Banfield Laboratory

University of California, Berkeley




Voutsinos, M.Y., Banfield, J.F., Moreau, J.W. (2021). Secondary lanthanide phosphate mineralisation in weathering profiles of I-, S-and A-type granites. Mineralogical Magazine. DOI: 10.1180/mgm.2020.90




Meheust, R., Castelle, C.J., Matheus Carnevali, P.B., Farag, I.F., He, C., Chen, L.X., Amano, Y., Hug, L.A., Banfield, J.F. (2020). Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog. ISME Journal. DOI: 10.1038/s41396-020-0716-1


Jaffe, A.L., Castelle, C.J., Matheus Carnevali, P.B., Gribaldo, S., Banfield, J.F. (2020). The rise of diversity in metabolic platforms across the Candidate Phyla Radiation. BMC Biology. DOI: 10.1186/s12915-020-00804-5


Matheus Carnevali, P.B., Lavy, A., Thomas, A.D., Crits-Christoph, A., Diamond, S., Meheust, R., Olm, M.R., Sharrar, A., Lei, S., Dong, W., Falco, N., Bouskill, N., Newcomer, M., Nico, P., Wainwright, H., Dwivedi, D., Williams, K.H., Hubbard, S., Banfield, J.F. (2020). Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale. bioRxiv. DOI: 10.1101/2020.05.14.086363


Pausch, P., Al-Shayeb, B., Bisom-Rapp, E., Tsuchida, C.A., Li, Z., Cress, B.F., Knott, G.J., Jacobsen, S.E., Banfield, J.F., Doudna, J.A. (2020). CRISPR-CasΦ from huge phages is a hypercompact genome editor. Science. DOI: 10.1126/science.abb1400


Harrington, L.B., Ma, E., Chen, J.S., Witte, I.P., Gertz, D., Paez-Espino, D., Al-Shayeb, B., Kyrpides, N.C., Burstein, D., Banfield, J.F., Doudna, J.A.(2020). A scoutRNA Is Required for Some Type V CRISPR-Cas Systems. Molecular Cell. DOI: 10.1016/j.molcel.2020.06.022


Sharrar, A.M., Crits-Christoph, A., Meheust, R., Diamond, S., Starr, E.P., Banfield, J.F. (2020). Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type. mBio. DOI: 10.1128/mBio.00416-20


Mu, A., Thomas, B.C., Banfield, J.F., Moreau, J.W. (2020). Subsurface carbon monoxide oxidation capacity revealed through genome‐resolved metagenomics of a carboxydotroph. Environmental Microbiology Reports. DOI: 10.1111/1758-2229.12868


He, C., Keren, R., Whittaker, M., Farag, I.F., Doudna, J., Cate, J.H.D., Banfield, J.F. (2020). Huge and variable diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems. bioRxiv. DOI: 10.1101/2020.05.14.094862


Meheust, R., Castelle, C.J., Matheus Carnevali, P.B., Jaffe, A.L., Banfield, J.F. (2020). Early acquisition of conserved, lineage-specific proteins currently lacking functional predictions were central to the rise and diversification of archaea. bioRxiv. DOI: 10.1101/2020.07.16.207365


Rubin, B.E., Diamond, S., Cress, B.F., Crits-Christoph, A., He, C., Xu, M., Zhou, Z. Smock, D.C., Tang, K., Owens, T.K., Krishnappa, N., Sachdeva, R., Deutschbauer, A.M., Banfield, J.F., Doudna, J.A. (2020). Targeted Genome Editing of Bacteria Within Microbial Communities. bioRxiv. DOI: 10.1101/2020.07.17.209189


Crits-Christoph, A., Bhattacharya, N., Olm, M.R., Song, Y.S., Banfield, J.F.(2020). Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity. bioRxiv. DOI: 10.1101/2020.06.24.170084


Huddy, R.J., Sachdeva, R., Kadzinga, F., Kantor, R., Harrison, S.T.L., Banfield, J.F.(2020). Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophic Afipia and Thiobacillus strains within complex microbiomes. bioRxiv. DOI: 10.1101/2020.04.29.067207


Al-Shayeb, B., Sachdeva, R., Chen, L.X., Ward, F., Munk, P., Devoto, A., Castelle, C.J., Olm, M.R., Bouma-Gregson, K., Amano, Y., He, C., Meheust, R., Brooks, B., Thomas, A., Lavy, A., Matheus Carnevali, P.B., Sun, C., Goltsman, D.S.A., Borton, M.A., Sharrar, A., Jaffe, A.L., Nelson, T.C., Kantor, R., Keren, R., Lane, K.R., Farag. I.F., Lei, S.F., Finstad, K., Amundson, R., Anantharaman, K., Zhou, J.L., Probst, A.L., Power, M.E., Tringe, S.G., Li. W.J., Wrighton, K., Harrison, S., Morowitz, M., Relman, D.A., Doudna, J.A., Lehours, A.C., Warren, L., Cate, J.H.D., Santini, J.M., Banfield, J.F.(2020). Clades of huge phages from across Earth’s ecosystems. Nature. DOI: 10.1038/s41586-020-2007-4


Olm, M.R., Crits-Christoph, A., Diamond, S., Lavy, A., Matheus Carnevali, P.B., Banfield, J.F.(2020). Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries. mSystems. DOI: 10.1128/mSystems.00731-19


Whittaker, M.L., Comolli, L.R., Gilbert, B., Banfield, J.F.(2020). Layer size polydispersity in hydrated montmorillonite creates multiscale porosity networks. Applied Clay Science. DOI: 10.1016/j.clay.2020.105548


Crits-Christoph, A., Olm, M.R., Diamond, S., Bouma-Gregson, K., P.B., Banfield, J.F.(2020). Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. ISME Journal. DOI: 10.1038/s41396-020-0655-x


West, P.T., Peters, S.L., Olm, M.R., Yu, F.Q.B, Lou, Y.C., Firek, B.A., Baker, R., Johnson, A.D., Morowitz, M.J., Hettich, R.L., Banfield, J.F.(2020). Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics and proteomics. bioRxiv. DOI: 10.1101/2020.03.23.004093


Gionfriddo, C.M., Stott, M.B., Power, J.F., Ogorek, J.M, Krabbenhoft, D.P., Wick, R., Holt, K., Chen, L.X., Thomas, B.C., Banfield, J.F., Moreau, J.W.(2020). Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs. bioRxiv. DOI: 10.1101/2020.02.03.933291


Olm, M.R., Crits-Christoph, A., Diamond, S., Lavy, A., Matheus Carnevali, P.B., Banfield, J.F.(2020). Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries. mSystems. DOI: 10.1128/mSystems.00731-19


Olm, M.R., Crits-Christoph, A., Diamond, S., Bouma-Gregson, K., Firek, B., Morowitz, M.J., Banfield, J.F.(2020). InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains. bioRxiv. DOI: 10.1101/2020.01.22.915579


Sher, Y., Olm, M.R., Raveh-Sadka, T., Brown, C.T., Sher, R., Firek, B., Baker, R., Morowitz, M.J., Banfield, J.F.(2020). Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut. PLOS ONE. DOI: 10.1371/journal.pone.0229537


Probst, A.J., Elling, F.J., Castelle, C.J., Zhu, Q.Z., Elvert, M., Birarda, G., Holman, H.Y.N., Lane, K.R., Ladd, B., Ryan, M.C., Woyke, T., Hinrichs, K.U., Banfield, J.F.(2020). Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria. ISME Journal. DOI: 10.1038/s41396-020-0624-4


