Skip to main content Skip to navigation

Departments & Programs

More

Chris Francis

Chris  Francis
Title:Associate Professor
Primary Affiliation:Department of Environmental Earth System Science
Other Affiliations:Earth Systems
Office Location:Green Earth Sci.  235
Research Group:Environmental Microbiology
Phone:(620) 724-0301
Fax:(650) 725-2199
E-mail:caf@stanford.edu

Research

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

Teaching

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

Professional Activities

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

 

Co-Organizer/Chair of " Populations and Activity of Ammonia-Oxidizing and Denitrifying Organisms in Coastal Waters" Session SS52 at the American Society for Limnology and Oceanography (ASLO) Aquatic Sciences Meeting, New Orleans, Louisiana, February 2013; Co-Organizer/Chair of "Linking Microbial Communities to Geochemical Cycling" Session at the American Society for Limnology and Oceanography (ASLO) Aquatic Sciences Meeting, Nice, France, 2009; Co-Organizer/Chair of "Saline Environments" Session at the US-China Geomicrobiology Workshop, Beijing, China, 2008; School of Earth Sciences (SES) Council Member, 2007-present; Woods Institute Environmental Venture Project (EVP) Committee Member, 2008-present; Editorial Board member, Applied and Environmental Microbiology journal, 2008-present; Co-Organizer of "Microbial communities along environmental gradients: Linking microbial ecology and the ecosystem" Symposium at the Ecologicial Society of America/SER Joint Meeting, San Jose, CA, 2007; Stanford University Nominee, Packard Fellowship in Science and Engineering, 2006; GES Undergraduate Environmental Earth Science Curriculum Committee, 2006; SES Diversity Committee, 2005-06; Review Panel Member for NSF Antarctic Biology and Biomedicine (ABM; 2006), and Microbial Interactions and Processes (MIP; 2007) programs; editorial advisory board member, Geobiology journal, 2006-present; co-chair, "Archaea in the Earth System" Session at the AGU Fall Meeting, 2006; Terman Fellow, Stanford University; 2004-present; founder/organizer, Geomicrobiology and Microbial Geochemistry Seminar Series, Stanford University, 2003-present

Education

  • 2000 | Ph.D. Marine Biology, Scripps Institution of Oceanography, University of California - San Diego (UCSD)
  • 1998 | Microbial Diversity (Summer) | Course, Marine Biological Laboratory, Woods Hole, MA
  • 1994 | B.A. (Highest Honors) Biology University of California - Santa Cruz (UCSC)

Professional Experience

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

Honors & Awards

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

University Service

  • 2013-present | EESS Faculty Search Committee for Coastal Human-Environment Systems position
  • 2011-present | Chair, EESS Graduate Admissions Committee
  • 2011-present | Co-Chair, School of Earth Sciences GeoBiology Faculty Search Committee
  • 2010-2012 | Co-Chair, Environmental Venture Project (EVP) Selection Committee - Woods Institute for the Environment
  • 2011 | Organizer, Environmental Earth System Science (EESS) Departmental Seminar
  • 2010-Present | Member, Woods Faculty Leadership Working Group
  • 2010 | Environmental Venture Project (EVP) Committee/Panel Member - Woods Institute for the Environment
  • 2009 | Green Earth Sciences Building Space Committee
  • 2009 - Present | Earth Sciences Council Member
  • 2009 | Environmental Venture Project (EVP) Committee/Panel Member - Woods Institute for the Environment
  • 2008 - 2011 | EESS Graduate Admissions Committee
  • 2008 - Present | EESS Faculty Search Committee for Marine Chemist position
  • 2008 - 2009 | Hopkins Marine Station (HMS) Faculty Search Committee for Marine Cell Biologist position
  • 2008 Environmental Venture Project (EVP) Committee/Panel Member - Woods Institute for the Environment
  • 2007 - 2009 | Earth Sciences Council Member
  • 2006 - 2007 | SES Faculty Search Committe Member for Physical Oceanographer position
  • 2006 | Environmental Earth Science (EES) Undergraduate Curriculum Committee Member
  • 2005 - 2006 | SES Diversity Committee Member
  • 2005 - 2008 | GES Graduate Admissions Committee Member
  • 2003 - Present | Ph.D. Dissertation Committee Member for 27 students
  • 2003 - Present | University Chair of Oral Examination (Ph.D. Dissertation Defense) for 12 Stanford Ph.D. students (from 6 departments)

