recoverable in fecal matter or tissue. Flow-through systems located at an urban impaired lake in San Francisco, CA were utilized to determine uptake kinetics under environmentally relevant conditions. The bivalves maintained a 1-log removal of E. coli for the duration of exposure. The calculated uptake rates can be used in conjunction with hydrologic models to determine the number of bivalves needed to maintain removal of E. coli in different freshwater systems. The outcomes of this study support the use of native freshwater bivalves to achieve the co-benefits of rehabilitating a freshwater ecosystem and improving water quality via reduction of E. coli in contaminated freshwater systems.

    View details for DOI 10.1021/es5033212

    View details for PubMedID 25587628

  • Hand-to-Mouth Contacts Result in Greater Ingestion of Feces than Dietary Water Consumption in Tanzania: A Quantitative Fecal Exposure Assessment Model. Environmental science & technology Mattioli, M. C., Davis, J., Boehm, A. B. 2015; 49 (3): 1912-1920


    Diarrheal diseases kill 1800 children under the age of five die each day, and nearly half of these deaths occur in sub-Saharan Africa. Contaminated drinking water and hands are two important environmental transmission routes of diarrhea-causing pathogens to young children in low-income countries. The objective of this research is to evaluate the relative contribution of these two major exposure pathways in a low-income country setting. A Monte Carlo simulation was used to model the amount of human feces ingested by children under five years old from exposure via hand-to-mouth contacts and stored drinking water ingestion in Bagamoyo, Tanzania. Child specific exposure data were obtained from the USEPA 2011 Exposure Factors Handbook, and fecal contamination was estimated using hand rinse and stored water fecal indicator bacteria concentrations from over 1200 Tanzanian households. The model outcome is a distribution of a child's daily dose of feces via each exposure route. The model results show that Tanzanian children ingest a significantly greater amount of feces each day from hand-to-mouth contacts than from drinking water, which may help elucidate why interventions focused on water without also addressing hygiene often see little to no effect on reported incidence of diarrhea.

    View details for DOI 10.1021/es505555f

    View details for PubMedID 25559008

  • Sunny with a chance of gastroenteritis: predicting swimmer risk at california beaches. Environmental science & technology Thoe, W., Gold, M., Griesbach, A., Grimmer, M., Taggart, M. L., Boehm, A. B. 2015; 49 (1): 423-431


    Traditional beach management that uses concentrations of cultivatable fecal indicator bacteria (FIB) may lead to delayed notification of unsafe swimming conditions. Predictive, nowcast models of beach water quality may help reduce beach management errors and enhance protection of public health. This study compares performances of five different types of statistical, data-driven predictive models: multiple linear regression model, binary logistic regression model, partial least-squares regression model, artificial neural network, and classification tree, in predicting advisories due to FIB contamination at 25 beaches along the California coastline. Classification tree and the binary logistic regression model with threshold tuning are consistently the best performing model types for California beaches. Beaches with good performing models usually have a rainfall/flow related dominating factor affecting beach water quality, while beaches having a deteriorating water quality trend or low FIB exceedance rates are less likely to have a good performing model. This study identifies circumstances when predictive models are the most effective, and suggests that using predictive models for public notification of unsafe swimming conditions may improve public health protection at California beaches relative to current practices.

    View details for DOI 10.1021/es504701j

    View details for PubMedID 25489920

  • Mobilization of Microspheres from a Fractured Soil during Intermittent Infiltration Events VADOSE ZONE JOURNAL Mohanty, S. K., Bulicek, M. C., Metge, D. W., Harvey, R. W., Ryan, J. N., Boehm, A. B. 2015; 14 (1)
  • Predicting water quality at Santa Monica Beach: Evaluation of five different models for public notification of unsafe swimming conditions WATER RESEARCH Thoe, W., Gold, M., Griesbach, A., Grimmer, M., Taggart, M. L., Boehm, A. B. 2014; 67: 105-117


    Bathing beaches are monitored for fecal indicator bacteria (FIB) to protect swimmers from unsafe conditions. However, FIB assays take ∼24 h and water quality conditions can change dramatically in that time, so unsafe conditions cannot presently be identified in a timely manner. Statistical, data-driven predictive models use information on environmental conditions (i.e., rainfall, turbidity) to provide nowcasts of FIB concentrations. Their ability to predict real time FIB concentrations can make them more accurate at identifying unsafe conditions than the current method of using day or older FIB measurements. Predictive models are used in the Great Lakes, Hong Kong, and Scotland for beach management, but they are presently not used in California - the location of some of the world's most popular beaches. California beaches are unique as point source pollution has generally been mitigated, the summer bathing season receives little to no rainfall, and in situ measurements of turbidity and salinity are not readily available. These characteristics may make modeling FIB difficult, as many current FIB models rely heavily on rainfall or salinity. The current study investigates the potential for FIB models to predict water quality at a quintessential California Beach: Santa Monica Beach. This study compares the performance of five predictive models, multiple linear regression model, binary logistic regression model, partial least square regression model, artificial neural network, and classification tree, to predict concentrations of summertime fecal coliform and enterococci concentrations. Past measurements of bacterial concentration, storm drain condition, and tide level are found to be critical factors in the predictive models. The models perform better than the current beach management method. The classification tree models perform the best; for example they correctly predict 42% of beach postings due to fecal coliform exceedances during model validation, as compared to 28% by the current method. Artificial neural network is the second best model which minimizes the number of incorrect beach postings. The binary logistic regression model also gives promising results, comparable to classification tree, by adjusting the posting decision thresholds to maximize correct beach postings. This study indicates that predictive models hold promise as a beach management tool at Santa Monica Beach. However, there are opportunities to further refine predictive models.

    View details for DOI 10.1016/j.watres.2014.09.001

    View details for Web of Science ID 000346394900011

    View details for PubMedID 25262555

  • Human health risk implications of multiple sources of faecal indicator bacteria in a recreational waterbody WATER RESEARCH Soller, J. A., Schoen, M. E., Varghese, A., Ichida, A. M., Boehm, A. B., Eftim, S., Ashbolt, N. J., Ravenscroft, J. E. 2014; 66: 254-264


    We simulate the influence of multiple sources of enterococci (ENT) as faecal indicator bacteria (FIB) in recreational water bodies on potential human health risk by considering waters impacted by human and animal sources, human and non-pathogenic sources, and animal and non-pathogenic sources. We illustrate that risks vary with the proportion of culturable ENT in water bodies derived from these sources and estimate corresponding ENT densities that yield the same level of health protection that the recreational water quality criteria in the United States seeks (benchmark risk). The benchmark risk is based on epidemiological studies conducted in water bodies predominantly impacted by human faecal sources. The key result is that the risks from mixed sources are driven predominantly by the proportion of the contamination source with the greatest ability to cause human infection (potency), not necessarily the greatest source(s) of FIB. Predicted risks from exposures to mixtures comprised of approximately 30% ENT from human sources were up to 50% lower than the risks expected from purely human sources when contamination is recent and ENT levels are at the current water quality criteria levels (35 CFU 100 mL(-1)). For human/non-pathogenic, human/gull, human/pig, and human/chicken faecal mixtures with relatively low human contribution, the predicted culturable enterococci densities that correspond to the benchmark risk are substantially greater than the current water quality criteria values. These findings are important because they highlight the potential applicability of site specific water quality criteria for waters that are predominantly un-impacted by human sources.

    View details for DOI 10.1016/j.watres.2014.08.026

    View details for Web of Science ID 000344823500024

    View details for PubMedID 25222329

  • Escherichia coli Removal in Biochar-Augmented Biofilter: Effect of Infiltration Rate, Initial Bacterial Concentration, Biochar Particle Size, and Presence of Compost ENVIRONMENTAL SCIENCE & TECHNOLOGY Mohanty, S. K., Boehm, A. B. 2014; 48 (19): 11535-11542

    View details for DOI 10.1021/es5033162

    View details for Web of Science ID 000343016600065

  • Escherichia coli removal in biochar-augmented biofilter: effect of infiltration rate, initial bacterial concentration, biochar particle size, and presence of compost. Environmental science & technology Mohanty, S. K., Boehm, A. B. 2014; 48 (19): 11535-11542


    Bioretention systems and biofilters are used in low impact development to passively treat urban stormwater. However, these engineered natural systems are not efficient at removing fecal indicator bacteria, the contaminants responsible for a majority of surface water impairments. The present study investigates the efficacy of biochar-augmented model sand biofilters for Escherichia coli removal under a variety of stormwater bacterial concentrations and infiltration rates. Additionally, we test the role of biochar particle size and "presence of compost on model" biofilter performance. Our results show that E. coli removal in a biochar-augmented sand biofilter is ∼ 96% and is not greatly affected by increases in stormwater infiltration rates and influent bacterial concentrations, particularly within the ranges expected in field. Removal of fine (<125 μm) biochar particles from the biochar-sand biofilter decreased the removal capacity from 95% to 62%, indicating biochar size is important. Addition of compost to biochar-sand biofilters not only lowered E. coli removal capacity but also increased the mobilization of deposited bacteria during intermittent infiltration. This result is attributed to exhaustion of attachment sites on biochar by the dissolved organic carbon leached from compost. Overall, our study indicates that biochar has potential to remove bacteria from stormwater under a wide range of field conditions, but for biochar to be effective, the size should be small and biochar should be applied without compost. Although the results aid in the optimization of biofilter design, further studies are needed to examine biochar potential in the field over an entire rainy season.

    View details for DOI 10.1021/es5033162

    View details for PubMedID 25222640

  • Static Electricity Powered Copper Oxide Nanowire Microbicidal Electroporation for Water Disinfection NANO LETTERS Liu, C., Xie, X., Zhao, W., Yao, J., Kong, D., Boehm, A. B., Cui, Y. 2014; 14 (10): 5603-5608

    View details for DOI 10.1021/nl5020958

    View details for Web of Science ID 000343016400019

  • Efficacy of biochar to remove Escherichia coli from stormwater under steady and intermittent flow. Water research Mohanty, S. K., Cantrell, K. B., Nelson, K. L., Boehm, A. B. 2014; 61: 288-296


    Biofilters, designed to facilitate the infiltration of stormwater into soil, are generally ineffective in removing bacteria from stormwater, thereby causing pollution of groundwater and receiving surface waters. The bacterial removal capacity of biofilters has been shown to be lower in the presence of natural organic matter (NOM) and during intermittent infiltration of stormwater. To improve the removal of fecal indicator bacteria (Escherichia coli) under these conditions, we amended sand with 5% (by weight) biochar, a carbonaceous geomedia produced by pyrolysis of biomass, and investigated the removal and remobilization of E. coli. Three types of biochar were used to evaluate the role of biochar properties on the removal. Compared to sand, biochar not only retained up to 3 orders of magnitude more E. coli, but also prevented their mobilization during successive intermittent flows. In the presence of NOM, the removal capacity of biochar was lower, but remained higher than sand alone. The improved retention with the biochar amendment is attributed to an increase in the attachment of E. coli at the primary minimum and to an increase in the water-holding capacity of biochar-amended sand, which renders driving forces such as moving air-water interfaces less effective in detaching bacteria from grain surfaces. Biochars with lower volatile matter and polarity appear to be more effective in removing bacteria from stormwater. Overall, our results suggest that a biochar amendment to biofilter media has the potential to effectively remove bacteria from stormwater.

    View details for DOI 10.1016/j.watres.2014.05.026

    View details for PubMedID 24952272

  • Effect of submarine groundwater discharge on bacterial indicators and swimmer health at Avalon Beach, CA, USA. Water research Yau, V. M., Schiff, K. C., Arnold, B. F., Griffith, J. F., Gruber, J. S., Wright, C. C., Wade, T. J., Burns, S., Hayes, J. M., Mcgee, C., Gold, M., Cao, Y., Boehm, A. B., Weisberg, S. B., Colford, J. M. 2014; 59: 23-36


    Use of fecal indicator bacteria (FIB) for monitoring beach water quality is based on their co-occurrence with human pathogens, a relationship that can be dramatically altered by fate and transport processes after leaving the human intestine. We conducted a prospective cohort study at Avalon Beach, California (USA), where the indicator relationship is potentially affected by the discharge of sewage-contaminated groundwater and by solar radiation levels at this shallow, relatively quiescent beach. The goals of this study were to determine: 1) if swimmers exposed to marine water were at higher risk of illness than non-swimmers; 2) if FIB measured in marine water were associated with swimmer illness, and; 3) if the associations between FIB and swimmer health were modified by either submarine groundwater discharge or solar radiation levels. There were 7317 individuals recruited during the summers of 2007-08, 6165 (84%) of whom completed follow-up within two weeks of the beach visit. A total of 703 water quality samples were collected across multiple sites and time periods during recruitment days and analyzed for FIB using both culture-based and molecular methods. Adjusted odds ratios (AOR) indicated that swimmers who swallowed water were more likely to experience Gastrointestinal Illness (GI Illness) within three days of their beach visit than non-swimmers, and that this risk was significantly elevated when either submarine groundwater discharge was high (AOR [95% CI]:2.18 [1.22-3.89]) or solar radiation was low (2.45 [1.25-4.79]). The risk of GI Illness was not significantly elevated for swimmers who swallowed water when groundwater discharge was low or solar radiation was high. Associations between GI Illness incidence and FIB levels (Enterococcus EPA Method 1600) among swimmers who swallowed water were not significant when we did not account for groundwater discharge, but were strongly associated when groundwater discharge was high (1.85 [1.06, 3.23]) compared to when it was low (0.77 [0.42, 1.42]; test of interaction: P = 0.03). These results demonstrate the need to account for local environmental conditions when monitoring for, and making decisions about, public health at recreational beaches. The views expressed in this article are those of the authors and do not necessarily reflect the views or policies of the U.S. Environmental Protection Agency.

    View details for DOI 10.1016/j.watres.2014.03.050

    View details for PubMedID 24776951

  • Diversity and Transport of Microorganisms in Intertidal Sands of the California Coast APPLIED AND ENVIRONMENTAL MICROBIOLOGY Boehm, A. B., Yamahara, K. M., Sassoubre, L. M. 2014; 80 (13): 3943-3951
  • Diversity and transport of microorganisms in intertidal sands of the California coast. Applied and environmental microbiology Boehm, A. B., Yamahara, K. M., Sassoubre, L. M. 2014; 80 (13): 3943-3951


    Forced by tides and waves, large volumes of seawater are flushed through the beach daily. Organic material and nutrients in seawater are remineralized and cycled as they pass through the beach. Microorganisms are responsible for most of the biogeochemical cycling in the beach; however, few studies have characterized their diversity in intertidal sands, and little work has characterized the extent to which microbes are transported between different compartments of the beach. The present study uses next-generation massively parallel sequencing to characterize the microbial community present at 49 beaches along the coast of California. In addition, we characterize the transport of microorganisms within intertidal sands using laboratory column experiments. We identified extensive diversity in the beach sands. Nearly 1,000 unique taxa were identified in sands from 10 or more unique beaches, suggesting the existence of a group of "cosmopolitan" sand microorganisms. A biogeographical analysis identified a taxon-distance relationship among the beaches. In addition, sands with similar grain size, organic carbon content, exposed to a similar wave climate, and having the same degree of anthropogenic influence tended to have similar microbial communities. Column experiments identified microbes readily mobilized by seawater infiltrating through unsaturated intertidal sands. The ease with which microbes were mobilized suggests that intertidal sands may represent a reservoir of bacteria that seed the beach aquifer where they may partake in biogeochemical cycling.

    View details for DOI 10.1128/AEM.00513-14

    View details for PubMedID 24747906

  • Hand bacterial communities vary across two different human populations. Microbiology (Reading, England) Hospodsky, D., Pickering, A. J., Julian, T. R., Miller, D., Gorthala, S., Boehm, A. B., Peccia, J. 2014; 160: 1144-1152


    This study utilized pyrosequencing-based phylogenetic library results to assess bacterial communities on the hands of women in Tanzania and compared these communities with bacteria assemblages on the hands of US women. Bacterial population profiles and phylogenetically based ordinate analysis demonstrated that the bacterial communities on hands were more similar for selected populations within a country than between the two countries considered. Organisms that have commonly been identified in prior human skin microbiome studies, including members of the Propionibacteriaceae, Staphylococcaceae and Streptococceacea families, were highly abundant on US hands and drove the clustering of US hand microbial communities into a distinct group. The most abundant bacterial taxa on Tanzanian hands were the soil-associated Rhodobacteraceae and Nocardioidaceae. These results help to expand human microbiome results beyond US and European populations, and the identification and abundance of soil-associated bacteria on Tanzanian hands demonstrated the important role of the environment in shaping the microbial communities on human hands.

    View details for DOI 10.1099/mic.0.075390-0

    View details for PubMedID 24817404

  • Mechanisms for Photoinactivation of Enterococcus faecalis in Seawater. Applied and environmental microbiology Sassoubre, L. M., Nelson, K. L., Boehm, A. B. 2014; 80 (9): 2964-?

    View details for DOI 10.1128/AEM.00913-14

    View details for PubMedID 24732731

  • Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters. Journal of environmental management Riedel, T. E., Zimmer-Faust, A. G., Thulsiraj, V., Madi, T., Hanley, K. T., Ebentier, D. L., Byappanahalli, M., Layton, B., Raith, M., Boehm, A. B., Griffith, J. F., Holden, P. A., Shanks, O. C., Weisberg, S. B., Jay, J. A. 2014; 136: 112-120


    Some molecular methods for tracking fecal pollution in environmental waters have both PCR and quantitative PCR (qPCR) assays available for use. To assist managers in deciding whether to implement newer qPCR techniques in routine monitoring programs, we compared detection limits (LODs) and costs of PCR and qPCR assays with identical targets that are relevant to beach water quality assessment. For human-associated assays targeting Bacteroidales HF183 genetic marker, qPCR LODs were 70 times lower and there was no effect of target matrix (artificial freshwater, environmental creek water, and environmental marine water) on PCR or qPCR LODs. The PCR startup and annual costs were the lowest, while the per reaction cost was 62% lower than the Taqman based qPCR and 180% higher than the SYBR based qPCR. For gull-associated assays, there was no significant difference between PCR and qPCR LODs, target matrix did not effect PCR or qPCR LODs, and PCR startup, annual, and per reaction costs were lower. Upgrading to qPCR involves greater startup and annual costs, but this increase may be justified in the case of the human-associated assays with lower detection limits and reduced cost per sample.

    View details for DOI 10.1016/j.jenvman.2014.01.029

    View details for PubMedID 24583609

  • Impacts of Beach Wrack Removal via Grooming on Surf Zone Water Quality. Environmental science & technology Russell, T. L., Sassoubre, L. M., Zhou, C., French-Owen, D., Hassaballah, A., Boehm, A. B. 2014; 48 (4): 2203-2211


    Fecal indicator bacteria (FIB) are used to assess the microbial water quality of recreational waters. Increasingly, nonfecal sources of FIB have been implicated as causes of poor microbial water quality in the coastal environment. These sources are challenging to quantify and difficult to remediate. The present study investigates one nonfecal FIB source, beach wrack (decaying aquatic plants), and its impacts on water quality along the Central California coast. The prevalence of FIB on wrack was studied using a multibeach survey, collecting wrack throughout Central California. The impacts of beach grooming, to remove wrack, were investigated at Cowell Beach in Santa Cruz, California using a long-term survey (two summers, one with and one without grooming) and a 48 h survey during the first ever intensive grooming event. FIB were prevalent on wrack but highly variable spatially and temporally along the nine beaches sampled in Central California. Beach grooming was generally associated with either no change or a slight increase in coastal FIB concentrations and increases in surf zone turbidity and silicate, phosphate, and dissolved inorganic nitrogen concentrations. The findings suggest that beach grooming for wrack removal is not justified as a microbial pollution remediation strategy.

