Christopher Francis

All Publications

• Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus. Communications biology Johnson, J., Tolar, B. B., Tosun, B., Yoshikuni, Y., Francis, C. A., Wakatsuki, S., DeMirci, H. 2024; 7 (1): 1364

  Abstract

  The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA synthetase (ADP-forming; Nmar_0206) represents one of several enzymes from this cycle that exhibit increased efficiency over crenarchaeal counterparts. This enzyme reduces energy requirements on the cell, reflecting thaumarchaeal success in adapting to low-nutrient environments. Here we show the structure of Nmar_0206 from Nitrosopumilus maritimus SCM1, which reveals a highly conserved interdomain linker loop between the CoA-binding and ATP-grasp domains. Phylogenetic analysis suggests the widespread prevalence of this loop and highlights both its underrepresentation within the PDB and structural importance within the (ATP-forming) acyl-CoA synthetase (ACD) superfamily. This linker is shown to have a possible influence on conserved interface interactions between domains, thereby influencing homodimer stability. These results provide a structural basis for the energy efficiency of this key enzyme in the modified 3HP/4HB cycle of Thaumarchaeota.

  View details for DOI 10.1038/s42003-024-06432-x

  View details for PubMedID 39433970

  View details for PubMedCentralID 3067309

• Globally distributed marine Gemmatimonadota have unique genomic potentials. Microbiome Gong, X., Xu, L., Langwig, M. V., Chen, Z., Huang, S., Zhao, D., Su, L., Zhang, Y., Francis, C. A., Liu, J., Li, J., Baker, B. J. 2024; 12 (1): 149

  Abstract

  Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood.Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to "hijack" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts.This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.

  View details for DOI 10.1186/s40168-024-01871-4

  View details for PubMedID 39123272

  View details for PubMedCentralID PMC11316326

• Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay. The ISME journal Rasmussen, A., Francis, C. A. 2024

  Abstract

  Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay (SFB). Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South SFB during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in qPCR data and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Ca. Nitrosomarinus catalina-like AOA metagenome-assembled genome (MAG) that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria (NOB) MAG from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier MAGs. This study confirms AOA are not only abundant, but also highly active during blooms oxidizing large amounts of ammonia to nitrite - a key intermediate in the microbial nitrogen cycle - and producing reactive compounds that may impact other members of the microbial community.

  View details for DOI 10.1093/ismejo/wrae148

  View details for PubMedID 39077992

• Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA. mSystems Rasmussen, A. N., Tolar, B. B., Bargar, J. R., Boye, K., Francis, C. A. 2024: e0031424

  Abstract

  We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (n = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (Methanoregulaceae, Methanotrichaceae, and Methanomassiliicoccales), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (Candidatus Methanoperedens) in anoxic depths and uncultured bacteria (Ca. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. Ca. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the Ca. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured Thermoplasmata archaea in the Ca. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the Ca. Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.

  View details for DOI 10.1128/msystems.00314-24

  View details for PubMedID 38940520

• Pelagic metagenome-assembled genomes from an estuarine salinity gradient in San Francisco Bay. Microbiology resource announcements Rasmussen, A. N., Francis, C. A. 2023: e0080023

  Abstract

  San Francisco Bay (SFB) is a large and highly human-impacted estuarine system. We produced 449 metagenome-assembled genomes from SFB waters, collected along the salinity gradient, providing a rich data set to compare the metabolic potential of microorganisms from different salinity zones within SFB and to other estuarine systems.

  View details for DOI 10.1128/MRA.00800-23

  View details for PubMedID 37929976

• Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa. The ISME journal Lanclos, V. C., Rasmussen, A. N., Kojima, C. Y., Cheng, C., Henson, M. W., Faircloth, B. C., Francis, C. A., Thrash, J. C. 2023

  Abstract

  The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 460 highly complete publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided detailed IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.

