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Publications

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(1998-present)

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Francis, C. A., E.-M. Co, and B. M. Tebo. 2001. Enzymatic manganese(II) oxidation by a marine alpha-proteobacterium. Applied and Environmental Microbiology 67: 4024-4029.
  • 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.
  • 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.
  • 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.
  • Taroncher-Oldenburg, G., E. M. Griner, C. A. Francis, and B. B. Ward. 2003. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Applied and Environmental Microbiology 69:1159-1171.
  • Francis, C. A., G. D. O'Mullan, and B. B. Ward.  2003. Diversity of ammonia monooxygnenase (amoA) genes across environmental gradients in Chesapeake Bay sediments. Geobiology 1:129-140.
  • Jayakumar, D. A., C. A. Francis, S. W. A. Naqvi, and B. B. Ward. 2004. Diversity of nitrite reductase genes (nirS) in the denitrifying water column of the coastal Arabian Sea. Aquatic Microbial Ecology 34:69-78.
  • Francis, C. A., K. J. Roberts, J. M. Beman, A. E. Santoro, and B. B. Oakley. 2005. 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.
  • Santoro, A. E., A. B. Boehm, and C. A. Francis. 2006. Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer. Applied and Environmental Microbiology 72:2102-2109.
  • Glatz., R. E., P. W. Lepp, B. B. Ward, and C. A. Francis. 2006. Planktonic microbial community composition across steep physical/chemical gradients in permanently ice-covered Lake Bonney, Antarctica. Geobiology 4:53-67.
  • Hansel, C. M., and C. A. Francis. 2006. Coupled Mn(II) oxidation pathways of a planktonic Roseobacter-like bacterium. Applied and Environmental Microbiology 72:3543-3549.
  • Wankel, S. D., C. Kendall, C. A. Francis, and A. Paytan. 2006. Nitrogen sources and cycling in the San Francisco Bay Estuary: A nitrate dual isotopic composition approach. Limnology and Oceanography 51:1654-1664.
  • Park, H-D., G. F. Wells, H. Bae, C. S. Criddle, and C. A. Francis. 2006. Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Applied and Environmental Microbiology 72: 5643-5647.
  • Beman, J. M., and C. A. Francis. 2006. 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.
  • Oakley, B. B., C. A. Francis., K. J. Roberts, C. A. Fuchsman, S. Srinivasan, and J. T. Staley. 2007. 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: 119-130.
  • Francis, C. A., J. M. Beman, and M. M. M. Kuypers. 2007. New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME Journal 1: 19-27.
  • Beman, J. M., K. J. Roberts, L. Wegley, F. Rohwer, and C.A. Francis. 2007. Distribution and diversity of archaeal ammonia monooxygenase (amoA) genes associated with corals. Applied and Environmental Microbiology 73:5642-5647.
  • Spear, J. R., H. A. Barton, C. E. Robertson, C. A. Francis, and N. R. Pace. 2007. Microbial community biofabrics in a geothermal mine adit. Applied and Environmental Microbiology 73:6172-6180.
  • Hansel, C. M., S. Fendorf, P. M. Jardine, and C. A. Francis. 2008. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Applied and Environmental Microbiology 74:1620-1633.
  • Santoro, A. E., C. A. Francis, N. R. de Sieyes, and A. B. Boehm. 2008. Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. Environmental Microbiology 10:1068-1079.
  • Beman, J. M., B. N. Popp, and C. A. Francis. 2008. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. The ISME Journal 2:429-441.
  • Mosier, A. C., and C. A. Francis. 2008. Relative abundance of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environmental Microbiology 10:3002-3016.
  • Bulow, S. E., C. A. Francis, G. A. Jackson, and B. B. Ward. 2008. Sediment denitrifier community composition and nirS gene expression investigated with functional gene microarrays. Environmental Microbiology 10:3057-3069.
  • Wells, G. F., H-D. Park, C-H. Yeung, B. Eggleston, C. A. Francis, and C. S. Criddle. 2009. Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environmental Microbiology 11:2310-2328.
  • Santoro, A. E., K. L. Casciotti, and C. A. Francis. 2010. Activity, abundance, and diversity of nitrifying archaea and bacteria in the central California Current. Environmental Microbiology 12: 1989-2006.
  • Mosier, A. C., and C. A. Francis. 2010. Denitrifier abundance and activity across the San Francisco Bay estuary. Environmental Microbiology Reports 2: 667-676..
  • Reed, D. W., J. M. Smith, C. A. Francis, and Y. Fujita. 2010. Response of ammonia-oxidizing bacterial and archaeal populations to organic nitrogen amendments in low-nutrient groundwater. Applied and Environmental Microbiology 76:2517-2523.
  • Ofiteru, I. D., M. Lunn, T. P. Curtis, G. F. Wells, C. S. Criddle, C. A. Francis, and W. T. Sloan. 2010. Combined niche and neutral effects in a microbial wastewater treatment community. Proceedings of the National Academy of Sciences 107: 15345-15350.