    View details for DOI 10.1021/es405536q

    View details for PubMedID 24437501

  • Transcriptional response of Enterococcus faecalis to sunlight. Journal of photochemistry and photobiology. B, Biology Sassoubre, L. M., Ramsey, M. M., Gilmore, M. S., Boehm, A. B. 2014; 130: 349-356


    Microarrays were used to investigate the transcriptional response of Enterococcus faecalis to photostress. E. faecalis are Gram-positive bacteria used as indicators of water quality and have been shown to vary diurnally in response to sunlight. E. faecalis in filtered seawater microcosms were exposed to artificial sunlight for 12h and then placed in the dark for 12h. Transcript abundance was measured at 0, 2, 6, 12, and 24h in the sunlit microcosm and a dark control using microarrays. Culturable E. faecalis concentrations decreased 6-7 orders of magnitude within the first 6h of light exposure. After 12h in the dark, no evidence of dark-repair was observed. Expression data collected after 12h of sunlight exposure revealed a difference in transcript abundance in the light relative to dark microcosms for 35 unique ORFs, 33 ORFs showed increased transcript abundance and 2 ORFs showed reduced transcript abundance. A majority (51%) of the ORFs with increased transcript abundance in the sunlit relative to dark microcosms encoded hypothetical proteins; others were associated with protein synthesis, oxidative stress and DNA repair. Results suggest that E. faecalis exposed to sunlight actively transcribe RNA in response to photostress.

    View details for DOI 10.1016/j.jphotobiol.2013.12.013

    View details for PubMedID 24434819

  • Enteric Pathogens in Stored Drinking Water and on Caregiver's Hands in Tanzanian Households with and without Reported Cases of Child Diarrhea PLOS ONE Mattioli, M. C., Boehm, A. B., Davis, J., Harris, A. R., Mrisho, M., Pickering, A. J. 2014; 9 (1)

    View details for DOI 10.1371/journal.pone.0084939

    View details for Web of Science ID 000329460100084

    View details for PubMedID 24392161

  • Enteric pathogens in stored drinking water and on caregiver's hands in Tanzanian households with and without reported cases of child diarrhea. PLoS One Mattioli, M., C., Boehm, A., B., Davis, J., Harris, A., R., Mrisho, M., Pickering., A., J. 2014; 9: e84939
  • Enteric pathogens in stored drinking water and on caregiver's hands in Tanzanian households with and without reported cases of child diarrhea. PloS one Mattioli, M. C., Boehm, A. B., Davis, J., Harris, A. R., Mrisho, M., Pickering, A. J. 2014; 9 (1)


    Diarrhea is one of the leading causes of mortality in young children. Diarrheal pathogens are transmitted via the fecal-oral route, and for children the majority of this transmission is thought to occur within the home. However, very few studies have documented enteric pathogens within households of low-income countries.The presence of molecular markers for three enteric viruses (enterovirus, adenovirus, and rotavirus), seven Escherichia coli virulence genes (ECVG), and human-specific Bacteroidales was assessed in hand rinses and household stored drinking water in Bagamoyo, Tanzania. Using a matched case-control study design, we examined the relationship between contamination of hands and water with these markers and child diarrhea. We found that the presence of ECVG in household stored water was associated with a significant decrease in the odds of a child within the home having diarrhea (OR = 0.51; 95% confidence interval 0.27-0.93). We also evaluated water management and hygiene behaviors. Recent hand contact with water or food was positively associated with detection of enteric pathogen markers on hands, as was relatively lower volumes of water reportedly used for daily hand washing. Enteropathogen markers in stored drinking water were more likely found among households in which the markers were also detected on hands, as well as in households with unimproved water supply and sanitation infrastructure.The prevalence of enteric pathogen genes and the human-specific Bacteroidales fecal marker in stored water and on hands suggests extensive environmental contamination within homes both with and without reported child diarrhea. Better stored water quality among households with diarrhea indicates caregivers with sick children may be more likely to ensure safe drinking water in the home. Interventions to increase the quantity of water available for hand washing, and to improve food hygiene, may reduce exposure to enteric pathogens in the domestic environment.

    View details for DOI 10.1371/journal.pone.0084939

    View details for PubMedID 24392161

  • New Performance Metrics for Quantitative Polymerase Chain Reaction-Based Microbial Source Tracking Methods ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Wang, D., Green, H. C., Shanks, O. C., Boehm, A. B. 2014; 1 (1): 20-25

    View details for DOI 10.1021/ez400022t

    View details for Web of Science ID 000350830700005

  • New performance metrics for quantitative PCR microbial source tracking methods. Environmental Science & Technology Letters Wang, D., Green, H., Shanks, O., Boehm., A., B. 2014; 1: 20-25
  • Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods WATER RESEARCH Ebentier, D. L., Hanley, K. T., Cao, Y., Badgley, B. D., Boehm, A. B., Ervin, J. S., Goodwin, K. D., Gourmelon, M., Griffith, J. F., Holden, P. A., Kelty, C. A., Lozach, S., Mcgee, C., Peed, L. A., Raith, M., Ryu, H., Sadowsky, M. J., Scott, E. A., Domingo, J. S., Schriewer, A., Sinigalliano, C. D., Shanks, O. C., Van De Werfhorst, L. C., Wang, D., Wuertz, S., Jay, J. A. 2013; 47 (18): 6839-6848
  • Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study WATER RESEARCH Harwood, V. J., Boehm, A. B., Sassoubre, L. M., Vijayavel, K., Stewart, J. R., Fong, T., Caprais, M., Converse, R. R., Diston, D., Ebdon, J., Fuhrman, J. A., Gourmelon, M., Gentry-Shields, J., Griffith, J. F., Kashian, D. R., Noble, R. T., Taylor, H., Wicki, M. 2013; 47 (18): 6929-6943


    An inter-laboratory study of the accuracy of microbial source tracking (MST) methods was conducted using challenge fecal and sewage samples that were spiked into artificial freshwater and provided as unknowns (blind test samples) to the laboratories. The results of the Source Identification Protocol Project (SIPP) are presented in a series of papers that cover 41 MST methods. This contribution details the results of the virus and bacteriophage methods targeting human fecal or sewage contamination. Human viruses used as source identifiers included adenoviruses (HAdV), enteroviruses (EV), norovirus Groups I and II (NoVI and NoVII), and polyomaviruses (HPyVs). Bacteriophages were also employed, including somatic coliphages and F-specific RNA bacteriophages (FRNAPH) as general indicators of fecal contamination. Bacteriophage methods targeting human fecal sources included genotyping of FRNAPH isolates and plaque formation on bacterial hosts Enterococcus faecium MB-55, Bacteroides HB-73 and Bacteroides GB-124. The use of small sample volumes (≤50 ml) resulted in relatively insensitive theoretical limits of detection (10-50 gene copies or plaques × 50 ml(-1)) which, coupled with low virus concentrations in samples, resulted in high false-negative rates, low sensitivity, and low negative predictive values. On the other hand, the specificity of the human virus methods was generally close to 100% and positive predictive values were ∼40-70% with the exception of NoVs, which were not detected. The bacteriophage methods were generally much less specific toward human sewage than virus methods, although FRNAPH II genotyping was relatively successful, with 18% sensitivity and 85% specificity. While the specificity of the human virus methods engenders great confidence in a positive result, better concentration methods and larger sample volumes must be utilized for greater accuracy of negative results, i.e. the prediction that a human contamination source is absent.

    View details for DOI 10.1016/j.watres.2013.04.064

    View details for Web of Science ID 000328444000012

    View details for PubMedID 23886543

  • Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources WATER RESEARCH Raith, M. R., Kelty, C. A., Griffith, J. F., Schriewer, A., Wuertz, S., Mieszkin, S., Gourmelon, M., Reischer, G. H., Farnleitner, A. H., Ervin, J. S., Holden, P. A., Ebentier, D. L., Jay, J. A., Wang, D., Boehm, A. B., Aw, T. G., Rose, J. B., Balleste, E., Meijer, W. G., Sivaganesan, M., Shanks, O. C. 2013; 47 (18): 6921-6928


    The State of California has mandated the preparation of a guidance document on the application of fecal source identification methods for recreational water quality management. California contains the fifth highest population of cattle in the United States, making the inclusion of cow-associated methods a logical choice. Because the performance of these methods has been shown to change based on geography and/or local animal feeding practices, laboratory comparisons are needed to determine which assays are best suited for implementation. We describe the performance characterization of two end-point PCR assays (CF128 and CF193) and five real-time quantitative PCR (qPCR) assays (Rum2Bac, BacR, BacCow, CowM2, and CowM3) reported to be associated with either ruminant or cattle feces. Each assay was tested against a blinded set of 38 reference challenge filters (19 duplicate samples) containing fecal pollution from 12 different sources suspected to impact water quality. The abundance of each host-associated genetic marker was measured for qPCR-based assays in both target and non-target animals and compared to quantities of total DNA mass, wet mass of fecal material, as well as Bacteroidales, and enterococci determined by 16S rRNA qPCR and culture-based approaches (enterococci only). Ruminant- and cow-associated genetic markers were detected in all filters containing a cattle fecal source. However, some assays cross-reacted with non-target pollution sources. A large amount of variability was evident across laboratories when protocols were not fixed suggesting that protocol standardization will be necessary for widespread implementation. Finally, performance metrics indicate that the cattle-associated CowM2 qPCR method combined with either the BacR or Rum2Bac ruminant-associated methods are most suitable for implementation.

    View details for DOI 10.1016/j.watres.2013.03.061

    View details for Web of Science ID 000328444000011

    View details for PubMedID 23871256

  • Multi-laboratory evaluations of the performance of Catellicoccus marimammalium PCR assays developed to target gull fecal sources WATER RESEARCH Sinigalliano, C. D., Ervin, J. S., Van De Werfhorst, L. C., Badgley, B. D., Balleste, E., Bartkowiak, J., Boehm, A. B., Byappanahalli, M., Goodwin, K. D., Gourmelon, M., Griffith, J., Holden, P. A., Jay, J., Layton, B., Lee, C., Lee, J., Meijer, W. G., Noble, R., Raith, M., Ryu, H., Sadowsky, M. J., Schriewer, A., Wang, D., Wanless, D., Whitman, R., Wuertz, S., Domingo, J. W. 2013; 47 (18): 6883-6896


    Here we report results from a multi-laboratory (n = 11) evaluation of four different PCR methods targeting the 16S rRNA gene of Catellicoccus marimammalium originally developed to detect gull fecal contamination in coastal environments. The methods included a conventional end-point PCR method, a SYBR(®) Green qPCR method, and two TaqMan(®) qPCR methods. Different techniques for data normalization and analysis were tested. Data analysis methods had a pronounced impact on assay sensitivity and specificity calculations. Across-laboratory standardization of metrics including the lower limit of quantification (LLOQ), target detected but not quantifiable (DNQ), and target not detected (ND) significantly improved results compared to results submitted by individual laboratories prior to definition standardization. The unit of measure used for data normalization also had a pronounced effect on measured assay performance. Data normalization to DNA mass improved quantitative method performance as compared to enterococcus normalization. The MST methods tested here were originally designed for gulls but were found in this study to also detect feces from other birds, particularly feces composited from pigeons. Sequencing efforts showed that some pigeon feces from California contained sequences similar to C. marimammalium found in gull feces. These data suggest that the prevalence, geographic scope, and ecology of C. marimammalium in host birds other than gulls require further investigation. This study represents an important first step in the multi-laboratory assessment of these methods and highlights the need to broaden and standardize additional evaluations, including environmentally relevant target concentrations in ambient waters from diverse geographic regions.

    View details for DOI 10.1016/j.watres.2013.02.059

    View details for Web of Science ID 000328444000008

    View details for PubMedID 23916157

  • Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers - Is it feasible? Water research Wang, D., Farnleitner, A. H., Field, K. G., Green, H. C., Shanks, O. C., Boehm, A. B. 2013; 47 (18): 6849-6861


    Fecal pollution is measured in surface waters using culture-based measurements of enterococci and Escherichia coli bacteria. Source apportionment of these two fecal indicator bacteria is an urgent need for prioritizing remediation efforts and quantifying health risks associated with source-specific pathogens. There are a number of quantitative real-time PCR (QPCR) assays that estimate concentrations of source-associated genetic markers; however, their concentrations are not necessarily amenable to source apportionment because the markers may differ in prevalence across sources. Here we mathematically derive and test, under ideal conditions, a method that utilizes the ratios of fecal source-associated genetic markers and culture and molecular measurements of general fecal indicators to apportion enterococci and E. coli. The source contribution is approximately equal to the ratio of the source-associated and the general fecal indicator concentrations in a water sample divided by their ratio in the source material, so long as cross-reactivity is negligible. We illustrate the utility of the ratio method using samples consisting of mixtures of various fecal pollution sources. The results from the ratio method correlated well with the actual source apportionment in artificial samples. However, aging of contamination can confound source allocation predictions. In particular, culturable enterococci and E. coli, the organisms presently regulated in the United States and much of the world, decay at different rates compared to source-associated markers and as a result cannot be apportioned using this method. However, limited data suggest a similar decay rate between source-associated and QPCR-measured Enterococcus and E. coli genetic markers, indicating that apportionment may be possible for these organisms; however further work is needed to confirm.

    View details for DOI 10.1016/j.watres.2013.02.058

    View details for PubMedID 23890872

  • Characterization of fecal concentrations in human and other animal sources by physical, culture-based, and quantitative real-time PCR methods WATER RESEARCH Ervin, J. S., Russell, T. L., Layton, B. A., Yamahara, K. M., Wang, D., Sassoubre, L. M., Cao, Y., Kelty, C. A., Sivaganesan, M., Boehm, A. B., Holden, P. A., Weisberg, S. B., Shanks, O. C. 2013; 47 (18): 6873-6882


    The characteristics of fecal sources, and the ways in which they are measured, can profoundly influence the interpretation of which sources are contaminating a body of water. Although feces from various hosts are known to differ in mass and composition, it is not well understood how those differences compare across fecal sources and how differences depend on characterization methods. This study investigated how nine different fecal characterization methods provide different measures of fecal concentration in water, and how results varied across twelve different fecal pollution sources. Sources investigated included chicken, cow, deer, dog, goose, gull, horse, human, pig, pigeon, septage and sewage. A composite fecal slurry was prepared for each source by mixing feces from 6 to 22 individual samples with artificial freshwater. Fecal concentrations were estimated by physical (wet fecal mass added and total DNA mass extracted), culture-based (Escherichia coli and enterococci by membrane filtration and defined substrate), and quantitative real-time PCR (Bacteroidales, E. coli, and enterococci) characterization methods. The characteristics of each composite fecal slurry and the relationships between physical, culture-based and qPCR-based characteristics varied within and among different fecal sources. An in silico exercise was performed to assess how different characterization methods can impact identification of the dominant fecal pollution source in a mixed source sample. A comparison of simulated 10:90 mixtures based on enterococci by defined substrate predicted a source reversal in 27% of all possible combinations, while mixtures based on E. coli membrane filtration resulted in a reversal 29% of the time. This potential for disagreement in minor or dominant source identification based on different methods of measurement represents an important challenge for water quality managers and researchers.

    View details for DOI 10.1016/j.watres.2013.02.060

    View details for Web of Science ID 000328444000007

    View details for PubMedID 23871252

  • Recommendations following a multi-laboratory comparison of microbial source tracking methods WATER RESEARCH Stewart, J. R., Boehm, A. B., Dubinsky, E. A., Fong, T., Goodwin, K. D., Griffith, J. F., Noble, R. T., Shanks, O. C., Vijayavel, K., Weisberg, S. B. 2013; 47 (18): 6829-6838


    Microbial source tracking (MST) methods were evaluated in the Source Identification Protocol Project (SIPP), in which 27 laboratories compared methods to identify host sources of fecal pollution from blinded water samples containing either one or two different fecal types collected from California. This paper details lessons learned from the SIPP study and makes recommendations to further advance the field of MST. Overall, results from the SIPP study demonstrated that methods are available that can correctly identify whether particular host sources including humans, cows and birds have contributed to contamination in a body of water. However, differences between laboratory protocols and data processing affected results and complicated interpretation of MST method performance in some cases. This was an issue particularly for samples that tested positive (non-zero Ct values) but below the limits of quantification or detection of a PCR assay. Although false positives were observed, such samples in the SIPP study often contained the fecal pollution source that was being targeted, i.e., the samples were true positives. Given these results, and the fact that MST often requires detection of targets present in low concentrations, we propose that such samples be reported and identified in a unique category to facilitate data analysis and method comparisons. Important data can be lost when such samples are simply reported as positive or negative. Actionable thresholds were not derived in the SIPP study due to limitations that included geographic scope, age of samples, and difficulties interpreting low concentrations of target in environmental samples. Nevertheless, the results of the study support the use of MST for water management, especially to prioritize impaired waters in need of remediation. Future integration of MST data into quantitative microbial risk assessments and other models could allow managers to more efficiently protect public health based on site conditions.

    View details for DOI 10.1016/j.watres.2013.04.063

    View details for Web of Science ID 000328444000003

    View details for PubMedID 23891204

  • Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study WATER RESEARCH Layton, B. A., Cao, Y., Ebentier, D. L., Hanley, K., Balleste, E., Brandao, J., Byappanahalli, M., Converse, R., Farnleitner, A. H., Gentry-Shields, J., Gidley, M. L., Gourmelon, M., Lee, C. S., Lee, J., Lozach, S., Madi, T., Meijer, W. G., Noble, R., Peed, L., Reischer, G. H., Rodrigues, R., Rose, J. B., Schriewer, A., Sinigalliano, C., Srinivasan, S., Stewart, J., Van De Werfhorst, L. C., Wang, D., Whitman, R., Wuertz, S., Jay, J., Holden, P. A., Boehm, A. B., Shanks, O., Griffith, J. F. 2013; 47 (18): 6897-6908


    A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman(®), HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources. The assay results were assessed for presence/absence of the human markers and also quantitatively while varying the following: 1) classification of samples that were detected but not quantifiable (DNQ) as positive or negative; 2) reference fecal sample concentration unit of measure (such as culturable indicator bacteria, wet mass, total DNA, etc); and 3) human fecal source type (stool, sewage or septage). Assay performance using presence/absence metrics was found to depend on the classification of DNQ samples. The assays that performed best quantitatively varied based on the fecal concentration unit of measure and laboratory protocol. All methods were consistently more sensitive to human stools compared to sewage or septage in both the presence/absence and quantitative analysis. Overall, HF183 Taqman(®) was found to be the most effective marker of human fecal contamination in this California-based study.