Professional Activities

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

Courses Taught

  • 2012 (Summer) | EESS 253S/BIOHOPK 274/BIO 274S/CEE 274S Hopkins Microbiology Course
  • 2012 (Spring) | EESS 802 TGR Dissertation [Enrolled 1]
  • 2012 (Spring) | EESS 400 Graduate Research [Enrolled 4]
  • 2012 (Spring) | EESS 46N Exploring the Critical Interface Between the Land and Monterey Bay: Elkhorn Slough [Enrolled 8]
  • 2012 (Winter) | EESS 802 TGR Dissertation [Enrolled 1]
  • 2012 (Winter) | EESS 400 Graduate Research [Enrolled 2]
  • 2012 (Winter) |  EESS 258 Geomicrobiology [Enrolled 10]
  • 2012 (Fall) | EESS 802 TGR Dissertation [Enrolled 1]
  • 2012 (Fall) | EESS 400 Graduate Research [Enrolled 4]
  • 2012 (Fall) | EESS/GES 208 Topics in Geobiology [Enrolled 11]
  • 2011 (Summer) | EESS 253S/BIOHOPK 274/BIO 274S/CEE 274S Hopkins Microbiology Course
  • 2011 (Summer) | EESS 400 Graduate Research [Enrolled 2]
  • 2011 (Summer) | EESS 802 TGR DISSERTATION [Enrolled 1]
  • 2011 (Spring) | EESS 802 TGR DISSERTATION [Enrolled 1]
  • 2011 (Winter) | EESS 802 TGR DISSERTATION [Enrolled 1]
  • 2011 (Fall) | EESS 802 TGR DISSERTATION [Enrolled 1]
  • 2011 (Spring) | EESS 49N Multi-Disciplinary Perspectives on a Large Urban Estuary: San Francisco Bay
  • 2011 (Winter) | EESS 400 Graduate Research [Enrolled 2]
  • 2011 (Fall) | EESS 301 Topics in EESS [Enrolled 24]
  • 2011 (Fall) | EESS/GES 208 Topics in Geobiology [Enrolled 10]
  • 2011 (Fall) | EESS 400 Graduate Research [Enrolled 2]
  • 2010 (Summer) | EESS 253S/BIOHOPK 274/BIO 274S/CEE 274S Hopkins Microbiology Course [Enrolled 4]
  • 2010 (Summer) | EESS 802 TGR DISSERTATION [Enrolled 1]
  • 2010 (Spring) | EESS 802 TGR DISSERTATION [Enrolled 1]
  • 2010 (Winter) | EESS 802 TGR DISSERTATION [Enrolled 1]
  • 2010 (Fall) | EESS 802 TGR DISSERTATION [Enrolled 2]
  • 2010 (Spring) | EESS 400 Graduate Research [Enrolled 3]
  • 2010 (Winter) | EESS 400 Graduate Research [Enrolled 3]
  • 2010 (Fall) | EESS 400 Graduate Research [Enrolled 3]
  • 2010 (Spring) | EESS 46N Exploring the Critical Interface Between the Land and Monterey Bay: Elkhorn Slough [Enrolled 9]
  • 2010 (Spring) | EESS 301 Topics in EESS (Seminar)
  • 2010 (Winter) | EESS 259 Environmental Microbial Genomics [Enrolled 11]
  • 2010 (Winter) | EESS 301 Topics in EESS (Seminar) [Enrolled 17)
  • 2009 (Summer) | EESS 253S/BIOHOPK 274/BIO 274S/CEE 274S Hopkins Microbiology Course [Enrolled 4]
  • 2009 (Summer) | EESS 802 TGR DISSERTATION [Enrolled 1]
  • 2009 (Summer) | EESS 400 Graduate Research [Enrolled 3]
  • 2009 (Spring) | EESS 802 TGR DISSERTATION [Enrolled 2]
  • 2009 (Winter) | EESS 802 TGR DISSERTATION [Enrolled 2]
  • 2009 (Fall) | EESS 802 TGR DISSERTATION [Enrolled 2]
  • 2009 (Spring) | EESS 400 Graduate Research [Enrolled 2]
  • 2009 (Winter) | EESS 400 Graduate Research [Enrolled 1]
  • 2009 (Fall) | EESS 400 Graduate Research [Enrolled 2]