  View details for DOI 10.1038/s41396-023-01376-2

  View details for PubMedID 36739346

• Simulation of anoxic lenses as exporters of reactivity in alluvial aquifer sediments GEOCHIMICA ET COSMOCHIMICA ACTA Babey, T., Boye, K., Tolar, B., Engel, M., Noel, V., Perzan, Z., Kumar, N., Francis, C. A., Bargar, J. R., Maher, K. 2022; 334: 119-134

  View details for DOI 10.1016/j.gca.2022.07.018

  View details for Web of Science ID 000855258500004

• Thousands of small, novel genes predicted in global phage genomes. Cell reports Fremin, B. J., Bhatt, A. S., Kyrpides, N. C. 2022; 39 (12): 110984

  Abstract

  Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

  View details for DOI 10.1016/j.celrep.2022.110984

  View details for PubMedID 35732113

• Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay. mSystems Rasmussen, A. N., Francis, C. A. 1800: e0127021

  Abstract

  Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of "Candidatus Nitrosomarinus catalina" SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10muM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB. IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)-the largest estuary on the west coast of North America-and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.

  View details for DOI 10.1128/msystems.01270-21

  View details for PubMedID 35076275

• Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay MSYSTEMS Rasmussen, A. N., Francis, C. A. 2022; 7 (1)

  View details for Web of Science ID 000760939200002

• Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics. The ISME journal Reji, L., Cardarelli, E. L., Boye, K., Bargar, J. R., Francis, C. A. 2021

  Abstract

  The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.

  View details for DOI 10.1038/s41396-021-01167-7

  View details for PubMedID 34873295

• Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus. Scientific reports Destan, E., Yuksel, B., Tolar, B. B., Ayan, E., Deutsch, S., Yoshikuni, Y., Wakatsuki, S., Francis, C. A., DeMirci, H. 2021; 11 (1): 22849

  Abstract

  The ammonia-oxidizing thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle is one of the most energy-efficient CO2 fixation cycles discovered thus far. The protein encoded by Nmar_1308 (from Nitrosopumilus maritimus SCM1) is a promiscuous enzyme that catalyzes two essential reactions within the thaumarchaeal 3HP/4HB cycle, functioning as both a crotonyl-CoA hydratase (CCAH) and 3-hydroxypropionyl-CoA dehydratase (3HPD). In performing both hydratase and dehydratase activities, Nmar_1308 reduces the total number of enzymes necessary for CO2 fixation in Thaumarchaeota, reducing the overall cost for biosynthesis. Here, we present the first high-resolution crystal structure of this bifunctional enzyme with key catalytic residues in the thaumarchaeal 3HP/4HB pathway.

  View details for DOI 10.1038/s41598-021-02180-8

  View details for PubMedID 34819551

• Response of Lower Sacramento River phytoplankton to high-ammonium wastewater effluent Elementa: Science of the Anthropocene Strong, A. L., Mills, M. M., Huang, I. B., van Dijken, G. L., Driscoll, S. E., Berg, G. M., Kudela, R. M., Monismith, S. G., Francis, C. A., Arrigo, K. R. 2021; 9(1)

  View details for DOI 10.1525/elementa.2021.040

• The Beach Aquifer Microbiome: Research Gaps and Data Needs Frontiers in Environmental Science Archana, A., Francis, C. A., Boehm, A. B. 2021

  View details for DOI 10.3389/fenvs.2021.653568

• ` Stability of Floodplain Subsurface Microbial Communities Through Seasonal Hydrological and Geochemical Cycles FRONTIERS IN EARTH SCIENCE Tolar, B. B., Boye, K., Bobb, C., Maher, K., Bargar, J. R., Francis, C. A. 2020; 8

  View details for DOI 10.3389/feart.2020.00338

  View details for Web of Science ID 000566258600001

• Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage The ISME Journal Reji, L., Francis, C. A. 2020

  View details for DOI 10.1038/s41396-020-0675-6

• Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States. Microbial ecology Cardarelli, E. L., Bargar, J. R., Francis, C. A. 2020

  Abstract

  Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.

  View details for DOI 10.1007/s00248-020-01534-5

  View details for PubMedID 32535638

• Time series assessment of Thaumarchaeota ecotypes in Monterey Bay reveals the importance of water column position in predicting distribution-environment relationships Limnology and Oceanography Tolar, B. B., Reji, L., Smith, J. M., Blum, M., Pennington, J. T., Chavez, F. P., Francis, C. A. 2020

  View details for DOI 10.1002/LNO.11436

• In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay. Microbial ecology Rasmussen, A. N., Damashek, J. n., Eloe-Fadrosh, E. A., Francis, C. A. 2020

  Abstract

  Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.