    View details for DOI 10.1016/j.watres.2013.05.060

    View details for Web of Science ID 000328444000009

    View details for PubMedID 23992621

  • Performance of forty-one microbial source tracking methods: A twenty-seven lab evaluation study. Water research Boehm, A. B., Van De Werfhorst, L. C., Griffith, J. F., Holden, P. A., Jay, J. A., Shanks, O. C., Wang, D., Weisberg, S. B. 2013; 47 (18): 6812-6828


    The last decade has seen development of numerous new microbial source tracking (MST) methodologies, but many of these have been tested in just a few laboratories with a limited number of fecal samples. This method evaluation study examined the specificity and sensitivity of 41 MST methodologies by analyzing data generated in 27 laboratories. MST methodologies that targeted human, cow, ruminant, dog, gull, pig, horse, and sheep were tested against sewage, septage, human, cow, dog, deer, pig, chicken, pigeon, gull, horse, and goose fecal samples. Each laboratory received 64 blind samples containing a single source (singletons) or two sources (doubletons), as well as diluted singleton samples to assess method sensitivity. Laboratories utilized their own protocols when performing the methods and data were deposited in a central database before samples were unblinded. Between one and seven laboratories tested each method. The most sensitive and specific assays, based on an analysis of presence/absence of each marker in target and non-target fecal samples, were HF183 endpoint and HF183SYBR (human), CF193 and Rum2Bac (ruminant), CowM2 and CowM3 (cow), BacCan (dog), Gull2SYBR and LeeSeaGull (gull), PF163 and pigmtDNA (pig), HoF597 (horse), PhyloChip (pig, horse, chicken, deer), Universal 16S TRFLP (deer), and Bacteroidales 16S TRFLP (pig, horse, chicken, deer); all had sensitivity and specificity higher than 80% in all or the majority of laboratories. When the abundance of MST markers in target and non-target fecal samples was examined, some assays that performed well in the binary analysis were found to not be sensitive enough as median concentrations fell below a minimum abundance criterion (set at 50 copies per colony forming units of enterococci) in target fecal samples. Similarly, some assays that cross-reacted with non-target fecal sources in the binary analysis were found to perform well in a quantitative analysis because the cross-reaction occurred at very low levels. Based on a quantitative analysis, the best performing methods were HF183Taqman and BacH (human), Rum2Bac and BacR (ruminant), LeeSeaGull (gull), and Pig2Bac (pig); no cow or dog-specific assay met the quantitative specificity and sensitivity criteria. Some of the best performing assays in the study were run by just one laboratory so further testing of assay portability is needed. While this study evaluated the marker performance in defined samples, further field testing as well as development of frameworks for fecal source allocation and risk assessment are needed.

    View details for DOI 10.1016/j.watres.2012.12.046

    View details for PubMedID 23880218

  • Simple estimate of entrainment rate of pollutants from a coastal discharge into the surf zone. Environmental science & technology Wong, S. H., Monismith, S. G., Boehm, A. B. 2013; 47 (20): 11554-11561


    Microbial pollutants from coastal discharges can increase illness risks for swimmers and cause beach advisories. There is presently no predictive model for estimating the entrainment of pollution from coastal discharges into the surf zone. We present a novel, quantitative framework for estimating surf zone entrainment of pollution at a wave-dominant open beach. Using physical arguments, we identify a dimensionless parameter equal to the quotient of the surf zone width l(sz) and the cross-flow length scale of the discharge la = M(j) (1/2)/U(sz), where M(j) is the discharge's momentum flux and U(sz) is a representative alongshore velocity in the surf zone. We conducted numerical modeling of a nonbuoyant discharge at an alongshore uniform beach with constant slope using a wave-resolving hydrodynamic model. Using results from 144 numerical experiments we develop an empirical relationship between the surf zone entrainment rate α and l(sz)/(la). The empirical relationship can reasonably explain seven measurements of surf zone entrainment at three diverse coastal discharges. This predictive relationship can be a useful tool in coastal water quality management and can be used to develop predictive beach water quality models.

    View details for DOI 10.1021/es402492f

    View details for PubMedID 24006887

  • Engineering Solutions to Improve the Removal of Fecal Indicator Bacteria by Bioinfiltration Systems during Intermittent Flow of Stormwater. Environmental science & technology Mohanty, S. K., Torkelson, A. A., Dodd, H., Nelson, K. L., Boehm, A. B. 2013; 47 (19): 10791-10798


    Bioinfiltration systems facilitate the infiltration of urban stormwater into soil and reduce high flow events and flooding. Stormwater carries a myriad of pollutants including fecal indicator bacteria (FIB). Significant knowledge gaps exist about the ability of bioinfiltration systems to remove and retain FIB. The present study investigates the ability of model, simplified bioinfiltration systems containing quartz sand and iron oxide-coated quartz sand (IOCS) to remove two FIB (Enterococcus faecalis and Escherichia coli) suspended in synthetic stormwater with and without natural organic matter (NOM) as well as the potential for accumulated FIB to be remobilized during intermittent flow. The experiments were conducted in two phases: (1) the saturated columns packed with either sand or IOCS were contaminated by injecting stormwater with bacteria followed by injection of sterile stormwater and (2) the contaminated columns were subjected to intermittent infiltration of sterile stormwater preceded by a pause during which columns were either kept saturated or drained by gravity. During intermittent flow, fewer bacteria were released from the saturated column compared to the column drained by gravity: 12% of attached E. coli and 3% of attached Ent. faecalis were mobilized from the drained sand column compared to 3% of attached E. coli and 2% attached Ent. faecalis mobilized from the saturated sand column. Dry and wet cycles introduce moving air-water interfaces that can scour bacteria from grain surfaces. During intermittent flows, less than 0.2% of attached bacteria were mobilized from IOCS, which bound both bacteria irreversibly in the absence of NOM. Addition of NOM, however, increased bacterial mobilization from IOCS: 50% of attached E. coli and 8% of attached Ent. faecalis were released from IOCS columns during draining and rewetting. Results indicate that using geomedia such as IOCS that promote irreversible attachment of bacteria, and maintaining saturated condition, could minimize the mobilization of previous attached bacteria from bioinfiltration systems, although NOM may significantly decrease these benefits.

    View details for DOI 10.1021/es305136b

    View details for PubMedID 23721343

  • A Coupled Modeling and Molecular Biology Approach to Microbial Source Tracking at Cowell Beach, Santa Cruz, CA, United States. Environmental science & technology Russell, T. L., Sassoubre, L. M., Wang, D., Masuda, S., Chen, H., Soetjipto, C., Hassaballah, A., Boehm, A. B. 2013; 47 (18): 10231-10239


    Consistently high levels of bacterial indicators of fecal pollution rank Cowell Beach as the most polluted beach in California. High levels of fecal indicator bacteria (FIB), E. coli and enterococci, are measured throughout the summer, resulting in beach advisories with social and economic consequences. The source of FIB, however, is unknown. Speculations have been made that the wrack accumulating on the beach is a major source of FIB to the surf zone. The present study uses spatial and temporal sampling coupled with process-modeling to investigate potential FIB sources and the relative contributions of those sources. Temporal sampling showed consistently high FIB concentrations in the surf zone, sand, and wrack at Cowell Beach, and ruled out the storm drain, the river, the harbor, and the adjacent wharf as the sources of the high concentrations observed in the surf zone. Spatial sampling confirmed that the source of FIB to the beach is terrestrial rather than marine. Modeling results showed two dominant FIB sources to the surf zone: sand for enterococci and groundwater for E. coli. FIB from wrack represented a minor contribution to bacterial levels in the water. Molecular source tracking methods indicate the FIB at the beach is of human and bird origin. The microbial source tracking (MST) approach presented here provides a framework for future efforts.

    View details for DOI 10.1021/es402303w

    View details for PubMedID 23924260

  • A coupled modeling and molecular biology approach to microbial source tracking at Cowell Beach, Santa Cruz, CA, United States. Environmental science & technology Russell, T. L., Sassoubre, L. M., Wang, D., Masuda, S., Chen, H., Soetjipto, C., Hassaballah, A., Boehm, A. B. 2013; 47 (18): 10231-10239


    Consistently high levels of bacterial indicators of fecal pollution rank Cowell Beach as the most polluted beach in California. High levels of fecal indicator bacteria (FIB), E. coli and enterococci, are measured throughout the summer, resulting in beach advisories with social and economic consequences. The source of FIB, however, is unknown. Speculations have been made that the wrack accumulating on the beach is a major source of FIB to the surf zone. The present study uses spatial and temporal sampling coupled with process-modeling to investigate potential FIB sources and the relative contributions of those sources. Temporal sampling showed consistently high FIB concentrations in the surf zone, sand, and wrack at Cowell Beach, and ruled out the storm drain, the river, the harbor, and the adjacent wharf as the sources of the high concentrations observed in the surf zone. Spatial sampling confirmed that the source of FIB to the beach is terrestrial rather than marine. Modeling results showed two dominant FIB sources to the surf zone: sand for enterococci and groundwater for E. coli. FIB from wrack represented a minor contribution to bacterial levels in the water. Molecular source tracking methods indicate the FIB at the beach is of human and bird origin. The microbial source tracking (MST) approach presented here provides a framework for future efforts.

    View details for DOI 10.1021/es402303w

    View details for PubMedID 23924260

  • Conducting nanosponge electroporation for affordable and high-efficiency disinfection of bacteria and viruses in water. Nano letters Liu, C., Xie, X., Zhao, W., Liu, N., Maraccini, P. A., Sassoubre, L. M., Boehm, A. B., Cui, Y. 2013; 13 (9): 4288-4293


    High-efficiency, affordable, and low energy water disinfection methods are in great need to prevent diarrheal illness, which is one of the top five leading causes of death over the world. Traditional water disinfection methods have drawbacks including carcinogenic disinfection byproducts formation, energy and time intensiveness, and pathogen recovery. Here, we report an innovative method that achieves high-efficiency water disinfection by introducing nanomaterial-assisted electroporation implemented by a conducting nanosponge filtration device. The use of one-dimensional (1D) nanomaterials allows electroporation to occur at only several volts, which is 2 to 3 orders of magnitude lower than that in traditional electroporation applications. The disinfection mechanism of electroporation prevents harmful byproduct formation and ensures a fast treatment speed of 15 000 L/(h·m(2)), which is equal to a contact time of 1 s. The conducting nanosponge made from low-cost polyurethane sponge coated with carbon nanotubes and silver nanowires ensures the device's affordability. This method achieves more than 6 log (99.9999%) removal of four model bacteria, including Escherichia coli, Salmonella enterica Typhimirium, Enterococcus faecalis, and Bacillus subtilis, and more than 2 log (99%) removal of one model virus, bacteriophage MS2, with a low energy consumption of only 100 J/L.

    View details for DOI 10.1021/nl402053z

    View details for PubMedID 23987737

  • Mechanisms of post-supply contamination of drinking water in Bagamoyo, Tanzania. Journal of water and health Harris, A. R., Davis, J., Boehm, A. B. 2013; 11 (3): 543-554


    Access to household water connections remains low in sub-Saharan Africa, representing a public health concern. Previous studies have shown water stored in the home to be more contaminated than water at the source; however, the mechanisms of post-supply contamination remain unclear. Using water quality measurements and structured observations of households in Bagamoyo, Tanzania, this study elucidates the causal mechanisms of the microbial contamination of drinking water after collection from a communal water source. The study identifies statistically significant loadings of fecal indicator bacteria (FIB) occurring immediately after filling the storage container at the source and after extraction of the water from the container in the home. Statistically significant loadings of FIB also occur with various water extraction methods, including decanting from the container and use of a cup or ladle. Additionally, pathogenic genes of Escherichia coli were detected in stored drinking water but not in the source from which it was collected, highlighting the potential health risks of post-supply contamination. The results of the study confirm that storage containers and extraction utensils introduce microbial contamination into stored drinking water, and suggest that further research is needed to identify methods of water extraction that prevent microbial contamination of drinking water.

    View details for DOI 10.2166/wh.2013.023

    View details for PubMedID 23981881

  • Enterococcus spp on fomites and hands indicate increased risk of respiratory illness in child care centers AMERICAN JOURNAL OF INFECTION CONTROL Julian, T. R., Pickering, A. J., Leckie, J. O., Boehm, A. B. 2013; 41 (8): 728-733


    BACKGROUND: Surface-mediated transmission is a potential route for respiratory disease in child care centers, but evidence of its importance relative to other routes (eg, airborne) is limited. METHODS: We tracked respiratory disease and monitored bacteria contamination on hands and fomites over 4 months during 64 visits at 2 child care centers. Staff monitored health daily by recording respiratory symptoms. We measured concentrations of Escherichia coli, Enterococcus spp, and fecal coliform in hand rinses and on select fomites. RESULTS: We demonstrated that symptomatic respiratory illness was positively associated with microbial contamination on hands and fomites, as measured using Enterococcus spp. Enterococcus spp were 0.28 (95% confidence interval: 0.08-0.48)-log(10) (colony-forming units per 2 hands) higher when an individual had symptomatic respiratory illness. Susceptible individuals were 1.62 (95% confidence interval: 1.06-2.46) times more likely to develop respiratory illness within 4 days with every log(10) increase of Enterococcus spp on hands. CONCLUSION: The findings imply that hand contamination as measured using Enterococcus spp is a risk factor for onset of respiratory illness and highlight the utility of fecal indicator bacteria as a metric for hand and fomite contamination.

    View details for DOI 10.1016/j.ajic.2012.10.013

    View details for Web of Science ID 000322641100014

    View details for PubMedID 23394857

  • Engineered Infiltration Systems for Urban Stormwater Reclamation ENVIRONMENTAL ENGINEERING SCIENCE Grebel, J. E., Mohanty, S. K., Torkelson, A. A., Boehm, A. B., Higgins, C. P., Maxwell, R. M., Nelson, K. L., Sedlak, D. L. 2013; 30 (8): 437-454
  • Salmonella enterica Diversity in Central Californian Coastal Waterways. Applied and environmental microbiology Walters, S. P., González-Escalona, N., Son, I., Melka, D. C., Sassoubre, L. M., Boehm, A. B. 2013; 79 (14): 4199-4209


    Salmonella enterica is one of the most important bacterial enteric pathogens worldwide, however, little is known about its distribution and diversity in the environment. The present study explored the diversity of 104 strains of Salmonella enterica isolated over two years from twelve coastal waterways in central California. Pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to probe species diversity. Seventy-four PFGE patterns and 38 sequence types (STs) were found including 18 newly described ST. Nineteen of 25 PFGE patterns were indistinguishable from those of clinical isolates in PulseNet. The most common ST was consistent with S. enterica serovar Typhimurium; other frequently detected STs were associated with serovars Heidelberg and Enteritidis - all important etiologies of salmonellosis. An investigation into S. enterica biogeography was conducted at the level of ST and subspecies. At the ST and subspecies level, we found a taxa-time relationship, but no taxa-area or taxa-environmental distance relationships. STs collected during wet versus dry conditions tended to be more similar; however, STs collected from waterways adjacent to watersheds with similar land covers did not tend to be similar. The results suggest lack of dispersal limitation may be an important factor affecting the diversity of S. enterica in the region.

    View details for DOI 10.1128/AEM.00930-13

    View details for PubMedID 23624479

  • Sunlight Inactivation of Human Viruses and Bacteriophages in Coastal Waters Containing Natural Photosensitizers ENVIRONMENTAL SCIENCE & TECHNOLOGY Silverman, A. I., Peterson, B. M., Boehm, A. B., McNeill, K., Nelson, K. L. 2013; 47 (4): 1870-1878


    Sunlight inactivation of poliovirus type 3 (PV3), adenovirus type 2 (HAdV2), and two bacteriophage (MS2 and PRD1) was investigated in an array of coastal waters to better understand solar inactivation mechanisms and the effect of natural water constituents on observed inactivation rates (k(obs)). Reactor scale inactivation experiments were conducted using a solar simulator, and k(obs) for each virus was measured in a sensitizer-free control and five unfiltered surface water samples collected from different sources. k(obs) values varied between viruses in the same water matrix, and for each virus in different matrices, with PV3 having the fastest and MS2 the slowest k(obs) in all waters. When exposed to full-spectrum sunlight, the presence of photosensitizers increased k(obs) of HAdV2, PRD1 and MS2, but not PV3, which provides evidence that the exogenous sunlight inactivation mechanism, involving damage by exogenously produced reactive intermediates, played a greater role for these viruses. While PV3 inactivation was observed to be dominated by endogenous mechanisms, this may be due to a masking of exogenous k(obs) by significantly faster endogenous k(obs). Results illustrate that differences in water composition can shift absolute and relative inactivation rates of viruses, which has important implications for natural wastewater treatment systems, solar disinfection (SODIS), and the use of indicator organisms for monitoring water quality.

    View details for DOI 10.1021/es3036913

    View details for Web of Science ID 000315326700012

    View details for PubMedID 23384052

  • Hands and Water as Vectors of Diarrhea! Pathogens in Bagannoyo, Tanzania ENVIRONMENTAL SCIENCE & TECHNOLOGY Mattioli, M. C., Pickering, A. J., Gilsdorf, R. J., Davis, J., Boehm, A. B. 2013; 47 (1): 355-363


    Diarrheal disease is a leading cause of under-five childhood mortality worldwide, with at least half of these deaths occurring in sub-Saharan Africa. Transmission of diarrheal pathogens occurs through several exposure routes including drinking water and hands, but the relative importance of each route is not well understood. Using molecular methods, this study examines the relative importance of different exposure routes by measuring enteric bacteria (pathogenic Escherichia coli) and viruses (rotavirus, enterovirus, adenovirus) in hand rinses, stored water, and source waters in Bagamoyo, Tanzania. Viruses were most frequently found on hands, suggesting that hands are important vectors for viral illness. The occurrence of E. coli virulence genes (ECVG) was equivalent across all sample types, indicating that both water and hands are important for bacterial pathogen transmission. Fecal indicator bacteria and turbidity were good predictors of ECVG, whereas turbidity and human-specific Bacteroidales were good predictors of viruses. ECVG were more likely found in unimproved water sources, but both ECVG and viral genes were detected in improved water sources. ECVG were more likely found in stored water of households with unimproved sanitation facilities. The results provide insights into the distribution of pathogens in Tanzanian households and offer evidence that hand-washing and improved water management practices could alleviate viral and bacterial diarrhea.