  • Wankel, S. D., A. C., Mosier, C. M. Hansel, A. Paytan, and C. A. Francis. 2011. Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary. Applied and Environmental Microbiology 77: 269-280.
  • Mosier, A. C., and C. A. Francis. 2011. Determining the distribution of marine and coastal ammonia-oxidizing archaea and bacteria using a quantitative approach. Methods in Enzymology 486: 205-221.
  • *Blainey, P. C. , A. C. Mosier*, A. Potanina, C. A. Francis, and S. R. Quake. 2011. Genome of a low-salinity ammonia-oxidizing archaeon determined by sinlge-cell and metagenomic analysis. PLoS ONE 6: e16626. (* = authors contributed equally) 
  • 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. 2011. 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.
  • Wells, G. F., H-D. Park, B. Eggleston, C. A. Francis, and C. S. Criddle. 2011. Fine-scale bacterial community dynamics and the taxa–time relationship within a full-scale activated sludge bioreactor. Water Research 45: 5476-5488.
  • 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. 2012. Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation. The ISME Journal 6: 513-523.
  • 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.
  • 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.
  • Lund, M., J. M. Smith, and C. A. Francis. 2012. Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea. The ISME Journal 6: 1966-1977
  • Mosier, A.C., M. Lund, and C. A. Francis. 2012. Ecophysiology of an ammonia-oxidizing archaeon adapted to low-salinity habitats. Microbial Ecology 64: 955-963
  • Biller, S. J., A. C. Mosier, G. F. Wells, and C. A. Francis. 2012. Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat. Frontiers in Aquatic Microbiology doi:10.3389/fmicb.2012.00252
  • Yeung, C.-H., C. A. Francis, and C. S. Criddle. 2013. Adaptation of nitrifying microbial biomass to nickel in batch incubations. Applied Microbiology and Biotechnology 97: 847-857.
  • Ying, S. C., Y. Masue-Slowey, B. D. Kocar, S. D. Griffis, S. Webb, M. A. Marcus, C. A. Francis, and S. Fendorf. 2013. Distributed microbially- and chemically-mediated redox processes controlling arsenic dynamics within Mn-/Fe-oxide constructed aggregates. Geochimica et Cosmochimica Acta 104: 29-41.
  • Francis, C. A., G. D. O’Mullan, J. C. Cornwell, and B. B. Ward. 2013. Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary. Frontiers in Aquatic Microbiology doi:10.3389/fmicb.2013.00237
  • Santoro, A. E., C. M. Sakamoto, J. M. Smith, J. N. Plant, A. L. Gehman, A. Z. Worden, K. S. Johnson, C. A. Francis, and K. L. Casciotti. 2013. 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.
  • 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. Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes. Applied Microbiology and Biotechnology 98: 4723-4736.
  • Smith, J.M., K. L. Casciotti, F. P. Chavez, and C. A. Francis. 2014. Differential contributions of archaeal ammonia oxidizer ecotypes to nitrification in coastal surface waters. The ISME Journal 8: 1704-1714.
  • Smith, J. M., F. P. Chavez, and C. A. Francis. 2014. Ammonium uptake by phytoplankton regulates nitrification in the sunlit ocean. PLoS ONE 9(9): e108173. doi: 10.1371/journal.pone.0108173
  • Smith, J. M., A. C. Mosier, and C. A. Francis. 2015. Spatiotemporal relationships between the abundance, distribution and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments. Microbial Ecology 69: 13-24.
  • Damashek, J, J. M. Smith, A. C. Mosier, and C. A. Francis. 2015. Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine Delta. Frontiers in Aquatic Microbiology 5: 743 doi: 10.3389/fmicb.2014.00743
  • Ying, S. C., J. Damashek, S. Fendorf, and C. A. Francis. 2015. Indigenous arsenic(V)-reducing microbial communities in redox fluctuating near-surface sediments of the Mekong Delta. Geobiology 13: 581-587.
  • Smith, J. M., J. Damashek, F. P. Chavez, and C. A. Francis. 2016. Factors influencing nitrification rates and the abundance and transcriptional activity of ammonia-oxidizing microorganisms in the dark northeast Pacific Ocean. Limnology and Oceanography 61: 596-609. doi: 10.1002/lno.10235
  • Damashek, J., K. L. Casciotti, and C. A. Francis. 2016. 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.