Chen, L.X., Anantharaman, K., Shaiber, A., Murat Eren, A., Banfield, J.F.(2020). Accurate and complete genomes from metagenomes. Genome Research. DOI: 10.1101/gr.258640.119


Keren, R., Lawrence, J.E., Zhuang, W.Q., Jenkins, D., Banfield, J.F., Alvarez-Cohen, L., Zhou, L.J., Yu, K. (2020). Increased replication of dissimilatory nitrate-reducing bacteria leads to decreased anammox bioreactor performance. Microbiome. DOI: 10.1186/s40168-020-0786-3


Nuccio, E.E., Starr, E., Karaoz, U., Brodie, E.L., Zhou, J.Z., Tringe S.G., Malmstrom, R.R., Woyke, T., Banfield, J.F., Firestone, M.K., Pett-Ridge, J.(2020). Niche differentiation is spatially and temporally regulated in the rhizosphere. ISME Journal. DOI: 10.1038/s41396-019-0582-x


Arbour, T.J., Gilbert, B., Banfield, J.F. (2020). Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities. Frontiers in Microbiology. DOI: 10.3389/fmicb.2020.01694




Siber, C.M.K., Paul, B.G., Castelle, C.J., Hu, P., Tringe, S.G., Valentine, D.L., Andersen, G.L., Banfield, J.F. (2019). Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community. mSystems. DOI: 10.1128/mBio.02128-19


Olm, M.R., Bhattacharya, N., Crits-Christoph, A., Firek, B.A., Baker, R., Song, Y.S., Morowitz, M.J., Banfield, J.F. (2019). Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria. Science Advances. DOI: 10.1126/sciadv.aax5727


Light, S.H., Meheust, R., Ferrell, J.L., Cho, J.Y., Deng, D., Agostoni, M., Lavarone, A.T., Banfield, J.F., D'Orazio, S.E.F., Portnoy, D.A. (2019). Extracellular electron transfer powers flavinylated extracellular reductases in Gram-positive bacteria. PNAS. DOI: 10.1073/pnas.1915678116


Chen, L.X., Zhao, Y.L., McMahon, K.D., Mori, J.F., Jessen, G.L., Nelson, T.C., Warren, L.A., Banfield, J.F. (2019). Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria. mSystems. DOI: 10.1128/mSystems.00410-19


Starr, E., Nuccio, E.E., Pett-Ridge, J., Banfield, J.F., Firestone, M.K. (2019). Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. PNAS. DOI: 10.1073/pnas.1908291116


Chen, L.X., Al-Shayeb, B., Meheust, R., Li, W.J., Doudna, J.A., Banfield, J.F. (2019). Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems. Frontiers in Microbiology. DOI: 10.3389/fmicb.2019.00928


Chen, B., Huang, Y., Xu, J., Zhou, X., Chen, Z., Zhang, H., Zhang, J., Qi, J., Lu, T., Banfield, J., Yan, J., Raju, S.V., Gleason, A.E., Clark, S., MacDowell, A.A. (2019). Revealing the ductility of nanoceramic MgAl2O4. Journals of Materials Research. DOI: 10.1557/jmr.2019.114


Schwank, K., Bornemann, T.L.V., Dombrowski, N., Spang, A., Banfield, J.F., Probst, A.J. (2019). An archaeal symbiont-host association from the deep terrestrial subsurface. ISME Journal. DOI: 10.1038/s41396-019-0421-0


Diamond, S., Andeer, P.F., Li, Z., Crits-Christoph, A., Burstein, D., Anantharaman, K., Lane, K.R., Thomas, B.C., Pan, C., Northen, T.R., Banfield, J.F. (2019). Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nature Microbiology. DOI: 10.1038/s41564-019-0449-y


Poghosyan, L., Koch, H., Lavy, A., Frank, J., van Kessel, M.A.H.J, Jetten, M.S.M., Banfield, J.F., Lucker, S. (2019). Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface. Environmental Microbiology. DOI: 10.1111/1462-2920.14691


Lavy, A., McGrath, D.G., Matheus Carnevali, P., Wan, J.M., Dong, W.M, Tokunaga, T.K., Thomas, B.C., Williams, K.H., Hubbard, S.S., Banfield, J.F., Gilbert, B. (2019). Microbial communities across a hillslope‐riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock. Ecology and Evolution. DOI: 10.1002/ece3.5254


Mangiante, D.M., Schaller, R.D., Banfield, J.F., Gilbert, B. (2019). Pathways for the photoreduction of fumarate on ZnS. ACS. DOI: 10.1021/acsearthspacechem.9b00169


Wright, A.V., Wang, J.Y., Burstein, D., Harrington, L.B., Paez-Espino, D., Kyrpides, N.C., Iavarone, A.T., Banfield, J.F., Doudna, J.A. (2019). A Functional Mini-Integrase in a Two-Protein Type V-C CRISPR System. Molecular Cell. DOI: 10.1016/j.molcel.2018.12.015


Bouma-Gregson, K., Olm, M.R., Probst, A., Anantharaman, K., Power, M.E., Banfield, J.F. (2019). Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network. ISME Journal. DOI: 10.1038/s41396-019-0374-3


Borrel, G., Adam, P.S., McKay, L.J., Chen, L.X., Sierra-García, I.N., Sieber, C.M.K., Letourneur, Q., Ghozlane, A., Andersen, G.L., Li, W.J., Hallam, S.J., Muyzer, G., de Oliveira, V.M., Inskeep, W.P., Banfield, J.F., Gribaldo, S. (2019). Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nature Microbiology. DOI: 10.1038/s41564-019-0363-3


Olm, M.R., West, P.T., Brooks, B., Firek B.A., Baker, R., Morowitz, M.J., Banfield, J.F. (2019). Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms. Microbiome. DOI: 10.1186/s40168-019-0638-1


Watts, M.P., Spurr, L.P., Lê Cao, K., Wick, R., Banfield, J.F., Moreau, J.W. (2019). Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium. Elsevier. DOI: 10.1016/j.watres.2019.02.058


Devoto, A.E., Santini, J.M., Olm, M.R., Anantharaman, K., Munk, P., Tung, J., Archie, E.A., Turnbaugh, P.J., Seed, K.D., Blekhman, R., Aarestrup, F.M., Thomas, B.C., Banfield, J.F. (2019). Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nature Microbiology. DOI: 10.1038/s41564-018-0338-9


Matheus Carnevali, P.B., Schulz, F., Castelle, C.J., Kantor, R.S., Shih, P.M., Sharon, I., Santini, J.M., Olm, M.R., Amano, Y., Thomas, B.C., Anantharaman, K., Burstein, D., Becraft, E.D., Stepanauskas,R., Woyke, T., Banfield, J.F. (2019). Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nature Communications. DOI: 10.1038/s41467-018-08246-y


Whittaker, M., Carrero Romero, S., Gilbert, B., Banfield, J.F. (2019). Phase separation during ion exchange controls collapse and induces ordering in hydrated montmorillonite. EarthArXiv. DOI: 10.31223/




Harrington, L. B., Burstein, D., Chen, J. S., Paez-Espino, D., Ma, E., Witte, I.P., Cofsky, J.C., Banfield, J.F., Doudna, J.A. (2018). Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science. DOI: 10.1126/science.aav4294