    View details for DOI 10.1021/es303878d

    View details for Web of Science ID 000313220300046

    View details for PubMedID 23181394

  • Recommendations following a multi-laboratory comparison of microbial source tracking methods. Water Research. Stewart, J., Boehm, A., B, Dubinsky, E., A., Fong, T., T., Goodwin, K., D., Griffith, J., F. 2013; 47: 6829-6838
  • Performance of Viruses and Bacteriophages for Fecal Source Determination in a Multi-Laboratory, Comparative Study. Water Research. Harwood, V., J., Boehm, A., B., Sassoubre, L., M., Kannappan, V., Stewart, J., R., Fong, T., T. 2013; 47: 6929-6943
  • Multi-Laboratory Evaluations of the Performance of Catellicoccus marimamm\ alium PCR Assays Developed to Target Gull Fecal Sources Water Research. Sinigalliano, C., D., Ervin, J., Van De Werfhorst, L., Badgley, B., Balleste, E., Bartkowiak, J., Boehm, A. 2013; 47: 6883-6896
  • Fecal indicator bacteria on fomites and hands are associated with increased risk of respiratory illness in day care centers. American Journal of Infection Control Julian, T., R., Pickering, A., J., Leckie, J., O., Boehm., A., B. 2013; 41: 728-733
  • Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods. Water Research. Ebentier, D., L., Hanley, K., T., Cao, Y., Badgley, B., D., Boehm, A., B., Ervin, J., S. 2013; 47: 6839-6848
  • Characterization of fecal concentrations in human and other animal sources by physical, cutlure, and quantitative real-time PCR methods. Water Research. Ervin, J., S., Russell, T., L, Layton, B., A., Yamahara, K., M., Wang, D., Sassoubre, L., M., Boehm, A. 2013; 47: 6873-6882
  • A simple estimate of entrainment rate of pollutants from a coastal discharge into the surf zone. Environmental Science & Technology Wong, S.H., C., Monismith, S., G., Boehm, A., B. 2013; 47: 11554-11561
  • Performance of human fecal-associated PCR-based assays: an international source identificiaiton method evaluation. Water Research. Layton, B., Cao, Y., Ebentie, D., L., Hanley, K., T., Van De Werfhorst, L., Wang, D., Boehm, A. 2013; 47: 6897-6908
  • Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers -- Is it feasible? Water Research. Wang, D., Farnleitner, A., H., Field, K., G., Green, H., C., Shanks, O., C., Boehm., A., B. 2013; 47: 6849-6861
  • Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources. Water Research. Raith, M., Kelty, C., A., Griffith, J., F., Schriewer, A., Wuertz, S., Mieszkin, S., Boehm, A. 2013; 47: 6921-6928
  • Mechanisms for Photoinactivation of Enterococcus faecalis in Seawater APPLIED AND ENVIRONMENTAL MICROBIOLOGY Sassoubre, L. M., Nelson, K. L., Boehm, A. B. 2012; 78 (21): 7776-7785


    Field studies in fresh and marine waters consistently show diel fluctuations in concentrations of enterococci, indicators of water quality. We investigated sunlight inactivation of Enterococcus faecalis to gain insight into photoinactivation mechanisms and cellular responses to photostress. E. faecalis bacteria were exposed to natural sunlight in clear, filtered seawater under both oxic and anoxic conditions to test the relative importance of oxygen-mediated and non-oxygen-mediated photoinactivation mechanisms. Multiple methods were used to assess changes in bacterial concentration, including cultivation, quantitative PCR (qPCR), propidium monoazide (PMA)-qPCR, LIVE/DEAD staining using propidium iodide (PI), and cellular activity, including ATP concentrations and expression of the superoxide dismutase-encoding gene, sodA. Photoinactivation, based on numbers of cultivable cells, was faster in oxic than in anoxic microcosms exposed to sunlight, suggesting that oxygen-mediated photoinactivation dominated. There was little change in qPCR signal over the course of the experiment, demonstrating that the nucleic acid targets were not damaged to a significant extent. The PMA-qPCR signal was also fairly stable, consistent with the observation that the fraction of PI-permeable cells was constant. Thus, damage to the membrane was minimal. Microbial ATP concentrations decreased in all microcosms, particularly the sunlit oxic microcosms. The increase in relative expression of the sodA gene in the sunlit oxic microcosms suggests that cells were actively responding to oxidative stress. Dark repair was not observed. This research furthers our understanding of photoinactivation mechanisms and the conditions under which diel fluctuations in enterococci can be expected in natural and engineered systems.

    View details for DOI 10.1128/AEM.02375-12

    View details for Web of Science ID 000309678600032

    View details for PubMedID 22941072

  • Comparison of enterovirus and adenovirus concentration and enumeration methods in seawater from Southern California, USA and Baja Malibu, Mexico JOURNAL OF WATER AND HEALTH Sassoubre, L. M., Love, D. C., Silverman, A. I., Nelson, K. L., Boehm, A. B. 2012; 10 (3): 419-430


    Despite being important etiological agents of waterborne illness, the sources, transport and decay of human viruses in recreational waters are not well understood. This study examines enterovirus and adenovirus concentrations in coastal water samples collected from four beaches impacted by microbial pollution: (1) Malibu Lagoon, Malibu; (2) Tijuana River, Imperial Beach; (3) Baja Malibu, Baja California; and (4) Punta Bandera, Baja California. Water samples were concentrated using a flocculation-based skim milk method and dead-end membrane filtration (MF). Viruses were enumerated using cell culture infectivity assays and reverse transcription quantitative polymerase chain reaction (RT-QPCR). Across concentration and quantification methods, enteroviruses were detected more often than adenoviruses. For both viruses, MF followed by (RT)QPCR yielded higher concentrations than skim milk flocculation followed by (RT)QPCR or cell culture assays. Samples concentrated by skim milk flocculation and enumerated by (RT)QPCR agreed more closely with concentrations enumerated by cell culture assays than MF followed by (RT)QPCR. The detection of viruses by MF and (RT)QPCR was positively correlated with the presence of infectious viruses. Further research is needed to determine if detection of viruses by rapid methods such as (RT)QPCR can be a useful water quality monitoring tool to assess health risks in recreational waters.

    View details for DOI 10.2166/wh.2012.011

    View details for Web of Science ID 000309490300009

    View details for PubMedID 22960486

  • Mobilization and Transport of Naturally Occurring Enterococci in Beach Sands Subject to Transient Infiltration of Seawater ENVIRONMENTAL SCIENCE & TECHNOLOGY Russell, T. L., Yamahara, K. M., Boehm, A. B. 2012; 46 (11): 5988-5996


    This study explores the transport of enterococci (ENT) from naturally contaminated beach sands to the groundwater table via infiltrating seawater using field, laboratory, and modeling experiments. ENT were readily mobilized and transported through the unsaturated zone during infiltration events in both the field and laboratory column experiments. Detachment mechanisms were investigated using a modified version of HYDRUS-1D. Three models for detachment kinetics were tested. Detachment kinetics that are first order with respect to the rate of change in the water content and attached surface bacterial concentrations were found to provide a best fit between predicted and observed data. From these experimental and model results we conclude that detachment mechanisms associated with the rapid increases in pore water content such as air-water interface scouring and thin film expansion are likely drivers of ENT mobilization in the investigated system. These findings suggest that through-beach transport of ENT may be an important pathway through which ENT from beach sands are transported to beach groundwater where they may be discharged to coastal waters via submarine groundwater discharge.

    View details for DOI 10.1021/es300408z

    View details for Web of Science ID 000304783000046

    View details for PubMedID 22533299

  • Fecal Contamination and Diarrheal Pathogens on Surfaces and in Soils among Tanzanian Households with and without Improved Sanitation ENVIRONMENTAL SCIENCE & TECHNOLOGY Pickering, A. J., Julian, T. R., Marks, S. J., Mattioli, M. C., Boehm, A. B., Schwab, K. J., Davis, J. 2012; 46 (11): 5736-5743


    Little is known about the extent or pattern of environmental fecal contamination among households using low-cost, on-site sanitation facilities, or what role environmental contamination plays in the transmission of diarrheal disease. A microbial survey of fecal contamination and selected diarrheal pathogens in soil (n = 200), surface (n = 120), and produce samples (n = 24) was conducted in peri-urban Bagamoyo, Tanzania, among 20 households using private pit latrines. All samples were analyzed for E. coli and enterococci. A subset was analyzed for enterovirus, rotavirus, norovirus GI, norovirus GII, diarrheagenic E. coli, and general and human-specific Bacteroidales fecal markers using molecular methods. Soil collected from the house floor had significantly higher concentrations of E. coli and enterococci than soil collected from the latrine floor. There was no significant difference in fecal indicator bacteria levels between households using pit latrines with a concrete slab (improved sanitation) versus those without a slab. These findings imply that the presence of a concrete slab does not affect the level of fecal contamination in the household environment in this setting. Human Bacteroidales, pathogenic E. coli, enterovirus, and rotavirus genes were detected in soil samples, suggesting that soil should be given more attention as a transmission pathway of diarrheal illness in low-income countries.

    View details for DOI 10.1021/es300022c

    View details for Web of Science ID 000304783000017

    View details for PubMedID 22545817

  • Occurrence and Persistence of Bacterial Pathogens and Indicator Organisms in Beach Sand along the California Coast APPLIED AND ENVIRONMENTAL MICROBIOLOGY Yamahara, K. M., Sassoubre, L. M., Goodwin, K. D., Boehm, A. B. 2012; 78 (6): 1733-1745


    This report documents the presence of fecal indicators and bacterial pathogens in sand at 53 California marine beaches using both culture-dependent and -independent (PCR and quantitative PCR [QPCR]) methods. Fecal indicator bacteria were widespread in California beach sand, with Escherichia coli and enterococci detected at 68% and 94% of the beaches surveyed, respectively. Somatic coliphages and a Bacteroidales human-specific fecal marker were detected at 43% and 13% of the beaches, respectively. Dry sand samples from almost 30% of the beaches contained at least one of the following pathogens: Salmonella spp., Campylobacter spp., Staphylococcus aureus, and methicillin-resistant Staphylococcus aureus (MRSA), which were detected at 15%, 13%, 14%, and 3% of tested beaches, respectively. Fecal indicators and pathogens were poorly correlated to one another and to land cover. Sands were dry at the time of collection, and those with relatively high moisture tended to have higher concentrations or a more frequent occurrence of both indicators and pathogens. Using culture-dependent assays, fecal indicators decayed faster than pathogens in microcosm experiments using unaltered beach sand seeded with sewage and assessed by culture-dependent assays. The following order of persistence was observed (listed from most to least persistent): Campylobacter > Salmonella > somatic coliphages > enterococci > E. coli > F(+) phages. In contrast, pathogens decayed faster than fecal indicators in culture-independent assays: enterococci > Bacteroidales human-specific marker > Salmonella > Campylobacter. Microcosm experiments demonstrated that both indicators and pathogens were mobilized by wetting with seawater. Decay rates measured by QPCR were lower than those measured with culture-dependent methods. Enterococcal persistence and possible growth were observed for wetted microcosms relative to unwetted controls.

    View details for DOI 10.1128/AEM.06185-11

    View details for Web of Science ID 000300629800014

    View details for PubMedID 22247142

  • Coupled physical, chemical, and microbiological measurements suggest a connection between internal waves and surf zone water quality in the Southern California Bight CONTINENTAL SHELF RESEARCH Wong, S. H., Santoro, A. E., Nidzieko, N. J., Hench, J. L., Boehm, A. B. 2012; 34: 64-78
  • Solar inactivation of four Salmonella serovars in fresh and marine waters JOURNAL OF WATER AND HEALTH Boehm, A. B., Soetjipto, C., Wang, D. 2012; 10 (4): 504-510


    Sunlight-mediated disinfection of water is of interest to both the drinking and recreational water quality community of researchers due to its potential to reduce microbial contamination and waterborne illness. Photo-inactivation of enteric bacteria has primarily been investigated using Escherichia coli and laboratory strains of model bacteria. The present study sought to document the photo-inactivation of environmental isolates of Salmonella in filter-sterilized natural seawater and freshwater and to test the hypothesis that diverse Salmonella serovars decay at similar rates both within and between water matrices. The inactivation of Salmonella enterica Typhimurium LT2, Typhimurium ST19, Heidelberg, and Mbandaka was examined in sunlit and dark microcosms. First order decay was observed in sunlit microcosms; the time until 90% inactivation was of the order of 10 min. A significant shoulder, of the order of 1 hr in length, was observed in the freshwater microcosms during which concentrations were stable. Serovar Mdandaka decayed more slowly than other serovars in both seawater and freshwater. The serovars were extremely stable in the dark microcosms showing little to no decay over 53 days. The results document intra-species variation in photo-inactivation, likely owing to differences in intracellular concentrations of photo-sensitizing molecules or molecules that quench reactive species.

    View details for DOI 10.2166/wh.2012.084

    View details for Web of Science ID 000311341300002

    View details for PubMedID 23165707

  • Marine and Freshwater Fecal Indicators and Source Identification. Encyclopedia of Sustainability Science and Technology McLellan, S., L., Boehm, A., B., Shanks, O., C. edited by Grimes, D., J. 2012
  • Photoinactivation mechanisms of Enterococcus faecalis in seawater. Applied and Environmental Microbiology Sassoubre, L., M., Nelson, K., L., Boehm., A., B. 2012; 78: 7776-7785
  • Diurnal Variation in Enterococcus Species Composition in Polluted Ocean Water and a Potential Role for the Enterococcal Carotenoid in Protection against Photoinactivation APPLIED AND ENVIRONMENTAL MICROBIOLOGY Maraccini, P. A., Ferguson, D. M., Boehm, A. B. 2012; 78 (2): 305-310


    Enterococcus species composition was determined each hour for 72 h at a polluted marine beach in Avalon, Santa Catalina Island, CA. Species composition during the day was significantly different from that at night, based on an analysis of similarity. Enterococcus faecium and E. faecalis were more prevalent at night than during the day, while E. hirae and other Enterococcus species were more prevalent during the day than the night. Enterococcus spp. containing a yellow pigment were more common during the day than the night, suggesting that the pigmented phenotype may offer a competitive advantage under sunlit conditions. A laboratory microcosm experiment established that the pigmented E. casseliflavus isolate and a pigmented E. faecalis isolate recovered from the field site decay slower than a nonpigmented E. faecalis isolate in a solar simulator in simulated, clear seawater. This further supports the idea that the yellow carotenoid pigment in Enterococcus provides protection under sunlit conditions. The findings are in accordance with previous work with other carotenoid-containing nonphotosynthetic and photosynthetic bacteria that suggests that the carotenoid is able to quench reactive oxygen species capable of causing photoinactivation and photostress. The results suggest that using enterococcal species composition as a microbial source tracking tool may be hindered by the differential environmental persistence of pigmented and nonpigmented enterococci.

    View details for DOI 10.1128/AEM.06821-11

    View details for Web of Science ID 000299018800002

    View details for PubMedID 22081569

  • Quantitative PCR-based detection of pathogenic Leptospira in Hawai'ian coastal streams JOURNAL OF WATER AND HEALTH Viau, E. J., Boehm, A. B. 2011; 9 (4): 637-646


    Pathogenic Leptospira, the causative agents of leptospirosis, are mainly associated with tropical freshwaters, but little is known about their fate in the environment. This study analyzed the distribution of pathogenic Leptospira genomes in 22 tropical coastal streams using quantitative polymerase chain reaction (qPCR). Statistical analyses were conducted to understand pathogenic Leptospira associations with water quality parameters, land use, microbial source tracking (MST) markers, and fecal indicators. Results indicated that pathogenic Leptospira genomes were widespread in O'ahu coastal streams during the Hawai'ian rainy season, with slightly higher concentrations in December when compared with March. Leptospira showed a strong positive association to turbidity, a finding consistent with studies showing increased Leptospira survival when aggregated to particles. Positive correlations to salinity may also indicate survival of Leptospira in relatively saline stream waters. A positive association to the human Bacteroidales fecal marker, no correlation to pig or cow Bacteroidales markers, and a negative association to agricultural land coverage may suggest human or other non-agricultural animal sources of Leptospira (e.g., rats or dogs). Future studies of Leptospira in the Hawai'ian environment are recommended to investigate Leptospira survival in saline waters, to determine both primary and secondary Hawai'ian animal hosts of Leptospira, and to correlate environmental exposures with epidemiological studies of leptospirosis.

    View details for DOI 10.2166/wh.2011.064

    View details for Web of Science ID 000297599300003

    View details for PubMedID 22048423

  • Effective detection of human noroviruses in Hawaiian waters using enhanced RT-PCR methods WATER RESEARCH Tong, H., Connell, C., Boehm, A. B., Lu, Y. 2011; 45 (18): 5837-5848


    The current recreational water quality criteria using growth-based measurements of fecal indicator bacteria (FIB) concentration have their limitations for swimmer protection. To evaluate the possible use of enteric viruses as an improved indicator of human sewage contamination in recreational waters for enhanced health risk assessment, human norovirus (huNoV) was tested as a model in this study. To establish a highly sensitive protocol for effective huNoV detection in waters, 16 published and newly designed reverse transcription polymerase chain reaction (RT-PCR) primer pairs specific for huNoV genogroup I (GI) and genogroup II (GII) were comparatively evaluated side-by-side using single sources of huNoV RNA stock extracted from local clinical isolates. Under optimized conditions, these RT-PCR protocols shared a very different pattern of detection sensitivity for huNoV. The primer sets COG2F/COG2R and QNIF4/NV1LCR were determined to be the most sensitive ones for huNoV GII and GI, respectively, with up to 10(5)- and 10(6)-fold more sensitive as compared to other sets tested. These two sensitive protocols were validated by positive detection of huNoV in untreated and treated urban wastewater samples. In addition, these RT-PCR protocols enabled detection of the prevalence of huNoV in 5 (GI) and 10 (GII) of 16 recreational water samples collected around the island of O'ahu, which was confirmed by DNA sequencing and sequence analysis. Findings from this study support the possible use of enteric viral pathogens for environmental monitoring and argue the importance and essentiality for such monitoring activity to ensure a safe use of recreational waters.

    View details for DOI 10.1016/j.watres.2011.08.030

    View details for Web of Science ID 000296826200003

    View details for PubMedID 21945082

  • Comparison of Surface Sampling Methods for Virus Recovery from Fomites APPLIED AND ENVIRONMENTAL MICROBIOLOGY Julian, T. R., Tamayo, F. J., Leckie, J. O., Boehm, A. B. 2011; 77 (19): 6918-6925


    The role of fomites in infectious disease transmission relative to other exposure routes is difficult to discern due, in part, to the lack of information on the level and distribution of virus contamination on surfaces. Comparisons of studies intending to fill this gap are difficult because multiple different sampling methods are employed and authors rarely report their method's lower limit of detection. In the present study, we compare a subset of sampling methods identified from a literature review to demonstrate that sampling method significantly influences study outcomes. We then compare a subset of methods identified from the review to determine the most efficient methods for recovering virus from surfaces in a laboratory trial using MS2 bacteriophage as a model virus. Recoveries of infective MS2 and MS2 RNA are determined using both a plaque assay and quantitative reverse transcription-PCR, respectively. We conclude that the method that most effectively recovers virus from nonporous fomites uses polyester-tipped swabs prewetted in either one-quarter-strength Ringer's solution or saline solution. This method recovers a median fraction for infective MS2 of 0.40 and for MS2 RNA of 0.07. Use of the proposed method for virus recovery in future fomite sampling studies would provide opportunities to compare findings across multiple studies.

    View details for DOI 10.1128/AEM.05709-11

    View details for Web of Science ID 000295123300023

    View details for PubMedID 21821742

  • Swimmer Risk of Gastrointestinal Illness from Exposure to Tropical Coastal Waters Impacted by Terrestrial Dry-Weather Runoff ENVIRONMENTAL SCIENCE & TECHNOLOGY Viau, E. J., Lee, D., Boehm, A. B. 2011; 45 (17): 7158-7165


    This study used molecular methods to measure concentrations of four enteric viruses (adenovirus, enterovirus, norovirus GI, and norovirus GII) and fecal source tracking markers (human, ruminant, and pig Bacteroidales) in land-based runoff from 22 tropical streams on O'ahu, Hawai'i. Each stream was sampled twice in the morning and afternoon during dry weather. Viruses and human Bacteroidales were widespread in the streams. Watershed septic tank densities were positively associated with higher occurrence of human Bacteroidales and norovirus. There were no associations between occurrence of viruses and fecal indicator concentrations. Virus concentrations and previously reported culturable Salmonella and Campylobacter were used as inputs to a quantitative microbial risk assessment (QMRA) model to estimate the risk of acquiring gastrointestinal (GI) illness from swimming in tropical marine waters adjacent to discharging streams. Monte Carlo methods were used to incorporate uncertainties in the dilution of stream discharge with seawater, swimmer ingestion volumes, pathogen concentrations, and dose-response parameters into the model. Median GI illness risk to swimmers from exposure to coastal waters adjacent to the 22 streams ranged from 0 to 21/1000. GI illness risks from viral exposures were generally orders of magnitude greater than bacterial exposures. Swimming adjacent to streams positive for norovirus or adenovirus resulted in the highest risks. The median risk adjacent to each stream was positively, significantly correlated to the concentration of Clostridium perfringens in the stream. Although a number of important assumptions were made to complete the QMRA, results suggest land-based runoff in the tropics as a potential source of GI illness risk, with pathogens coming from both human and nonhuman nonpoint sources including septic tanks.