  • 2009 (Winter) | EESS 158/258 Geomicrobiology [Enrolled 8]
  • 2008 (Fall) | EESS 400 Graduate Research [Enrolled 3]
  • 2008 (Winter) | EESS 259 Environmental Microbial Genomics [Enrolled 7]
  • 2008 (Spring) | EESS 46N Exploring the Critical Interface Between the Land and Monterey Bay: Elkhorn Slough [Enrolled 12]
  • 2008 (Summer) | EESS 253S/BIOHOPK 274/BIO 274S/CEE 274S Hopkins Microbiology Course [Enrolled 4]
  • 2008 (Summer) | EESS 250 Elkhorn Slough Microbiology [Enrolled 3]
  • 2008 (Winter) | EESS 400 Graduate Research [Enrolled 3]
  • 2008 (Spring) | EESS 400 Graduate Research [Enrolled 2]
  • 2008 (Summer) | EESS 400 Graduate Research [Enrolled 3]
  • 2007 (Fall) | GES 299 Field Research [Enrolled 1]
  • 2007 (Spring) | GES 400 Graduate Research [Enrolled 4]
  • 2007 (Summer) | GES 400 Graduate Research [Enrolled 4]
  • 2007 (Winter) | GES 400 Graduate Research [Enrolled 4]
  • 2007 (Summer) | GES 270 Elkhorn Slough Microbiology [Enrolled 1]
  • 2007 (Summer) | BIOHOPK 274/CEE 274S Hopkins Microbiology [Enrolled 3]
  • 2007 (Spring) | GES 46N Exploring the Critical Interface Between the Land and Monterey Bay: Elkhorn Slough [Enrolled 10]
  • 2007 (Fall) | GES 400 Graduate Research [Enrolled 4]
  • 2007 (Winter) | GES 268 Geomicrobiology [Enrolled 10]
  • 2006 (Summer) | GES 274 Hopkins Microbiology Course [Enrolled 2]
  • 2006 (Summer) | GES 801 TGR Project [Enrolled 1]
  • 2006 (Winter) | GES 266A Recent Developments in Microbial Redox Transformations [Enrolled 10]
  • 2006 (Spring) | GES 269 Environmntal Microbial Genomics [Enrolled 4]
  • 2006 (Winter) | GES 400 Graduate Research [Enrolled 2]
  • 2006 (Spring) | GES 400 Graduate Research [Enrolled 2]
  • 2006 (Fall) | GES 400 Graduate Research [Enrolled 2]
  •  2005 (Summer) | GES 400 Graduate Research [Enrolled 3]
  • 2005 (Winter) | GES 268 Geomicrobiology [Enrolled 16]
  • 2005 (Summer) | GES 270 Elkhorn Slough Microbiology [Enrolled 2]
  • 2005 (Fall) | GES 400 Graduate Research [Enrolled 2]
  • 2005 (Winter) | GES 400 Graduate Research [Enrolled 3]
  • 2005 (Spring) | GES 400 Graduate Research [Enrolled 3]
  • 2005 (Summer) | GES 274 Hopkins Microbiology Course [Enrolled 6]
  • 2004 (Winter) | GES 400 Graduate Research [Enrolled 2]
  • 2004 (Summer) | GES400 Graduate Research [Enrolled 1]
  • 2004 (Fall) | GES 400 Graduate Research [Enrolled 2]
  • 2004 (Winter) | GES 265 Microbially Mediated Redox Processes (w/ Fendorf) [Enrolled 12]
  • 2004 (Spring) | GES 269 Environmental Microbial Genomics [Enrolled 10]
  • 2004 (Spring) | GES 400 Graduate Research [Enrolled 2]
  • 2003 (Fall) | GES400 Graduate Research [Enrolled 1]
  • 2003 (Spring) | GES400 Graduate Research [Enrolled 1]
  • 2003 (Spring) | GES266A Recent Developments in Microbial Redox Transformations (w/ Fendorf) [Enrolled 6]
  • 2003 (Winter) | GES 400 Graduate Research [Enrolled 1]