Castelle, C.J., Brown, C.T., Anantharaman, K., Probst, A.J., Huang, R.H., Banfield, J.F. (2018). Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nature Reviews Microbiology. DOI: 10.1038/s41579-018-0076-2


Whittaker, M.L., Kisielowski, C., Montabana, E.A., Gilbert, B., Banfield, J.F. (2018). Atomic Structure, Defects, and Stacking of Clay Particles by Low-Dose, High Resolution (Cryo)-TEM. MSA. DOI: 10.1017/S1431927618010279


Starr, E.P., Shi, S., Blazewicz, S.J., Prost, A., Herman, D.J., Firestone, M.K., Banfield, J.F. (2018). Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon. Microbiome. DOI: 10.1186/s40168-018-0499-z


Crits-Christoph, A., Diamond, S., Butterfield, C.N., Thomas, B., Banfield, J.F. (2018). Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature. DOI: 10.1038/s41586-018-0207-y


Brooks, B., Olm, M.R., Firek, B.A., Baker, R., Geller-McGrath, D., Reimer, S.R., Soenjoyo, K.R., Yip, J.S., Dahan, D., Thomas, B.C., Morowitz, M.J., Banfield, J.F. (2018). The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms. Microbiome. DOI: 10.1186/s40168-018-0493-5


Liu, X., Castelle, C., Probst, A.J., Zhou, Z., Pan, J., Liu, Y., Banfield, J.F., Gu, J. (2018). Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages. Microbiome. DOI: 10.1186/s40168-018-0488-2


Goltsman, D.S.A., Sun, C.L., Proctor, D.M., DiGiulio, D.B., Robaczewska, A., Thomas, B.C., Shaw, G.M., Stevenson, D.K., Holmes, S.P., Banfield, J.F., Relman, D.A. (2018). Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome. bioRxiv. DOI: 10.1101/266700


Sieber, C.M.K, Probst, A., Sharrar, A., Thomas, B.C., Hess, M., Tringe, S.G., Banfield, J.F. (2018). Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nature Microbiology. DOI: 10.1038/s41564-018-0171-1


Bouma-Gregson, K. Olm, M.R., Probst, A.J., Anantharaman, K., Power, M.E., Banfield, J.F. (2018). Microbial diversity and metabolic potential in cyanotoxin producing cyanobacterial mats throughout a river network. bioRxiv. DOI: 10.1101/294421


Olm, M.R., West, P.T., Brooks, B., Firek, B.A., Baker, R., Morowitz, M.J., Banfield, J.F. (2018). Strain-level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes. bioRxiv. DOI: 10.1101/324566


Brown, C.T., Xiong, W., Olm, M.R., Thomas, B., Baker, R., Morowitz, M.J., Firek, B.A., Hettich, R.L., Banfield, J.F. (2018). Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles. mBio. DOI: 10.1128/mBio.00441-18


Probst, A.J., Banfield, J.F. (2018). Homologous Recombination and Transposon Propagation Shape the Population Structure of an Organism from the Deep Subsurface with Minimal Metabolism. Genome Biology and Evolution. DOI: 10.1093/gbe/evy067


Matheus-Carnevali, P.B., Schulz, F., Castelle, C.J., Kantor, R., Shih, P., Sharon, I., Santini, J., Olm, M., Amano, Y., Thomas, B.C., Anantharaman, K., Burstein, D., Becraft, E.D., Stepanauskas, R., Woyke, T., Banfield, J.F. (2018). Hydrogen-based metabolism - An ancestral trait in lineages sibling to the Cyanobacteria. bioRxiv. DOI: 10.1101/328856


Castelle, C.J., Banfield, J.F. (2018). Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life. Cell. DOI: 10.1016/j.cell.2018.02.016


Meheust, R., Burstein, D., Castelle, C.J., Banfield, J.F. (2018). Biological capacities clearly define a major subdivision in Domain Bacteria. bioRxiv. DOI: 10.1101/335083


West, P.T., Probst, A.J., Grigoriev, I.V., Thomas, B., Banfield, J.F. (2018). Genome-reconstruction for eukaryotes from complex natural microbial communities. Genome Research. DOI: 10.1101/gr.228429.117


Hubbard, S., Williams, K.H., Agarwal, D., Banfield, J.F., Beller, H., Bouskill, N., Brodie, E., Carroll, R., Dafflon, B., Dwivedi, D., Falco, N., Faybishenko, B., Maxwell, R., Nico, P., Steelfel, C., Steltzer, H., Tokunaga, T., Tran, P.A., Wainwright, H., Varadharajan, C. (2018). The East River, Colorado, Watershed: A Mountainous Community Testbed for Improving Predictive Understanding of Multiscale Hydrological–Biogeochemical Dynamics. ACCESS. DOI: 10.2136/vzj2018.03.0061


Lavy, A., Keren, R., Yu, K., Thomas, B.C., Alvarez-Cohen, L., Banfield, J.F., Ilan, M. (2018). A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges. Environmental Microbiology. DOI: 10.1111/1462-2920.14013


Anantharaman, K., Hausmann, B., Jungbluth, S.P., Kantor, R.S., Lavy, A., Warren, L.A., Rappe, M.S., Pester, M., Loy, A., Thomas, B.C., Banfield, J.F. (2018). Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME Journal. DOI: 10.1038/s41396-018-0078-0


Probst, A.J., Ladd, B., Jarette, J.K., Geller-McGrath, D.E., Sieber, C.M.K, Emerson, J.B., Anantharaman, K., Thomas, B.C., Malmstrom, R.R., Stieglmeier, M., Klingl, A., Woyke, T., Ryan, M.C., Banfield, J.F. (2018). Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nature Microbiology. DOI: 10.1038/s41564-017-0098-y


Rahman, S.F., Olm, M.R., Morowitz, M.J., Banfield, J.F. (2018). Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome. mSystems. DOI: 10.1128/mSystems.00123-17




Fakra, S.C., Luef, B., Castelle, C.J., Mullin, S.W., Williams, K.H., Marcus, M.A., Schichnes, D., Banfield, J.F. (2017). Correlative Cryogenic Spectromicroscopy to Investigate Selenium Bioreduction Products. Environmental Science & Technology. DOI: 10.1021/acs.est.5b01409


Dudek, N.K., Sun, C.L., Burstein, D., Kantor, R.S., Goltsman, D.S.A., Bik, E.M., Thomas, B.C., Banfield, J.F., Relman, D.A. (2017). Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome. Current Biology. DOI: 10.1016/j.cub.2017.10.040


Xiong, W., Brown, C.T., Morowitz, M.J., Banfield, J.F., Hettich, R.L. (2017). Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life. Microbiome. DOI: 10.1186/s40168-017-0290-6


Brooks, B., Olm, M.R., Firek, B.A., Baker, R., Thomas, B.C., Morowitz, M.J., Banfield, J.F. (2017). Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. Nature Communications. Article Number: 1814 DOI: 10.1038/s41467-017-02018-w


Banfield, J.F., Anantharaman, K., Williams, K.H., Thomas, B.C. (2017). Complete 4.55-Megabase-Pair Genome of “Candidatus Fluviicola riflensis,” Curated from Short-Read Metagenomic Sequences. Genome Announcements. DOI: 10.1128/genomeA.01299-17