  View details for DOI 10.1007/s00248-020-01621-7

  View details for PubMedID 33150499

• Depth-differentiation and seasonality of planktonic microbial assemblages in the Monterey Bay upwelling system Frontiers in Microbiology Reji, L., Tolar, B. B., Chavez, F. P., Francis, C. A. 2020

  View details for DOI 10.3389/fmicb.2020.01075

• Depth distributions of Nitrite Reductase (nirK) Gene Variants Reveal Spatial Dynamics of Thaumarchaeal Ecotype Populations in Coastal Monterey Bay. Environmental microbiology Reji, L., Tolar, B. B., Smith, J. M., Chavez, F. P., Francis, C. A. 2019

  Abstract

  Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper-containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three 'ecotype' populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer-scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker. This article is protected by copyright. All rights reserved.

  View details for DOI 10.1111/1462-2920.14753

  View details for PubMedID 31330081

• Differential co-occurrence relationships shaping ecotype diversification within Thaumarchaeota populations in the coastal ocean water column ISME JOURNAL Reji, L., Tolar, B. B., Smith, J. M., Chavez, F. P., Francis, C. A. 2019; 13 (5): 1144–58

  View details for DOI 10.1038/s41396-018-0311-x

  View details for Web of Science ID 000464960400003

• Nitrosarchaeum Bergey's Manual of Systematics of Archaea and Bacteria Tolar, B. B., Mosier, A. C., Lund, M. B., Francis, C. A. John Wile & Sons, Inc. in association with Bergey's Manual Trust. 2019

  View details for DOI 10.1002/9781118960608

• Microbial Nitrogen Cycling in Estuaries: From Genes to Ecosystem Processes ESTUARIES AND COASTS Damashek, J., Francis, C. A. 2018; 41 (3): 626–60

  View details for DOI 10.1007/s12237-017-0306-2

  View details for Web of Science ID 000428847700002

• Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins. The ISME journal Li, P. N., Herrmann, J. n., Tolar, B. B., Poitevin, F. n., Ramdasi, R. n., Bargar, J. R., Stahl, D. A., Jensen, G. J., Francis, C. A., Wakatsuki, S. n., van den Bedem, H. n. 2018

  Abstract

  Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown. Nano-scale lattices affect the diffusion behavior of low-concentration solutes, even if they are significantly smaller than the pore size. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ammonia-oxidizing archaea (AOA) as a model for S-layer geometry, and a 2D electrodiffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium (NH4+), we find that the characteristic length scales of nanoporous S-layers elevate the concentration of NH4+ in the pseudo-periplasmic space. Our simulations suggest an evolutionary, mechanistic basis for S-layer charge and shed light on the unique ability of some AOA to oxidize ammonia in environments with nanomolar NH4+ availability, with broad implications for comparisons of ecologically distinct populations.

  View details for PubMedID 29899515

• Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition ENVIRONMENTAL MICROBIOLOGY Lee, J. A., Francis, C. A. 2017; 19 (12): 4897–4912

  Abstract

  Denitrification is a dominant nitrogen loss process in the sediments of San Francisco Bay. In this study, we sought to understand the ecology of denitrifying bacteria by using next-generation sequencing (NGS) to survey the diversity of a denitrification functional gene, nirS (encoding cytchrome-cd1 nitrite reductase), along the salinity gradient of San Francisco Bay over the course of a year. We compared our dataset to a library of nirS sequences obtained previously from the same samples by standard PCR cloning and Sanger sequencing, and showed that both methods similarly demonstrated geography, salinity and, to a lesser extent, nitrogen, to be strong determinants of community composition. Furthermore, the depth afforded by NGS enabled novel techniques for measuring the association between environment and community composition. We used Random Forests modelling to demonstrate that the site and salinity of a sample could be predicted from its nirS sequences, and to identify indicator taxa associated with those environmental characteristics. This work contributes significantly to our understanding of the distribution and dynamics of denitrifying communities in San Francisco Bay, and provides valuable tools for the further study of this key N-cycling guild in all estuarine systems.

