Academic Appointments


Administrative Appointments


  • Graduate Student, Research, Scripps Institution of Oceanography (UCSD) (1994 - 2000)
  • U.S. Environmental Protection Agency STAR Graduate Fellow, University of California, San Diego (1995 - 1998)
  • Harry Hess Postdoctoral Fellow, Geosciences, Princeton University (2001 - 2002)
  • NSF Postdoctoral Research Fellow, Microbial Biology, Princeton University (2002 - 2003)
  • Assistant Professor of Geological & Environmental Sciences, Stanford University (2003 - 2008)
  • Assistant Professor, Environmental Earth System Science, Stanford University (2008 - Present)
  • Affiliated Faculty Member, Woods Institute for the Environment , Stanford University (2009 - 2011)
  • Associate Professor, Environmental Earth System Science, Stanford University (2010 - Present)
  • Senior Fellow, Woods Institute for the Environment, Stanford University (2011 - Present)

Honors & Awards


  • Highest Honors, Biol.; Cowell College Honors; Mark T. MacMillan Award, Undergrad Research,..., University of California, San Diego (1994)
  • STAR (Science To Achieve Results) Graduate Fellow, U.S. Environmental Protection Agency (1995-1998)
  • Harry Hess Postdoctoral Fellow, Geosciences, Princeton University (2001)
  • Postdoctoral Research Fellow, Microbial Biology, National Science Foundation (2002-2003)
  • Frederick E. Terman Fellow, Stanford University (2004)
  • Nominee - Packard Fellowship in Science and Engineering, Stanford University (2006)
  • Faculty Early Career Development (CAREER) Award Recipient, National Science Foundation, Division of Ocean Sciences (2009-present)

Boards, Advisory Committees, Professional Organizations


  • Co-Organizer and Chair, "Populations and Activity of Ammonia-Oxidizing and Denitrifying Organisms in Coastal Waters" Session at the American Society for Limnology and Oceanography (ASLO) Aquatic Sciences Meeting, New Orleans, Louisiana, February 2013, American Society for Limnology and Oceanography (ASLO) (2013 - 2013)
  • EESS Faculty Search Committee for Coastal Human-Environment Systems position, Stanford University (2013 - Present)
  • Chair, EESS Graduate Admissions Committee, Stanford University (2011 - 2013)
  • Organizer, Environmental Earth System Science (EESS) Departmental Seminar, Stanford University (2011 - 2011)
  • Co-Chair, School of Earth Sciences GeoBiology Faculty Search Committee, Stanford University (2011 - Present)
  • Associate Editor, Frontiers in Aquatic Microbiology (2010 - Present)
  • Invited Speaker for the 13th International Symposium on Microbial Ecology (ISME- 13) symposium entitled “Shifting Paradigms in Major Biogeochemical Cycles”, (August 22- 27, 2010; Seattle, WA), International Symposium on Microbial Ecology (ISME- 13) (2010 - 2010)
  • Environmental Venture Project (EVP) Committee/Panel Member, Woods Institute for the Environment (2010 - 2010)
  • Co-Chair, Environmental Venture Project (EVP) Selection Committee, Woods Institute for the Environment (2010 - 2012)
  • Member, Woods Faculty Leadership Working Group, Woods Institute for the Environment (2010 - Present)
  • Invited Speaker for the 2010 Gordon Research Conference on “Marine Microbes: From Genes to Global Cycles”, (July 4-9, 2010; Tilton School, Tilton, NH), Gordon Research Conference (2010 - 2010)
  • Chair/Organizer of “New Processes and Players in the Marine Microbial Nitrogen Cycle” Symposium at the 110th General Meeting of the American Society for Microbiology (ASM) General Meeting, San Diego, CA, May 2010, American Society for Microbiology (ASM) (2010 - 2010)
  • Co-Organizer and Chair of “Linking Microbial Communities to Geochemical Cycling” Session at the American Society for Limnology and Oceanography (ASLO) Aquatic Sciences Meeting, Nice, France, January 2009, American Society for Limnology and Oceanography (ASLO) (2009 - 2009)
  • Green Earth Sciences Building Space Committee, Stanford University (2009 - 2009)
  • Earth Sciences Council Member, Stanford University (2009 - Present)
  • Invited speaker - Ocean Sciences Seminar Series, University of California-Santa Cruz (May 2009), University of California-Santa Cruz (2009 - 2009)
  • Environmental Venture Project (EVP) Committee/Panel Member, Woods Institute for the Environment (2009 - 2009)
  • Invited speaker - Environmental Microbiology/Microbial Ecology (EMME) Seminar Series, University of California-Santa Barbara (May 2009), University of California-Santa Barbara (2009 - 2009)
  • Co-Chair/Organizer of “Functional Diversity in Nitrifying Organisms: Response to stress and substrate availability, evolution and niche differentiation” Session at the 1st International Conference on Nitrification (ICoN1), Louisville, KY, July 2009, International Conference on Nitrification (ICoN1) (2009 - 2009)
  • Reviewer for ‘Nitrification’ textbook, published by American Society for Microbiology (ASM) Press, American Society for Microbiology (ASM) (2009 - 2009)
  • Invited Speaker for the 1st International Conference on Nitrification (ICoN1), special session on “Diversity and abundance of nitrifier communities and their contributions to nitrification, nitrifier denitrification and anammox processes”, University of Louisville, Louisville, KY (July 2009), International Conference on Nitrification (ICoN1 (2009 - 2009)
  • Invited Speaker - Scripps Institution of Oceanography, University of California at San Diego, Marine Biology Seminar (November 2009), Scripps Institution of Oceanography, University of California at San Diego (2009 - 2009)
  • Editorial Board member, Applied and Environmental Microbiology journal (2008 - Present)
  • EESS Graduate Admissions Committee, Stanford University (2008 - 2011)
  • Invited speaker - Department of Biological Sciences, Northern Arizona University (2008 - 2008)
  • Environmental Venture Project (EVP) Committee/Panel Member, Woods Institute for the Environment (2008 - 2008)
  • Co-Organizer and Chair of “Saline Environments” Session at the US-China Geomicrobiology Workshop, Beijing, China, October 2008, US-China Geomicrobiology Workshop (2008 - 2008)
  • EESS Faculty Search Committee for Marine Chemist position, Stanford University (2008 - Present)
  • Hopkins Marine Station (HMS) Faculty Search Committee for Marine Cell Biologist position, Stanford University, (2008 - 2009)
  • Invited speaker - Environmental Microbiology Seminar Series, University of California-Berkeley (May 2008), University of California-Berkeley (2008 - 2008)
  • Invited speaker - Environmental Engineering Seminar Series, University of California-Berkeley (October 2008), University of California-Berkeley (2008 - 2008)
  • Panelist - National Science Foundation, Microbial Interactions & Processes (MIP) Program, National Science Foundation (2007 - 2007)
  • Invited speaker - Department of Microbiology, University of Tennessee (2007 - 2007)
  • Co-Organizer of “Microbial communities along environmental gradients: Linking microbial ecology and the ecosystem” Symposium at the Ecologicial Society of America/SER Joint Meeting, San Jose, CA, August 2007, Ecologicial Society of America/SER (2007 - 2007)
  • Earth Sciences Council Member, Stanford University (2007 - 2009)
  • Panelist - National Science Foundation, Antarctic Biology & Medicine (ABM) Program, National Science Foundation (2006 - 2006)
  • Environmental Earth Science (EES) Undergraduate Curriculum Committee Member, Stanford University (2006 - 2006)
  • SES Faculty Search Committe Member for Physical Oceanographer position, Stanford University (2006 - 2007)
  • Editorial Advisory Board member, Geobiology journal (2006 - Present)
  • Co-Chair of “Archaea in the Earth System” Session at the American Geophysical Union National (Fall) | Meeting, San Francisco, CA, American Geophysical Union (2006 - 2006)
  • Invited Speaker - ‘Functional Genes’ Symposium, International Geobiology 2006 Course, University of Southern Californa - Wrigley Marine Science Center (Catalina Island, CA), University of Southern Californa - Wrigley Marine Science Center (2006 - 2006)
  • Invited Speaker - 2006 Gordon Research Conference on Organic Geochemistry, special session on “Molecular Signatures of Archaea and Archaeal Processes” (Holderness School, Plymouth, NH), Gordon Research Conference (2006 - 2006)
  • Speaker, School of Earth Sciences Faculty Forum, Stanford University (2006 - 2006)
  • Speaker, Inaugural Global Bioreactor Network (GBN) Workshop, Nanyang Technological University (November 2006), Inaugural Global Bioreactor Network (GBN) (2006 - 2006)
  • Invited Participant, American Academy of Microbiology Colloquium on Marine Microbial Diversity: The Key to Earth's Habitability, San Francisco, CA, American Academy of Microbiology (2005 - 2005)
  • Invited Speaker - Agouron Institute Microbial Mat Meeting, La Jolla, CA, Agouron Institute (2005 - 2005)
  • SES Diversity Committee Member, Stanford University (2005 - 2006)
  • GES Graduate Admissions Committee Member, Stanford University (2005 - 2008)
  • Invited speaker - Ocean Sciences Department, University of California at Santa Cruz (2004 - 2004)
  • Invited speaker - Environmental Engineering and Science Seminar, Department of Civil & Environmental Engineering, Stanford University (2004 - 2004)
  • Invited Speaker - Biological Oceanography Seminar, School of Oceanography, University of Washington (2004 - 2004)
  • Invited Speaker - Division of Geological and Planetary Sciences,, California Institute of Technology (2004 - 2004)
  • University Chair of Oral Examination (Ph.D. Dissertation Defense) for 12 Stanford Ph.D. students (from 6 departments), Stanford University (2003 - Present)
  • Invited speaker - Department of Geography and Environmental Engineering, Johns Hopkins University (2003 - 2003)
  • Founder and Organizer, Geomicrobiology & Microbial Geochemistry (GMG) Seminar Series, Stanford University (2003 - Present)
  • Ph.D. Dissertation Committee Member for 27 students, Stanford University (2003 - Present)
  • Manuscript Reviewer for Applied and Environmental Microbiology, Aquatic Microbial Ecology, Aquatic Sciences, Archives of Microbiology, Biogeosciences Discussions, Environmental Microbiology, Environmental Science & Technology, FEMS Microbiology Ecology, FEMS Microbiology Reviews, Geochimica et Cosmochimica Acta, Geomicrobiology Journal, Journal of Applied Microbiology, Limnology & Oceanography, Microbiology, Molecular Ecology, Proceedings of the National Academy of Sciences USA, The ISME Journal, and Trends in Microbiology journals, Professional Journals (2003 - Present)
  • Proposal Reviewer for NSF Antarctic Biology and Medicine, Biocomplexity, Biogeosciences, Biological Oceanography, CAREER, Chemical Oceanography, Ecological Biology, Ecosystem Studies, Environmental Genomics, Geobiology and Low- Temperature Geochemistry, Microbial Genome Sequencing, and Microbial Observatories & Microbial Interactions and Processes (MO/MIP) programs, Various (2003 - Present)
  • Invited speaker - Department of Microbiology and Immunology, University of British Columbia (2002 - 2002)
  • Invited speaker - Department of Geological & Environmental Sciences, Stanford University (2002 - 2002)