Probst, A.J., Hu, P., Sun, C.L., Dubinsky, E.A., Sieber, C.M.K., Banfield, J.F., Andersen, G.L. (2017). Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill. PNAS. DOI: 10.1073/pnas.1712466114


Ino, K., Hernsdorf, A.W., Konno, U., Kouduka, M., Yanagawa, K., Kato, S., Sunamura, M., Hirota, A., Togo, Y.S. Ito, K., Fukuda, A., Iwatsuki, T., Mizuno, T., Komatsu, D.D., Tsunogai, U., Ishimura, T., Amano, Y., Thomas, B.C., Banfield, J.F., Suzuki, Y. (2017). Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment. ISME. Volume: 12. DOI: 10.1038/ismej.2017.140


Bowers, R.M., Kyrpides, N.C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T.B.K., Schulz, F., Jarett, J., Rivers, A.R., Eloe-Fadrosh, E.A., Tringe, S.G., Ivanova, N.N., Copeland, A., Clum, A., Becraft, E.D., Malmstrom, R.R., Birren, B., Podar, M., Bork, P., Weinstock, G.M., Garrity, G., Dodsworth, J.A., Yooseph, S., Sutton, G., Glockner, F.O., Gilbert, J.A., Nelson, W.C., Hallam, S.J., Jungbluth, S.P., Ettema, T.J.G, Tighe, S., Konstantinidis, K.T., Liu, W., Baker, B.J., Rattei, T., Eisen, J.A., Hedlund, B., MacMahon, K.D., Fierer, N., Knight, R., Finn, R., Cochrane, G., Karsch-Mizrachi, I., Tyson, G.W., Rinke, C., The Genome Standards Consortium, Lapidus, A., Meyer, F., Yilmaz, P., Parks, D.H., Eren, A.M., Schriml, L., Banfield, J.F., Hugenholtz, P., Woyke, T. (2017). Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. Volume: 35. DOI: 10.1038/nbt.3893


Hernsdorf, A.W., Amano, Y., Miyakawa, K., Ise, K., Suzuki, Y., Anantharaman, K., Probst, A., Burstein, D., Thomas, B.C., Banfield, J.F. (2017). Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME. Volume: 11. DOI: 10.1038/ismej.2017.39


Finstad, K.M., Probst, A.J., Thomas, B.C., Andersen, G.L., Demergasso, C., Echeverria, A., Amundson, R.G., Banfield, J.F. (2017). Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics. Frontiers in Microbiology. DOI: 10.3389/fmicb.2017.01435


Hu, P., Dubinsky, E.A., Probst, A.J., Wang, J., Sieber, C.M.K., Tom, L.M., Gardinali, P.R., Banfield, J.F., Atlas, R.M., Andersen, G.L. (2017). Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. PNAS. DOI: 10.1073/pnas.1703424114


Mangiante, D.M., Schaller, R.D., Zarzycki, P., Banfield, J.F., Gilbert, B. (2017). Mechanism of Ferric Oxalate Photolysis. ACS Earth and Space Chemistry. Volume 1, Issue 5. DOI: 10.1021/acsearthspacechem.7b00026


Costello, E.K., Sun, C.L., Carlisle, E.M., Morowitz, M.J., Banfield, J.F., Relman, D.A. (2017). Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant. Scientific Reports. Article number: 3764. DOI: 10.1038/s41598-017-03821-7


Huddy, R.J., Kadzinga, F., Rahman, S.F., Kantor, R., Banfield, J.F., Harrison, S.T.L. (2017). Analysis of Microbial Communities Associated with Bioremediation Systems for Thiocyanate-Laden Mine Water Effluents. Solid State Phenomena. Volume 262. DOI: 10.4028/


Paul, B.G., Burstein, D., Castelle C.J., Handa, S., Arambula, D., Czornyj, E., Thomas, B.C., Ghosh, P., Miller, J.F., Banfield, J.F., Valentine, D.L. (2017). Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea. Nature Microbiology. 2, 17045. DOI: 10.1038/nmicrobiol.2017.45


Hernsdorf, A.W., Amano, Y., Miyakawa, K., Ise, K., Suzuki, Y., Anantharaman, K., Probst, A.J., Burstein, D., Thomas, B.C., Banfield, J.F. (2017). Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME. 28 March 2017. DOI: 10.1038/ismej.2017.39


Olm, M.R., Butterfield, C.N., Copeland, A., Boles, T.C., Thomas, B.C., Banfield, J.F. (2017). The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis. mBio. 8, e01969-16. DOI: 10.1128/mBio.01969-16


Kantor, R.S., Huddy, R.J., Iyer, R.M., Thomas, B.C., Brown, C.T., Anantharaman, K., Tringe, S.G., Hettich, R.L., Harrison, S.T.L., Banfield, J.F. (2017). Genome-resolved meta-omics ties microbial dynamics to process performance in biotechnology for thiocyanate degradation. Environmental Science & Technology. DOI: 10.1021/acs.est.6b04477


Rogers, M.B., Aveson, V., Firek, B., Yeh, A., Brooks, B., Brower-Sinning, R., Steve, J., Banfield, J.F., Zureikat, A., Hogg, M., Boone, B.A., Zeh, H.J., Morowitz, M.J. (2017). Disturbances of the Perioperative Microbiome Across Multiple Body Sites in Patients Undergoing Pancreaticoduodenectomy. Pancreas. 46, 260-267. DOI: 10.1097/MPA.0000000000000726


Zaremba-Niedzwiedzka, K., Caceres, E.F., Saw, J.H., Bäckström, D., Juzokaite, L., Vancaester, E., Seitz, K.W., Anantharaman, K., Starnawski, P., Kjeldsen, K.U., Stott, M.B., Nunoura, T., Banfield, J.F., Schramm, A., Baker, B.J., Spang, A., Ettema, T.J.G. (2017). Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature. 541, 353-358. DOI: 10.1038/nature21031


Olm, M.R., Brown, C.T., Brooks, B., Firek, B., Baker, R., Burstein, D., Soenjoyo, K., Thomas, B.C., Morowitz, M., Banfield, J.F. (2017). Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Research. DOI: 10.1101/gr.213256.116


Castelle, C.J., Brown, C.T., Thomas, B.C., Williams, K.H., Banfield, J.F. (2017). Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation. Scientific Reports. 7, Article number: 40101. DOI: 10.1038/srep40101


Rahman, S.F., Kantor, R.S., Huddy, R., Thomas, B.C., Zyl, A.W., Harrison, S.T.L., Banfield, J.F. (2017). Genome‐resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings. MicrobiologyOpen. DOI: 10.1002/mbo3.446


Olm, M.R., Brown, C.T., Brooks, B., Banfield, J.F. (2017). dRep: A tool for fast and accurate genome de-replication that enables tracking of microbial genotypes and improved genome recovery from metagenomes. bioRxiv (preprint). 108142. DOI: 10.1101/108142


Sieber, C.M.K., Probst, A.J., Sharrar, A., Thomas, B.C., Hess, M., Tringe, S.G., Banfield, J.F. (2017). Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy. bioRxiv (preprint). 107789. DOI: 10.1101/107789




Burstein, D., Harrington, L.B., Strutt, S.C., Probst, A.J., Anantharaman, K., Thomas, B.C., Doudna, J.A., Banfield, J.F. (2016). New CRISPR–Cas systems from uncultivated microbes. Nature. 542, 237–241. DOI: 10.1038/nature21059


