Christopher A. Francis, Ph.D. - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
 2000 University of California, San Diego, La Jolla, CA 
Area:
Microbiology Biology, Biogeochemistry, Oceanography Biology, Molecular Biology
Website:
https://earthsci.stanford.edu/~caf/

55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 von Sperber C, Chadwick OA, Casciotti KL, Peay KG, Francis CA, Kim AE, Vitousek PM. Controls of nitrogen cycling evaluated along a well-characterized climate gradient. Ecology. PMID 28130777 DOI: 10.1002/ecy.1751  0.44
2016 Damashek J, Casciotti KL, Francis CA. Variable Nitrification Rates Across Environmental Gradients in Turbid, Nutrient-Rich Estuary Waters of San Francisco Bay Estuaries and Coasts. 39: 1050-1071. DOI: 10.1007/s12237-016-0071-7  1
2015 Ying SC, Damashek J, Fendorf S, Francis CA. Indigenous arsenic(V)-reducing microbial communities in redox-fluctuating near-surface sediments of the Mekong Delta. Geobiology. 13: 581-7. PMID 26466963 DOI: 10.1111/gbi.12152  0.52
2015 Smith JM, Mosier AC, Francis CA. Spatiotemporal relationships between the abundance, distribution, and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments. Microbial Ecology. 69: 13-24. PMID 25038845 DOI: 10.1007/s00248-014-0450-1  1
2015 Smith JM, Damashek J, Chavez FP, Francis CA. Factors influencing nitrification rates and the abundance and transcriptional activity of ammonia-oxidizing microorganisms in the dark northeast Pacific Ocean Limnology and Oceanography. DOI: 10.1002/lno.10235  1
2014 Damashek J, Smith JM, Mosier AC, Francis CA. Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta. Frontiers in Microbiology. 5: 743. PMID 25620958 DOI: 10.3389/fmicb.2014.00743  1
2014 Smith JM, Chavez FP, Francis CA. Ammonium uptake by phytoplankton regulates nitrification in the sunlit ocean. Plos One. 9: e108173. PMID 25251022 DOI: 10.1371/journal.pone.0108173  1
2014 Wells GF, Wu CH, Piceno YM, Eggleston B, Brodie EL, Desantis TZ, Andersen GL, Hazen TC, Francis CA, Criddle CS. Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes. Applied Microbiology and Biotechnology. 98: 4723-36. PMID 24553968 DOI: 10.1007/s00253-014-5564-3  1
2014 Smith JM, Casciotti KL, Chavez FP, Francis CA. Differential contributions of archaeal ammonia oxidizer ecotypes to nitrification in coastal surface waters. The Isme Journal. 8: 1704-14. PMID 24553472 DOI: 10.1038/ismej.2014.11  1
2013 Yeung CH, Francis CA, Criddle CS. Adaptation of nitrifying microbial biomass to nickel in batch incubations. Applied Microbiology and Biotechnology. 97: 847-57. PMID 22374414 DOI: 10.1007/s00253-012-3947-x  1
2013 Santoro AE, Sakamoto CM, Smith JM, Plant JN, Gehman AL, Worden AZ, Johnson KS, Francis CA, Casciotti KL. Measurements of nitrite production in and around the primary nitrite maximum in the central California Current Biogeosciences. 10: 7395-7410. DOI: 10.5194/bg-10-7395-2013  1
2013 Ying SC, Masue-Slowey Y, Kocar BD, Griffis SD, Webb S, Marcus MA, Francis CA, Fendorf S. Distributed microbially- and chemically-mediated redox processes controlling arsenic dynamics within Mn-/Fe-oxide constructed aggregates Geochimica Et Cosmochimica Acta. 104: 29-41. DOI: 10.1016/j.gca.2012.08.020  1
2012 Biller SJ, Mosier AC, Wells GF, Francis CA. Global Biodiversity of Aquatic Ammonia-Oxidizing Archaea is Partitioned by Habitat. Frontiers in Microbiology. 3: 252. PMID 22826704 DOI: 10.3389/fmicb.2012.00252  1
2012 Mosier AC, Lund MB, Francis CA. Ecophysiology of an ammonia-oxidizing archaeon adapted to low-salinity habitats. Microbial Ecology. 64: 955-63. PMID 22644483 DOI: 10.1007/s00248-012-0075-1  1
2012 Lund MB, Smith JM, Francis CA. Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea. The Isme Journal. 6: 1966-77. PMID 22592819 DOI: 10.1038/ismej.2012.40  1
2012 Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA. Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary. Journal of Bacteriology. 194: 2121-2. PMID 22461555 DOI: 10.1128/JB.00013-12  1
2012 Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA. Genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay estuary. Journal of Bacteriology. 194: 2119-20. PMID 22461554 DOI: 10.1128/JB.00007-12  1