Professional Education


  • Ph.D., Scripps Institution of Oceanography, University of California, San Diego (UCSD), Marine Biology (2000)
  • B.A., University of California, Santa Cruz (UCSC), Biology (1994)

Current Research and Scholarly Interests


Research
My research interests center on the molecular, biogeochemical, and ecological aspects of the microbially-mediated cycling of nitrogen and metals in the environment. In particular, the major research avenues actively pursued in my laboratory are focused on examining the diversity and activity of microorganisms involved in manganese cycling, denitrification, and especially nitrification within coastal, estuarine, and select terrestrial systems. We use a combination of molecular, genomic, cultivation, and biogeochemical approaches to study functionally-important groups of bacteria and archaea in both the laboratory and the field.

Teaching
My courses emphasize the critical role of microbes in shaping the geochemistry of our planet, over modern or geological time scales. Topically, these courses span the 'geo-microbiology' continuum from redox chemistry to molecular phylogeny, and from metagenomics to the hands-on cultivation of environmental microbes that catalyze key redox transformations. The unifying theme of all my courses is the emphasis on the immense metabolic and phylogenetic diversity of prokaryotes that drive the biogeochemical cycling of elements in nature. Collectively, these courses provide a strong 'microbial foundation' for students with backgrounds in biogeochemistry, geosciences, environmental engineering, as well as microbiology.

Professional Activities
Graduate Admissions Chair, Environmental Earth System Science (EESS) Department, 2011-2013; Co-Chair, Stanford School of Earth Sciences GeoBiology Faculty Search, 2011-present; Co-Chair, Stanford's Woods Institute Environmental Venture Project (EVP) Program 2010-2012; Associate Editor, Frontiers in Aquatic Microbiology, 2010-present; NSF CAREER Grant Recipient, 2009.

2016-17 Courses


Stanford Advisees


All Publications


  • Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient. FEMS microbiology ecology Peay, K. G., von Sperber, C., Cardarelli, E., Toju, H., Francis, C. A., Chadwick, O. A., Vitousek, P. M. 2017; 93 (5)

    Abstract

    Changes in species richness along climatological gradients have been instrumental in developing theories about the general drivers of biodiversity. Previous studies on microbial communities along climate gradients on mountainsides have revealed positive, negative and neutral richness trends. We examined changes in richness and composition of Fungi, Bacteria and Archaea in soil along a 50-1000 m elevation, 280-3280 mm/yr precipitation gradient in Hawai'i. Soil properties and their drivers are exceptionally well understood along this gradient. All three microbial groups responded strongly to the gradient, with community ordinations being similar along axes of environmental conditions (pH, rainfall) and resource availability (nitrogen, phosphorus). However, the form of the richness-climate relationship varied between Fungi (positive linear), Bacteria (unimodal) and Archaea (negative linear). These differences were related to resource-ecology and limiting conditions for each group, with fungal richness increasing most strongly with soil carbon, ammonia-oxidizing Archaea increasing with nitrogen mineralization rate, and Bacteria increasing with both carbon and pH. Reponses to the gradient became increasingly variable at finer taxonomic scales and within any taxonomic group most individual OTUs occurred in narrow climate-elevation ranges. These results show that microbial responses to climate gradients are heterogeneous due to complexity of underlying environmental changes and the diverse ecologies of microbial taxa.

    View details for DOI 10.1093/femsec/fix045

    View details for PubMedID 28402397

  • Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance. Microbial ecology Lee, J. A., Francis, C. A. 2016: -?

    Abstract

    Denitrifying bacteria play a critical role in the estuarine nitrogen cycle. Through the transformation of nitrate into nitrogen gas, these organisms contribute to the loss of bioavailable (i.e., fixed) nitrogen from low-oxygen environments such as estuary sediments. Denitrifiers have been shown to vary in abundance and diversity across the spatial environmental gradients that characterize estuaries, such as salinity and nitrogen availability; however, little is known about how their communities change in response to temporal changes in those environmental properties. Here, we present a 1-year survey of sediment denitrifier communities along the estuarine salinity gradient of San Francisco Bay. We used quantitative PCR and sequencing of functional genes coding for a key denitrifying enzyme, dissimilatory nitrite reductase, to compare two groups of denitrifiers: those with nirK (encoding copper-dependent nitrite reductase) and those with nirS (encoding the cytochrome-cd 1-dependent variant). We found that nirS was consistently more abundant and more diverse than nirK in all parts of the estuary. The abundances of the two genes were tightly linked across space but differed temporally, with nirK peaking when temperature was low and nirS peaking when nitrate was high. Likewise, the diversity and composition of nirK- versus nirS-type communities differed in their responses to seasonal variations, though both were strongly determined by site. Furthermore, our sequence libraries detected deeply branching clades with no cultured isolates, evidence of enormous diversity within the denitrifiers that remains to be explored.

    View details for PubMedID 27709247

  • Variable Nitrification Rates Across Environmental Gradients in Turbid, Nutrient-Rich Estuary Waters of San Francisco Bay ESTUARIES AND COASTS Damashek, J., Casciotti, K. L., Francis, C. A. 2016; 39 (4): 1050-1071
  • Factors influencing nitrification rates and the abundance and transcriptional activity of ammonia-oxidizing microorganisms in the dark northeast Pacific Ocean LIMNOLOGY AND OCEANOGRAPHY Smith, J. M., Damashek, J., Chavez, F. P., Francis, C. A. 2016; 61 (2): 596-609

    View details for DOI 10.1002/lno.10235

    View details for Web of Science ID 000372166500008

  • Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta FRONTIERS IN MICROBIOLOGY Damashek, J., Smith, J. M., Mosier, A. C., Francis, C. A. 2015; 5
  • Spatiotemporal relationships between the abundance, distribution, and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments. Microbial ecology Smith, J. M., Mosier, A. C., Francis, C. A. 2015; 69 (1): 13-24

    Abstract

    The primary objective of this study was to gain an understanding of how key microbial communities involved in nitrogen cycling in estuarine sediments vary over a 12-month period. Furthermore, we sought to determine whether changes in the size of these communities are related to, or indicative of, seasonal patterns in fixed nitrogen dynamics in Elkhorn Slough-a small, agriculturally impacted estuary with a direct connection to Monterey Bay. We assessed sediment and pore water characteristics, abundance of functional genes for nitrification (bacterial and archaeal amoA, encoding ammonia monooxygenase subunit A) and denitrification (nirS and nirK, encoding nitrite reductase), and measurements of potential nitrification and denitrification activities at six sites. No seasonality in the abundance of denitrifier or ammonia oxidizer genes was observed. A strong association between potential nitrification activity and the size of ammonia-oxidizing bacterial communities was observed across the estuary. In contrast, ammonia-oxidizing archaeal abundances remained relatively constant in space and time. Unlike many other estuaries, salinity does not appear to regulate the distribution of ammonia-oxidizing communities in Elkhorn Slough. Instead, their distributions appear to be governed over two different time scales. Long-term niche characteristics selected for the gross size of archaeal and bacterial ammonia-oxidizing communities, yet covariation in their abundances between monthly samples suggests that they respond in a similar manner to short-term changes in their environment. Abundances of denitrifier and ammonia oxidizer genes also covaried, but site-specific differences in this relationship suggest differing levels of interaction (or coupling) between nitrification and denitrification.