Anantharaman, K., Brown, C.T., Hug, L.A., Sharon, I., Castelle, C.J., Probst, A.J., Thomas, B.C., Singh, A., Wilkins, M.J., Karaoz, U., Brodie, E.L., Williams, K.H., Hubbard, S.S., Banfield, J.F. (2016). Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nature Communications. Article number: 13219. DOI: 10.1038/ncomms13219


Tester, C.C., Aloni, S., Gilbert, B., Banfield J.F. (2016). Short-and Long-Range Attractive Forces That Influence the Structure of Montmorillonite Osmotic Hydrates. American Chemical Society. 32, 12039-12046. DOI: 10.1021/acs.langmuir.6b03265


Butterfield, C.N., Li, Z., Andeer, P.F., Spaulding, S., Thomas, B.C., Singh, A., Hettich, R.L., Suttle, K.B., Probst, A.J., Tringe, S.G., Northen, T., Pan, C., Banfield, J.F. (2016). Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ. 4, e2687. DOI: 10.7717/peerj.2687


Brown, C.T., Olm, M.R., Thomas, B.C., Banfield, J.F. (2016). Measurement of bacterial replication rates in microbial communities. Nature Biotechnology. 34, 1256–1263. DOI: 10.1038/nbt.3704


Legg, B.A., Zhu, M., Zhang, H., Waychunas, G., Gilbert, B., Banfield, J.F. (2016). A Model for Nucleation When Nuclei Are Nonstoichiometric: Understanding the Precipitation of Iron Oxyhydroxide Nanoparticles. Crystal Growth & Design. 16, 5726-5737. DOI: 10.1021/acs.cgd.6b00809


Raveh-Sadka, T., Firek, B., Sharon, I., Baker, R., Brown, C.T., Thomas, B.C., Morowitz, M.J., Banfield, J.F. (2016). Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants. ISME Journal. 10, 2817-2830. DOI: 10.1038/ismej.2016.83


Emerson, J.B., Thomas, B.C., Alvarez, W., Banfield, J.F. (2016). Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. Environmental Microbiology. 18, 1686-1703. DOI: 10.1111/1462-2920.12817


Varaljay, SV.A., Satagopan, S., North, J.A., Witte, B., Dourado, M.N., Anantharaman, K., Arbing, M.A., Hoeft McCann, S., Oremland, R.S., Banfield, J.F., Wrighton, K.C., Tabita, F.R. (2016) Functional metagenomic selection of RubisCO from uncultivated bacteria. Environmental Microbiology, DOI:10.1111/1462-2920.13138


Zhu, M., Frandsen, C., Wallace, A.W., Legg, B., Khalid, S., Zhang, H., Mørup, S., Banfield, J.F., and Waychunas, G.A. (2016) Precipitation pathways for ferrihydrite formation in acidic solutions. DOI: 10.1016/j.gca.2015.09.015 Geochimica et Cosmochimica Acta, 72, 247-264


Burstein, D., Sun, C.L., Brown, C.T., Sharon, I., Anantharaman, K., Probst, A.J, Thomas, B.C., and Banfield, J.F. (2016) Major bacterial lineages are essentially devoid of CRISPR-Cas viral defense systems. Nature Communications, 7:10613, DOI: 10.1038/ncomms10613


Hu, P., Tom, L., Singh, A., Thomas, B.C., Baker, B.J., Piceno, Y.M., Andersen, G.L. and Banfield, J.F. (2016) Genome-resolved metagenomic analysis reveals roles for candidate phyla and other microbial community members in biogeochemical transformations in oil reservoirs. mBio, 7, :e01669-15. DOI:10.1128/mBio.01669-15.


Hug, L.A., Thomas, B.C. Sharon, I., Brown, C.T., Sharma, R., Hettich, R.L., Wilkins, M.J., Williams, K.H., Singh, A. and Banfield, J.F. (2016) Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. Environmental Microbiology, 18, 159-173, DOI: 10.1111/1462-2920.12930.


Anantharaman, K., Brown, C.T., Burstein, D., Castelle, C.J., Probst, A.J., Thomas, B.C., Williams, K.H., and Banfield, J.F. (2016) Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. PeerJ, 4, e1607, PubMed 26844018, DOI: 10.7717/peerj.1607.


Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T.,  Probst, A.J.,  Castelle, C.J., Butterfield, C.N., Hernsdorf, A.W., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman, D.A., Finstad, K.M., Amundson, R., Thomas, B.C., and Banfield, J.F. (2016) A new view of The Tree and life’s diversity. Nature Microbiology, DOI:10.1038/nmicrobiol.2016.48.


Baker, B.J. and Banfield, J.F. (2016) Metagenomics of Acid Mine Drainage at Iron Mountain California, Expanding Our View from Individual Genes and Cultures to Entire Communities. Ch. 13. In: Acidophiles: Life in Extremely Acidic Environments, Quatrini and Johnson, Eds. Caister Academic Press, ISBN: 978-1-910190-34-0, DOI: 10.21775/9781910190333


Wrighton, K.C., Castelle, C.J., Varaljay, V.A., Satagopan, S., Brown, C.T., Wilkins, M.J., Thomas, B.C., Sharon, I., Williams, K.H., Tabita, F.R., and Banfield, J.F. (2016) RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria. ISME Journal, DOI: 10.1038/ismej.2016.53


Probst, A.J., Castelle, C.J., Singh, A., Brown, C.T., Anantharaman, K., Sharon, I., Hug, L.A., Burstein, D., Emerson, J.B., Thomas, B.C., Banfield, J.F. (2016) Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations. Environmental microbiology, DOI: 10.1111/1462-2920.13362


Bhangar, S. Brooks, B., Firek, B., Licina, D., Tang, X., Morowitz, M.J., Banfield, J.F. and Nazaroff, W.W. (2016) Pilot study of sources and concentrations of size-resolved airborne particles in a neonatal intensive care unit. Building and Environment, 106, 10-19, DOI: 10.1016/j.buildenv.2016.06.020


Raveh-Sadka, T., Firek, B., Sharon, I., Baker, R., Brown, C.T., Thomas, B.C, Morowitz, M.J., and Banfield, J.F. (2016) ISME Journal, DOI:10.1038/ismej.2016.83


Licina, D., Bhangar, S., Brooks, B., Baker, R., Firek, B., Tang, X., Morowitz, M.J., Banfield, J.F. and Nazaroff, W.W. (2016) Concentrations and Sources of Airborne Particles in a Neonatal Intensive Care Unit, PloS one 11 (5), e0154991, DOI: 10.1371/journal.pone.0154991


Long, P.E., Williams, K.H., Hubbard, S.S. and Banfield, J.F. (2016) Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes. Trends in microbiology, 10.1016/j.tim.2016.04.006


Mosier A.C., Miller C.S., Frischkorn, K.R., Ohm, R.A., Li Z., LaButti K., Lapidus A., Lipzen A., Chen C., Johnson J., Lindquist E.A., Pan C., Hettich R.L., Grigoriev I.V., Singer S.W., Banfield J.F. (2016) Fungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acid mine drainage. Frontiers in Microbiology. Mar 3;7:238. DOI: 10.3389/fmicb.2016.00238. eCollection 2016.