  View details for PubMedID 28892301

• 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. 2017; 73 (2): 271-284

  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 DOI 10.1007/s00248-016-0865-y

  View details for Web of Science ID 000393713800003

• Controls of nitrogen cycling evaluated along a well-characterized climate gradient. Ecology von Sperber, C., Chadwick, O. A., Casciotti, K. L., Peay, K. G., Francis, C. A., Kim, A. E., Vitousek, P. M. 2017

  Abstract

  The supply of nitrogen (N) constrains primary productivity in many ecosystems, raising the question "what controls the availability and cycling of N"? As a step toward answering this question, we evaluated N cycling processes and aspects of their regulation on a climate gradient on Kohala Volcano, Hawaii, USA. The gradient extends from sites receiving <300 mm/yr of rain to those receiving >3,000 mm/yr, and the pedology and dynamics of rock-derived nutrients in soils on the gradient are well understood. In particular, there is a soil process domain at intermediate rainfall within which ongoing weathering and biological uplift have enriched total and available pools of rock-derived nutrients substantially; sites at higher rainfall than this domain are acid and infertile as a consequence of depletion of rock-derived nutrients, while sites at lower rainfall are unproductive and subject to wind erosion. We found elevated rates of potential net N mineralization in the domain where rock-derived nutrients are enriched. Higher-rainfall sites have low rates of potential net N mineralization and high rates of microbial N immobilization, despite relatively high rates of gross N mineralization. Lower-rainfall sites have moderately low potential net N mineralization, relatively low rates of gross N mineralization, and rates of microbial N immobilization sufficient to sequester almost all the mineral N produced. Bulk soil δ(15) N also varied along the gradient, from +4‰ at high rainfall sites to +14‰ at low rainfall sites, indicating differences in the sources and dynamics of soil N. Our analysis shows that there is a strong association between N cycling and soil process domains that are defined using soil characteristics independent of N along this gradient, and that short-term controls of N cycling can be understood in terms of the supply of and demand for N.

  View details for DOI 10.1002/ecy.1751

  View details for PubMedID 28130777

• Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea. Environmental microbiology reports Tolar, B. B., Herrmann, J. n., Bargar, J. R., van den Bedem, H. n., Wakatsuki, S. n., Francis, C. A. 2017; 9 (5): 484–91

  Abstract

  Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK).

  View details for PubMedID 28677304

• Regional patterns in ammonia-oxidizing communities throughout Chukchi Sea waters from the Bering Strait to the Beaufort Sea AQUATIC MICROBIAL ECOLOGY Damashek, J., Pettie, K. P., Brown, Z. W., Mills, M. M., Arrigo, K. R., Francis, C. A. 2017; 79 (3): 273–86

  View details for DOI 10.3354/ame01834

  View details for Web of Science ID 000406130800008

• 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

  View details for DOI 10.1007/s12237-016-0071-7

  View details for Web of Science ID 000377798600012

• 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

• Indigenous arsenic(V)-reducing microbial communities in redox-fluctuating near-surface sediments of the Mekong Delta GEOBIOLOGY Ying, S. C., DAMASHEK, J., Fendorf, S., Francis, C. A. 2015; 13 (6): 581-587

  Abstract

  Arsenic (As) cycling within soils and sediments of the Mekong Delta of Cambodia is affected by drastic redox fluctuations caused by seasonal monsoons. Extensive flooding during monsoon seasons creates anoxic soil conditions that favor anaerobic microbial processes, including arsenate [As(V)] respiration-a process contributing to the mobilization of As. Repeated oxidation and reduction in near-surface sediments, which contain 10-40 mg kg(-1) As, lead to the eventual downward movement of As to the underlying aquifer. Amplification of a highly conserved functional gene encoding dissimilatory As(V) reductase, arrA, can be used as a molecular marker to detect the genetic potential for As(V) respiration in environmental samples. However, few studies have successfully amplified arrA from sediments without prior enrichment, which can drastically shift community structure. In the present study, we examine the distribution and diversity of arrA genes amplified from multiple sites within the Cambodian Mekong Delta as a function of near-surface depth (10, 50, 100, 200, and 400 cm), where sediments undergo seasonal redox fluctuations. We report successful amplification of 302 arrA gene sequences (72 OTUs) from near-surface Cambodian soils (without prior enrichment or stimulation with carbon amendments), where a large majority (>70%) formed a well-supported clade that is phylogenetically distinct from previously reported sequences from Cambodia and other South and Southeast Asian sediments, with highest sequence similarity to known Geobacter species capable of As(V) respiration, further supporting the potentially important role of Geobacter sp. in arsenic mobilization in these regions.