    View details for DOI 10.1007/s00248-014-0450-1

    View details for PubMedID 25038845

  • Ammonium Uptake by Phytoplankton Regulates Nitrification in the Sunlit Ocean PLOS ONE Smith, J. M., Chavez, F. P., Francis, C. A. 2014; 9 (9)
  • Differential contributions of archaeal ammonia oxidizer ecotypes to nitrification in coastal surface waters. ISME journal Smith, J. M., Casciotti, K. L., Chavez, F. P., Francis, C. A. 2014; 8 (8): 1704-1714

    Abstract

    The occurrence of nitrification in the oceanic water column has implications extending from local effects on the structure and activity of phytoplankton communities to broader impacts on the speciation of nitrogenous nutrients and production of nitrous oxide. The ammonia-oxidizing archaea, responsible for carrying out the majority of nitrification in the sea, are present in the marine water column as two taxonomically distinct groups. Water column group A (WCA) organisms are detected at all depths, whereas Water column group B (WCB) are present primarily below the photic zone. An open question in marine biogeochemistry is whether the taxonomic definition of WCA and WCB organisms and their observed distributions correspond to distinct ecological and biogeochemical niches. We used the natural gradients in physicochemical and biological properties that upwelling establishes in surface waters to study their roles in nitrification, and how their activity-ascertained from quantification of ecotype-specific ammonia monooxygenase (amoA) genes and transcripts-varies in response to environmental fluctuations. Our results indicate a role for both ecotypes in nitrification in Monterey Bay surface waters. However, their respective contributions vary, due to their different sensitivities to surface water conditions. WCA organisms exhibited a remarkably consistent level of activity and their contribution to nitrification appears to be related to community size. WCB activity was less consistent and primarily constrained to colder, high nutrient and low chlorophyll waters. Overall, the results of our characterization yielded a strong, potentially predictive, relationship between archaeal amoA gene abundance and the rate of nitrification.

    View details for DOI 10.1038/ismej.2014.11

    View details for PubMedID 24553472

  • Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes APPLIED MICROBIOLOGY AND BIOTECHNOLOGY Wells, G. F., Wu, C. H., Piceno, Y. M., Eggleston, B., Brodie, E. L., DeSantis, T. Z., Andersen, G. L., Hazen, T. C., Francis, C. A., Criddle, C. S. 2014; 98 (10): 4723-4736

    Abstract

    Wastewater treatment plants use a variety of bioreactor types and configurations to remove organic matter and nutrients. Little is known regarding the effects of different configurations and within-plant immigration on microbial community dynamics. Previously, we found that the structure of ammonia-oxidizing bacterial (AOB) communities in a full-scale dispersed growth activated sludge bioreactor correlated strongly with levels of NO2 (-) entering the reactor from an upstream trickling filter. Here, to further examine this puzzling association, we profile within-plant microbial biogeography (spatial variation) and test the hypothesis that substantial microbial immigration occurs along a transect (raw influent, trickling filter biofilm, trickling filter effluent, and activated sludge) at the same full-scale wastewater treatment plant. AOB amoA gene abundance increased >30-fold between influent and trickling filter effluent concomitant with NO2 (-) production, indicating unexpected growth and activity of AOB within the trickling filter. Nitrosomonas europaea was the dominant AOB phylotype in trickling filter biofilm and effluent, while a distinct "Nitrosomonas-like" lineage dominated in activated sludge. Prior time series indicated that this "Nitrosomonas-like" lineage was dominant when NO2 (-) levels in the trickling filter effluent (i.e., activated sludge influent) were low, while N. europaea became dominant in the activated sludge when NO2 (-) levels were high. This is consistent with the hypothesis that NO2 (-) production may cooccur with biofilm sloughing, releasing N. europaea from the trickling filter into the activated sludge bioreactor. Phylogenetic microarray (PhyloChip) analyses revealed significant spatial variation in taxonomic diversity, including a large excess of methanogens in the trickling filter relative to activated sludge and attenuation of Enterobacteriaceae across the transect, and demonstrated transport of a highly diverse microbial community via the trickling filter effluent to the activated sludge bioreactor. Our results provide compelling evidence that substantial immigration between coupled process units occurs and may exert significant influence over microbial community dynamics within staged bioreactors.

    View details for DOI 10.1007/s00253-014-5564-3

    View details for Web of Science ID 000335460700039

    View details for PubMedID 24553968

  • Spatiotemporal relationships between the abundance, distribution and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments Microbial Ecology Smith, J. M., Mosier, A. C., Francis, C. A. 2014
  • Ammonium uptake by phytoplankton regulates nitrification in the sunlit ocean. PloS one Smith, J. M., Chavez, F. P., Francis, C. A. 2014; 9 (9)

    Abstract

    Nitrification, the microbial oxidation of ammonium to nitrate, is a central part of the nitrogen cycle. In the ocean's surface layer, the process alters the distribution of inorganic nitrogen species available to phytoplankton and produces nitrous oxide. A widely held idea among oceanographers is that nitrification is inhibited by light in the ocean. However, recent evidence that the primary organisms involved in nitrification, the ammonia-oxidizing archaea (AOA), are present and active throughout the surface ocean has challenged this idea. Here we show, through field experiments coupling molecular genetic and biogeochemical approaches, that competition for ammonium with phytoplankton is the strongest regulator of nitrification in the photic zone. During multiday experiments at high irradiance a single ecotype of AOA remained active in the presence of rapidly growing phytoplankton. Over the course of this three day experiment, variability in the intensity of competition with phytoplankton caused nitrification rates to decline from those typical of the lower photic zone (60 nmol L-1 d-1) to those in well-lit layers (<1 nmol L-1 d-1). During another set of experiments, nitrification rates exhibited a diel periodicity throughout much of the photic zone, with the highest rates occurring at night when competition with phytoplankton is lowest. Together, the results of our experiments indicate that nitrification rates in the photic zone are more strongly regulated by competition with phytoplankton for ammonium than they are by light itself. This finding advances our ability to model the impact of nitrification on estimates of new primary production, and emphasizes the need to more strongly consider the effects of organismal interactions on nutrient standing stocks and biogeochemical cycling in the surface of the ocean.

    View details for DOI 10.1371/journal.pone.0108173

    View details for PubMedID 25251022

  • Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta. Frontiers in microbiology Damashek, J., Smith, J. M., Mosier, A. C., Francis, C. A. 2014; 5: 743-?

    Abstract

    Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic nitrification, is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.

    View details for DOI 10.3389/fmicb.2014.00743

    View details for PubMedID 25620958

  • Distributed microbially- and chemically-mediated redox processes controlling arsenic dynamics within Mn-/Fe-oxide constructed aggregates GEOCHIMICA ET COSMOCHIMICA ACTA Ying, S. C., Masue-Slowey, Y., Kocar, B. D., Griffis, S. D., Webb, S., Marcus, M. A., Francis, C. A., Fendorf, S. 2013; 104: 29-41
  • Adaptation of nitrifying microbial biomass to nickel in batch incubations APPLIED MICROBIOLOGY AND BIOTECHNOLOGY Yeung, C., Francis, C. A., Criddle, C. S. 2013; 97 (2): 847-857

    Abstract

    Nitrification-microbial oxidation of ammonia to nitrate-is sensitive to an array of inhibitors. Currently, little is known regarding the ecological processes that enable adaptation to inhibitors and recovery of nitrification. This study evaluated inhibition and recovery of nitrification in batch cultures of activated sludge incubated with different levels of nickel (Ni), a model inhibitor. Incubation with 1 mg/L of added Ni did not adversely affect nitrification, and little inhibition occurred at 5 and 10 mg/L Ni. Incubation with 50 mg/L Ni resulted in significant inhibition, decreased amoA transcript abundance, and delayed recovery of nitrification until amoA transcript abundance rebounded after 24 h. For this dosage, recovery of nitrification occurred without a significant change in ammonia-oxidizing bacteria (AOB) community structure. By contrast, incubation with 150 mg/L of added Ni strongly inhibited nitrification and delayed recovery until a shift in AOB community structure occurred after ∼6 weeks of incubation. The results indicate that inhibitor-resistant nitrifying cultures can be obtained from long-term batch incubations of decaying activated sludge incubated with high levels of added inhibitor.

    View details for DOI 10.1007/s00253-012-3947-x

    View details for Web of Science ID 000313651700035

    View details for PubMedID 22374414

  • Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary. Frontiers in microbiology Francis, C. A., O'Mullan, G. D., Cornwell, J. C., Ward, B. B. 2013; 4: 237-?

    Abstract

    Chesapeake Bay, the largest estuary in North America, can be characterized as having steep and opposing gradients in salinity and dissolved inorganic nitrogen along the main axis of the Bay. In this study, the diversity of nirS gene fragments (encoding cytochrome cd 1-type nitrite reductase), physical/chemical parameters, and benthic N2-fluxes were analyzed in order to determine how denitrifier communities and biogeochemical activity vary along the estuary salinity gradient. The nirS gene fragments were PCR-amplified, cloned, and sequenced from sediment cores collected at five stations. Sequence analysis of 96-123 nirS clones from each station revealed extensive overall diversity in this estuary, as well as distinct spatial structure in the nirS sequence distributions. Both nirS-based richness and community composition varied among stations, with the most dramatic shifts occurring between low-salinity (oligohaline) and moderate-salinity (mesohaline) sites. For four samples collected in April, the nirS-based richness, nitrate concentrations, and N2-fluxes all decreased in parallel along the salinity gradient from the oligohaline northernmost station to the highest salinity (polyhaline) station near the mouth of the Bay. The vast majority of the 550 nirS sequences were distinct from cultivated denitrifiers, although many were closely related to environmental clones from other coastal and estuarine systems. Interestingly, 8 of the 172 OTUs identified accounted for 42% of the total nirS clones, implying the presence of a few dominant and many rare genotypes, which were distributed in a non-random manner along the salinity gradient of Chesapeake Bay. These data, comprising the largest dataset to investigate nirS clone sequence diversity from an estuarine environment, also provided information that was required for the development of nirS microarrays to investigate the interaction of microbial diversity, environmental gradients, and biogeochemical activity.