Hendricks, U., Rodriguez Pascual, M., Banfield, J.F., Lewis, A.E. (2015) Measuring precipitation kinetics of sparingly soluble salts using Shock-Freeze Cryo-TEM. Journal of Crystal Growth, 432, 108-15, DOI: 10.1016/j.jcrysgro.2015.09.017


Zhang, H.Z., Waychunas, G.A., Banfield, J.F. (2015) Molecular Dynamics Simulation Study of the Early Stages of Nucleation of Iron Oxyhydroxide Nanoparticles in Aqueous Solutions. Journal of Physical Chemistry B, 119, 10630-10642, DOI: 10.1021/acs.jpcb.5b03801


Young, J.C., Pan, C.L., Adams, R.M., Brooks, B., Banfield, J.F., Morowitz, M.J., Hettich, R.L. (2015) Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case. Proteomics, 15, 3463-3473, DOI: 10.1002/pmic.201400563


Brooks, B., Mueller, R.S., Young, J.C., Morowitz, M.J., Hettich, R.L, Banfield, J.F. (2015) Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Frontiers in Microbiology, 6, Article Number: 654, DOI: 10.3389/fmicb.2015.00654


Long, P.E., Williams, K.H., Davis, J.A., Fox, P.M., Wilkins, M.J., Yabusaki, S.B., Fang, Y.L., Waichler, S.R., Berman, E.S.F., Gupta, M., Chandler, D.P., Murray, C., Peacock, A.D., Giloteaux, L., Handley, K.M., Lovley, D.R., Banfield, J.F. (2015) Bicarbonate impact on U(VI) bioreduction in a shallow alluvial aquifer. Geochimica et Cosmochimica Acta, 150, 106-124, DOI: 10.1016/j.gca.2014.11.013


Dideriksen, K., Frandsen, C., Bovet, N., Wallace, A.F., Sel, O., Arbour, T., Navrotsky, A., De Yoreo, J.J., Banfield, J.F. (2015) Formation and transformation of a short range ordered iron carbonate precursor. Geochimica et Cosmochimica Acta, 164, 94-109, DOI: 10.1016/j.gca.2015.05.005


Sharon, I., Kertesz, M., Hug, L.A., Pushkarev, D., Blauwkamp, T.A., Castelle, C.J., Amirebrahimi, M., Thomas, B.C., Burstein, D., Tringe, S.G., Williams, K.H., Banfield, J.F. (2015) Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Research, 25, 534-543, DOI: 10.1101/gr.183012.114


Hug, L.A., Thomas, B.C., Brown, C.T., Frischkorn, K.R., Williams, K.H., Tringe, S.G., Banfield, J.F. (2015) Aquifer environment selects for microbial species cohorts in sediment and groundwater. ISME Journal, 9, 1846-1856, DOI: 10.1038/ismej.2015.2 De Yoreo, J.J., Gilbert, P.U.P.A., Sommerdijk, N.A.J.M., Penn, R.L., Whitelam, S., Joester, D., Zhang, H.Z., Rimer, J.D., Navrotsky, A., Banfield, J.F., Wallace, A.F., Michel, F.M., Meldrum, F.C., Colfen, H., Dove, P.M. (2015) Crystallization by particle attachment in synthetic, biogenic, and geologic environments. Science, 349, DOI: 10.1126/science.aaa6760


Brown, C.T., Hug, L.A., Thomas, B.C., Sharon, I., Castelle, C.J., Singh, A., Wilkins, M.J., Wrighton, K.C., Williams, K.H., Banfield, J.F. (2015) Unusual biology across a group comprising more than 15% of domain Bacteria. Nature, 523, 208-U173, DOI: 10.1038/nature14486


Castelle, C.J., Wrighton, K.C., Thomas, B.C., Hug, L.A., Brown, C.T., Wilkins, M.J., Frischkorn, K.R., Tringe, S.G., Singh, A., Markillie, L.M., Taylor, R.C., Williams, K.H., Banfield, J.F. (2015) Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling. Current Biology, 690-701, DOI: 10.1016/j.cub.2015.01.014


Handley, K.M., Wrighton, K.C., Miller, C.S., Wilkins, M.J., Kantor, R.S., Thomas, B.C., Williams, K.H., Gilbert, J.A., Long, P.E., Banfield, J.F. (2015) Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points. Environmental Microbiology, 17, 622-636, DOI: 10.1111/1462-2920.12467


Raveh-Sadka, T., Thomas, B.C., Singh, A., Firek, B., Brooks, B., Castelle, C.J., Sharon, I., Baker, R., Good, M., Morowitz, M.J., Banfield, J.F. (2015) Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. eLife, 4, Article Number: UNSP e05477, DOI: 10.7554/eLife.05477


Paez-Espino, D., Sharon, I., Morovic, W., Stahl, B., Thomas, B.C., Barrangou, R., Banfield, J.F. (2015) CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus. mBio, 6, Article Number: e00262-15, DOI: 10.1128/mBio.00262-15


Raveh-Sadka, T., Thomas, B.C., Singh, A., Firek, B., Brooks, B., Castelle, C.J., Sharon, I., Baker, R., Good, M., Morowitz, M.J., Banfield, J.F. (2014) Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. eLife, e05477, DOI: 10.7554/eLife.05477


Tully, B.J., Emerson, J.B., Andrade, K., Brocks, J.J., Allen, E.E., Banfield, J.F., Heidelberg, K.B. (2014) De Novo Sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, Reveal a Variable Genomic Landscape. Archaea-An International Microbiological Journal, Article Number: 875784, DOI: 10.1155/2015/875784


Justice, N.B., Norman, A., Brown, C.T., Singh, A., Thomas, B.C., Banfield, J.F. (2014) Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics, 15, Article Number: 1107, DOI: 10.1186/1471-2164-15-1107


Legg, B.A., Zhu, M.Q., Comolli, L.R., Gilbert, B., Banfield, J.F. (2014) Impacts of Ionic Strength on Three-Dimensional Nanoparticle Aggregate Structure and Consequences for Environmental Transport and Deposition. Environmental Science & Technology, 48, 13703-13710, DOI: 10.1021/es502654q


Zhang, H.Z., Banfield, J.F. (2014) Structural Characteristics and Mechanical and Thermodynamic Properties of Nanocrystalline TiO2. Chemical Reviews, 114, 9613-9644, DOI: 10.1021/cr500072j


Luef, B., Frischkorn, K.R., Wrighton, K.C., Holman, H.Y.N., Birarda, G., Thomas, B.C., Singh, A., Williams, K.H., Siegerist, C.E., Tringe, S.G., Downing, K.H., Comolli, L.R., Banfield, J.F. (2014) Diverse uncultivated ultra-small bacterial cells in groundwater. Nature Communications, 6, Article Number: 6372, DOI: 10.1038/ncomms7372


Mosier, A.C., Li, Z., Thomas, B.C., Hettich, R.L., Pan, C.L., Banfield, J.F. (2014) Elevated temperature alters proteomic responses of individual organisms within a biofilm community. ISME Journal, 9, 180-194, DOI: 10.1038/ismej.2014.113


Xiong, W.L., Giannone, R.J., Morowitz, M.J., Banfield, J.F., Hettich, R.L. (2014) Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut. Journal of Proteome Research, 14, 133-141, DOI: 10.1021/pr500936p





Legg, B.A., Zhu, M.Q., Comolli, L.R., Gilbert, B., Banfield, J.F. (2014) Determination of the Three-Dimensional Structure of Ferrihydrite Nanoparticle Aggregates. LangMuir, 30, 9931-9940, DOI: 10.1021/la502128d