  View details for DOI 10.1111/gbi.12152

  View details for Web of Science ID 000362958500005

  View details for PubMedID 26466963

• 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

  View details for DOI 10.3389/fmicb.2014.00743

  View details for Web of Science ID 000348707300001

• 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)

  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 Web of Science ID 000342492700088

  View details for PubMedCentralID PMC4177112

• 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: 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

• 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

  View details for PubMedCentralID PMC4287051

• 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

  View details for DOI 10.1016/j.gca.2012.08.020

  View details for Web of Science ID 000314664500003

• 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

• Measurements of nitrite production 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 (11): 7395-7410

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

  View details for Web of Science ID 000327814700042

• 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

  View details for PubMedCentralID PMC3757304

• 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

  View details for PubMedCentralID PMC3446794

• 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

  View details for PubMedCentralID PMC3318490

• 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

  View details for PubMedCentralID PMC3318456

• 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

  View details for PubMedCentralID PMC3280143

• 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

  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 Web of Science ID 000208863600300

  View details for PubMedCentralID PMC3399221

• 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

  View details for PubMedCentralID PMC3126447

• 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

  View details for PubMedCentralID PMC3043068

• 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

  View details for PubMedCentralID PMC3019697

• 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

  View details for PubMedCentralID PMC2932620

• 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

  View details for PubMedCentralID PMC2849197

• 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

• 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 (11): 3057-3069

  Abstract

  A functional gene microarray was used to investigate denitrifier community composition and nitrite reductase (nirS) gene expression in sediments along the estuarine gradient in Chesapeake Bay, USA. The nirS oligonucleotide probe set was designed to represent a sequence database containing 539 Chesapeake Bay clones, as well as sequences from many other environments. Greatest nirS diversity was detected at the freshwater station at the head of the bay and least diversity at the higher salinity station near the mouth of the Bay. The most common OTUs from the sequence database were detected on the array with high signal strength in most samples. One of the most abundant OTUs, CB2-S-138, was identified as dominant at the mid-bay site by both microarray and quantitative PCR assays, but it comprised a much smaller fraction of the assemblage in the north and south bay samples. cDNA (transcribed from total RNA extracts) targets were hybridized to the same array to compare the profiles of community composition at the DNA (relative abundance) and mRNA (gene expression) levels. Only the three dominant denitrifying groups (in terms of relative strength of DNA hybridization signal) were detected at the mRNA level. These results suggest that the most actively denitrifying groups are responsible for most nirS expression as well.

  View details for DOI 10.1111/j.1462-2920.2008.01765.x

  View details for Web of Science ID 000259680300015

  View details for PubMedID 18973624

• 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

  View details for PubMedCentralID PMC2258623

• 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

  View details for PubMedCentralID PMC2075011

• 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

  View details for PubMedCentralID PMC2042080

• 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

• 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

  View details for PubMedCentralID PMC1694203

• 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

  View details for PubMedCentralID PMC1538709

• 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

  View details for Web of Science ID 000239262200010

• 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

  View details for PubMedCentralID PMC1472357

• 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

  View details for DOI 10.1111/j.1472-4669.2006.00057.x

  View details for Web of Science ID 000207172100006

• 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

  View details for PubMedCentralID PMC1393195

• 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

  View details for PubMedCentralID PMC1253578

• 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

  View details for Web of Science ID 000188829700007

• 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

  View details for DOI 10.1046/j.1472-4669.2003.00010.x

  View details for Web of Science ID 000207171200004

• Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment APPLIED AND ENVIRONMENTAL MICROBIOLOGY Taroncher-Oldenburg, G., Griner, E. M., Francis, C. A., Ward, B. B. 2003; 69 (2): 1159-1171