    View details for DOI 10.1021/es200984b

    View details for Web of Science ID 000294373400012

    View details for PubMedID 21780808

  • Dissolved Inorganic Nitrogen, Soluble Reactive Phosphorous, and Microbial Pollutant Loading from Tropical Rural Watersheds in Hawai'i to the Coastal Ocean During Non-Storm Conditions ESTUARIES AND COASTS Boehm, A. B., Yamahara, K. M., Walters, S. P., Layton, B. A., Keymer, D. P., Thompson, R. S., Knee, K. L., Rosener, M. 2011; 34 (5): 925-936
  • Using radium isotopes to characterize water ages and coastal mixing rates: A sensitivity analysis LIMNOLOGY AND OCEANOGRAPHY-METHODS Knee, K. L., Garcia-Solsona, E., Garcia-Orellana, J., Boehm, A. B., Paytan, A. 2011; 9: 380-395
  • Sources and fate of Salmonella and fecal indicator bacteria in an urban creek JOURNAL OF ENVIRONMENTAL MONITORING Sassoubre, L. M., Walters, S. P., Russell, T. L., Boehm, A. B. 2011; 13 (8): 2206-2212


    This research aimed to understand the sources and fate of Salmonella and fecal bacteria in urban surface waters. An urban creek (San Pedro Creek, California, USA) that had unusually high levels of Salmonella and fecal bacteria relative to other nearby waterbodies was chosen as a model field site. State of the art microbiological methods were used in concert with modeling to investigate Salmonella and fecal bacteria sources, and determine field-relevant dark inactivation and photoinactivation rates. Three along-creek surveys that spanned reaches adjacent to both urban and forested land covers were conducted to measure Salmonella, enterococci, Escherichia coli, and horse- and human-specific Bacteroidales. Salmonella were detected adjacent to and downstream of urban land cover, but not adjacent to forested land cover. No human or horse-specific Bacteroidales fecal markers were detected implicating other urban animal sources of bacteria. Two locations along the creek where Salmonella was consistently detected were sampled hourly for 25 hours and a mass-balance model was applied to determine field-relevant light and dark inactivation rates for Salmonella, enterococci, and E. coli. Sunlight inactivation did not appear to be important in modulating concentrations of Salmonella, but was important in modulating both enterococci and E. coli concentrations. Dark inactivation was important for all three organisms. This is the first study to quantitatively examine the fate of Salmonella within an urban surface water. Although the work is carried out at a single site, the methodologies are extendable to source tracking in other waterbodies. Additionally, the rate constants determined through the modeling will be useful for modeling these organisms in other surface waters, and represent useful benchmarks for comparison to laboratory-derived inactivation rates.

    View details for DOI 10.1039/c1em10213c

    View details for Web of Science ID 000293502600012

    View details for PubMedID 21687857

  • Wrack promotes the persistence of fecal indicator bacteria in marine sands and seawater FEMS MICROBIOLOGY ECOLOGY Imamura, G. J., Thompson, R. S., Boehm, A. B., Jay, J. A. 2011; 77 (1): 40-49


    Algae on freshwater beaches can serve as reservoirs for fecal indicator bacteria (FIB). Wrack (especially kelp) at marine beaches might sustain FIB as well. This study examines the relationship between beach wrack, FIB, and surrounding water and sediment at marine beaches along the California coast. Surveys of southern and central California beaches were conducted to observe environmental wrack-associated FIB concentrations. FIB concentrations normalized to dry weight were the highest in stranded dry wrack, followed by stranded wet and suspended 'surf' wrack. Laboratory microcosms were conducted to examine the effect of wrack on FIB persistence in seawater and sediment. Indigenous enterococci and Escherichia coli incubated in a seawater microcosm containing wrack showed increased persistence relative to those incubated in a microcosm without wrack. FIB concentrations in microcosms containing wrack-covered sand were significantly higher than those in uncovered sand after several days. These findings implicate beach wrack as an important FIB reservoir. The presence of wrack may increase water and sediment FIB levels, altering the relationship between FIB levels and actual health risk while possibly leading to beach closures. Further work will need to investigate the possibility of FIB growth on wrack and the potential for pathogen presence.

    View details for DOI 10.1111/j.1574-6941.2011.01082.x

    View details for Web of Science ID 000291312500004

    View details for PubMedID 21385189

  • Bacterial pathogens in Hawaiian coastal streams-Associations with fecal indicators, land cover, and water quality WATER RESEARCH Viau, E. J., Goodwin, K. D., Yamahara, K. M., Layton, B. A., Sassoubre, L. M., Burns, S. L., Tong, H., Wong, S. H., Lu, Y., Boehm, A. B. 2011; 45 (11): 3279-3290


    This work aimed to understand the distribution of five bacterial pathogens in O'ahu coastal streams and relate their presence to microbial indicator concentrations, land cover of the surrounding watersheds, and physical-chemical measures of stream water quality. Twenty-two streams were sampled four times (in December and March, before sunrise and at high noon) to capture seasonal and time of day variation. Salmonella, Campylobacter, Staphylococcus aureus, Vibrio vulnificus, and V. parahaemolyticus were widespread -12 of 22 O'ahu streams had all five pathogens. All stream waters also had detectable concentrations of four fecal indicators and total vibrio with log mean ± standard deviation densities of 2.2 ± 0.8 enterococci, 2.7 ± 0.7 Escherichia coli, 1.1 ± 0.7 Clostridium perfringens, 1.2 ± 0.8 F(+) coliphages, and 3.6 ± 0.7 total vibrio per 100 ml. Bivariate associations between pathogens and indicators showed enterococci positively associated with the greatest number of bacterial pathogens. Higher concentrations of enterococci and higher incidence of Campylobacter were found in stream waters collected before sunrise, suggesting these organisms are sensitive to sunlight. Multivariate regression models of microbes as a function of land cover and physical-chemical water quality showed positive associations between Salmonella and agricultural and forested land covers, and between S. aureus and urban and agricultural land covers; these results suggested that sources specific to those land covers may contribute these pathogens to streams. Further, significant associations between some microbial targets and physical-chemical stream water quality (i.e., temperature, nutrients, turbidity) suggested that organism persistence may be affected by stream characteristics. Results implicate streams as a source of pathogens to coastal waters. Future work is recommended to determine infectious risks of recreational waterborne illness related to O'ahu stream exposures and to mitigate these risks through control of land-based runoff sources.

    View details for DOI 10.1016/j.watres.2011.03.033

    View details for Web of Science ID 000291499100002

    View details for PubMedID 21492899

  • Submarine Groundwater Discharge to a High-Energy Surf Zone at Stinson Beach, California, Estimated Using Radium Isotopes ESTUARIES AND COASTS de Sieyes, N. R., Yamahara, K. M., Paytan, A., Boehm, A. B. 2011; 34 (2): 256-268
  • Impact of urbanization and agriculture on the occurrence of bacterial pathogens and stx genes in coastal waterbodies of central California WATER RESEARCH Walters, S. P., Thebo, A. L., Boehm, A. B. 2011; 45 (4): 1752-1762


    Fecal pollution enters coastal waters through multiple routes, many of which originate from land-based activities. Runoff from pervious and impervious land surfaces transports pollutants from land to sea and can cause impairment of coastal ocean waters. To understand how land use practices and water characteristics influence concentrations of fecal indicator bacteria (FIB) and pathogens in natural waters, fourteen coastal streams, rivers, and tidal lagoons, surrounded by variable land use and animal densities, were sampled every six weeks over two years (2008 & 2009). Fecal indicator bacteria (FIB; Escherichia coli and Enterococci) and Salmonella concentrations, the occurrence of Bacteroidales human, ruminant, and pig-specific fecal markers, E. coli O157:H7, and Shiga toxin (stx) genes present in E. coli, were measured. In addition, environmental and climatic variables (e.g., temperature, salinity, rainfall), as well as human and livestock population densities and land cover were quantified. Concentrations of FIB and Salmonella were correlated with each other, but the occurrence of host-specific Bacteroidales markers did not correlate with FIB or pathogens. FIB and Salmonella concentrations, as well as the occurrence of E. coli harboring stx genes, were positively associated with the fraction of the surrounding subwatershed that was urban, while the occurrence of E. coli O157:H7 was positively associated with the agricultural fraction. FIB and Salmonella concentrations were negatively correlated to salinity and temperature, and positively correlated to rainfall. Areal loading rates of FIB, Salmonella and E. coli O157:H7 to the coastal ocean were calculated for stream and river sites and varied with land cover, salinity, temperature, and rainfall. Results suggest that FIB and pathogen concentrations are influenced, in part, by their flux from the land, which is exacerbated during rainfall; once waterborne, bacterial persistence is affected by water temperature and salinity.

    View details for DOI 10.1016/j.watres.2010.11.032

    View details for Web of Science ID 000286995000025

    View details for PubMedID 21168181

  • The Effects of Informational Interventions on Household Water Management, Hygiene Behaviors, Stored Drinking Water Quality, and Hand Contamination in Peri-Urban Tanzania AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Davis, J., Pickering, A. J., Rogers, K., Mamuya, S., Boehm, A. B. 2011; 84 (2): 184-191


    Safe water storage and hand hygiene have been shown to reduce fecal contamination and improve health in experimental settings; however, triggering and sustaining such behaviors is challenging. This study investigates the extent to which personalized information about Escherichia coli contamination of stored water and hands influenced knowledge, reported behaviors, and subsequent contamination levels among 334 households with less than 5-year-old children in peri-urban Dar es Salaam, Tanzania. One-quarter of the study participants received information about strategies to reduce risk of water- and sanitation-related illness. Respondents in another three study cohorts received this same information, along with their household's water and/or hand-rinse test results. Findings from this study suggest that additional work is needed to elucidate the conditions under which such testing represents a cost-effective strategy to motivate improved household water management and hand hygiene.

    View details for DOI 10.4269/ajtmh.2011.10-0126

    View details for Web of Science ID 000287003900002

    View details for PubMedID 21292883

    View details for PubMedCentralID PMC3029166

  • Bacterial hand contamination among Tanzanian mothers varies temporally and following household activities TROPICAL MEDICINE & INTERNATIONAL HEALTH Pickering, A. J., Julian, T. R., Mamuya, S., Boehm, A. B., Davis, J. 2011; 16 (2): 233-239


    To characterize mechanisms of hand contamination with faecal indicator bacteria and to assess the presence of selected pathogens on mothers' hands in Tanzania.A household observational study combined with repeated microbiological hand rinse sampling was conducted among 119 mothers in Dar es Salaam, Tanzania. All hand rinse samples were analysed for enterococci and Escherichia coli, and selected samples were analysed for genetic markers of Bacteroidales, enterovirus and pathogenic E. coli.Using the toilet, cleaning up a child's faeces, sweeping, cleaning dishes, preparing food and bathing were all found to increase faecal indicator bacterial levels on hands. Geometric mean increases in colony forming units per two hands ranged from 50 (cleaning dishes) to 6310 (food preparation). Multivariate modelling of hand faecal indicator bacteria as a function of activities recently performed shows that food handling, exiting the household premises and longer time since last handwashing with soap are positively associated with bacterial levels on hands, while bathing is negatively associated. Genetic markers of Bacteroidales, enterovirus and pathogenic E. coli were each detected on a subset of mothers' hands.Escherichia coli and enterococci on hands can be significantly increased by various household activities, including those involving the use of soap and water. Thus, faecal indicator bacteria should be considered highly variable when used as indicators of handwashing behaviour. This work corroborates hands as important vectors of disease among Tanzanian mothers and highlights the difficulty of good personal hygiene in an environment characterized by the lack of networked sanitation and water supply services.

    View details for DOI 10.1111/j.1365-3156.2010.02677.x

    View details for Web of Science ID 000286116500015

    View details for PubMedID 21091858

  • Efficacy of alcohol-based hand sanitizer on hands soiled with dirt and cooking oil JOURNAL OF WATER AND HEALTH Pickering, A. J., Davis, J., Boehm, A. B. 2011; 9 (3): 429-433


    Handwashing education and promotion are well established as effective strategies to reduce diarrhea and respiratory illness in countries around the world. However, access to reliable water supplies has been identified as an important barrier to regular handwashing in low-income countries. Alcohol-based hand sanitizer (ABHS) is an effective hand hygiene method that does not require water, but its use is not currently recommended when hands are visibly soiled. This study evaluated the efficacy of ABHS on volunteers' hands artificially contaminated with Escherichia coli in the presence of dirt (soil from Tanzania) and cooking oil. ABHS reduced levels of E. coli by a mean of 2.33 log colony forming units (CFU) per clean hand, 2.32 log CFU per dirt-covered hand, and 2.13 log CFU per oil-coated hand. No significant difference in efficacy was detected between hands that were clean versus dirty or oily. ABHS may be an appropriate hand hygiene method for hands that are moderately soiled, and an attractive option for field settings in which access to water and soap is limited.

    View details for DOI 10.2166/wh.2011.138

    View details for Web of Science ID 000293624300001

    View details for PubMedID 21976190

  • Oceans and human health. Encyclopedia of Environmental Health Boehm, A., B., Bischel, H., N. edited by Nriagu, J. Burlington, Elsevier.. 2011: 223–230
  • Recombination Shapes the Structure of an Environmental Vibrio cholerae Population APPLIED AND ENVIRONMENTAL MICROBIOLOGY Keymer, D. P., Boehm, A. B. 2011; 77 (2): 537-544


    Vibrio cholerae consists of pathogenic strains that cause sporadic gastrointestinal illness or epidemic cholera disease and nonpathogenic strains that grow and persist in coastal aquatic ecosystems. Previous studies of disease-causing strains have shown V. cholerae to be a primarily clonal bacterial species, but isolates analyzed have been strongly biased toward pathogenic genotypes, while representing only a small sample of the vast diversity in environmental strains. In this study, we characterized homologous recombination and structure among 152 environmental V. cholerae isolates and 13 other putative Vibrio isolates from coastal waters and sediments in central California, as well as four clinical V. cholerae isolates, using multilocus sequence analysis of seven housekeeping genes. Recombinant regions were identified by at least three detection methods in 72% of our V. cholerae isolates. Despite frequent recombination, significant linkage disequilibrium was still detected among the V. cholerae sequence types. Incongruent but nonrandom associations were observed for maximum likelihood topologies from the individual loci. Overall, our estimated recombination rate in V. cholerae of 6.5 times the mutation rate is similar to those of other sexual bacteria and appears frequently enough to restrict selection from purging much of the neutral intraspecies diversity. These data suggest that frequent recombination among V. cholerae may hinder the identification of ecotypes in this bacterioplankton population.

    View details for DOI 10.1128/AEM.02062-10

    View details for Web of Science ID 000286147300019

    View details for PubMedID 21075874

  • Case Studies: Beach Environments. Microbial Source Tracking: Methods, Applications, and Case Studies Solo-Gabriele, H., M., Boehm, A., B., Scott, T., M., Sinigalliano, C. edited by Hagedorn, C., Blanch, A., Harwood, J. Springer. 2011
  • Recreational Water risk: Pathogens and Fecal Indicators. Encyclopedia of Sustainability Science and Technology Boehm, A., B., Soller, J., A. edited by Meyers, R., A. Springer. 2011
  • Beach wrack is a reservoir for faecal indicator bacteria along the California coast FEMS Microbiology Ecology Imamura, G., Strickfaden, R., M., Boehm, A., B., Jay., J., A. 2011; 77: 40-49
  • A comparison of surface sampling methods for virus recovery from fomites. Applied and Environmental Microbiology Julian, T., R., Tamayo, F., J., Leckie, J., O., Boehm, A., B. 2011; 77: 6918-6925
  • Prominent human health impacts from several marine microbes: History, ecology, and public health implications. International Journal of Microbiology Bienfang, P., K., DeFelice, S., V., Laws, E., A., Brand, L., E., Bidigare, R., R., Christensen, S., Boehm, A. 2011

    View details for DOI 10.1155/2011/152815

  • Hand fecal contamination among Tanzanian mothers varies temporally and following household activities. Tropical Medicine and International Health Pickering, A., J., Julian, T., R., Mamuya, S., Boehm, A., B., Davis, J. 2011; 16: 233-239
  • Contributions of Foot Traffic and Outdoor Concentrations to Indoor Airborne Aspergillus AEROSOL SCIENCE AND TECHNOLOGY Goebes, M. D., Boehm, A. B., Hildemann, L. M. 2011; 45 (3): 352-363
  • Virus transfer between fingerpads and fomites JOURNAL OF APPLIED MICROBIOLOGY JULIAN, T. R., Leckie, J. O., Boehm, A. B. 2010; 109 (6): 1868-1874


    Virus transfer between individuals and fomites is an important route of transmission for both gastrointestinal and respiratory illness. The present study examines how direction of transfer, virus species, time since last handwashing, gender, and titre affect viral transfer between fingerpads and glass.Six hundred fifty-six total transfer events, performed by 20 volunteers using MS2, φX174, and fr indicated 0·23 ± 0·22 (mean and standard deviation) of virus is readily transferred on contact. Virus transfer is significantly influenced by virus species and time since last handwashing. Transfer of fr bacteriophage is significantly higher than both MS2 and φX174. Virus transfer between surfaces is reduced for recently washed hands.Viruses are readily transferred between skin and surfaces on contact. The fraction of virus transferred is dependent on multiple factors including virus species, recently washing hands, and direction of transfer likely because of surface physicochemical interactions.The study is the first to provide a large data set of virus transfer events describing the central tendency and distribution of fraction virus transferred between fingers and glass. The data set from the study, along with the quantified effect sizes of the factors explored, inform studies examining role of fomites in disease transmission.

    View details for DOI 10.1111/j.1365-2672.2010.04814.x

    View details for Web of Science ID 000284170300002

    View details for PubMedID 20659186

  • Enterococcus species distribution among human and animal hosts using multiplex PCR JOURNAL OF APPLIED MICROBIOLOGY Layton, B. A., Walters, S. P., Lam, L. H., Boehm, A. B. 2010; 109 (2): 539-547


    This study evaluated the use of Enterococcus species differentiation as a tool for microbial source tracking (MST) in recreational waters.Avian, mammalian and human faecal samples were screened for the occurrence of Enterococcus avium, Enterococcus casseliflavus, Enterococcus durans, Enterococcus gallinarum, Enterococcus faecium, Enterococcus faecalis, Enterococcus hirae and Enterococcus saccharolyticus using multiplex PCR. Host-specific patterns of Enterococcus species presence were observed only when data for multiple Enterococcus species were considered in aggregate.The results suggest that no single Enterococcus species is a reliable indicator of the host faecal source. However, Enterococcus species composite 'fingerprints' may offer auxiliary evidence for bacterial source identification.This study presents novel information on the enterococci species assemblages present in avian and mammalian hosts proximate to the nearshore ocean. These data will aid the development of appropriate MST strategies, and the approach used in this study could potentially assist in the identification of faecal pollution sources.