Zhang, H.Z., De Yoreo, J.J., Banfield, J.F. (2014) A Unified Description of Attachment-Based Crystal Growth. ACS Nano, 8, 6526-6530, DOI: 10.1021/nn503145w


Nielsen, M.H., Li, D.S., Zhang, H.Z., Aloni, S., Han, T.Y.J., Frandsen, C., Seto, J., Banfield, J.F., Colfen, H., De Yoreo, J.J. (2014) Investigating Processes of Nanocrystal Formation and Transformation via Liquid Cell TEM. Microscopy and Microanalysis, 20, 425-436, DOI: 10.1017/S1431927614000294


Frandsen, C., Legg, B.A., Comolli, L.R., Zhang, H.Z., Gilbert, B., Johnson, E., Banfield, J.F. (2014) Aggregation-induced growth and transformation of beta-FeOOH nanorods to micron-sized alpha-Fe2O3 spindles. CrystEngComm, 16, 1451-1458, DOI: 10.1039/c3ce40983j


Vu, T.A., Reagan, M.M., Li, D.S., Legg, B., De Yorea, J.J., Banfield, J.F., Zhang, H.Z. (2014) Kinetics of crystal growth of nanogoethite in aqueous solutions containing nitrate and sulfate anions. CrystEngComm, 16, 1466-1471, DOI: 10.1039/c3ce41685b


Zhang, H.Z., Banfield, J.F. (2014) Interatomic Coulombic interactions as the driving force for oriented attachment. CrystEngComm, 16, 1568-1578, DOI: 10.1039/c3ce41929k


Wallace, A.F., Hedges, L.O., Fernandez-Martinez, A., Raiteri, P., Gale, J.D., Waychunas, G.A., Whitelam, S., Banfield, J.F., De Yoreo, J.J. (2013) Microscopic Evidence for Liquid-Liquid Separation in Supersaturated CaCO3 Solutions. Science, 341, 885-889, DOI: 10.1126/science.1230915


Singer, D. M.; Chatman, S. M.; Ilton, E. S.; Rosso, K. M.; Banfield, J. F.; Waychunas, G. A. (2012) Identification of Simultaneous U(VI) Sorption Complexes and U(IV) Nanoprecipitates on the Magnetite (111) Surface. Environmental Science & Technology, 46, (7), 3811-3820, DOI: 10.1021/es203877x


Li, D., Nielsen, M.H., Lee, J.R., Frandsen, C., Banfield, J.F., and De Yoreo, J.J. (2012) Direction-specific interactions control crystal growth by oriented attachment. Science, 336, 1014-1018, DOI: 10.1126/science.1219643


Zhang, H., and Banfield, J.F. (2012) Energy Calculations Predict Nanoparticle Attachment Orientations and Asymmetric Crystal Formation. Journal of Physical Chemistry Letters, 3, 2882-2886 DOI: 10.1021/jz301161j


Zhu, M.Q., Legg, B., Zhang, H.Z., Gilbert, B., Ren, Y., Banfield, J.F., and Waychunas, G.A. (2012) Early stage formation of iron oxyhydroxides during neutralization of simulated acid mine drainage solutions. Environmental Science and Technology, 46, 8140-8147, DOI: 10.1021/es301268g


Zhang, H., Bayne, M., Fernando, S., Legg, B., Zhu, M., Penn, R.L., and Banfield, J.F. (2011) Size-dependent bandgap of nanogoethite. The Journal of Physical Chemistry C, 115, 17704-17710, DOI: 10.1021/jp205192a


Zhang, H., Chen, B., Banfield, J.F., and Waychunas, G.A. (2008) Atomic structure of nanometer-sized amorphous TiO2. Physical Review B, 78,(21) article number:214106, DOI: 10.1103/PhysRevB.78.214106.


Parker, S., Spagnoli, D. Banfield, J.F. (2008) Free energy change of aggregation of nanoparticles. Journal of Physical Chemistry B, 112, 14731-14736, DOI: 10.1021/jp804966c


Goodell, C., Gilbert, B., Weigand, S., Banfield, J.F.(2008) Kinetics of water adsorption driven structural transformation of ZnS nanoparticles. The Journal of Physical Chemistry C, 112, 4791-4796, DOI: 10.1021/jp077189m


Finnegan, M.P., Zhang, H., and Banfield, J.F. (2008) Anatase coarsening kinetics under hydrothermal conditions as a function of pH and temperature. Chemistry of Materials 20, 3443-3449, DOI: 10.1021/cm071057o.


Zhang, H., Rustad, J.R., and Banfield, J.F. (2007) Interaction between water and ZnS nanoparticles studied by temperature-programmed desorption (TPD) and molecular dynamics simulations. Journal of Physical Chemistry A3, 111, 5008-5014, DOI: 10.1021/jp0688916.


Zhang, H. and Banfield, J.F. (2007) Polymorphic transformations and particle coarsening in nanocrystalline titania ceramic powders and membranes. The Journal of Physical Chemistry C, 111, 6621-6629, DOI: 10.1021/jp067665t.


Chen, B., Zhang, H., Gilbert, B., and Banfield, J.F. (2007) Mechanism of inhibition of nanoparticle growth and phase transformation by surface impurities. Physical Review Letters, 98, 106103-1-4, DOI: 10.1103/PhysRevLett.98.106103.


Finnegan, M.P., Zhang, H., and Banfield J.F. (2007) Phase stability and transformation in titania nanoparticles in aqueous solutions dominated by surface energy. Journal of Physical Chemistry C, 111, 1962-1968, DOI: 10.1021/jp063822c.


Guzman, K.A.D., Finnegan, M.P., and Banfield, J.F. (2006) Influence of surface potential on aggregation and transport of titania nanoparticles. Environmental Science and Technology, 40, 7688-7693, DOI: 10.1021/es060847g.


Zhang, H., Chen, B., Gilbert, B., and Banfield, J.F. (2006) Kinetically controlled formation of a novel nanoparticulate ZnS with mixed cubic and hexagonal stacking. Journal of Materials Chemistry, 16, 249-254, DOI: 10.1039/B512580D.


Gilbert, B., Huang , F., Lin Z., Goodell , C., Zhang, H., Banfield J.F. (2006) Surface chemistry controls crystallinity of ZnS nanoparticles. Nano Letters, 6, 605-610, DOI: 10.1021/nl052201c


Gilbert, B. Zhang, H. Chen, B., Kunz, M, Huang F., and Banfield J.F. (2006) Compressibility of zinc sulfide nanoparticles. Physical Review B, 74, 115405, DOI: 10.1103/PhysRevB.74.115405


Zhang, H., Gilbert, B., Chen, B., Banfield J.F. (2006) WAXS and PDF-based analyses of chromium doping in titania (anatase and brookite). Mat. Res. Soc. Symp. Proc. 915, 0915-R07-02, DOI:10.1557/PROC-0915-R07-02



Geomicrobiology, nanoparticles, microorganisms, geophysics


Probst, A.J., Weinmaier, T., Raymann, K., Perras, A., Emerson, J.B., Rattei, T., Wanner, G., Klingl, A., Berg, I.A., Yoshinaga, M., Viehweger, B., Hinrichs, K.U., Thomas, B.C., Meck, S., Auerbach, A.K., Heise, M., Schintlmeiser, A., Schmid, M., Wagner, M., Gribaldo, S., Banfield, J.F., Moissl-Eichinger, C. (2014) Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nature Communications, 5, Article Number: 5497, DOI: 10.1038/ncomms6497