    View details for DOI 10.3389/fmicb.2013.00237

    View details for PubMedID 24009603

  • Measurements of nitrite production and nitrite-producing organisms in and around the primary nitrite maximum in the central California Current Biogeosciences Santoro, A. E., Sakamoto, C. M., Smith, J. M., Plant, J. N., Gehman, A. L., Worden, A. Z., Johnson, K. S., Francis, C. A., Casciotti, K. L. 2013; 10: 7395-7410

    View details for DOI 10.5194/bg-10-7395-2013

  • Ecophysiology of an Ammonia-Oxidizing Archaeon Adapted to Low-Salinity Habitats MICROBIAL ECOLOGY Mosier, A. C., Lund, M. B., Francis, C. A. 2012; 64 (4): 955-963

    Abstract

    Ammonia oxidation in marine and terrestrial ecosystems plays a pivotal role in the cycling of nitrogen and carbon. Recent discoveries have shown that ammonia-oxidizing archaea (AOA) are both abundant and diverse in these systems, yet very little is known about their physiology. Here we report a physiological analysis of a novel low-salinity-type AOA enriched from the San Francisco Bay estuary, Candidatus Nitrosoarchaeum limnia strain SFB1. N. limnia has a slower growth rate than Nitrosopumilus maritimus and Nitrososphaera viennensis EN76, the only pure AOA isolates described to date, but the growth rate is comparable to the growth of marine AOA enrichment cultures. The growth rate only slightly decreased when N. limnia was grown under lower-oxygen conditions (5.5 % oxygen in the headspace). Although N. limnia was capable of growth at 75 % of seawater salinity, there was a longer lag time, incomplete oxidation of ammonia to nitrite, and slower overall growth rate. Allylthiourea (ATU) only partially inhibited growth and ammonia oxidation by N. limnia at concentrations known to completely inhibit bacterial ammonia oxidation. Using electron microscopy, we confirmed the presence of flagella as suggested by various flagellar biosynthesis genes in the N. limnia genome. We demonstrate that N. limnia is representative of a low-salinity estuarine AOA ecotype and that more than 85 % of its proteins have highest identity to other coastal and estuarine metagenomic sequences. Our findings further highlight the physiology of N. limnia and help explain its ecological adaptation to low-salinity niches.

    View details for DOI 10.1007/s00248-012-0075-1

    View details for Web of Science ID 000310127900010

    View details for PubMedID 22644483

  • Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea ISME JOURNAL Lund, M. B., Smith, J. M., Francis, C. A. 2012; 6 (10): 1966-1977

    Abstract

    Ammonia-oxidizing archaea (AOA) are widespread and abundant in aquatic and terrestrial habitats and appear to have a significant impact on the global nitrogen cycle. Like the ammonia-oxidizing bacteria, AOA encode a gene homologous to copper-containing nitrite reductases (nirK), which has been studied very little to date. In this study, the diversity, abundance and expression of thaumarchaeal nirK genes from coastal and marine environments were investigated using two mutually excluding primer pairs, which amplify the nirK variants designated as AnirKa and AnirKb. Only the AnirKa variant could be detected in sediment samples from San Francisco Bay and these sequences grouped with the nirK from Candidatus Nitrosopumilus maritimus and Candidatus Nitrosoarchaeum limnia. The two nirK variants had contrasting distributions in the water column in Monterey Bay and the California Current. AnirKa was more abundant in the epi- to mesopelagic Monterey Bay water column, whereas AnirKb was more abundant in the meso- to bathypelagic California Current water. The abundance and community composition of AnirKb, but not AnirKa, followed that of thaumarchaeal amoA, suggesting that either AnirKa is not exclusively associated with AOA or that commonly used amoA primers may be missing a significant fraction of AOA diversity in the epipelagic. Interestingly, thaumarchaeal nirK was expressed 10-100-fold more than amoA in Monterey Bay. Overall, this study provides valuable new insights into the distribution, diversity, abundance and expression of this alternative molecular marker for AOA in the ocean.

    View details for DOI 10.1038/ismej.2012.40

    View details for Web of Science ID 000309056300014

    View details for PubMedID 22592819

  • Genome Sequence of "Candidatus Nitrosopumilus salaria" BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary JOURNAL OF BACTERIOLOGY Mosier, A. C., Allen, E. E., Kim, M., Ferriera, S., Francis, C. A. 2012; 194 (8): 2121-2122

    Abstract

    Ammonia-oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine and terrestrial ecosystems. Here, we present the draft genome sequence for the ammonia-oxidizing archaeon "Candidatus Nitrosopumilus salaria" BD31, which was enriched in culture from sediments of the San Francisco Bay estuary. The genome sequences revealed many similarities to the genome of Nitrosopumilus maritimus.

    View details for DOI 10.1128/JB.00013-12

    View details for Web of Science ID 000302180200041

    View details for PubMedID 22461555

  • Genome Sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a Low-Salinity Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary JOURNAL OF BACTERIOLOGY Mosier, A. C., Allen, E. E., Kim, M., Ferriera, S., Francis, C. A. 2012; 194 (8): 2119-2120

    Abstract

    Here, we present the draft genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, an ammonia-oxidizing archaeon enriched in culture from low-salinity sediments of the San Francisco Bay estuary. The genome sequence revealed many similarities to the previously sequenced genome of "Ca. Nitrosoarchaeum limnia" SFB1 (enriched from a nearby site in San Francisco Bay) and is representative of a clade of ammonia-oxidizing archaea (AOA) found in low-salinity habitats worldwide.

    View details for DOI 10.1128/JB.00007-12

    View details for Web of Science ID 000302180200040

    View details for PubMedID 22461554

  • Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation ISME JOURNAL Robidart, J. C., Preston, C. M., Paerl, R. W., Turk, K. A., Mosier, A. C., Francis, C. A., Scholin, C. A., Zehr, J. P. 2012; 6 (3): 513-523

    Abstract

    Monterey Bay, CA is an Eastern boundary upwelling system that is nitrogen limited much of the year. In order to resolve population dynamics of microorganisms important for nutrient cycling in this region, we deployed the Environmental Sample Processor with quantitative PCR assays targeting both ribosomal RNA genes and functional genes for subclades of cyanobacteria (Synechococcus) and ammonia-oxidizing Archaea (Thaumarchaeota) populations. Results showed a strong correlation between Thaumarchaea abundances and nitrate during the spring upwelling but not the fall sampling period. In relatively stratified fall waters, the Thaumarchaeota community reached higher numbers than in the spring, and an unexpected positive correlation with chlorophyll concentration was observed. Further, we detected drops in Synechococcus abundance that occurred on short (that is, daily) time scales. Upwelling intensity and blooms of eukaryotic phytoplankton strongly influenced Synechococcus distributions in the spring and fall, revealing what appear to be the environmental limitations of Synechococcus populations in this region. Each of these findings has implications for Monterey Bay biogeochemistry. High-resolution sampling provides a better-resolved framework within which to observe changes in the plankton community. We conclude that controls on these ecosystems change on smaller scales than are routinely assessed, and that more predictable trends will be uncovered if they are evaluated within seasonal (monthly), rather than on annual or interannual scales.

    View details for DOI 10.1038/ismej.2011.127

    View details for Web of Science ID 000300883200004

    View details for PubMedID 21975596

  • Global Biodiversity of Aquatic Ammonia-Oxidizing Archaea is Partitioned by Habitat. Frontiers in microbiology Biller, S. J., Mosier, A. C., Wells, G. F., Francis, C. A. 2012; 3: 252-?

    Abstract

    Archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon and nitrogen cycles. Since the initial discovery of an ammonia monooxygenase α-subunit (amoA) gene associated with an archaeal metagenomic fragment, archaeal amoA sequences have been detected in a wide variety of nitrifying environments. Recent sequencing efforts have revealed extensive diversity of archaeal amoA sequences within different habitats. In this study, we have examined over 8000 amoA sequences from the literature and public databases in an effort to understand the ecological factors influencing the distribution and diversity of ammonia-oxidizing archaea (AOA), with a particular focus on sequences from aquatic habitats. This broad survey provides strong statistical support for the hypothesis that different environments contain distinct clusters of AOA amoA sequences, as surprisingly few sequences are found in more than one habitat type. Within aquatic environments, salinity, depth in the water column, and temperature were significantly correlated with the distribution of sequence types. These findings support the existence of multiple distinct aquatic AOA populations in the environment and suggest some possible selective pressures driving the partitioning of AOA amoA diversity.

    View details for DOI 10.3389/fmicb.2012.00252

    View details for PubMedID 22826704

  • Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat FRONTIERS IN MICROBIOLOGY Biller, S. J., Mosier, A. C., Wells, G. F., Francis, C. A. 2012; 3
  • Fine-scale bacterial community dynamics and the taxa-time relationship within a full-scale activated sludge bioreactor WATER RESEARCH Wells, G. F., Park, H., Eggleston, B., Francis, C. A., Criddle, C. S. 2011; 45 (17): 5476-5488

    Abstract

    In activated sludge bioreactors, aerobic heterotrophic communities efficiently remove organics, nutrients, toxic substances, and pathogens from wastewater, but the dynamics of these communities are as yet poorly understood. A macroecology metric used to quantify community shifts is the taxa-time relationship, a temporal analog of the species-area curve. To determine whether this metric can be applied to full-scale bioreactors, activated sludge samples were collected weekly over a one-year period at a local municipal wastewater treatment plant. Bacterial community dynamics were evaluated by monitoring 16S rRNA genes using Terminal Restriction Fragment Length Polymorphism (T-RFLP), corroborated by clone libraries. Observed taxa richness increased with time according to a power law model, as predicted by macroecological theory, with a power law exponent of w = 0.209. The results reveal strong long-term temporal dynamics during a period of stable performance (BOD removal and nitrification). Community dynamics followed a gradual succession away from initial conditions rather than periodicity around a mean "equilibrium", with greater within-month then among-month community similarities. Changes in community structure were significantly associated via multivariate statistical analyses with dissolved oxygen, temperature, influent silver, biomass (MLSS), flow rate, and influent nitrite, cadmium and chromium concentrations. Overall, our results suggest patterns of bacterial community dynamics likely regulated in part by operational parameters and provide evidence that the taxa-time relationship may be a fundamental ecological pattern in macro- and microbial systems.