  Abstract

  The analysis of functional diversity and its dynamics in the environment is essential for understanding the microbial ecology and biogeochemistry of aquatic systems. Here we describe the development and optimization of a DNA microarray method for the detection and quantification of functional genes in the environment and report on their preliminary application to the study of the denitrification gene nirS in the Choptank River-Chesapeake Bay system. Intergenic and intragenic resolution constraints were determined by an oligonucleotide (70-mer) microarray approach. Complete signal separation was achieved when comparing unrelated genes within the nitrogen cycle (amoA, nifH, nirK, and nirS) and detecting different variants of the same gene, nirK, corresponding to organisms with two different physiological modes, ammonia oxidizers and denitrifying halobenzoate degraders. The limits of intragenic resolution were investigated with a microarray containing 64 nirS sequences comprising 14 cultured organisms and 50 clones obtained from the Choptank River in Maryland. The nirS oligonucleotides covered a range of sequence identities from approximately 40 to 100%. The threshold values for specificity were determined to be 87% sequence identity and a target-to-probe perfect match-to-mismatch binding free-energy ratio of 0.56. The lower detection limit was 10 pg of DNA (equivalent to approximately 10(7) copies) per target per microarray. Hybridization patterns on the microarray differed between sediment samples from two stations in the Choptank River, implying important differences in the composition of the denitirifer community along an environmental gradient of salinity, inorganic nitrogen, and dissolved organic carbon. This work establishes a useful set of design constraints (independent of the target gene) for the implementation of functional gene microarrays for environmental applications.

  View details for DOI 10.1128/AEM.69.2.1159-1171.2003

  View details for Web of Science ID 000180927100056

  View details for PubMedID 12571043

• 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 (2): 874-880

  Abstract

  Bacterial spores are renowned for their longevity, ubiquity, and resistance to environmental insults, but virtually nothing is known regarding whether these metabolically dormant structures impact their surrounding chemical environments. In the present study, a number of spore-forming bacteria that produce dormant spores which enzymatically oxidize soluble Mn(II) to insoluble Mn(IV) oxides were isolated from coastal marine sediments. The highly charged and reactive surfaces of biogenic metal oxides dramatically influence the oxidation and sorption of both trace metals and organics in the environment. Prior to this study, the only known Mn(II)-oxidizing sporeformer was the marine Bacillus sp. strain SG-1, an extensively studied bacterium in which Mn(II) oxidation is believed to be catalyzed by a multicopper oxidase, MnxG. Phylogenetic analysis based on 16S rRNA and mnxG sequences obtained from 15 different Mn(II)-oxidizing sporeformers (including SG-1) revealed extensive diversity within the genus Bacillus, with organisms falling into several distinct clusters and lineages. In addition, active Mn(II)-oxidizing proteins of various sizes, as observed in sodium dodecyl sulfate-polyacrylamide electrophoresis gels, were recovered from the outer layers of purified dormant spores of the isolates. These are the first active Mn(II)-oxidizing enzymes identified in spores or gram-positive bacteria. Although extremely resistant to denaturation, the activities of these enzymes were inhibited by azide and o-phenanthroline, consistent with the involvement of multicopper oxidases. Overall, these studies suggest that the commonly held view that bacterial spores are merely inactive structures in the environment should be revised.

  View details for Web of Science ID 000173588600055

  View details for PubMedID 11823231

• Sulfur disproportionation by the facultative anaerobe Pantoea agglomerans SP1 as a mechanism for chromium(VI) reduction GEOMICROBIOLOGY JOURNAL Obraztsova, A. Y., Francis, C. A., Tebo, B. M. 2002; 19 (1): 121-132

  View details for Web of Science ID 000173790100010

• Enzymatic manganese(II) oxidation by a marine alpha-proteobacterium APPLIED AND ENVIRONMENTAL MICROBIOLOGY Francis, C. A., Co, E. M., Tebo, B. M. 2001; 67 (9): 4024-4029