Publications

  • (Submitted)* | Smith, J.M., A.C. Mosier, and C. A. Francis. Spatiotemporal relationships between the abundance, distribution and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments
  • (Submitted)* | Wells, G. F., C. H. Wu, Y. M. Piceno, B. Eggleston, E.L. Brodie, T. Z. DeSantis, G. L. Andersen, T. C. Hazen, C. A. Francis, and C. S. Criddle.  Microbial Biogeography across a Full-Scale Wastewater Treatment Plant Transect: Evidence for Immigration Between Coupled Processes.  
  • 2013* |  Ying, S.C., Y. Masue-Slowey, B.D. Kocar, S.D. Griffis, S.M. Webb, M.A. Marcus, C.A. Francis, and. S. Fendorf. Distributed microbially- and chemically-mediated redox processes controlling arsenic dynamics within Mn-/Fe-oxide constructed aggregates. Geochimica et Cosmochimica Acta 104: 29–41.
  • 2013* | Yeung, C.-H., C. A. Francis, and C. S. Criddle. Adaptation of nitrifying microbial biomass to nickel in batch incubations. Applied Microbiology and Biotechnology 97:847-857.
  • 2012* | Biller, S. J., A. C. Mosier, G. F. Wells, and C. A. Francis. Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat. Frontiers in Aquatic Microbiology doi:10.3389/fmicb.2012.00252
  • 2012* | Lund, M., J. M. Smith, and C. A. Francis. Diversity, abundance, and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea. The ISME Journal 6:1966-1977.
  • 2012* | Mosier, A.C., M. Lund, and C. A. Francis. Ecophysiology of an ammonia-oxidizing archaeon adapted to low-salinity habitats. Microbial Ecology 64: 955-63.
  • 2012* | Mosier, A. C., E. A. Allen, S. Ferriera, and C. A. Francis. 2012. Genome sequence of a low-salinity ammonia oxidizing archaeon from the San Francisco Bay estuary, "Candidatus Nitrosoarchaeum limnia" BG20. J. Bacteriology 194:2121-2122.
  • 2012* | Mosier, A. C., E. A. Allen, S. Ferriera, and C. A. Francis. 2012. Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia oxidizing archaeon enriched from the San Francisco Bay estuary. J. Bacteriology 194:2119-2120
  • 2012 * | Robidart, J. C., C.M. Preston, R.W. Paerl, K. A. Turk, A. C. Mosier, C. A. Francis, C. A. Scholin, and J.P. Zehr. Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation. ISME Journal 6: 513-523.
  • 2011 * | Wells, G. F., H-D. Park, B. Eggleston, C. A. Francis, and C. S. Criddle. Fine-Scale Bacterial Community Dynamics and a Taxa-Time Relationship in a Full-Scale Activated Sludge Wastewater Treatment Plant. Water Research 45: 5476-5488.
  • 2011 * | Pitcher, A., E. C. Hopmans, A. C. Mosier, S J. Park, S. K. Rhee C. A. Francis, S. Schouten S, and J.S. Sinninghe Damsté. Core and intact polar glycerol dibiphytanyl glycerol tetraether lipids of ammonia-oxidizing Archaea enriched from marine and estuarine sediments. Applied and Environmental Microbiology 77: 3468-3477.
  • 2011 * | Blainey**, P. C. , A. C. Mosier**, A. Potanina, C. A. Francis, and S. R. Quake. Genome of a low-salinity ammonia-oxidizing archaeon by sinlge-cell and metagenomic analysis. PLoS ONE 6: e16626. (** = authors contributed equally) 
  • 2011 * | Mosier, A. C., and C. A. Francis. Determining the distribution of marine and coastal ammonia-oxidizing archaea and bacteria using a quantitative approach. Methods in Enzymology 486: 205-221.
  • 2011 * | Wankel, S. D., A. C., Mosier, C. M. Hansel, A. Paytan, and C. A. Francis. Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary. Applied and Environmental Microbiology 77: 269-280.