    View details for DOI 10.1016/j.watres.2011.08.006

    View details for Web of Science ID 000295894600013

    View details for PubMedID 21875739

  • Core and Intact Polar Glycerol Dibiphytanyl Glycerol Tetraether Lipids of Ammonia-Oxidizing Archaea Enriched from Marine and Estuarine Sediments APPLIED AND ENVIRONMENTAL MICROBIOLOGY Pitcher, A., Hopmans, E. C., Mosier, A. C., Park, S., Rhee, S., Francis, C. A., Schouten, S., Damste, J. S. 2011; 77 (10): 3468-3477

    Abstract

    Glycerol dibiphytanyl glycerol tetraether (GDGT)-based intact membrane lipids are increasingly being used as complements to conventional molecular methods in ecological studies of ammonia-oxidizing archaea (AOA) in the marine environment. However, the few studies that have been done on the detailed lipid structures synthesized by AOA in (enrichment) culture are based on species enriched from nonmarine environments, i.e., a hot spring, an aquarium filter, and a sponge. Here we have analyzed core and intact polar lipid (IPL)-GDGTs synthesized by three newly available AOA enriched directly from marine sediments taken from the San Francisco Bay estuary ("Candidatus Nitrosoarchaeum limnia"), and coastal marine sediments from Svalbard, Norway, and South Korea. Like previously screened AOA, the sedimentary AOA all synthesize crenarchaeol (a GDGT containing a cyclohexane moiety and four cyclopentane moieties) as a major core GDGT, thereby supporting the hypothesis that crenarchaeol is a biomarker lipid for AOA. The IPL headgroups synthesized by sedimentary AOA comprised mainly monohexose, dihexose, phosphohexose, and hexose-phosphohexose moieties. The hexose-phosphohexose headgroup bound to crenarchaeol was common to all enrichments and, in fact, the only IPL common to every AOA enrichment analyzed to date. This apparent specificity, in combination with its inferred lability, suggests that it may be the most suitable biomarker lipid to trace living AOA. GDGTs bound to headgroups with a mass of 180 Da of unknown structure appear to be specific to the marine group I.1a AOA: they were synthesized by all three sedimentary AOA and "Candidatus Nitrosopumilus maritimus"; however, they were absent in the group I.1b AOA "Candidatus Nitrososphaera gargensis."

    View details for DOI 10.1128/AEM.02758-10

    View details for Web of Science ID 000290473200036

    View details for PubMedID 21441324

  • Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis PLOS ONE Blainey, P. C., Mosier, A. C., Potanina, A., Francis, C. A., Quake, S. R. 2011; 6 (2)

    Abstract

    Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles. We sequenced the genome of AOA in an enrichment culture from low-salinity sediments in San Francisco Bay using single-cell and metagenomic genome sequence data. Five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells' genomic DNA was amplified by multiple displacement amplification (MDA) in 50 nL volumes and then sequenced by high-throughput DNA pyrosequencing. This microscopy-based approach to single-cell genomics minimizes contamination and allows correlation of high-resolution cell images with genomic sequences. Statistical properties of coverage across the five single cells, in combination with the contrasting properties of the metagenomic dataset allowed the assembly of a high-quality draft genome. The genome of this AOA, which we designate Candidatus Nitrosoarchaeum limnia SFB1, is ∼1.77 Mb with >2100 genes and a G+C content of 32%. Across the entire genome, the average nucleotide identity to Nitrosopumilus maritimus, the only AOA in pure culture, is ∼70%, suggesting this AOA represents a new genus of Crenarchaeota. Phylogenetically, the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes of this AOA are most closely related to sequences reported from a wide variety of freshwater ecosystems. Like N. maritimus, the low-salinity AOA genome appears to have an ammonia oxidation pathway distinct from ammonia oxidizing bacteria (AOB). In contrast to other described AOA, these low-salinity AOA appear to be motile, based on the presence of numerous motility- and chemotaxis-associated genes in the genome. This genome data will be used to inform targeted physiological and metabolic studies of this novel group of AOA, which may ultimately advance our understanding of AOA metabolism and their impacts on the global carbon and nitrogen cycles.

    View details for DOI 10.1371/journal.pone.0016626

    View details for Web of Science ID 000287656600009

    View details for PubMedID 21364937

  • Spatial Variability in Nitrification Rates and Ammonia-Oxidizing Microbial Communities in the Agriculturally Impacted Elkhorn Slough Estuary, California APPLIED AND ENVIRONMENTAL MICROBIOLOGY Wankel, S. D., Mosier, A. C., Hansel, C. M., Paytan, A., Francis, C. A. 2011; 77 (1): 269-280

    Abstract

    Ammonia oxidation-the microbial oxidation of ammonia to nitrite and the first step in nitrification-plays a central role in nitrogen cycling in coastal and estuarine systems. Nevertheless, questions remain regarding the connection between this biogeochemical process and the diversity and abundance of the mediating microbial community. In this study, we measured nutrient fluxes and rates of sediment nitrification in conjunction with the diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing betaproteobacteria (β-AOB). Sediments were examined from four sites in Elkhorn Slough, a small agriculturally impacted coastal California estuary that opens into Monterey Bay. Using an intact sediment core flowthrough incubation system, we observed significant correlations among NO(3)(-), NO(2)(-), NH(4)(+), and PO(4)(3+) fluxes, indicating a tight coupling of sediment biogeochemical processes. (15)N-based measurements of nitrification rates revealed higher rates at the less impacted, lower-nutrient sites than at the more heavily impacted, nutrient-rich sites. Quantitative PCR analyses revealed that β-AOB amoA (encoding ammonia monooxygenase subunit A) gene copies outnumbered AOA amoA gene copies by factors ranging from 2- to 236-fold across the four sites. Sites with high nitrification rates primarily contained marine/estuarine Nitrosospira-like bacterial amoA sequences and phylogenetically diverse archaeal amoA sequences. Sites with low nitrification rates were dominated by estuarine Nitrosomonas-like amoA sequences and archaeal amoA sequences similar to those previously described in soils. This is the first report measuring AOA and β-AOB amoA abundance in conjunction with (15)N-based nitrification rates in estuary sediments.

    View details for DOI 10.1128/AEM.01318-10

    View details for Web of Science ID 000285550300029

    View details for PubMedID 21057023

  • DETERMINING THE DISTRIBUTION OF MARINE AND COASTAL AMMONIA-OXIDIZING ARCHAEA AND BACTERIA USING A QUANTITATIVE APPROACH METHODS IN ENZYMOLOGY: RESEARCH ON NITRIFICATION AND RELATED PROCESSES, VOL 486, PART A Mosier, A. C., Francis, C. A. 2011; 486: 205-221

    Abstract

    The oxidation of ammonia to nitrite is the first and often rate-limiting step in nitrification and plays an important role in both nitrogen and carbon cycling. This process is carried out by two distinct groups of microorganisms: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This chapter describes methods for measuring the abundance of AOA and AOB using ammonia monooxygenase subunit A (amoA) genes, with a particular emphasis on marine and coastal systems. We also describe quantitative measures designed to target two specific clades of marine AOA: the "shallow" (group A) and "deep" (group B) water column AOA.

    View details for DOI 10.1016/S0076-6879(11)86009-X

    View details for Web of Science ID 000286404100009

    View details for PubMedID 21185437

  • Denitrifier abundance and activity across the San Francisco Bay estuary ENVIRONMENTAL MICROBIOLOGY REPORTS Mosier, A. C., Francis, C. A. 2010; 2 (5): 667-676

    Abstract

    Over 50% of external dissolved inorganic nitrogen inputs to estuaries are removed by denitrification - the microbial conversion of nitrate to nitrogen gas under anaerobic conditions. In this study, denitrifier abundance, potential rates and community structure were examined in sediments from the San Francisco Bay estuary. Abundance of nirK genes (encoding Cu-containing nitrite reductase) ranged from 9.7 × 10(3) to 4.4 × 10(6) copies per gram of sediment, while the abundance of nirS genes (encoding cytochrome cd1 nitrite reductase) ranged from 5.4 × 10(5) to 5.4 × 10(7) copies per gram of sediment. nirK gene abundance was highest in the riverine North Bay, whereas nirS gene abundance was highest in the more marine Central and South Bays. Denitrification potential (DNP) rate measurements were highest in the San Pablo and Central Bays and lowest in the North Bay. nirS-type denitrifiers may be more biogeochemically important than nirK-type denitrifiers in this estuary, because DNP rates were positively correlated with nirS abundance, nirS abundance was higher than nirK abundance at every site and time point, and nirS richness was higher than nirK richness at every site. Statistical analyses demonstrated that salinity, organic carbon, nitrogen and several metals were key factors influencing denitrification rates, nir abundance and community structure. Overall, this study provides valuable new insights into the abundance, diversity and biogeochemical activity of estuarine denitrifying communities and suggests that nirS-type denitrifiers likely play an important role in nitrogen removal in San Francisco Bay, particularly at high-salinity sites.