  Abstract

  A yellow-pigmented marine bacterium, designated strain SD-21, was isolated from surface sediments of San Diego Bay, San Diego, Calif., based on its ability to oxidize soluble Mn(II) to insoluble Mn(III, IV) oxides. 16S rRNA analysis revealed that this organism was most closely related to members of the genus Erythrobacter, aerobic anoxygenic phototrophic bacteria within the alpha-4 subgroup of the Proteobacteria (alpha-4 Proteobacteria). SD-21, however, has a number of distinguishing phenotypic features relative to Erythrobacter species, including the ability to oxidize Mn(II). During the logarithmic phase of growth, this organism produces Mn(II)-oxidizing factors of approximately 250 and 150 kDa that are heat labile and inhibited by both azide and o-phenanthroline, suggesting the involvement of a metalloenzyme. Although the expression of the Mn(II) oxidase was not dependent on the presence of Mn(II), higher overall growth yields were reached in cultures incubated with Mn(II) in the culture medium. In addition, the rate of Mn(II) oxidation appeared to be slower in cultures grown in the light. This is the first report of Mn(II) oxidation within the alpha-4 Proteobacteria as well as the first Mn(II)-oxidizing proteins identified in a marine gram-negative bacterium.

  View details for Web of Science ID 000170747100035

  View details for PubMedID 11526000

• 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 (9): 4272-4278

  Abstract

  A multicopper oxidase gene, cumA, required for Mn(II) oxidation was recently identified in Pseudomonas putida strain GB-1. In the present study, degenerate primers based on the putative copper-binding regions of the cumA gene product were used to PCR amplify cumA gene sequences from a variety of Pseudomonas strains, including both Mn(II)-oxidizing and non-Mn(II)-oxidizing strains. The presence of highly conserved cumA gene sequences in several apparently non-Mn(II)-oxidizing Pseudomonas strains suggests that this gene may not be expressed, may not be sufficient alone to confer the ability to oxidize Mn(II), or may have an alternative function in these organisms. Phylogenetic analysis of both CumA and 16S rRNA sequences revealed similar topologies between the respective trees, including the presence of several distinct phylogenetic clusters. Overall, our results indicate that both the cumA gene and the capacity to oxidize Mn(II) occur in phylogenetically diverse Pseudomonas strains.

  View details for Web of Science ID 000170747100068

  View details for PubMedID 11526033

• 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 (2): 543-548

  Abstract

  Anaerobic enrichments with acetate as the electron donor and Fe(III) as the terminal electron acceptor were obtained from sediments of Salt Pond, a coastal marine basin near Woods Hole, Mass. A pure culture of a facultatively anaerobic Fe(III) reducer was isolated, and 16S rRNA analysis demonstrated that this organism was most closely related to Pantoea (formerly Enterobacter) agglomerans, a member of the family Enterobacteriaceae within the gamma subdivision of the Proteobacteria. This organism, designated strain SP1, can grow by coupling the oxidation of acetate or H(2) to the reduction of a variety of electron acceptors, including Fe(III), Mn(IV), Cr(VI), and the humic substance analog 2,6-anthraquinone disulfonate, but not sulfate. To our knowledge, this is the first mesophilic facultative anaerobe reported to couple acetate oxidation to dissimilatory metal reduction.

  View details for Web of Science ID 000085125900013

  View details for PubMedID 10653716

• 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 (1): 71-78

  Abstract

  The oxidation of soluble manganese(II) to insoluble Mn(III,IV) oxide precipitates plays an important role in the environment. These Mn oxides are known to oxidize numerous organic and inorganic compounds, scavenge a variety of other metals on their highly charged surfaces, and serve as electron acceptors for anaerobic respiration. Although the oxidation of Mn(II) in most environments is believed to be bacterially-mediated, the underlying mechanisms of catalysis are not well understood. In recent years, however, the application of molecular biological approaches has provided new insights into these mechanisms. Genes involved in Mn oxidation were first identified in our model organism, the marine Bacillus sp. strain SG-1, and subsequently have been identified in two other phylogenetically distinct organisms, Leptothrix discophora and Pseudomonas putida. In all three cases, enzymes related to multicopper oxidases appear to be involved, suggesting that copper may play a universal role in Mn(II) oxidation. In addition to catalyzing an environmentally important process, organisms capable of Mn(II) oxidation are potential candidates for the removal, detoxification, and recovery of metals from the environment. The Mn(II)-oxidizing spores of the marine Bacillus sp. strain SG-1 show particular promise, due to their inherent physically tough nature and unique capacity to bind and oxidatively precipitate metals without having to sustain growth.

  View details for PubMedID 10941787

• 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. S., Ward, B. B. 1998; 15 (3): 225-231

  View details for Web of Science ID 000075783800003

• 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

  View details for DOI 10.1007/978-1-4757-5983-9_37