2012 Robidart JC, Preston CM, Paerl RW, Turk KA, Mosier AC, Francis CA, Scholin CA, Zehr JP. Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation. The Isme Journal. 6: 513-23. PMID 21975596 DOI: 10.1038/ismej.2011.127  1
2011 Wells GF, Park HD, Eggleston B, Francis CA, Criddle CS. Fine-scale bacterial community dynamics and the taxa-time relationship within a full-scale activated sludge bioreactor. Water Research. 45: 5476-88. PMID 21875739 DOI: 10.1016/j.watres.2011.08.006  1
2011 Pitcher A, Hopmans EC, Mosier AC, Park SJ, Rhee SK, Francis CA, Schouten S, Sinninghe Damsté JS. 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. PMID 21441324 DOI: 10.1128/AEM.02758-10  1
2011 Mosier AC, Francis CA. Determining the distribution of marine and coastal ammonia-oxidizing archaea and bacteria using a quantitative approach. Methods in Enzymology. 486: 205-21. PMID 21185437 DOI: 10.1016/B978-0-12-381294-0.00009-2  1
2011 Wankel SD, Mosier AC, Hansel CM, Paytan A, Francis CA. Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary, California. Applied and Environmental Microbiology. 77: 269-80. PMID 21057023 DOI: 10.1128/AEM.01318-10  1
2011 Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR. Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis Plos One. 6. DOI: 10.1371/journal.pone.0016626  1
2010 Mosier AC, Francis CA. Denitrifier abundance and activity across the San Francisco Bay estuary. Environmental Microbiology Reports. 2: 667-76. PMID 23766254 DOI: 10.1111/j.1758-2229.2010.00156.x  1
2010 Ofiteru ID, Lunn M, Curtis TP, Wells GF, Criddle CS, Francis CA, Sloan WT. Combined niche and neutral effects in a microbial wastewater treatment community. Proceedings of the National Academy of Sciences of the United States of America. 107: 15345-50. PMID 20705897 DOI: 10.1073/pnas.1000604107  1
2010 Santoro AE, Casciotti KL, Francis CA. Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environmental Microbiology. 12: 1989-2006. PMID 20345944 DOI: 10.1111/j.1462-2920.2010.02205.x  1
2010 Reed DW, Smith JM, Francis CA, Fujita Y. Responses of ammonia-oxidizing bacterial and archaeal populations to organic nitrogen amendments in low-nutrient groundwater. Applied and Environmental Microbiology. 76: 2517-23. PMID 20190081 DOI: 10.1128/AEM.02436-09  1
2009 Wells GF, Park HD, Yeung CH, Eggleston B, Francis CA, Criddle CS. Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environmental Microbiology. 11: 2310-28. PMID 19515200 DOI: 10.1111/j.1462-2920.2009.01958.x  1
2008 Bulow SE, Francis CA, Jackson GA, Ward BB. Sediment denitrifier community composition and nirS gene expression investigated with functional gene microarrays. Environmental Microbiology. 10: 3057-69. PMID 18973624 DOI: 10.1111/j.1462-2920.2008.01765.x  1
2008 Mosier AC, Francis CA. Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environmental Microbiology. 10: 3002-16. PMID 18973621 DOI: 10.1111/j.1462-2920.2008.01764.x  1
2008 Santoro AE, Francis CA, de Sieyes NR, Boehm AB. Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. Environmental Microbiology. 10: 1068-79. PMID 18266758 DOI: 10.1111/j.1462-2920.2007.01547.x  1
2008 Beman JM, Popp BN, Francis CA. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. The Isme Journal. 2: 429-41. PMID 18200070 DOI: 10.1038/ismej.2007.118  1
2008 Hansel CM, Fendorf S, Jardine PM, Francis CA. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Applied and Environmental Microbiology. 74: 1620-33. PMID 18192411 DOI: 10.1128/AEM.01787-07  1
2007 Francis CA, Beman JM, Kuypers MM. New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. The Isme Journal. 1: 19-27. PMID 18043610 DOI: 10.1038/ismej.2007.8  1
2007 Spear JR, Barton HA, Robertson CE, Francis CA, Pace NR. Microbial community biofabrics in a geothermal mine adit. Applied and Environmental Microbiology. 73: 6172-80. PMID 17693567 DOI: 10.1128/AEM.00393-07  1