    View details for DOI 10.1111/j.1758-2229.2010.00156.x

    View details for Web of Science ID 000283157900007

    View details for PubMedID 23766254

  • Combined niche and neutral effects in a microbial wastewater treatment community PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ofiteru, I. D., Lunn, M., Curtis, T. P., Wells, G. F., Criddle, C. S., Francis, C. A., Sloan, W. T. 2010; 107 (35): 15345-15350

    Abstract

    It has long been assumed that differences in the relative abundance of taxa in microbial communities reflect differences in environmental conditions. Here we show that in the economically and environmentally important microbial communities in a wastewater treatment plant, the population dynamics are consistent with neutral community assembly, where chance and random immigration play an important and predictable role in shaping the communities. Using dynamic observations, we demonstrate a straightforward calibration of a purely neutral model and a parsimonious method to incorporate environmental influence on the reproduction (or birth) rate of individual taxa. The calibrated model parameters are biologically plausible, with the population turnover and diversity in the heterotrophic community being higher than for the ammonia oxidizing bacteria (AOB) and immigration into AOB community being relatively higher. When environmental factors were incorporated more of the variance in the observations could be explained but immigration and random reproduction and deaths remained the dominant driver in determining the relative abundance of the common taxa. Consequently we suggest that neutral community models should be the foundation of any description of an open biological system.

    View details for DOI 10.1073/pnas.1000604107

    View details for Web of Science ID 000281468500012

    View details for PubMedID 20705897

  • Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current ENVIRONMENTAL MICROBIOLOGY Santoro, A. E., Casciotti, K. L., Francis, C. A. 2010; 12 (7): 1989-2006

    Abstract

    A combination of stable isotope and molecular biological approaches was used to determine the activity, abundance and diversity of nitrifying organisms in the central California Current. Using (15)NH(4)(+) incubations, nitrification was detectable in the upper water column down to 500 m; maximal rates were observed just below the euphotic zone. Crenarchaeal and betaproteobacterial ammonia monooxygenase subunit A genes (amoA), and 16S ribosomal RNA (rRNA) genes of Marine Group I Crenarchaeota and a putative nitrite-oxidizing genus, Nitrospina, were quantified using quantitative PCR. Crenarchaeal amoA abundance ranged from three to six genes ml(-1) in oligotrophic surface waters to > 8.7 x 10(4) genes ml(-1) just below the core of the California Current at 200 m depth. Bacterial amoA abundance was lower than archaeal amoA and ranged from below detection levels to 400 genes ml(-1). Nitrification rates were not directly correlated to bacterial or archaeal amoA abundance. Archaeal amoA and Marine Group I crenarchaeal 16S rRNA gene abundances were correlated with Nitrospina 16S rRNA gene abundance at all stations, indicating that similar factors may control the distribution of these two groups. Putatively shallow water-associated archaeal amoA types ('Cluster A') decreased in relative abundance with depth, while a deep water-associated amoA type ('Cluster B') increased with depth. Although some Cluster B amoA sequences were found in surface waters, expressed amoA gene sequences were predominantly from Cluster A. Cluster B amoA transcripts were detected between 100 and 500 m depths, suggesting an active role in ammonia oxidation in the mesopelagic. Expression of marine Nitrosospira-like bacterial amoA genes was detected throughout the euphotic zone down to 200 m. Natural abundance stable isotope ratios (delta(15)N and delta(18)O) in nitrate (NO(3)(-)) and nitrous oxide (N(2)O) were used to evaluate the importance of nitrification over longer time scales. Using an isotope mass balance model, we calculate that nitrification could produce between 0.45 and 2.93 micromol m(-2) day(-1) N(2)O in the central California Current, or approximately 1.5-4 times the local N(2)O flux from deep water.

    View details for DOI 10.1111/j.1462-2920.2010.02205.x

    View details for Web of Science ID 000280101200016

    View details for PubMedID 20345944

  • Responses of Ammonia-Oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater APPLIED AND ENVIRONMENTAL MICROBIOLOGY Reed, D. W., Smith, J. M., Francis, C. A., Fujita, Y. 2010; 76 (8): 2517-2523

    Abstract

    To evaluate the potential for organic nitrogen addition to stimulate the in situ growth of ammonia oxidizers during a field scale bioremediation trial, samples collected from the Eastern Snake River Plain Aquifer in Idaho before, during, and after the addition of molasses and urea were subjected to PCR analysis of ammonia monooxygenase subunit A (amoA) genes. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were present in all of the samples tested, with AOA amoA genes outnumbering AOB amoA genes in all of the samples. Following urea addition, nitrate levels rose and bacterial amoA copy numbers increased dramatically, suggesting that urea hydrolysis stimulated nitrification. Bacterial amoA diversity was limited to two Nitrosomonas phylotypes, whereas archaeal amoA analyses revealed 20 distinct operational taxonomic units, including several that were markedly different from all previously reported sequences. Results from this study demonstrate the likelihood of stimulating ammonia-oxidizing communities during field scale manipulation of groundwater conditions to promote urea hydrolysis.

    View details for DOI 10.1128/AEM.02436-09

    View details for Web of Science ID 000276280100018

    View details for PubMedID 20190081

  • Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea ENVIRONMENTAL MICROBIOLOGY Wells, G. F., Park, H., Yeung, C., Eggleston, B., Francis, C. A., Criddle, C. S. 2009; 11 (9): 2310-2328

    Abstract

    Ammonia-oxidizing bacteria (AOB) have long been considered key to the removal of nitrogen in activated sludge bioreactors. Culture-independent molecular analyses have established that AOB lineages in bioreactors are dynamic, but the underlying operational or environmental factors are unclear. Furthermore, the contribution of ammonia-oxidizing archaea (AOA) to nitrogen removal in bioreactors has not been studied. To this end, we investigated the abundance of AOA and AOB as well as correlations between dynamics in AOB lineages and operational parameters at a municipal wastewater treatment plant sampled weekly over a 1 year period. Quantitative PCR measurements of bacterial and archaeal ammonia monooxygenase subunit A (amoA) genes revealed that the bacterial homologue predominated by at least three orders of magnitude in all samples. Archaeal amoA was only detectable in approximately 15% of these samples. Using terminal restriction fragment length polymorphism analysis, we monitored AOB lineages based on amoA genes. The Nitrosomonas europaea lineage and a novel Nitrosomonas-like cluster were the dominant AOB signatures, with a Nitrosospira lineage present at lower relative abundance. These lineages exhibited strong temporal oscillations, with one becoming sequentially dominant over the other. Using non-metric multidimensional scaling and redundancy analyses, we tested correlations between terminal restriction fragment length polymorphism profiles and 20 operational and environmental parameters. The redundancy analyses indicated that the dynamics of AOB lineages correlated most strongly with temperature, dissolved oxygen and influent nitrite and chromium. The Nitrosospira lineage signal had a strong negative correlation to dissolved oxygen and temperature, while the Nitrosomonas-like (negative correlations) and N. europaea lineages (positive correlations) were inversely linked (relative to one another) to influent nitrite and chromium. Overall, this study suggests that AOA may be minor contributors to ammonia oxidation in highly aerated activated sludge, and provides insight into parameters controlling the diversity and dominance of AOB lineages within bioreactors during periods of stable nitrification.

    View details for DOI 10.1111/j.1462-2920.2009.01958.x

    View details for Web of Science ID 000269539700013

    View details for PubMedID 19515200

  • Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary ENVIRONMENTAL MICROBIOLOGY Mosier, A. C., Francis, C. A. 2008; 10 (11): 3002-3016

    Abstract

    Ammonia oxidation in marine and estuarine sediments plays a pivotal role in the cycling and removal of nitrogen. Recent reports have shown that the newly discovered ammonia-oxidizing archaea can be both abundant and diverse in aquatic and terrestrial ecosystems. In this study, we examined the abundance and diversity of ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) across physicochemical gradients in San Francisco Bay--the largest estuary on the west coast of the USA. In contrast to reports that AOA are far more abundant than beta-AOB in both terrestrial and marine systems, our quantitative PCR estimates indicated that beta-AOB amoA (encoding ammonia monooxygenase subunit A) copy numbers were greater than AOA amoA in most of the estuary. Ammonia-oxidizing archaea were only more pervasive than beta-AOB in the low-salinity region of the estuary. Both AOA and beta-AOB communities exhibited distinct spatial structure within the estuary. AOA amoA sequences from the north part of the estuary formed a large and distinct low-salinity phylogenetic group. The majority of the beta-AOB sequences were closely related to other marine/estuarine Nitrosomonas-like and Nitrosospira-like sequences. Both ammonia-oxidizer community composition and abundance were strongly correlated with salinity. Ammonia-oxidizing enrichment cultures contained AOA and beta-AOB amoA sequences with high similarity to environmental sequences. Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and beta-AOB phylotypes may thrive.

    View details for DOI 10.1111/j.1462-2920.2008.01764.x

    View details for Web of Science ID 000259680300010

    View details for PubMedID 18973621

  • 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

    Abstract

    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

  • Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California ISME JOURNAL Beman, J. M., Popp, B. N., Francis, C. A. 2008; 2 (4): 429-441

    Abstract

    Nitrification plays an important role in marine biogeochemistry, yet efforts to link this process to the microorganisms that mediate it are surprisingly limited. In particular, ammonia oxidation is the first and rate-limiting step of nitrification, yet ammonia oxidation rates and the abundance of ammonia-oxidizing bacteria (AOB) have rarely been measured in tandem. Ammonia oxidation rates have not been directly quantified in conjunction with ammonia-oxidizing archaea (AOA), although mounting evidence indicates that marine Crenarchaeota are capable of ammonia oxidation, and they are among the most abundant microbial groups in the ocean. Here, we have directly quantified ammonia oxidation rates by 15N labeling, and AOA and AOB abundances by quantitative PCR analysis of ammonia monooxygenase subunit A (amoA) genes, in the Gulf of California. Based on markedly different archaeal amoA sequence types in the upper water column (60 m) and oxygen minimum zone (OMZ; 450 m), novel amoA PCR primers were designed to specifically target and quantify 'shallow' (group A) and 'deep' (group B) clades. These primers recovered extensive variability with depth. Within the OMZ, AOA were most abundant where nitrification may be coupled to denitrification. In the upper water column, group A tracked variations in nitrogen biogeochemistry with depth and between basins, whereas AOB were present in relatively low numbers or undetectable. Overall, 15NH4+ oxidation rates were remarkably well correlated with AOA group A amoA gene copies (r2=0.90, P<0.001), and with 16S rRNA gene copies from marine Crenarchaeota (r2=0.85, P<0.005). These findings represent compelling evidence for an archaeal role in oceanic nitrification.