    View details for DOI 10.1111/j.1365-2672.2010.04675.x

    View details for Web of Science ID 000279733700016

    View details for PubMedID 20132375

  • Caffeine and agricultural pesticide concentrations in surface water and groundwater on the north shore of Kauai (Hawaii, USA) MARINE POLLUTION BULLETIN Knee, K. L., Gossett, R., Boehm, A. B., Paytan, A. 2010; 60 (8): 1376-1382


    Caffeine has been associated with wastewater pollution in temperate and subtropical locations, but environmental caffeine concentrations in tropical locations have not been reported. The objectives of this study were to measure caffeine and agricultural pesticide (carbaryl, metalaxyl, and metribuzin) concentrations in environmental waters on the tropical north shore of Kauai (Hawaii, USA) and assess whether patterns in caffeine concentration were consistent with a wastewater caffeine source. Groundwater, river, stream and coastal ocean samples were collected in August 2006 and February 2007. Caffeine was detected in all August 2006 samples and in 33% of February 2007 samples at concentrations up to 88ngL(-1). Metribuzin was detected in five samples collected in February 2007. Carbaryl and metalaxyl were not detected in any sample. Caffeine was not detected in offshore ocean samples or river samples upstream of human development. A positive correlation between caffeine and enterococci suggested a possible wastewater caffeine source.

    View details for DOI 10.1016/j.marpolbul.2010.04.019

    View details for Web of Science ID 000281474000039

    View details for PubMedID 20557899

  • Relationship and Variation of qPCR and Culturable Enterococci Estimates in Ambient Surface Waters Are Predictable ENVIRONMENTAL SCIENCE & TECHNOLOGY Whitman, R. L., Ge, Z., Nevers, M. B., Boehm, A. B., Chern, E. C., Haugland, R. A., Lukasik, A. M., Molina, M., Przybyla-Kelly, K., Shively, D. A., White, E. M., Zepp, R. G., Byappanahalli, M. N. 2010; 44 (13): 5049-5054


    The quantitative polymerase chain reaction (qPCR) method provides rapid estimates of fecal indicator bacteria densities that have been indicated to be useful in the assessment of water quality. Primarily because this method provides faster results than standard culture-based methods, the U.S. Environmental Protection Agency is currently considering its use as a basis for revised ambient water quality criteria. In anticipation of this possibility, we sought to examine the relationship between qPCR-based and culture-based estimates of enterococci in surface waters. Using data from several research groups, we compared enterococci estimates by the two methods in water samples collected from 37 sites across the United States. A consistent linear pattern in the relationship between cell equivalents (CCE), based on the qPCR method, and colony-forming units (CFU), based on the traditional culturable method, was significant (P < 0.05) at most sites. A linearly decreasing variance of CCE with increasing CFU levels was significant (P < 0.05) or evident for all sites. Both marine and freshwater sites under continuous influence of point-source contamination tended to reveal a relatively constant proportion of CCE to CFU. The consistency in the mean and variance patterns of CCE versus CFU indicates that the relationship of results based on these two methods is more predictable at high CFU levels (e.g., log(10)CFU > 2.0/100 mL) while uncertainty increases at lower CFU values. It was further noted that the relative error in replicated qPCR estimates was generally higher than that in replicated culture counts even at relatively high target levels, suggesting a greater need for replicated analyses in the qPCR method to reduce relative error. Further studies evaluating the relationship between culture and qPCR should take into account analytical uncertainty as well as potential differences in results of these methods that may arise from sample variability, different sources of pollution, and environmental factors.

    View details for DOI 10.1021/es9028974

    View details for Web of Science ID 000279304700038

    View details for PubMedID 20527919

  • Nutrient inputs to the coastal ocean from submarine groundwater discharge in a groundwater-dominated system: Relation to land use (Kona coast, Hawaii, USA) LIMNOLOGY AND OCEANOGRAPHY Knee, K. L., Street, J. H., Grossman, E. E., Boehm, A. B., Paytan, A. 2010; 55 (3): 1105-1122
  • Hands, Water, and Health: Fecal Contamination in Tanzanian Communities with Improved, Non-Networked Water Supplies ENVIRONMENTAL SCIENCE & TECHNOLOGY Pickering, A. J., Davis, J., Walters, S. P., Horak, H. M., Keymer, D. P., Mushi, D., Strickfaden, B., Chynoweth, J. S., Liu, J., Blum, A., Rogers, K., Boehm, A. B. 2010; 44 (9): 3267-3272


    Almost half of the world's population relies on non-networked water supply services, which necessitates in-home water storage. It has been suggested that dirty hands play a role in microbial contamination of drinking water during collection, transport, and storage. However, little work has been done to evaluate quantitatively the association between hand contamination and stored water quality within households. This study measured levels of E. coli, fecal streptococci, and occurrence of the general Bacteroidales fecal DNA marker in source water, in stored water, and on hands in 334 households among communities in Dar es Salaam, Tanzania, where residents use non-networked water sources. Levels of fecal contamination on hands of mothers and children were positively correlated to fecal contamination in stored drinking water within households. Household characteristics associated with hand contamination included mother's educational attainment, use of an improved toilet, an infant in the household, and dissatisfaction with the quantity of water available for hygiene. In addition, fecal contamination on hands was associated with the prevalence of gastrointestinal and respiratory symptoms within a household. The results suggest that reducing fecal contamination on hands should be investigated as a strategy for improving stored drinking water quality and health among households using non-networked water supplies.

    View details for DOI 10.1021/es903524m

    View details for Web of Science ID 000277067000014

    View details for PubMedID 20222746

  • Efficacy of Waterless Hand Hygiene Compared with Handwashing with Soap: A Field Study in Dar es Salaam, Tanzania AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Pickering, A. J., Boehm, A. B., Mwanjali, M., Davis, J. 2010; 82 (2): 270-278


    Effective handwashing with soap requires reliable access to water supplies. However, more than three billion persons do not have household-level access to piped water. This research addresses the challenge of improving hand hygiene within water-constrained environments. The antimicrobial efficacy of alcohol-based hand sanitizer, a waterless hand hygiene product, was evaluated and compared with handwashing with soap and water in field conditions in Dar es Salaam, Tanzania. Hand sanitizer use by mothers resulted in 0.66 and 0.64 log reductions per hand of Escherichia coli and fecal streptococci, respectively. In comparison, handwashing with soap resulted in 0.50 and 0.25 log reductions per hand of E. coli and fecal streptococci, respectively. Hand sanitizer was significantly better than handwashing with respect to reduction in levels of fecal streptococci (P = 0.01). The feasibility and health impacts of promoting hand sanitizer as an alternative hand hygiene option for water-constrained environments should be assessed.

    View details for DOI 10.4269/ajtmh.2010.09-0220

    View details for Web of Science ID 000274263300018

    View details for PubMedID 20134005

  • Contrasting spring and summer phytoplankton dynamics in the nearshore Southern California Bight LIMNOLOGY AND OCEANOGRAPHY Santoro, A. E., Nidzieko, N. J., Van Dijken, G. L., Arrigo, K. R., Boehm, A. B. 2010; 55 (1): 264-278
  • Classical and Molecular Methods to Measure Fecal Bacteria. The Fecal Indicator Bacteria Edge, T., A., Boehm, A., B. edited by Sadowsky, M., Whitman, R. ASM Press. 2010: 328
  • Modeling Fate and Transport of Fecal Bacteria in Surface Water. The Fecal Indicator Bacteria Nevers, M., N., Boehm, A., B. edited by Sadowsky, M., Whitman, R. ASM Press. 2010: 328
  • Microbial and metal water quality in rain catchments compared with traditional drinking water sources in the East Sepik Province, Papua New Guinea JOURNAL OF WATER AND HEALTH Horak, H. M., Chynoweth, J. S., Myers, W. P., Davis, J., Fendorf, S., Boehm, A. B. 2010; 8 (1): 126-138


    In Papua New Guinea, a significant portion of morbidity and mortality is attributed to water-borne diseases. To reduce incidence of disease, communities and non-governmental organizations have installed rain catchments to provide drinking water of improved quality. However, little work has been done to determine whether these rain catchments provide drinking water of better quality than traditional drinking water sources, and if morbidity is decreased in villages with rain catchments. The specific aim of this study was to evaluate the quality of water produced by rain catchments in comparison with traditional drinking water sources in rural villages in the East Sepik Province. Fifty-four water sources in 22 villages were evaluated for enterococci and Escherichia coli densities as well as 14 health-relevant metals. In addition, we examined how the prevalence of diarrhoeal illness in villages relates to the type of primary drinking water source. The majority of tested metals were below World Health Organization safety limits. Catchment water sources had lower enterococci and E. coli than other water sources. Individuals in villages using Sepik River water as their primary water source had significantly higher incidence of diarrhoea than those primarily using other water sources (streams, dug wells and catchments).

    View details for Web of Science ID 000275310700014

    View details for PubMedID 20009255

  • Persistence of nucleic acid markers of health-relevant organisms in seawater microcosms: Implications for their use in assessing risk in recreational waters WATER RESEARCH Walters, S. P., Yamahara, K. M., Boehm, A. B. 2009; 43 (19): 4929-4939


    In the last decade, the use of culture-independent methods for detecting indicator organisms and pathogens in recreational waters has increased and has led to heightened interest in their use for routine water quality monitoring. However, a thorough understanding of the persistence of genetic markers in environmental waters is lacking. In the present study, we evaluate the persistence of enterococci, enterovirus, and human-specific Bacteroidales in seawater microcosms. Two microcosms consisted of seawater seeded with human sewage. Two additional seawater microcosms were seeded with naked Enterococcus faecium DNA and poliovirus RNA. One of each replicate microcosm was exposed to natural sunlight; the other was kept in complete darkness. In the sewage microcosms, concentrations of enterococci and enterovirus were measured using standard culture-dependent methods as well as QPCR and RT-QPCR respectively. Concentrations of human-specific Bacteroidales were determined with QPCR. In the naked-genome microcosms, enterococci and enterovirus markers were enumerated using QPCR and RT-QPCR, respectively. In the sewage microcosm exposed to sunlight, concentrations of culturable enterococci fell below the detection limit within 5 days, but the QPCR signal persisted until the end of the experiment (day 28). Culturable enterococci did not persist as long as infectious enteroviruses. The ability to culture enteroviruses and enterococci was lost before detection of the genetic markers was lost, but the human-specific Bacteroidales QPCR signal persisted for a similar duration as infectious enteroviruses in the sewage microcosm exposed to sunlight. In the naked-genome microcosms, DNA and RNA from enterococci and enterovirus, respectively, persisted for over 10d and did not vary between the light and dark treatments. These results indicate differential persistence of genetic markers and culturable organisms of public health relevance in an environmental matrix and have important management implications.

    View details for DOI 10.1016/j.watres.2009.05.047

    View details for Web of Science ID 000272057000017

    View details for PubMedID 19616273

  • Faecal indicator bacteria enumeration in beach sand: a comparison study of extraction methods in medium to coarse sands JOURNAL OF APPLIED MICROBIOLOGY Boehm, A. B., Griffith, J., Mcgee, C., Edge, T. A., Solo-Gabriele, H. M., Whitman, R., Cao, Y., Getrich, M., Jay, J. A., Ferguson, D., Goodwin, K. D., Lee, C. M., Madison, M., Weisberg, S. B. 2009; 107 (5): 1740-1750


    The absence of standardized methods for quantifying faecal indicator bacteria (FIB) in sand hinders comparison of results across studies. The purpose of the study was to compare methods for extraction of faecal bacteria from sands and recommend a standardized extraction technique.Twenty-two methods of extracting enterococci and Escherichia coli from sand were evaluated, including multiple permutations of hand shaking, mechanical shaking, blending, sonication, number of rinses, settling time, eluant-to-sand ratio, eluant composition, prefiltration and type of decantation. Tests were performed on sands from California, Florida and Lake Michigan. Most extraction parameters did not significantly affect bacterial enumeration. anova revealed significant effects of eluant composition and blending; with both sodium metaphosphate buffer and blending producing reduced counts.The simplest extraction method that produced the highest FIB recoveries consisted of 2 min of hand shaking in phosphate-buffered saline or deionized water, a 30-s settling time, one-rinse step and a 10 : 1 eluant volume to sand weight ratio. This result was consistent across the sand compositions tested in this study but could vary for other sand types.Method standardization will improve the understanding of how sands affect surface water quality.

    View details for DOI 10.1111/j.1365-2672.2009.04440.x

    View details for Web of Science ID 000270658100036

    View details for PubMedID 19659700

    View details for PubMedCentralID PMC2810257

  • Covariation and Photoinactivation of Traditional and Novel Indicator Organisms and Human Viruses at a Sewage-Impacted Marine Beach ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Yamahara, K. M., Love, D. C., Peterson, B. M., McNeill, K., Nelson, K. L. 2009; 43 (21): 8046-8052


    Sunlight modulates concentrations of Escherichia coli and enterococci in marine waters. However, the mechanism of photoinactivation is poorly understood. Additionally, little is known about photoinactivation of other fecal indicators and human viruses in recreational waters. We sampled nearshore waters at Avalon Beach, California hourly for 72 h for reactive oxygen species (ROS), traditional indicator bacteria (E. coli and enterococci, and QPCR-based detection of enterococci), F+ (DNA and RNA) and somatic coliphages, the human-specific marker in Bacteroidales (HF marker), human enterovirus, and human adenovirus. E. coli and enterococci (regardless of measurement technique) covaried with each other and the coliphages suggesting similar sources and fates. The occurrence of the HF and enterovirus markers was correlated, but their occurrence was not positively correlated with the other indicators. Lower concentrations or occurrence of all microbes, excluding the HF and enterovirus markers, were observed during sunlit as opposed to dark hours, pointing to the importance of photoinactivation. Empirical-deterministic models for a subset of microbial indicators were created to determine field-relevant sunlight inactivation rates while accounting for time dependent sources and sinks. Photoinactivation rates of enterococci and E. coli, enterococci measured by QPCR, and somatic coliphage were estimated at 7, 6, 3, and 28 d(-1) I(-1), respectively, where I is UVB intensity in W/m(2). Average H(2)O(2) was 183 nM and the maximum singlet oxygen steady state concentration was 6.6 fM. Given the clarity of the water, direct genomic damage of bacteria and coliphage, as well as indirect endogenous damage of bacteria, were likely the most important inactivation mechanisms, but we cannot rule out a contribution by indirect mechanisms involving the H(2)O(2) and singlet oxygen produced exogenously.

    View details for DOI 10.1021/es9015124

    View details for Web of Science ID 000271106300015

    View details for PubMedID 19924921

  • A Model of Exposure to Rotavirus from Nondietary Ingestion Iterated by Simulated Intermittent Contacts RISK ANALYSIS Julian, T. R., Canales, R. A., Leckie, J. O., Boehm, A. B. 2009; 29 (5): 617-632


    Existing microbial risk assessment models rarely incorporate detailed descriptions of human interaction with fomites. We develop a stochastic-mechanistic model of exposure to rotavirus from nondietary ingestion iterated by simulated intermittent fomes-mouth, hand-mouth, and hand-fomes contacts typical of a child under six years of age. This exposure is subsequently translated to risk using a simple static dose-response relationship. Through laboratory experiments, we quantified the mean rate of inactivation for MS2 phage on glass (0.0052/hr) and mean transfer between fingertips and glass (36%). Simulations using these parameters demonstrated that a child's ingested dose from a rotavirus-contaminated ball ranges from 2 to 1,000 virus over a period of one hour, with a median value of 42 virus. These results were heavily influenced by selected values of model parameters, most notably the concentration of rotavirus on fomes, frequency of fomes-mouth contacts, frequency of hand-mouth contacts, and virus transferred from fomes to mouth. The model demonstrated that mouthing of fomes is the primary exposure route, with hand mouthing contributions accounting for less than one-fifth of the child's dose over the first 10 minutes of interaction.

    View details for DOI 10.1111/j.1539-6924.2008.01193.x

    View details for Web of Science ID 000264892100002

    View details for PubMedID 19187484

  • Distribution and diversity of the enterococcal surface protein (esp) gene in animal hosts and the Pacific coast environment JOURNAL OF APPLIED MICROBIOLOGY Layton, B. A., Walters, S. P., Boehm, A. B. 2009; 106 (5): 1521-1531


    This study sought to evaluate the distribution of the enterococcal surface protein (esp) gene in Enterococcus faecium in the Pacific coast environment as well as the distribution and diversity of the gene in Northern California animal hosts.Over 150 environmental samples from the Pacific coast environment (sand, surf zone, fresh/estuarine, groundwater, and storm drain) were screened for the esp gene marker in E. faecium, and the marker was found in 37% of the environmental samples. We examined the host specificity of the gene by screening various avian and mammalian faecal samples, and found the esp gene to be widespread in nonhuman animal faeces. DNA sequence analysis performed on esp polymerase chain reaction amplicons revealed that esp gene sequences were not divergent between hosts.Our data confirm recent findings that the E. faecium variant of the esp gene is not human-specific.Our results suggest that the use of the esp gene for microbial source tracking applications may not be appropriate at all recreational beaches.

    View details for DOI 10.1111/j.1365-2672.2008.04113.x

    View details for Web of Science ID 000264958000012

    View details for PubMedID 19187132

  • Growth of Enterococci in Unaltered, Unseeded Beach Sands Subjected to Tidal Wetting (vol 75, pg 1517, 2009) APPLIED AND ENVIRONMENTAL MICROBIOLOGY Yamahara, K. M., Walters, S. P., Boehm, A. B. 2009; 75 (9): 2997-2997
  • Biogeographic Patterns in Genomic Diversity among a Large Collection of Vibrio cholerae Isolates APPLIED AND ENVIRONMENTAL MICROBIOLOGY Keymer, D. P., Lam, L. H., Boehm, A. B. 2009; 75 (6): 1658-1666


    Vibrio cholerae strains are capable of inhabiting multiple niches in the aquatic environment and in some cases cause disease in humans. However, the ecology and biodiversity of these bacteria in environmental settings remains poorly understood. We used the genomic fingerprinting technique enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) to profile 835 environmental isolates from waters and sediments obtained at nine sites along the central California coast. We identified 115 ERIC-PCR genotypes from 998 fingerprints, with a reproducibility of 98.5% and a discriminatory power of 0.971. When the temporal dynamics at a subset of sampling sites were explored, several genotypes provided evidence for cosmopolitan or geographically restricted distributions, and other genotypes displayed nonrandom patterns of cooccurrence. Partial Mantel tests confirmed that genotypic similarity of isolates across all sampling events was correlated with environmental similarity (0.04 < or = r < or = 0.05), temporal proximity (r = 0.09), and geographic distance (r = 0.09). A neutral community model for all sampling events explained 61% of the variation in genotype abundance. Cooccurrence indices (C-score, C-board, and Combo) were significantly different than expected by chance, suggesting that the V. cholerae population may have a competitive structure, especially at the regional scale. Even though stochastic processes are undoubtedly important in generating biogeographic patterns in diversity, deterministic factors appear to play a significant, albeit small, role in shaping the V. cholerae population structure in this system.