  • Lee, J. A., and C. A. Francis. 2017. Spatiotemporal characterization of San Francisco Bay denitrifying communities: a comparison of nirK and nirS diversity and abundance. Microbial Ecology 73: 271-284. doi: 10.1007/s00248-016-0865-y
  • von Sperber, C., O. A. Chadwick, K. L. Casciotti, K. G. Peay, C. A. Francis, A. E. Kim, and P. M. Vitousek. 2017. Controls of nitrogen cycling evaluated along a well-characterized climate gradient. Ecology 98: 1117–1129. doi: 10.1002/ecy.1751
  • Peay, K., C. von Sperber, E. Cardarelli, H. Toju, C. A. Francis, O. Chadwick, and P. Vitousek. 2017. Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient. FEMS Microbiology Ecology 93: fix045. doi.org/10.1093/femsec/fix045
  • Damashek, J., K.P. Pettie, Z.W. Brown, M. M. Mills, K. R. Arrigo, and C. A. Francis. 2017. Regional patterns in ammonia-oxidizing communities throughout Chukchi Sea waters from the Bering Strait to the Beaufort Sea. Aquatic Microbial Ecology 79: 273-286. doi.org/10.3354/ame01834
  • Tolar, B. B., J. Herrmann, J. R. Bargar, H. van den Bedem, S. Wakatsuki, and C. A. Francis. 2017. Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing Archaea. Environmental Microbiology Reports 9: 484-491. doi: 10.1111/1758-2229.12567
  • Lee, J. A., and C. A. Francis. 2017. Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition. Environmental Microbiology 19: 4897-4912. doi: 10.1111/1462-2920.13920
  • Damashek, J., and C.A. Francis. 2018. Microbial nitrogen cycling in estuaries: from genes to ecosystem processes. Estuaries and Coasts 41: 626-660. doi: 10.1007/s12237-017-0306-2
  • Li, P. N., J. Herrmann, B.B. Tolar, F. Poitevin, R. Ramdasi, J.R. Bargar, D.A. Stahl, G. J. Jensen, C.A. Francis, S. Wakatsuki, and H. van den Bedem. 2018. Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins. The ISME Journal 12: 2389-2402. doi: 10.1038/s41396-018-0191-0.
  • Reji, L. B.B. Tolar, J.M. Smith, F.P. Chavez, and C.A. Francis. 2019. Differential co-occurrence relationships shaping ecotype diversification within Thaumarchaeota populations in the coastal ocean water column. The ISME Journal 13: 1144–1158. doi: 10.1038/s41396-018-0311-x
  • Reji, L., B.B. Tolar, J.M. Smith, F.P. Chavez, and C.A. Francis. 2019. Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay. Environmental Microbiology 21: 4032-4045. doi: 10.1111/1462-2920.14753.
  • Tolar, B.B., A.C. Mosier, M.B. Lund, and C.A. Francis. 2019. Nitrosarchaeum. In Bergey’s Manual of Systematics of Archaea and Bacteria, (John Wiley & Sons, Inc., in association with Bergey’s Manual Trust), pp. 1–9. doi 10.1002/9781118960608.gbm01289
  • Tolar, B.B., L. Reji, J.M. Smith, M. Blum, J.T. Pennington, F.P. Chavez, and C.A. Francis. 2020. Time series assessment of Thaumarchaeota ecotypes in Monterey Bay reveals the importance of water column position in predicting distribution-environment relationships. Limnology and Oceanography 65: 20141-2055. doi: 10.1002/LNO.11436.
  • Reji, L., B.B. Tolar, F.P. Chavez, and C.A. Francis.. 2020. Depth-differentiation and seasonality of planktonic microbial assemblages in the Monterey Bay upwelling system. Frontiers in Aquatic Microbiology 11:1075. doi: 10.3389/fmicb.2020.01075.
  • Reji, L., and C.A. Francis.. 2020. Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage. The ISME Journal 14: 2105–2115. doi: 10.1038/s41396-020-0675-6.
  • Cardarelli, E.L., J.R. Bargar, and C.A. Francis. 2020. Diverse Thaumarchaeota dominate subsurface ammonia-oxidizing communities in semi-arid floodplains in the Western United States. Microbial Ecology 80: 778-792. doi: 10.1007/s00248-020-01534-5
  • Tolar, B.B., K. Boye, C. Bobb, K. Maher, J.R. Bargar, and C.A. Francis. 2020. Stability of floodplain subsurface microbial communities through seasonal hydrological and geochemical cycles. Frontiers in Earth Science (Biogeoscience) 8:338.  doi: 10.3389/feart.2020.00338
  • Rasmussen, A.N., J. Damashek, E. Eloe-Fadrosh, and C.A. Francis. 2021. In-depth spatiotemporal characterization of planktonic archaeal and bacterial communities in North and South San Francisco Bay. Microbial Ecology 81: 601-616. doi: 10.1007/s00248-020-01621-7
  • Strong, A. L., M. M. Mills, I. B. Huang, G. L. van Dijken, S. E. Driscoll, G. M. Berg, R. M. Kudela, S. G. Monismith, C. A. Francis, and K. R. Arrigo. 2021. Response of Lower Sacramento River phytoplankton to high-ammonium wastewater effluent. Elementa: Science of the Anthropocene 9(1). https://doi.org/10.1525/elementa.2021.040
  • Archana, A., C. A. Francis, and A. B. Boehm. 2021. The Beach Aquifer Microbiome: Research Gaps and Data Needs. Frontiers in Environmental Science (Biogeochemical Dynamics) 9:653568. https://doi.org/10.3389/fenvs.2021.653568