    View details for DOI 10.1038/ismej.2007.118

    View details for Web of Science ID 000255288700008

    View details for PubMedID 18200070

  • Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile APPLIED AND ENVIRONMENTAL MICROBIOLOGY Hansel, C. M., Fendorf, S., Jardine, P. M., Francis, C. A. 2008; 74 (5): 1620-1633

    Abstract

    Spatial heterogeneity in physical, chemical, and biological properties of soils allows for the proliferation of diverse microbial communities. Factors influencing the structuring of microbial communities, including availability of nutrients and water, pH, and soil texture, can vary considerably with soil depth and within soil aggregates. Here we investigated changes in the microbial and functional communities within soil aggregates obtained along a soil profile spanning the surface, vadose zone, and saturated soil environments. The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes (amoA and dsrAB) as well as cultivation-based analysis of Fe(III)-reducing organisms. Here we found that the microbial communities and putative ammonia-oxidizing and Fe(III)-reducing communities varied greatly along the soil profile, likely reflecting differences in carbon availability, water content, and pH. In particular, the Crenarchaeota 16S rRNA sequences are largely unique to each horizon, sharing a distribution and diversity similar to those of the putative (amoA-based) ammonia-oxidizing archaeal community. Anaerobic microenvironments within soil aggregates also appear to allow for both anaerobic- and aerobic-based metabolisms, further highlighting the complexity and spatial heterogeneity impacting microbial community structure and metabolic potential within soils.

    View details for DOI 10.1128/AEM.01787-07

    View details for Web of Science ID 000253792700037

    View details for PubMedID 18192411

  • Sediment denitrifier community composition and nirS gene expression investigated with functional gene microarrays Environmental Microbiology Bulow, S. E., Francis, C. A., Jackson, G. A., Ward, B. B. 2008; 10: 3057-3069
  • Microbial community biofabrics in a geothermal mine adit APPLIED AND ENVIRONMENTAL MICROBIOLOGY Spear, J. R., Barton, H. A., Robertson, C. E., Francis, C. A., Pace, N. R. 2007; 73 (19): 6172-6180

    Abstract

    Speleothems such as stalactites and stalagmites are usually considered to be mineralogical in composition and origin; however, microorganisms have been implicated in the development of some speleothems. We have identified and characterized the biological and mineralogical composition of mat-like biofabrics in two novel kinds of speleothems from a 50 degrees C geothermal mine adit near Glenwood Springs, CO. One type of structure consists of 2- to 3-cm-long, 3- to 4-mm-wide, leather-like, hollow, soda straw stalactites. Light and electron microscopy indicated that the stalactites are composed of a mineralized biofabric with several cell morphotypes in a laminated form, with gypsum and sulfur as the dominant mineral components. A small-subunit rRNA gene phylogenetic community analysis along the stalactite length yielded a diverse gradient of organisms, with a relatively simple suite of main constituents: Thermus spp., crenarchaeotes, Chloroflexi, and Gammaproteobacteria. PCR analysis also detected putative crenarchaeal ammonia monooxygenase subunit A (amoA) genes in this community, the majority related to sequences from other geothermal systems. The second type of speleothem, dumpling-like rafts floating on a 50 degrees C pool on the floor of the adit, showed a mat-like fabric of evidently living organisms on the outside of the dumpling, with a multimineral, amorphous, gypsum-based internal composition. These two novel types of biofabrics are examples of the complex roles that microbes can play in mineralization, weathering, and deposition processes in karst environments.

    View details for DOI 10.1128/AEM.00393-07

    View details for Web of Science ID 000249969000025

    View details for PubMedID 17693567

  • Distribution and diversity of archaeal ammonia monooxygenase genes associated with corals APPLIED AND ENVIRONMENTAL MICROBIOLOGY Beman, J. M., Roberts, K. J., Wegley, L., Rohwer, F., Francis, C. A. 2007; 73 (17): 5642-5647

    Abstract

    Corals are known to harbor diverse microbial communities of Bacteria and Archaea, yet the ecological role of these microorganisms remains largely unknown. Here we report putative ammonia monooxygenase subunit A (amoA) genes of archaeal origin associated with corals. Multiple DNA samples drawn from nine coral species and four different reef locations were PCR screened for archaeal and bacterial amoA genes, and archaeal amoA gene sequences were obtained from five different species of coral collected in Bocas del Toro, Panama. The 210 coral-associated archaeal amoA sequences recovered in this study were broadly distributed phylogenetically, with most only distantly related to previously reported sequences from coastal/estuarine sediments and oceanic water columns. In contrast, the bacterial amoA gene could not be amplified from any of these samples. These results offer further evidence for the widespread presence of the archaeal amoA gene in marine ecosystems, including coral reefs.

    View details for DOI 10.1128/AEM.00461-07

    View details for Web of Science ID 000249246700032

    View details for PubMedID 17586663

  • New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation ISME JOURNAL Francis, C. A., Beman, J. M., Kuypers, M. M. 2007; 1 (1): 19-27

    Abstract

    Microbial activities drive the global nitrogen cycle, and in the past few years, our understanding of nitrogen cycling processes and the micro-organisms that mediate them has changed dramatically. During this time, the processes of anaerobic ammonium oxidation (anammox), and ammonia oxidation within the domain Archaea, have been recognized as two new links in the global nitrogen cycle. All available evidence indicates that these processes and organisms are critically important in the environment, and particularly in the ocean. Here we review what is currently known about the microbial ecology of anaerobic and archaeal ammonia oxidation, highlight relevant unknowns and discuss the implications of these discoveries for the global nitrogen and carbon cycles.

    View details for DOI 10.1038/ismej.2007.8

    View details for Web of Science ID 000249215800005

    View details for PubMedID 18043610

  • Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria in the Black Sea suboxic zone ENVIRONMENTAL MICROBIOLOGY Oakley, B. B., Francis, C. A., Roberts, K. J., Fuchsman, C. A., Srinivasan, S., Staley, J. T. 2007; 9 (1): 118-130

    Abstract

    Chemical profiles of the Black Sea suboxic zone show a distribution of nitrogen species which is traditionally associated with denitrification, i.e. a secondary nitrite maximum associated with nitrate depletion and a N(2) gas peak. To better understand the distribution and diversity of the denitrifier community in the Black Sea suboxic zone, we combined a cultivation approach with cloning and sequencing of PCR-amplified nitrite reductase (nirS and nirK) genes. The Black Sea suboxic zone appears to harbour a homogeneous community of denitrifiers. For nirK, over 94% of the sequences fell into only three distinct phylogenetic clusters, and for nirS, a single closely related sequence type accounted for 91% of the sequences retrieved. Both nirS and nirK genes showed a dramatic shift in community composition at the bottom of the suboxic zone, but overall, nirK-based community composition showed much greater variation across depths compared with the highly uniform distribution of nirS sequences throughout the suboxic zone. The dominant nirK and nirS sequences differed at the amino acid level by at least 17% and 8%, respectively, from their nearest database matches. Denitrifying isolates recovered from the suboxic zone shared 97% 16S rRNA gene sequence similarity with Marinobacter maritimus. Analysis of the recently discovered nirS gene from the anammox bacterium Candidatus'Kuenenia stuttgartiensis' revealed that mismatches with commonly used primers may have prevented the previous detection of this divergent sequence.

    View details for DOI 10.1111/j.1462-2920.2006.01121.x

    View details for Web of Science ID 000243294900020

    View details for PubMedID 17227417

  • Microbial community biofbrics in a geothermal mine adit Applied and Environmental Microbiology Spear, J. R., Barton, H. A., Robertson, C. E., Francis, C. A., Pace, N. R. 2007; 73: 6172-6180
  • Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico APPLIED AND ENVIRONMENTAL MICROBIOLOGY Beman, J. M., Francis, C. A. 2006; 72 (12): 7767-7777

    Abstract

    Nitrification within estuarine sediments plays an important role in the nitrogen cycle, both at the global scale and in individual estuaries. Although bacteria were once thought to be solely responsible for catalyzing the first and rate-limiting step of this process, several recent studies have suggested that mesophilic Crenarchaeota are capable of performing ammonia oxidation. Here we examine the diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of Bahía del Tóbari, a hypernutrified estuary receiving substantial amounts of ammonium in agricultural runoff. Using PCR primers designed to specifically target the archaeal ammonia monooxygenase alpha-subunit (amoA) gene, we found AOA to be present at five sampling sites within this estuary and at two sampling time points (January and October 2004). In contrast, the bacterial amoA gene was PCR amplifiable from only 40% of samples. Bacterial amoA libraries were dominated by a few widely distributed Nitrosomonas-like sequence types, whereas AOA diversity showed significant variation in both richness and community composition. AOA communities nevertheless exhibited consistent spatial structuring, with two distinct end member assemblages recovered from the interior and the mouths of the estuary and a mixed assemblage from an intermediate site. These findings represent the first detailed examination of archaeal amoA diversity in estuarine sediments and demonstrate that diverse communities of Crenarchaeota capable of ammonia oxidation are present within estuaries, where they may be actively involved in nitrification.