  • 2010 * | Ofiteru, I. D., M. Lunn, T. P. Curtis, G. F. Wells, C. S. Criddle, C. A. Francis, and W. T. Sloan. Combined niche and neutral effects in a microbial wastewater treatment community. Proceedings of the National Academy of Sciences 107: 15345-15350.
  • 2010 * | Reed, D.W, J. M. Smith, C. A. Francis, and Y. Fujita. Responses of Ammonia-oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater. Applied and Environmental Microbiology 76: 2517-2523.
  • 2010 * | Santoro, A. E., K. L. Casciotti, and C. A. Francis. Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environmental Microbiology 12: 1989-2006.
  • 2010 * | Mosier, A. C., and C. A. Francis. Denitrifier abundance and activity across the San Francisco Bay estuary. Environmental Microbiology Reports 2: 667-676.
  • 2009 * | Wells, G. F., H-D. Park, H-D., C. H. Yeung, Brad Eggleston, C. A. Francis, and C. S. Criddle. Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environmental Microbiology 11:2310-2318
  • 2008 * | Hansel, C. M., S. Fendorf, P. M. Jardine, and C. A. Francis. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Applied and Environmental Microbiology 74:1620-1633.
  • 2008 * | Beman, J. M., B. N. Popp, and C. A. Francis. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. The ISME Journal 2:429-441.
  • 2008 * | Santoro, A. E., C. A. Francis, N. R. de Sieyes, and A. B. Boehm. Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. Environmental Microbiology 10:1068-1079.
  • 2008 * | Mosier, A. C., and C. A. Francis. Relative abundance of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environmental Microbiology 10:3002-3016.
  • 2008 * | Bulow, S. E., C. A. Francis, G. A. Jackson, and B. B. Ward. Sediment denitrifier community composition and nirS gene expression investigated with functional gene microarrays. Environmental Microbiology 10:3057-3069.
  • 2007 * | Oakley, B. B., C. A. Francis, K. J. Roberts, C. Fuchsman, S. Srinivasan, and J. T. Staley. Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria unique to the Black Sea suboxic zone. Environmental Microbiology 9:118-130
  • 2007 | Francis, C. A., J. M. Beman, and M. M. M. Kuypers. New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. The ISME Journal 1:19-27.
  • 2007 * | Beman, J. M., K. J. Roberts, L.E. Wegley, F. L. Rohwer, and C. A. Francis. Distribution and diversity of archaeal ammonia monooxygenase (amoA) genes associated with corals. Applied and Environmental Microbiology 73:5642-5647.
  • 2007 * | Spear, J. R., H. A. Barton, C. E. Robertson, C. A. Francis, and N. R. Pace. Microbial community biofbrics in a geothermal mine adit. Applied and Environmental Microbiology 73:6172-6180.
  • 2006 * | Glatz, R.E., P.W. Lepp, B.B. Ward, and C.A. Francis. Planktonic microbial community composition across steep physical/chemical gradients in permanently ice-covered Lake Bonney, Antarctica. Geobiology 4:53-67.
  • 2006 * | Santoro, A. E., A. B. Boehm, and C. A. Francis. Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer. Applied and Environmental Microbiology 72:2102-2109.
  • 2006 * | Park, H-D., G. F. Wells, H. Bae, C. S. Criddle, and C. A. Francis. Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Applied and Environmental Microbiology 72: 5643-5647.
  • 2006 * | Beman, J. M., and C. A. Francis. Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico. Applied and Environmental Microbiology 72: 7767-7777