    View details for DOI 10.1128/AEM.01304-08

    View details for Web of Science ID 000263920900024

    View details for PubMedID 19139224

  • A sea change ahead for recreational water quality criteria JOURNAL OF WATER AND HEALTH Boehm, A. B., Ashbolt, N. J., Colford, J. M., Dunbar, L. E., Fleming, L. E., Gold, M. A., Hansel, J. A., Hunter, P. R., Ichida, A. M., McGee, C. D., Soller, J. A., Weisberg, S. B. 2009; 7 (1): 9-20


    The United States Environmental Protection Agency is committed to developing new recreational water quality criteria for coastal waters by 2012 to provide increased protection to swimmers. We review the uncertainties and shortcomings of the current recreational water quality criteria, describe critical research needs for the development of new criteria, as well as recommend a path forward for new criteria development. We believe that among the most needed research needs are the completion of epidemiology studies in tropical waters and in waters adversely impacted by urban runoff and animal feces, as well as studies aimed to validate the use of models for indicator and pathogen concentration and health risk predictions.

    View details for DOI 10.2166/wh.2009.122

    View details for Web of Science ID 000264052900002

    View details for PubMedID 18957771

  • Growth of Enterococci in Unaltered, Unseeded Beach Sands Subjected to Tidal Wetting APPLIED AND ENVIRONMENTAL MICROBIOLOGY Yamahara, K. M., Walters, S. P., Boehm, A. B. 2009; 75 (6): 1517-1524


    Enterococci are indicator bacteria used to assess the risk of acquiring enteric disease from swimming in marine waters. Previous work identified beach sands as reservoirs of enterococci which can be transported from the sand to the sea, where they may instigate beach advisories. The present study establishes that naturally occurring enterococci can replicate in beach sands under environmentally relevant conditions. In unseeded, nonsterile microcosm experiments, it was shown that intermittent wetting of sands by seawater, like that which would occur at the high tide line, stimulates the transient replication of enterococci at rates of 0.20 to 0.63 per day (equivalent to doubling times of 1.1 to 3.5 days). Replication was not observed in control microcosms that were not subjected to wetting. Enterococci were enumerated using both culture-dependent (membrane filtration and mEI media) and culture-independent (quantitative PCR [QPCR], 23S rRNA gene based) techniques, which allowed tracking of both culturable and total enterococcus populations. Inhibition of QPCR and DNA extraction efficiencies were accounted for in the interpretation of the QPCR results. The results provide evidence that enterococci may not be an appropriate indicator of enteric disease risk at recreational beaches subject to nonpoint sources of pollution.

    View details for DOI 10.1128/AEM.02278-08

    View details for Web of Science ID 000263920900006

    View details for PubMedID 19151188

  • Sources of nutrients and fecal indicator bacteria to nearshore waters on the north shore of Kauai (Hawaii, USA) ESTUARIES AND COASTS Knee, K. L., Layton, B. A., Street, J. H., Boehm, A. B., Paytan, A. 2008; 31 (4): 607-622
  • Submarine discharge of nutrient-enriched fresh groundwater at Stinson Beach, California is enhanced during neap tides LIMNOLOGY AND OCEANOGRAPHY de Sieyes, N. R., Yamahara, K. M., Layton, B. A., Joyce, E. H., Boehm, A. B. 2008; 53 (4): 1434-1445
  • Fecal indicator bacteria and Salmonella in ponds managed as bird habitat, San Francisco Bay, California, USA WATER RESEARCH Shellenbarger, G. G., Athearn, N. D., Takekawa, J. Y., Boehm, A. B. 2008; 42 (12): 2921-2930


    Throughout the world, coastal resource managers are encouraging the restoration of previously modified coastal habitats back into wetlands and managed ponds for their ecosystem value. Because many coastal wetlands are adjacent to urban centers and waters used for human recreation, it is important to understand how wildlife can affect water quality. We measured fecal indicator bacteria (FIB) concentrations, presence/absence of Salmonella, bird abundance, and physico-chemical parameters in two coastal, managed ponds and adjacent sloughs for 4 weeks during the summer and winter in 2006. We characterized the microbial water quality in these waters relative to state water-quality standards and examined the relationship between FIB, bird abundance, and physico-chemical parameters. A box model approach was utilized to determine the net source or sink of FIB in the ponds during the study periods. FIB concentrations often exceeded state standards, particularly in the summer, and microbial water quality in the sloughs was generally lower than in ponds during both seasons. Specifically, the inflow of water from the sloughs to the ponds during the summer, more so than waterfowl use, appeared to increase the FIB concentrations in the ponds. The box model results suggested that the ponds served as net wetland sources and sinks for FIB, and high bird abundances in the winter likely contributed to net winter source terms for two of the three FIB in both ponds. Eight serovars of the human pathogen Salmonella were isolated from slough and pond waters, although the source of the pathogen to these wetlands was not identified. Thus, it appeared that factors other than bird abundance were most important in modulating FIB concentrations in these ponds.

    View details for DOI 10.1016/j.watres.2008.03.006

    View details for Web of Science ID 000257649100009

    View details for PubMedID 18457857

  • Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary ENVIRONMENTAL MICROBIOLOGY Santoro, A. E., Francis, C. A., de Sieyes, N. R., Boehm, A. B. 2008; 10 (4): 1068-1079


    Submarine groundwater discharge to coastal waters can be a significant source of both contaminants and biologically limiting nutrients. Nitrogen cycling across steep gradients in salinity, oxygen and dissolved inorganic nitrogen in sandy 'subterranean estuaries' controls both the amount and form of nitrogen discharged to the coastal ocean. We determined the effect of these gradients on betaproteobacterial ammonia-oxidizing bacteria (beta-AOB) and ammonia-oxidizing archaea (AOA) in a subterranean estuary using the functional gene encoding ammonia monooxygenase subunit A (amoA). The abundance of beta-AOB was dramatically lower in the freshwater stations compared with saline stations, while AOA abundance remained nearly constant across the study site. This differing response to salinity altered the ratio of beta-AOB to AOA such that bacterial amoA was 30 times more abundant than crenarchaeal amoA at the oxic marine station, but nearly 10 times less abundant at the low-oxygen fresh and brackish stations. As the location of the brackish mixing zone within the aquifer shifted from landward in winter to oceanward in summer, the location of the transition from a beta-AOB-dominated to an AOA-dominated community also shifted, demonstrating the intimate link between microbial communities and coastal hydrology. Analysis of ammonia-oxidizing enrichment cultures at a range of salinities revealed that AOA persisted solely in the freshwater enrichments where they actively express amoA. Diversity (as measured by total richness) of crenarchaeal amoA was high at all stations and time points, in sharp contrast to betaproteobacterial amoA for which only two sequence types were found. These results offer new insights into the ecology of AOA and beta-AOB by elucidating conditions that may favour the numerical dominance of beta-AOB over AOA in coastal sediments.

    View details for DOI 10.1111/j.1462-2920.2007.01547.x

    View details for Web of Science ID 000254124100023

    View details for PubMedID 18266758

  • Enterococci concentrations in diverse coastal environments exhibit extreme variability ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B. 2007; 41 (24): 8227-8232


    Fecal indicator bacteria (FIB) concentrations in a single grab sample of water are used to notify the public about the safety of swimming in coastal waters. If concentrations are over a single-sample standard, waters are closed or placed under an advisory. Previous work has shown that notification errors occur often because FIB vary more quickly than monitoring results can be obtained (typically 24 h). Rapid detection technologies (such as quantitative polymerase chain reaction) that allow FIB quantification in hours have been suggested as a solution to notification errors. In the present study, I explore variability of enterococci (ENT) over time scales less than a day that might affect interpretation of FIB concentrations from a single grab sample, even if obtained rapidly. Five new data sets of ENT collected at 10 and 1 min periodicities for 24 and 1 h, respectively, are presented. Data sets are collected in diverse marine environments from a turbulent surf zone to a quiescent bay. ENT vary with solar and tidal cycles, as has been observed in previous studies. Over short time scales, ENT are extremely variable in each environment even the quiescent bay. Changes in ENT concentrations between consecutive samples (1 or 10 min apart) greater than the single-sample standard (104 most probable number per 100 mL) are not unusual. Variability, defined as the change in concentration between consecutive samples, is not distinct between environments. ENT change by 60% on average between consecutive samples, and by as much as 700%. Spectral analyses reveal no spectral peaks, but power-law decline of spectral density with frequency. Power-law exponents are close to 1 suggesting ENT time series share properties with 1/f noise and are fractal in nature. Since fractal time series have no characteristic time scale associated with them, it is not obvious how the fractal nature of ENT can be exploited for adaptive sampling or management. Policy makers, as well as scientists designing field campaigns for microbial source tracking and epidemiology studies, are cautioned that a single sample of water reveals little about the true water quality at a beach. Multiple samples must be taken to gain a snapshot into the patchy structure of microbial water quality and associated human health risk.

    View details for DOI 10.1021/es071807v

    View details for Web of Science ID 000251582800007

    View details for PubMedID 18200844

  • Frequent occurrence of the human-specific Bacteroides fecal marker at an open coast marine beach: relationship to waves, tides and traditional indicators ENVIRONMENTAL MICROBIOLOGY Santoro, A. E., Boehm, A. B. 2007; 9 (8): 2038-2049


    Molecular genetic markers, such as those from fecal Bacteroides microorganisms, can link microbial pollution with its source, and have been used successfully in studies of sheltered aquatic environments. Their applicability to wave-driven, open coast environments has not been tested. We assessed the contribution of a tidal outlet to surf zone water quality in coastal Orange County, California, USA by measuring three traditional culture-based fecal indicator bacteria (FIB) as well as the human-specific Bacteroides molecular marker (HF marker) at four shoreline locations. We found that total and fecal coliform levels were higher during low tides than high tides at two of the four stations, and that this effect was strongest at the mouth of the tidal lagoon and decayed with distance from the outlet. The HF marker was detected in 23% and 47% of samples from the tidal outlet and 26% and 41% of samples from an adjacent recreational beach in 2005 and 2006 respectively. Surprisingly, the station farthest from the tidal outlet had the highest occurrence of the HF marker. We found no relationship between FIB abundance and occurrence of the HF marker for individual samples, but that when the data were considered together by year, higher FIB abundance was correlated with a higher incidence of the HF marker. DNA sequences of the HF marker recovered from this site were > 99% similar to those recovered from other states and countries, suggesting low global diversity of this marker. These data provide strong support for the idea that multiple time points and physical conditions should be considered when assessing coastal water quality.

    View details for DOI 10.1111/j.1462-2920.2007.01319.x

    View details for Web of Science ID 000248451600014

    View details for PubMedID 17635548

  • Beach sands along the California coast are diffuse sources of fecal bacteria to coastal waters ENVIRONMENTAL SCIENCE & TECHNOLOGY Yamahara, K. M., Layton, B. A., Santoro, A. E., Boehm, A. B. 2007; 41 (13): 4515-4521


    Fecal indicator bacteria (FIB) are nearly ubiquitous in California (CA) beach sands. Sands were collected from 55 beaches along the CA coast. Ninety-one percent of the beaches had detectable enterococci (ENT) while 62% had detectable E. coli (EC) in their sands. The presence of a putative bacterial source (such as a river), the degree of wave shelter, and surrounding land use explained a significant (p < 0.05) fraction of the variation in both ENT and EC densities between beaches. Sand characteristics including moisture content, organic carbon, and percentfines, significantly (p < 0.05) influenced only EC densities in beach sand. We assayed 34 of 163 sand samples for salmonellae, but did not detect this bacterial pathogen. The potential for FIB to be transported from the sand to sea was investigated at a single wave-sheltered beach with high densities of ENT in beach sand: Lovers Point, CA (LP). We collected samples of exposed and submerged sands as well as water over a 24 h period in order to compare the disappearance or appearance of ENT in sand and the water column. Exposed sands had significantly higher densities of ENT than submerged sands with the highest densities located near the high tide line. Water column ENT densities began low, increased sharply during the first flood tide and slowly decreased over the remainder of the study. During the first flood tide, the number of ENT that entered the water column was nearly equivalent to the number of ENT lost from exposed sands when they were submerged by seawater. The decrease in nearshore ENT concentrations after the initial influx can be explained by ENT die-off and dilution with clean ocean water. While some ENT in the water and sand at LP might be of human origin because they were positive for the esp gene, others lacked the esp gene and were therefore equivocal with respect to their origin. Follow-up sampling at LP revealed the presence of the human specific Bacteroides marker in water and sand.

    View details for DOI 10.1021/es062822n

    View details for Web of Science ID 000247782500014

    View details for PubMedID 17695890

  • Genomic and phenotypic diversity of coastal Vibrio cholerae strains is linked to environmental factors APPLIED AND ENVIRONMENTAL MICROBIOLOGY Keymer, D. P., Miller, M. C., Schoolnik, G. K., Boehm, A. B. 2007; 73 (11): 3705-3714


    Studies of Vibrio cholerae diversity have focused primarily on pathogenic isolates of the O1 and O139 serotypes. However, autochthonous environmental isolates of this species routinely display more extensive genetic diversity than the primarily clonal pathogenic strains. In this study, genomic and metabolic profiles of 41 non-O1/O139 environmental isolates from central California coastal waters and four clinical strains are used to characterize the core genome and metabolome of V. cholerae. Comparative genome hybridization using microarrays constructed from the fully sequenced V. cholerae O1 El Tor N16961 genome identified 2,787 core genes that approximated the projected species core genome within 1.6%. Core genes are almost universally present in strains with widely different niches, suggesting that these genes are essential for persistence in diverse aquatic environments. In contrast, the dispensable genes and phenotypic traits identified in this study should provide increased fitness for certain niche environments. Environmental parameters, measured in situ during sample collection, are correlated to the presence of specific dispensable genes and metabolic capabilities, including utilization of mannose, sialic acid, citrate, and chitosan oligosaccharides. These results identify gene content and metabolic pathways that are likely selected for in certain coastal environments and may influence V. cholerae population structure in aquatic environments.

    View details for DOI 10.1128/AEM.02736-06

    View details for Web of Science ID 000247016600030

    View details for PubMedID 17449702

    View details for PubMedCentralID PMC1932678

  • Detection and transformation of genome segments that differ within a coastal population of Vibrio cholerae strains APPLIED AND ENVIRONMENTAL MICROBIOLOGY Miller, M. C., Keymer, D. P., Avelar, A., Boehm, A. B., Schoolnik, G. K. 2007; 73 (11): 3695-3704


    Vibrio cholerae is an autochthonous member of diverse aquatic ecosystems around the globe. Collectively, the genomes of environmental V. cholerae strains comprise a large repository of encoded functions which can be acquired by individual V. cholerae lineages through uptake and recombination. To characterize the genomic diversity of environmental V. cholerae, we used comparative genome hybridization to study 41 environmental strains isolated from diverse habitats along the central California coast, a region free of endemic cholera. These data were used to classify genes of the epidemic V. cholerae O1 sequenced strain N16961 as conserved, variably present, or absent from the isolates. For the most part, absent genes were restricted to large mobile elements and have known functions in pathogenesis. Conversely, genes present in some, but not all, California isolates were in smaller contiguous clusters and were less likely to be near genes with functions in DNA mobility. Two such clusters of variable genes encoding different selectable metabolic phenotypes (mannose and diglucosamine utilization) were transformed into the genomes of environmental isolates by chitin-dependent competence, indicating that this mechanism of general genetic exchange is conserved among V. cholerae. The transformed DNA had an average size of 22.7 kbp, demonstrating that natural competence can mediate the movement of large chromosome fragments. Thus, whether variable genes arise through the acquisition of new sequences by horizontal gene transfer or by the loss of preexisting DNA though deletion, natural transformation provides a mechanism by which V. cholerae clones can gain access to the V. cholerae pan-genome.

    View details for DOI 10.1128/AEM.02735-06

    View details for Web of Science ID 000247016600029

    View details for PubMedID 17449699

    View details for PubMedCentralID PMC1932674

  • Now-casting recreational water quality. Statistical Framework for Water Quality Criteria and Monitoring Boehm, A., B., Whitman, R., L., Nevers, M., B., Hou, D., Weisberg, S., B. edited by Wymer, L., Dufour, A. 2007
  • Beach sands along the California coast are diffuse sources of fecal bacteria to coastal waters. Environmental Science & Technology Yamahara, K., M., Layton, B., A., Santoro, A., E., Boehm., A., B. 2007; 41: 4515-4521
  • Human development is linked to multiple water body impairments along the California coast ESTUARIES AND COASTS Handler, N. B., Payran, A., Higgins, C. P., Luthy, R. G., Boehm, A. B. 2006; 29 (5): 860-870
  • Regional public health cost estimates of contaminated coastal waters: A case study of gastroenteritis at southern california beaches ENVIRONMENTAL SCIENCE & TECHNOLOGY Given, S., Pendleton, L. H., Boehm, A. B. 2006; 40 (16): 4851-4858


    We present estimates of annual public health impacts, both illnesses and cost of illness, attributable to excess gastrointestinal illnesses caused by swimming in contaminated coastal waters at beaches in southern California. Beach-specific enterococci densities are used as inputs to two epidemiological dose-response models to predict the risk of gastrointestinal illness at 28 beaches spanning 160 km of coastline in Los Angeles and Orange Counties. We use attendance data along with the health cost of gastrointestinal illness to estimate the number of illnesses among swimmers and their likely economic impact. We estimate that between 627,800 and 1,479,200 excess gastrointestinal illnesses occur at beaches in Los Angeles and Orange Counties each year. Using a conservative health cost of gastroenteritis, this corresponds to an annual economic loss of dollars 21 or dollars 51 million depending upon the underlying epidemiological model used (in year 2000 dollars). Results demonstrate that improving coastal water quality could result in a reduction of gastrointestinal illnesses locally and a concurrent savings in expenditures on related health care costs.

    View details for DOI 10.1021/es060679s

    View details for Web of Science ID 000239684900012

    View details for PubMedID 16955877

  • Enterococci predictions from partial least squares regression models in conjunction with a single-sample standard improve the efficacy of beach management advisories ENVIRONMENTAL SCIENCE & TECHNOLOGY Hou, D., Rabinovici, S. J., Boehm, A. B. 2006; 40 (6): 1737-1743


    Beach health advisories are issued if enterococci (ENT) densities exceed the 30-d geometric mean or single-sample water quality criteria. Current ENT enumeration procedures require 1 day of incubation; therefore, beach managers make policy decisions using 1-day-old data. This is tantamount to using a model that assumes ENT density on day t is equal to ENT density on day t-1. Research has shown that ENT densities vary over time scales shorterthan a day, calling into question the usefulness of the current model for decision-making. We created Dynamic Partial Least Square Regression (DPLSR) models for ENT at water quality monitoring stations within two adjacent marine recreational sites, Huntington State Beach (HSB) and Huntington City (HCB) Beach, California, using publicly available environmental data and tested whether these models overcome the drawbacks of the current model. The DPLSR models provide a better prediction of ENT than the current models based on comparisons of root-mean-square errors of prediction and the numbers of type 1 and 2 errors. We compared outcomes in terms of predicted illness, swimmers deterred from entering the water, and net benefits to swimmers for hypothetical management scenarios where beach advisories were issued based on (a) the previously collected sample's ENT density in conjunction with the two water quality criteria, and (b) predictions from DPLSR models in conjunction with the single-sample standard. At both HSB and HCB the DPLSR scenario produced a more favorable balance between illness prevention and recreational access. The results call into question the current method of beach management and show that model-informed decision-making and elimination of the geometric mean standard will aid beach managers in achieving more favorable outcomes in terms of illness and access than are presently achieved using 1-day-old measurements, especially at beaches where water quality problems are chronic.