2007 Beman JM, Roberts KJ, Wegley L, Rohwer F, Francis CA. Distribution and diversity of archaeal ammonia monooxygenase genes associated with corals. Applied and Environmental Microbiology. 73: 5642-7. PMID 17586663 DOI: 10.1128/AEM.00461-07  1
2007 Oakley BB, Francis CA, Roberts KJ, Fuchsman CA, Srinivasan S, Staley JT. Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria in the Black Sea suboxic zone. Environmental Microbiology. 9: 118-30. PMID 17227417 DOI: 10.1111/j.1462-2920.2006.01121.x  1
2006 Beman JM, Francis CA. Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahía del Tóbari, Mexico. Applied and Environmental Microbiology. 72: 7767-77. PMID 17012598 DOI: 10.1128/AEM.00946-06  1
2006 Park HD, Wells GF, Bae H, Criddle CS, Francis CA. Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Applied and Environmental Microbiology. 72: 5643-7. PMID 16885322 DOI: 10.1128/AEM.00402-06  1
2006 Hansel CM, Francis CA. Coupled photochemical and enzymatic Mn(II) oxidation pathways of a planktonic Roseobacter-Like bacterium. Applied and Environmental Microbiology. 72: 3543-9. PMID 16672501 DOI: 10.1128/AEM.72.5.3543-3549.2006  1
2006 Santoro AE, Boehm AB, Francis CA. Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer. Applied and Environmental Microbiology. 72: 2102-9. PMID 16517659 DOI: 10.1128/AEM.72.3.2102-2109.2006  1
2006 Glatz RE, Lepp PW, Ward BB, Francis CA. Planktonic microbial community composition across steep physical/chemical gradients in permanently ice-covered Lake Bonney, Antarctica Geobiology. 4: 53-67. DOI: 10.1111/j.1472-4669.2006.00057.x  1
2006 Wankel SD, Kendall C, Francis CA, Paytan A. Nitrogen sources and cycling in the San Francisco Bay estuary: A nitrate dual isotopic composition approach Limnology and Oceanography. 51: 1654-1664.  1
2005 Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB. 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. 102: 14683-8. PMID 16186488 DOI: 10.1073/pnas.0506625102  1
2004 Jayakumar DA, Francis CA, Naqvi SWA, Ward BB. Diversity of nitrite reductase genes (nirS) in the denitrifying water column of the coastal Arabian Sea Aquatic Microbial Ecology. 34: 69-78.  1
2003 Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Applied and Environmental Microbiology. 69: 1159-71. PMID 12571043 DOI: 10.1128/AEM.69.2.1159-1171.2003  1
2002 Francis CA, Casciotti KL, Tebo BM. 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: 450-6. PMID 12420165 DOI: 10.1007/s00203-002-0472-9  1
2002 Francis CA, Tebo BM. Enzymatic manganese(II) oxidation by metabolically dormant spores of diverse Bacillus species. Applied and Environmental Microbiology. 68: 874-80. PMID 11823231  1
2002 Obraztsova AY, Francis CA, Tebo BM. Sulfur disproportionation by the facultative anaerobe Pantoea agglomerans SP1 as a mechanism for chromium(VI) reduction Geomicrobiology Journal. 19: 121-132. DOI: 10.1080/014904502317246219  1
2001 Francis CA, Tebo BM. cumA multicopper oxidase genes from diverse Mn(II)-oxidizing and non-Mn(II)-oxidizing Pseudomonas strains. Applied and Environmental Microbiology. 67: 4272-8. PMID 11526033 DOI: 10.1128/AEM.67.9.4272-4278.2001  1
2001 Francis CA, Co EM, Tebo BM. Enzymatic manganese(II) oxidation by a marine alpha-proteobacterium. Applied and Environmental Microbiology. 67: 4024-9. PMID 11526000 DOI: 10.1128/AEM.67.9.4024-4029.2001  1
2000 Francis CA, Obraztsova AY, Tebo BM. Dissimilatory metal reduction by the facultative anaerobe Pantoea agglomerans SP1. Applied and Environmental Microbiology. 66: 543-8. PMID 10653716 DOI: 10.1128/AEM.66.2.543-548.2000  1
2000 Francis CA, Tebo BM. New insights into the diversity of genes and enzymes involved in bacterial Mn(II) oxidation Acs Division of Environmental Chemistry, Preprints. 40: 488-490.  1
1999 Francis CA, Tebo BM. Marine Bacillus spores as catalysts for oxidative precipitation and sorption of metals. Journal of Molecular Microbiology and Biotechnology. 1: 71-8. PMID 10941787  1
1998 Francis CA, Francis AK, Golet DS, Ward BB. Quantification of catechol 2,3-dioxygenase gene homology and benzoate utilization in intertidal sediments Aquatic Microbial Ecology. 15: 225-231.  1
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