  • 2006 * | Wankel, S. D., C. Kendall, C. A. Francis, and A. Paytan. Nitrogen sources and cycling in the San Francisco Bay estuary: A nitrate dual isotopic composition approach. Limnology and Oceanography 51:1654-1664.
  • 2006 * | Hansel, C. M., and C. A. Francis. Coupled photochemical and enzymatic Mn(II) oxidation pathways of a planktonic Roseobacter-like bacterium. Applied and Environmental Microbiology 72:3543-3549.
  • 2005 * | Francis, C. A., K. J. Roberts, J. M. Beman, A. E. Santoro, and B. B. Oakley. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences 102:14683-14688.
  • 2004 * | Jayakumar, D. A., C. A. Francis, S. W. A. Naqvi, and B. B. Ward. 2004. Diversity of nitrite reductase genes in the denitrifying water column of the coastal Arabian Sea. Aquatic Microbial Ecology. 34:69-78.
  • 2003 * | Taroncher-Oldenburg, G., E. M. Griner, C. A. Francis, B. B. Ward. 2003. Oligonucleotide microarray for the study of functional gene diversity of the nitrogen cycle in the environment. Applied and Environmental Microbiology 69: 1159-1171.
  • 2003 * | Francis, C. A., G. D. OMullan, and B. B. Ward. 2003. Diversity of ammonia monooxygnenase (amoA) genes across environmental gradients in Chesapeake Bay sediments. Geobiology 1:129-140.
  • 2002 * | Francis, C. A., and B. M. Tebo. 2002. Enzymatic manganese(II) oxidation by metabolically dormant spores of diverse Bacillus species. Applied and Environmental Microbiology 68: 874-880.
  • 2002 * | Obraztsova, A. Y., C. A. Francis, and B. M. Tebo. 2002. Sulfur disproportionation by the facultative anaerobe Pantoea agglomerans as a mechanism for chromium(VI) reduction. Geomicrobiology Journal 19: 121-132.
  • 2002 * | Francis, C. A., K. L. Casciotti, and B. M. Tebo. 2002. 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 178:450-456.
  • 2001 * | Francis, C. A., and B. M. Tebo. 2001. cumA multicopper oxidase genes from diverse Mn(II)-oxidizing and non-Mn(II)-oxidizing Pseudomonas strains. Applied and Environmental Microbiology 67: 4272-4278.
  • 2001 * | Francis, C. A., E.-M. Co, and B. M. Tebo. 2001. Enzymatic manganese(II) oxidation by a marine a-proteobacterium. Applied and Environmental Microbiology 67: 4024-4029.
  • 2000 * | Francis, C. A., A. Y. Obraztsova, and B. M. Tebo. 2000. Dissimilatory metal reduction by the facultative anaerobe Pantoea agglomerans SP1. Applied and Environmental Microbiology 66: 543-548.
  • 2000 | Francis, C. A., and B. M. Tebo. 2000. Marine Bacillus spores as catalysts for the oxidative precipitation and sorption of metals. In: D.H. Bartlett (Ed.) Molecular Marine Microbiology. Horizon Scientific Press, Norfolk, England.
  • 1999 | Francis, C. A., and B. M. Tebo. 1999. Marine Bacillus spores as catalysts for oxidative precipitation and sorption of metals. Journal of Molecular Microbiology and Biotechnology 1: 71-78.
  • 1998 | Tebo, B. M., L. van Waasbergen, C. A. Francis, L. M. He, D. B. Edwards, and K. Casciotti. 1998. Manganese oxidation by spores of the marine Bacillus sp. strain SG-1: Application for the bioremediation of metal pollution. In Y. Le Gal and H.O. Halvorson (Eds.) New Developments in Marine Biotechnology. Plenum Press, New York. p.177-180.
  • 1998 * | Francis, C. A., A. K. Francis, D. Golet, and B. B Ward. 1998. Quantification of catechol 2,3-dioxygenase gene homology and benzoate utilization in intertidal sediments. Aquatic Microbial Ecology 15: 225-231.