    View details for DOI 10.1021/es0515250

    View details for Web of Science ID 000236213900005

    View details for PubMedID 16570591

  • Composition and flux of groundwater from a California beach aquifer: Implications for nutrient supply to the surf zone (vol 26, pg 269, 2006) CONTINENTAL SHELF RESEARCH Boehm, A., Paytan, A., Shellenbarger, G. G., Davis, K. A. 2006; 26 (4): 554-554
  • Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer APPLIED AND ENVIRONMENTAL MICROBIOLOGY Santoro, A. E., Boehm, A. B., Francis, C. A. 2006; 72 (3): 2102-2109


    Nitrogen flux into the coastal environment via submarine groundwater discharge may be modulated by microbial processes such as denitrification, but the spatial scales at which microbial communities act and vary are not well understood. In this study, we examined the denitrifying community within the beach aquifer at Huntington Beach, California, where high-nitrate groundwater is a persistent feature. Nitrite reductase-encoding gene fragments (nirK and nirS), responsible for the key step in the denitrification pathway, were PCR amplified, cloned, and sequenced from DNAs extracted from aquifer sediments collected along a cross-shore transect, where groundwater ranged in salinity from 8 to 34 practical salinity units and in nitrate concentration from 0.5 to 330 muM. We found taxonomically rich and novel communities, with all nirK clones exhibiting <85% identity and nirS clones exhibiting <92% identity at the amino acid level to those of cultivated denitrifiers and other environmental clones in the database. Unique communities were found at each site, despite being located within 40 m of each other, suggesting that the spatial scale at which denitrifier diversity and community composition vary is small. Statistical analyses of nir sequences using the Monte Carlo-based program integral-Libshuff confirmed that some populations were indeed distinct, although further sequencing would be required to fully characterize the highly diverse denitrifying communities at this site.

    View details for DOI 10.1128/AEM.72.3.2102-2109.2006

    View details for Web of Science ID 000236069200045

    View details for PubMedID 16517659

    View details for PubMedCentralID PMC1393195

  • Composition and flux of groundwater from a California beach aquifer: Implications for nutrient supply to the surf zone CONTINENTAL SHELF RESEARCH Boehm, A. B., Paytan, A., Shellenbarger, G. G., Davis, K. A. 2006; 26 (2): 269-282
  • An analytical model of enterococci inactivation, grazing, and transport in the surf zone of a marine beach WATER RESEARCH Boehm, A. B., Keymer, D. P., Shellenbarger, G. G. 2005; 39 (15): 3565-3578


    An analytical model of enterococci (ENT) concentrations in the surf zone of a long sandy beach is constructed considering the physical processes of dilution by rip currents and alongshore littoral drift, and the biological processes of inactivation and mortality by grazing. The solution is used to construct an expression for the length of shoreline adversely impacted by ENT from a point source. Two non-dimensional parameters are developed whose magnitude can be used to ascertain whether dilution, inactivation, or grazing is the dominant sink for ENT in the surf zone. The model is applied to beaches in southern California, USA. Model input parameters related to physical processes and inactivation are compiled from the literature. Laboratory experiments are conducted to determine grazing mortality rates of ENT (6.5 x 10(-6) s(-1)). Results indicate that at the field sites, between 1000 and 5000 m of shoreline are typically impacted by a continuous point source of ENT. Dilution is the primary cause of decline in ENT concentrations within the surf zone, with inactivation secondary and grazing tertiary. Results recommend strategic positioning of point sources and timing of effluent releases to take advantage of high dilution conditions. Our estimates for grazing mortality rates are within the same order of magnitude as some published inactivation rates, thus we cannot rule out the possibility that grazing is an important sink for ENT, especially in low dilution environments like enclosed bays.

    View details for Web of Science ID 000232417800014

    View details for PubMedID 16095656

  • Tidal forcing of enterococci at marine recreational beaches at fortnightly and semidiurnal frequencies ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Weisberg, S. B. 2005; 39 (15): 5575-5583


    Marine beach water quality is typically monitored in early morning once a week without respect to tidal condition. To assess the effect of tide on this public health warning system, we analyzed enterococci (ENT) data from 60 southern California marine beaches with differing geomorphology, orientation, and proximity to runoff sources. ENT concentrations during spring tides were significantly higher (p < 0.1) than those during neap tides at 50 of the beaches, and at the majority of these, water samples were also more than twice as likely to be out of compliance with the ENT single-sample standard during spring tides compared to neap tides. When tide range (spring/neap) and tide stage (ebb/flood) conditions were considered together, spring-ebb tides yielded the highest ENT concentrations and the greatest chance of exceeding the single-sample standard at the majority of beaches. The proximity to a terrestrial runoff source, the slope of the runoff source, the slope of the beach, and the orientation of the beach had minimal influence on the tidal modulation of ENT concentrations. The presence of spring and spring-ebb tide signals at such a great percentage of beaches suggests that tide should be considered in the design and interpretation of beach monitoring program data. It also suggests that ENT delivered by tidally forced sources other than terrestrial surficial runoff are widespread. Possibilities include ENT-laden groundwater (saline and fresh) from the beach aquifer as well as ENT-enriched sands, decaying wrack, and bird feces near the high water line.

    View details for DOI 10.1021/es048175m

    View details for Web of Science ID 000230919800020

    View details for PubMedID 16124289

  • Groundwater discharge: Potential association with fecal indicator bacteria in the surf zone ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Shellenbarger, G. G., Paytan, A. 2004; 38 (13): 3558-3566


    Short-lived radium isotopes (223Ra and 224Ra) are used to investigate the potential association between groundwater discharge and microbial pollution at Huntington Beach, CA. We establish the tidally driven exchange of groundwater from the surficial beach aquifer across the beach face. Groundwater is found to be a source of nutrients (silica, inorganic nitrogen, and orthophosphate) to the surf zone, and these nutrients could possibly provide an environment for enhanced growth or increased persistence of fecal indicator bacteria (FIB). Ammonium and ortho-phosphate explain up to 12-20% of the variance in FIB levels in the surf zone. Elevated levels of FIB were only found in 1 of the 26 groundwater samples. However, FIB in the surf zone covary with radium at fortnightly, diurnal, and semi-diurnal tidal periods. In addition, radium accounts for up to 38% of the variance in log-FIB levels in the surf zone. A column experiment illustrates that Enterococcus suspended in Huntington Beach saline groundwater is not significantly filtered by sand collected from the field. This work establishes a mechanism for the subterranean delivery of FIB pollution to the surf zone from the surficial aquifer and presents evidence that supports an association between groundwater discharge and FIB.

    View details for DOI 10.1021/es035385a

    View details for Web of Science ID 000222396400021

    View details for PubMedID 15296305

  • Scaling and management of fecal indicator bacteria in runoff from a coastal urban watershed in southern California ENVIRONMENTAL SCIENCE & TECHNOLOGY Reeves, R. L., Grant, S. B., Mrse, R. D., Oancea, C. M., Sanders, B. F., Boehm, A. B. 2004; 38 (9): 2637-2648


    This paper describes a series of field studies aimed at identifying the spatial distribution and flow forcing of fecal indicator bacteria in dry and wet weather runoff from the Talbert watershed, a highly urbanized coastal watershed in southern California. Runoff from this watershed drains through tidal channels to a popular public beach, Huntington State Beach, which has experienced chronic surf zone water quality problems over the past several years. During dry weather, concentrations of fecal indicator bacteria are highest in inland urban runoff, intermediate in tidal channels harboring variable mixtures of urban runoff and ocean water, and lowest in ocean water at the base of the watershed. This inland-to-coastal gradient is consistent with the hypothesis that urban runoff from the watershed contributes to coastal pollution. On a year round basis, the vast majority (>99%) of fecal indicator bacteria loading occurs during storm events when runoff diversions, the management approach of choice, are not operating. During storms, the load of fecal indicator bacteria in runoff follows a power law of the form L approximately Qn, where L is the loading rate (in units of fecal indicator bacteria per time), Q is the volumetric flow rate (in units of volume per time), and the exponent n ranges from 1 to 1.5. This power law and the observed range of exponent values are consistent with the predictions of a mathematical model that assumes fecal indicator bacteria in storm runoff originate from the erosion of contaminated sediments in drainage channels or storm sewers. The theoretical analysis, which is based on a conventional model for the shear-induced erosion of particles from land and channel-bed surfaces, predicts that the magnitude of the exponent n reflects the geometry of the stormwater conveyance system from which the pollution derives. This raises the possibility that the scaling properties of pollutants in stormwater runoff (i.e., the value of n) may harbor information about the origin of nonpoint source pollution.

    View details for Web of Science ID 000221189900029

    View details for PubMedID 15180060

  • Covariation of coastal water temperature and microbial pollution at interannual to tidal periods GEOPHYSICAL RESEARCH LETTERS Boehm, A. B., Lluch-Cota, D. B., Davis, K. A., Winant, C. D., Monismith, S. G. 2004; 31 (6)
  • Bacterial Contamination and Submarine Groundwater Discharge-A Possible Link ENVIRONMENTAL CHEMISTRY Paytan, A., Boehm, A. B., Shellenbarger, G. G. 2004; 1 (1): 29-30

    View details for DOI 10.1071/EN04002

    View details for Web of Science ID 000207050400009

  • Sources, management, and scaling of fecal indicator bacteria in runoff from a coastal urban watershed in Southern California. Environmental Science and Technology Reeves, R., L., Grant, S., B., Mrse, R., D., Oancea, C., M. C., Sanders, B., F., Boehm., A., B. 2004; 38: 2637-2648
  • Model of microbial transport and inactivation in the surf zone and application to field measurements of total coliform in Northern Orange County, California ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B. 2003; 37 (24): 5511-5517


    The classic model of pollutant transport in the surf zone of a long, sandy beach developed by Inman et al. (J. Geophys. Res. 1971, 76, 3493) is altered to account for first-order pollutant inactivation in an effort to understand how rip cell dilution and bacterial inactivation control the length of shoreline adversely impacted by microbial pollution from a point source. A dimensionless number gamma dictates whether physical processes (dilution of microbes in the surf zone by rip cell mixing) or biological processes (microbial inactivation) control the distribution of pollution along the shoreline. Estimates of gamma for beaches in Northern Orange County, California, indicate that dilution is the primary factor controlling total coliform levels surrounding two drains that release nuisance runoff directly onto the beach. It is also shown that, even when alongshore currents are fast, pollutant levels will drop e-fold at distances under 4000 m from the point source due to dilution alone. Because dilution is ultimately controlled by wave climate and shoreline morphology, the results suggest the strategic position of drains and other point sources in high dilution wave environments will reduce potential adverse effects on beach water quality. In addition, the results stress the importance of understanding hydrodynamics when conducting microbial source tracking at wave-dominated marine beaches.

    View details for DOI 10.1021/es034321x

    View details for Web of Science ID 000187248000006

    View details for PubMedID 14717158

  • Tiered approach for identification of a human fecal pollution source at a recreational beach: Case study at Avalon Cay, Catalina Island, California ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Fuhrman, J. A., Mrse, R. D., Grant, S. B. 2003; 37 (4): 673-680


    Recreational marine beaches in California are posted as unfit for swimming when the concentration of fecal indicator bacteria (FIB) exceeds any of seven concentration standards. Finding and mitigating sources of shoreline FIB is complicated by the many potential human and nonhuman sources of these organisms and the complex fate and transport processes that control their concentrations. In this study, a three-tiered approach is used to identify human and nonhuman sources of FIB in Avalon Bay, a popular resort community on Catalina Island in southern California. The first and second tiers utilize standard FIB tests to spatially isolate the FIB signal, to characterize the variability of FIB over a range of temporal scales, and to measure FIB concentrations in potential sources of these organisms. In the third tier, water samples from FIB "hot spots" and sources are tested for human-specific bacteria Bacteroides/Prevotella and enterovirus to determine whether the FIB are from human sewage or from nonhuman sources such as bird feces. FIB in Avalon Bay appear to be from multiple, primarily land-based, sources including bird droppings, contaminated subsurface water, leaking drains, and runoff from street wash-down actvities. Multiple shoreline samples and two subsurface water samples tested positive for human-specific bacteria and enterovirus, suggesting that at least a portion of the FIB contamination is from human sewage.

    View details for DOI 10.1021/es025934x

    View details for Web of Science ID 000181067100003

    View details for PubMedID 12636264

  • A model of microbial transport and inactivation in the surf zone and application to field measurements of total coliform in Northern Orange County, California. Environmental Science and Technology Boehm., A., B. 2003; 37: 5511-5517
  • A tiered approach for identification of a human fecal pollution source at a recreational beach: Case study at Avalon Bay, Catalina Island, California, USA. Environmental Science and Technology Boehm., A., B., Fuhrman, J., A., Mrse, R., D., Grant., S., B. 2003; 37: 673-680
  • A scaling theory for number-flux distributions generated during steady-state coagulation and settling and application to particles in Lake Zurich, Switzerland JOURNAL OF COLLOID AND INTERFACE SCIENCE Boehm, A. B. 2002; 254 (2): 266-273


    In this study, we extend the established scaling theory for cluster size distributions generated during unsteady coagulation to number-flux distributions that arise during steady-state coagulation and settling in an unmixed water mass. The scaling theory predicts self-similar number-flux distributions and power-law decay of total number flux with depth. The shape of the number-flux distributions and the power-law exponent describing the decay of the total number flux are shown to depend on the homogeneity and small i/j limit of the coagulation kernel and the exponent kappa, which describes the variation in settling velocity with cluster volume. Particle field measurements from Lake Zurich, collected by U. Weilenmann and co-workers (Limnol. Oceanogr.34, 1 (1989)), are used to illustrate how the scaling predictions can be applied to a natural system. This effort indicates that within the mid-depth region of Lake Zurich, clusters of the same size preferentially interact and large clusters react with one another more quickly than small ones, indicative of clusters coagulating in a reaction-limited regime.

    View details for DOI 10.1006/jcis.2002.8599

    View details for Web of Science ID 000178935400009

    View details for PubMedID 12702397

  • Decadal and shorter period variability of surf zone water quality at Huntington Beach, California ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Grant, S. B., Kim, J. H., Mowbray, S. L., McGee, C. D., Clark, C. D., Foley, D. M., Wellman, D. E. 2002; 36 (18): 3885-3892


    The concentration of fecal indicator bacteria in the surf zone at Huntington Beach, CA, varies over time scales that span at least 7 orders of magnitude, from minutes to decades. Sources of this variability include historical changes in the treatment and disposal of wastewater and dry weather runoff, El Niño events, seasonal variations in rainfall, spring-neap tidal cycles, sunlight-induced mortality of bacteria, and nearshore mixing. On average, total coliform concentrations have decreased over the past 43 years, although point sources of shoreline contamination (storm drains, river outlets, and submarine outfalls) continue to cause transiently poor water quality. These transient point sources typically persist for 5-8 yr and are modulated by the phase of the moon, reflecting the influence of tides on the sourcing and transport of pollutants in the coastal ocean. Indicator bacteria are very sensitive to sunlight therefore, the time of day when samples are collected can influence the outcome of water quality testing. These results demonstrate that coastal water quality is forced by a complex combination of local and external processes and raise questions about the efficacy of existing marine bathing water monitoring and reporting programs.

    View details for DOI 10.1021/es020524u

    View details for Web of Science ID 000178016600001

    View details for PubMedID 12269739

  • Cross-shelf transport at Huntington Beach. Implications for the fate of sewage discharged through an offshore ocean outfall ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Sanders, B. F., Winant, C. D. 2002; 36 (9): 1899-1906


    In this study, we evaluate the potential for internal tides to transport wastewater effluent from the Orange County Sanitation District (OCSD) ocean outfall toward Huntington Beach. Results of plume tracking studies show that OCSD effluent occasionally moves shoreward into water less than 20 m deep. Analyses of current and temperature observations indicate cold water is regularly advected cross-shelf, in to and out of the nearshore, at both semi-diurnal and diurnal frequencies. Isotherms typically associated with the waste field near the outfall are observed just outside the Huntington Beach surf zone, where the total depth is less than 6 m, highlighting the extent of the cross-shelf transport. This advection is attributed to a mode 1 internal motion, or internal tide. On the basis of the analyses presented here, the OCSD plume cannot be ruled out as a contributor to poor bathing-water quality at Huntington Beach.

    View details for DOI 10.1021/es0111986

    View details for Web of Science ID 000175311900010

    View details for PubMedID 12026969

  • Decadal and shorter period variability of surf zone water quality at Huntington Beach, California. Environmental Science and Technology Boehm., A., B., Grant, S., B., Kim, J., H., Mowbray, S., L., McGee, C., D., Clark, C., D. 2002; 36: 3885-3892
  • Cross-shelf transport at Huntington Beach -Implications for the fate of sewage discharged through an offshore ocean outfall. Environmental Science and Technology Boehm., A., B., Sanders, B., F., Winant., C., D. 2002; 36: 1899-1906
  • A steady state model of particulate organic carbon flux below the mixed layer and application to the Joint Global Ocean Flux Study JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS Boehm, A. B., Grant, S. B. 2001; 106 (C12): 31227-31237
  • Generation of enterococci bacteria in a coastal saltwater marsh and its impact on surf zone water quality ENVIRONMENTAL SCIENCE & TECHNOLOGY Grant, S. B., Sanders, B. F., Boehm, A. B., Redman, J. A., Kim, J. H., Mrse, R. D., Chu, A. K., Gouldin, M., McGee, C. D., Gardiner, N. A., Jones, B. H., Svejkovsky, J., Leipzig, G. V. 2001; 35 (12): 2407-2416


    Elevated levels of enterococci bacteria, an indicator of fecal pollution, are routinely detected in the surf zone at Huntington State and City Beaches in southern California. A multidisciplinary study was carried out to identify sources of enterococci bacteria landward of the coastline. We find that enterococci bacteria are present at high concentrations in urban runoff, bird feces, marsh sediments, and on marine vegetation. Surprisingly, urban runoff appears to have relatively little impact on surf zone water quality because of the long time required for this water to travel from its source to the ocean. On the other hand, enterococci bacteria generated in a tidal saltwater marsh located near the beach significantly impact surf zone water quality. This study identifies a potential tradeoff between restoring coastal wetlands and protecting beach water quality and calls into question the use of ocean bathing water standards based on enterococci at locations near coastal wetlands.

    View details for Web of Science ID 000169343700002

    View details for PubMedID 11432541

  • A steady-state model of particulate organic carbon flux below the mixed layer and application to the Joint Global Ocean Flux Study. Journal of Geophysical Research-Oceans Boehm, A., B., Grant., S., B. 2001; 106: 31227-21237
  • Generation of enterococci bacteria in a coastal saltwater marsh and its impact on surf zone water quality. Environmental Science & Technology Grant, S., B., Sanders, B., F., Boehm, A., B., Redman, J., A., Kim, J., H., Mrse, R., D. 2001; 35: 2407-2416
  • Particle coagulation and the memory of initial conditions JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL Boehm, A. B., Poor, C., Grant, S. B. 1998; 31 (46): 9241-9254
  • Influence of coagulation, sedimentation, and grazing by zooplankton on phytoplankton aggregate distributions in aquatic systems JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS Boehm, A. B., Grant, S. B. 1998; 103 (C8): 15601-15612
  • Particle coagulation and the memory of initial conditions Journal of Physics A: Mathematics and General Boehm, A., B., Poor, C., Grant., S., B. 1998; 31: 9241-9254
  • The influence of coagulation, sedimentation, and grazing by zooplankton on phytoplankton aggregate size distributions in aquatic systems. Journal of Geophysical Research-Oceans Boehm, A., B., Grant., S., B. 1998; 103: 15601-15612