    View details for DOI 10.1128/AEM.00946-06

    View details for Web of Science ID 000242681300043

    View details for PubMedID 17012598

  • Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors APPLIED AND ENVIRONMENTAL MICROBIOLOGY Park, H., Wells, G. F., Bae, H., Criddle, C. S., Francis, C. A. 2006; 72 (8): 5643-5647

    Abstract

    We report molecular evidence that ammonia-oxidizing archaea (AOA) occur in activated sludge bioreactors used to remove ammonia from wastewater. Using PCR primers targeting archaeal ammonia monooxygenase subunit A (amoA) genes, we retrieved and compared 75 sequences from five wastewater treatment plants operating with low dissolved oxygen levels and long retention times. All of these sequences showed similarity to sequences previously found in soil and sediments, and they were distributed primarily in four major phylogenetic clusters. One of these clusters contained virtually identical amoA sequences obtained from all five activated sludge samples (from Oregon, Wisconsin, Pennsylvania, and New Jersey) and accounted for 67% of all the sequences, suggesting that this AOA phylotype may be widespread in nitrifying bioreactors.

    View details for DOI 10.1128/AEM.00402-06

    View details for Web of Science ID 000239780400065

    View details for PubMedID 16885322

  • Nitrogen sources and cycling in the San Francisco Bay Estuary: A nitrate dual isotopic composition approach LIMNOLOGY AND OCEANOGRAPHY Wankel, S. D., Kendall, C., Francis, C. A., Paytan, A. 2006; 51 (4): 1654-1664
  • Coupled photochemical and enzymatic Mn(II) oxidation pathways of a planktonic Roseobacter-like bacterium APPLIED AND ENVIRONMENTAL MICROBIOLOGY Hansel, C. M., Francis, C. A. 2006; 72 (5): 3543-3549

    Abstract

    Bacteria belonging to the Roseobacter clade of the alpha-Proteobacteria occupy a wide range of environmental niches and are numerically abundant in coastal waters. Here we reveal that Roseobacter-like bacteria may play a previously unrecognized role in the oxidation and cycling of manganese (Mn) in coastal waters. A diverse array of Mn(II)-oxidizing Roseobacter-like species were isolated from Elkhorn Slough, a coastal estuary adjacent to Monterey Bay in California. One isolate (designated AzwK-3b), in particular, rapidly oxidizes Mn(II) to insoluble Mn(III, IV) oxides. Interestingly, AzwK-3b is 100% identical (at the 16S rRNA gene level) to a previously described Pfiesteria-associated Roseobacter-like bacterium, which is not able to oxidize Mn(II). The rates of manganese(II) oxidation by live cultures and cell-free filtrates are substantially higher when the preparations are incubated in the presence of light. The rates of oxidation by washed cell extracts, however, are light independent. Thus, AzwK-3b invokes two Mn(II) oxidation mechanisms when it is incubated in the presence of light, in contrast to the predominantly direct enzymatic oxidation in the dark. In the presence of light, production of photochemically active metabolites is coupled with initial direct enzymatic Mn(II) oxidation, resulting in higher Mn(II) oxidation rates. Thus, Roseobacter-like bacteria may not only play a previously unrecognized role in Mn(II) oxidation and cycling in coastal surface waters but also induce a novel photooxidation pathway that provides an alternative means of Mn(II) oxidation in the photic zone.

    View details for DOI 10.1128/AEM.72.5.3543-3549.2006

    View details for Web of Science ID 000237491200057

    View details for PubMedID 16672501

  • 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

    Abstract

    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

  • Planktonic microbial community composition across steep physical/chemical gradients in permanently ice-covered Lake Bonney, Antarctica GEOBIOLOGY Glatz, R. E., Lepp, P. W., Ward, B. B., Francis, C. A. 2006; 4 (1): 53-67
  • Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., Oakley, B. B. 2005; 102 (41): 14683-14688

    Abstract

    Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, occurs in a wide variety of environments and plays a central role in the global nitrogen cycle. Catalyzed by the enzyme ammonia monooxygenase, the ability to oxidize ammonia was previously thought to be restricted to a few groups within the beta- and gamma-Proteobacteria. However, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase alpha-subunit (amoA) genes derived from uncultivated, nonextremophilic Crenarchaeota. Here, we report molecular evidence for the widespread presence of ammonia-oxidizing archaea (AOA) in marine water columns and sediments. Using PCR primers designed to specifically target archaeal amoA, we find AOA to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. Diverse and distinct AOA communities are associated with each of these habitats, with little overlap between water columns and sediments. Within marine sediments, most AOA sequences are unique to individual sampling locations, whereas a small number of sequences are evidently cosmopolitan in distribution. Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle.

    View details for DOI 10.1073/pnas.0506625102

    View details for Web of Science ID 000232603600038

    View details for PubMedID 16186488

  • Diversity of nitrite reductase genes (nirS) in the denitrifying water column of the coastal Arabian Sea AQUATIC MICROBIAL ECOLOGY Jayakumar, D. A., Francis, C. A., Naqvi, S. W., Ward, B. B. 2004; 34 (1): 69-78
  • Diversity of nitrite reductase genes in the denitrifying water column of the coastal Arabian Sea Aquatic Microbial Ecology Jayakumar, D. A., Francis, C. A., Naqvi, S. W. A., Ward, B. B. 2004; 34: 69-78
  • Diversity of ammonia monooxygenase (amoA) genes across environmental gradients in Chesapeake Bay sediments GEOBIOLOGY Francis, C. A., O'Mullan, G. D., Ward, B. B. 2003; 1 (2): 129-140
  • Diversity of ammonia monooxygnenase (amoA) genes across environmental gradients in Chesapeake Bay sediments Geobiology Francis, C. A., OMullan, G. D., Ward, B. B. 2003; 1: 129-140
  • Oligonucleotide microarray for the study of functional gene diversity of the nitrogen cycle in the environment Applied and Environmental Microbiology Taroncher-Oldenburg, G., Griner, E. M., Francis, C. A., Ward, B. B. 2003; 69: 1159-1171
  • Localization of Mn(II)-oxidizing activity and the putative multicopper oxidase, MnxG, to the exosporium of the marine Bacillus sp strain SG-1 ARCHIVES OF MICROBIOLOGY Francis, C. A., Casciotti, K. L., Tebo, B. M. 2002; 178 (6): 450-456

    Abstract

    Dormant spores of the marine Bacillus sp. strain SG-1 catalyze the oxidation of manganese(II), thereby becoming encrusted with insoluble Mn(III,IV) oxides. In this study, it was found that the Mn(II)-oxidizing activity could be removed from SG-1 spores using a French press and recovered in the supernatant following centrifugation of the spores. Transmission electron microscopy of thin sections of SG-1 spores revealed that the ridged outermost layer was removed by passage through the French press, leaving the remainder of the spore intact. Comparative chemical analysis of this layer with the underlying spore coats suggested that this outer layer is chemically distinct from the spore coat. Taken together, these results indicate that this outer layer is an exosporium. Previous genetic analysis of strain SG-1 identified a cluster of genes involved in Mn(II) oxidation, the mnx genes. The product of the most downstream gene in this cluster, MnxG, appears to be a multicopper oxidase and is essential for Mn(II) oxidation. In this study, MnxG was overexpressed in Escherichia coli and used to generate polyclonal antibodies. Western blot analysis demonstrated that MnxG is localized to the exosporium of wild-type spores but is absent in the non-oxidizing spores of transposon mutants within the mnx gene cluster. To our knowledge, Mn(II) oxidation is the first oxidase activity, and MnxG one of the first gene products, ever shown to be associated with an exosporium.

    View details for DOI 10.1007/s00203-002-0472-9

    View details for Web of Science ID 000179674200010

    View details for PubMedID 12420165

  • Enzymatic manganese(II) oxidation by metabolically dormant spores of diverse Bacillus species Applied and Environmental Microbiology Francis, C. A., Tebo, B. M. 2002; 68: 874-880
  • Sulfur disproportionation by the facultative anaerobe Pantoea agglomerans as a mechanism for chromium(VI) reduction Geomicrobiology Journal Obraztsova, A. Y., Francis, C. A., Tebo, B. M. 2002; 19: 121-132
  • cumA multicopper oxidase genes from diverse Mn(II)-oxidizing and non-Mn(II)-oxidizing Pseudomonas strains Applied and Environmental Microbiology Francis, C. A., Tebo, B. M. 2001; 67: 4272-4278
  • Enzymatic manganese(II) oxidation by a marine a-proteobacterium Applied and Environmental Microbiology Francis, C. A., Co, E.-M., Tebo, B. M. 2001; 67: 4024-4029
  • Dissimilatory metal reduction by the facultative anaerobe Pantoea agglomerans SP1 Applied and Environmental Microbiology Francis, C. A., Obraztsova, A. Y., Tebo, B. M. 2000; 66: 543-548
  • Marine Bacillus spores as catalysts for the oxidative precipitation and sorption of metals Molecular Marine Microbiology Francis, C. A., Tebo, B. M. edited by Bartlett, D. H. Horizon Scientific Press, Norfolk, England. 2000
  • Marine Bacillus spores as catalysts for oxidative precipitation and sorption of metals Journal of Molecular Microbiology and Biotechnology Francis, C. A., Tebo, B. M. 1999; 1: 71-78
  • Manganese oxidation by spores of the marine Bacillus sp. strain SG-1: Application for the bioremediation of metal pollution New Developments in Marine Biotechnology Tebo, B. M., Waasbergen , L. v., Francis, C. A., He, L. M., Edwards, D. B., Casciotti, K. edited by Gal, Y. L., Halvorson, H. O. Plenum Press, New York. 1998: 177–180
  • Quantification of catechol 2,3-dioxygenase gene homology and benzoate utilization in intertidal sediments Aquatic Microbial Ecology Francis, C. A., Francis, A. K., Golet, D., Ward, B. B 1998; 15: 225-231