Advisee Degrees

  • 2011 | Samantha Ying: Competitive Microbial and Geochemical Processes Controlling the Fate of Arsenic, Ph.D.
  • 2011 | Annika Mosier: Microbial Nitrogen Cycling Dynamics in Coastal Systems, Ph.D.
  • 2011 | George Wells: Reexamining the Engineered Nitrogen Cycle: Microbial Diversity, Community Dynamics, and Immigration in Nitrifying Bioreactors, Ph.D. (co-advised w/ Craig Criddle, CEE)
  • 2008 | Alyson Santoro: A multidisciplinary study of water quality along an urban coast: Nitrogen cycling, algal blooms, and microbial pollutants, Ph.D. (Woods Hole Oceanographic Institution)
  • 2006 | Katie Roberts: Spatial and Temporal Analysis of Denitrifying Microbes within a California Estuary: Elkhorn Slough, M.S. (UC Santa Cruz)
  • 2004 | Rebecca Glatz: Microbial Diversity in the Water Column of Permanently Ice-Covered Lake Bonney, Antarctica, M.S. 

Advisee Publications

  • (Submitted)* | Smith, J.M., A.C. Mosier, and C. A. Francis. Spatiotemporal relationships between the abundance, distribution and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments.
  • (Submitted)* | Wells, G. F., C. H. Wu, Y. M. Piceno, B. Eggleston, E.L. Brodie, T. Z. DeSantis, G. L. Andersen, T. C. Hazen, C. A. Francis, and C. S. Criddle.  Microbial Biogeography Across a Full-Scale Wastewater Treatment Plant Transect: Evidence for Immigration Between Coupled Processes.  
  • 2013* |  Ying, S.C., Y. Masue-Slowey, B.D. Kocar, S.D. Griffis, S.M. Webb, M.A. Marcus, C.A. Francis, and. S. Fendorf. Distributed microbially- and chemically-mediated redox processes controlling arsenic dynamics within Mn-/Fe-oxide constructed aggregates. Geochimica et Cosmochimica Acta 104: 29–41.
  • 2013* | Yeung, C.-H., C. A. Francis, and C. S. Criddle. Adaptation of nitrifying microbial biomass to nickel in batch incubations. Applied Microbiology and Biotechnology 97:847-857.
  • 2012* | Biller, S. J., A. C. Mosier, G. F. Wellsand C. A. Francis. Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat. Frontiers in Aquatic Microbiology doi:10.3389/fmicb.2012.00252
  • 2012* | Lund, M., J. M. Smith, and C. A. Francis. Diversity, abundance, and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea. The ISME Journal 6:1966-1977.
  • 2012* | Mosier, A.C., M. Lund, and C. A. Francis. Ecophysiology of an ammonia-oxidizing archaeon adapted to low-salinity habitats. Microbial Ecology 64: 955-63.
  • 2012* | Mosier, A. C., E. A. Allen, S. Ferriera, and C. A. Francis. 2012. Genome sequence of a low-salinity ammonia oxidizing archaeon from the San Francisco Bay estuary, "Candidatus Nitrosoarchaeum limnia" BG20. J. Bacteriology 194:2121-2122.
  • 2012* | Mosier, A. C., E. A. Allen, S. Ferriera, and C. A. Francis. 2012. Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia oxidizing archaeon enriched from the San Francisco Bay estuary. J. Bacteriology 194:2119-2120.
  • 2012 * | Robidart, J. C., C.M. Preston, R.W. Paerl, K. A. Turk, A. C. Mosier, C. A. Francis, C. A. Scholin, and J.P. Zehr. Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation. ISME Journal 6: 513-523.
  • 2011 * | Wells, G. F., H-D. Park, B. Eggleston, C. A. Francis, and C. S. Criddle. Fine-Scale Bacterial Community Dynamics and a Taxa-Time Relationship in a Full-Scale Activated Sludge Wastewater Treatment Plant. Water Research 45: 5476-5488.
  • 2011 * | Pitcher, A., E. C. Hopmans, A. C. Mosier, S J. Park, S. K. Rhee C. A. Francis, S. Schouten S, and J.S. Sinninghe Damsté. Core and intact polar glycerol dibiphytanyl glycerol tetraether lipids of ammonia-oxidizing Archaea enriched from marine and estuarine sediments. Applied and Environmental Microbiology 77: 3468-3477.
  • 2011 * | Blainey**, P. C. , A. C. Mosier**, A. Potanina, C. A. Francis, and S. R. Quake. Genome of a low-salinity ammonia-oxidizing archaeon by sinlge-cell and metagenomic analysis. PLoS ONE 6: e16626. (** = authors contributed equally) 
  • 2011 * | Mosier, A. C., and C. A. Francis. Determining the distribution of marine and coastal ammonia-oxidizing archaea and bacteria using a quantitative approach. Methods in Enzymology 486: 205-221.
  • 2011 * | Wankel, S. D., A. C., Mosier, C. M. Hansel, A. Paytan, and C. A. Francis. Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary. Applied and Environmental Microbiology 77: 269-280.
  • 2010 * | Ofiteru, I. D., M. Lunn, T. P. Curtis, G. F. Wells, C. S. Criddle, C. A. Francis, and W. T. Sloan. Combined niche and neutral effects in a microbial wastewater treatment community. Proceedings of the National Academy of Sciences 107: 15345-15350.
  • 2010 * | Reed, D.W, J. M. Smith, C. A. Francis, and Y. Fujita. Responses of Ammonia-oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater. Applied and Environmental Microbiology 76: 2517-2523.
  • 2010 * | Santoro, A. E., K. L. Casciotti, and C. A. Francis. Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environmental Microbiology 12: 1989-2006.
  • 2010 * | Mosier, A. C., and C. A. Francis. Denitrifier abundance and activity across the San Francisco Bay estuary. Environmental Microbiology Reports 2: 667-676.
  • 2009 * | Wells, G. F., H-D. Park, H-D., C. H. Yeung, Brad Eggleston, C. A. Francis, and C. S. Criddle. Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environmental Microbiology 11:2310-2318
  • 2008 * | Hansel, C. M., S. Fendorf, P. M. Jardine, and C. A. Francis. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Applied and Environmental Microbiology 74:1620-1633.
  • 2008 * | Beman, J. M., B. N. Popp, and C. A. Francis. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. The ISME Journal 2:429-441.
  • 2008 * | Santoro, A. E., C. A. Francis, N. R. de Sieyes, and A. B. Boehm. Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. Environmental Microbiology 10:1068-1079.
  • 2008 * | Mosier, A. C., and C. A. Francis. Relative abundance of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environmental Microbiology 10:3002-3016.
  • 2008 * | Bulow, S. E., C. A. Francis, G. A. Jackson, and B. B. Ward. Sediment denitrifier community composition and nirS gene expression investigated with functional gene microarrays. Environmental Microbiology 10:3057-3069.
  • 2007 * | Oakley, B. B., C. A. Francis, K. J. Roberts, C. Fuchsman, S. Srinivasan, and J. T. Staley. Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria unique to the Black Sea suboxic zone. Environmental Microbiology 9:118-130
  • 2007 | Francis, C. A., J. M. Beman, and M. M. M. Kuypers. New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. The ISME Journal 1:19-27.
  • 2007 * | Beman, J. M., K. J. Roberts, L.E. Wegley, F. L. Rohwer, and C. A. Francis. Distribution and diversity of archaeal ammonia monooxygenase (amoA) genes associated with corals. Applied and Environmental Microbiology 73:5642-5647.
  • 2007 * | Spear, J. R., H. A. Barton, C. E. Robertson, C. A. Francis, and N. R. Pace. Microbial community biofbrics in a geothermal mine adit. Applied and Environmental Microbiology 73:6172-6180.
  • 2006 * | Glatz, R.E., P.W. Lepp, B.B. Ward, and C.A. Francis. Planktonic microbial community composition across steep physical/chemical gradients in permanently ice-covered Lake Bonney, Antarctica. Geobiology 4:53-67.
  • 2006 * | Santoro, A. E., A. B. Boehm, and C. A. Francis. Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer. Applied and Environmental Microbiology 72:2102-2109.
  • 2006 * | Park, H-D., G. F. Wells, H. Bae, C. S. Criddle, and C. A. Francis. Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Applied and Environmental Microbiology 72: 5643-5647.
  • 2006 * | Beman, J. M., and C. A. Francis. Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico. Applied and Environmental Microbiology 72: 7767-7777
  • 2006 * | Wankel, S. D., C. Kendall, C. A. Francis, and A. Paytan. Nitrogen sources and cycling in the San Francisco Bay estuary: A nitrate dual isotopic composition approach. Limnology and Oceanography 51:1654-1664.
  • 2006 * | Hansel, C. M., and C. A. Francis. Coupled photochemical and enzymatic Mn(II) oxidation pathways of a planktonic Roseobacter-like bacterium. Applied and Environmental Microbiology 72:3543-3549.

News & Media