Justice, N.B., Li, Z., Wang, Y.F., Spaulding, S.E., Mosier, A.C., Hettich, R.L., Pan, C.L., Banfield, J.F. (2014) N-15- and H-2 proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity. Environmental Microbiology, 16, 3224-3237, DOI: DOI: 10.1111/1462-2920.12488


Wrighton, K.C., Castelle, C.J., Wilkins, M.J., Hug, L.A., Sharon, I., Thomas, B.C., Handley, K.M., Mullin, S.W., Nicora, C.D., Singh, A., Lipton, M.S., Long, P.E., Williams, K.H., Banfield, J.F. (2014) Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME Journal, 8, 1452-1463, DOI: 10.1038/ismej.2013.249


Castelle, C.J., Wrighton, K.C., Thomas, B.C., Hug, L.A., Wilkins, M.J., Frischkorn, K., Tringe, S.G., Singh, A., Williams, K.H., Banfield, J.F. (2014) Genomic Expansion Of The Domain Archaea Highlights Roles For Organisms From New Phyla In Subsurface Anaerobic Carbon Cycling. Abstracts of the General Meeting of the American Society for Microbiology, 114, 1319, DOI: 10.1016/j.cub.2015.01.014


Kantor, R.S., Wrighton, K.C., Handley, K.M., Sharon, I., Hug, L.A., Castelle, C.J., Thomas, B.C., Banfield, J.F. (2013) Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla. mBio, 5, e00708-13, DOI: 10.1128/mBio.00708-13


Yelton, A.P., Williams, K.H., Fournelle, J., Wrighton, K.C., Handley, K.M., Banfield, J.F. (2013) Vanadate and Acetate Biostimulation of Contaminated Sediments Decreases Diversity, Selects for Specific Taxa, and Decreases Aqueous V5+ Concentration. Environmental Science & Technology, 47, 6500-6509, DOI: 10.1021/es4006674


Moreau, J.W., Fournelle, J.H., and Banfield, J.F. (2013) Quantifying heavy metals sequestration by sulfate-reducing bacteria in an acid mine drainage-contaminated natural wetland. Frontiers in Microbiology, 4, p. 43, DOI: 10.3389/fmicb.2013.00043


Luef B., Fakra S.C., Csencsits R., Wrighton K.C., Williams K.H., Wilkins M.J., Downing K.H., Long P.E., Comolli L.R., Banfield J.F. (2013) Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth. ISME Journal. 7(2), 338-50. DOI: 10.1038/ismej.2012.103.


Singer, D. M., Chatman, S.M., Ilton, E.S., Rosso, K.M., Banfield, J.F., Waychunas, G.A. (2012) U(VI) Sorption and Reduction Kinetics on the Magnetite (111) Surface. Environmental Science & Technology, 46, (7), 3821-3830, DOI: 10.1021/es203878c.


Ma, S. and Banfield, J.F. (2011) Micron-scale Fe2+/Fe3+, intermediate sulfur species and O2 gradients across the biofilm-solution-sediment interface control biofilm organization. Geochemical et Cosmochimica Acta, 75, 3568-3580


Moreau, J.W., Zierenberg, R.A., and Banfield J.F. (2010) Diversity of dissimilatory sulfite reductase genes (dsrAB) in a salt marsh impacted by long-term acid mine drainage. Applied and Environmental Microbiology, 76, 4819-4828, DOI: 10.1128/AEM.03006-09


Williams, K. H., N'Guessan, A.L., Druhan, J., Long, P.E., Hubbard, S.S., Lovley, D.R., and Banfield, J.F. (2010) Electrodic voltages accompanying stimulated bioremediation of a uranium-contaminated aquifer. JGR-Biosciences, 115, article G00G05, DOI: 10.1029/2009JG001142.


Williams, KH; Kemna, A; Wilkins, MJ, et al. (2009) Geophysical Monitoring of Coupled Microbial and Geochemical Processes During Stimulated Subsurface Bioremediation. Environmental Science and Technology, 43 6717-6723, DOI: 10.1021/es900855j


Chan, C.S., Fakra, S., Emerson, D., Edwards, D., and Banfield, J.F. (2009) Iron oxyhydroxide mineralization on microbial extracellular polysaccharides. Geochimica et Cosmochimica Acta, Volume: 73: 3807-3818, DOI: 10.1016/j.gca.2009.02.036


Cervini-Silva, J., Gilbert, B., Falka, S., Friedlich, S., and Banfield, J.F. (2008) Coupled redox transformations of catechol and cerium at the surface of a cerium (III) phosphate mineral. Geochimica et Cosmochimica Acta, 72, 2454-2464, DOI: 10.1016/j.gca.2008.02.017


Moreau J.W., Weber, P.K., Martin, M.C., Gilbert, B., Hutcheon, I.D., and Banfield, J.F. (2007) Extracellular proteins limit the dispersal of biogenic nanoparticles. Science, 316, 1600-1603, DOI: 10.1126/science.1141064.


Williams K.H., Hubbard, S.S., and Banfield, J.F. (2007) Galvanic interpretation of self-potential signals associated with microbial sulfate reduction. Journal of Geophysical Research, 112, G03019, DOI:10.1029/2007JG000440


Rosling, A., Johansson, E., Suttle, K.B., van Hees, P.A.W., and Banfield J.F. (2007) Phosphorous availability influences the dissolution of apatite by soil fungi. Geobiology, 5, pp. 265-280, DOI: 10.1111/j.1472-4669.2007.00107.x


Green, E.G., Dietrich, W.E., and Banfield, J.F. (2006) Quantification of chemical weathering rates across an actively eroding hillslope. Earth and Planetary Science Letters, 242, 155-169, DOI: 10.1016/j.epsl.2005.11.039.



Ultrastructure and community organization


Goltsman, D.S.A., Comolli, L.R., Thomas, B.C., Banfield, J.F. (2015) Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities. ISME Journal. 1014-1023, DOI: 10.1038/ismej.2014.200


Wilmes, P., Remis, J.P., Hwang, M. Auer, M., Thelen, M.P., and Banfield, J.F. (2009) Natural acidophilic biofilm communities reflect distinct organismal and functional organization. ISME Journal, 3, 266-270, DOI: 10.1038/ismej.2008.90.


Comolli, L., Baker, B.J., Downing, K.H., Siergerist, C.E., and Banfield J.F. (2009) Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME Journal, 3, 159-167, DOI: 10.1038/ismej.2008.99.



Molecular microbial ecology: community proteogenomics


Comilli, L.R., Banfield, J.F. (2014) Inter-species interconnections in acid mine drainage microbial communities. Frontiers in Microbiology, 5, Article Number: 367, DOI: 10.3389/fmicb.2014.00367


Li, Z. Wang, Y.F., Yao, Q.M., Justice, N.B., Ahn, T.H., Xu, D., Hettich, R.L., Banfield, J.F., Pan, C.L. (2014) Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. Nature Communications, 5, Article Number: 4405, DOI: 10.1038/ncomms5405


Podell, S., Emerson, J.B., Jones, C.M., Ugalde, J.A., Welch, S. Heidelberg, K.B., Banfield, J.F., Allen, E.E. (2014) Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME Journal, 8, 979-990, DOI: 10.1038/ismej.2013.221


Brooks, B., Firek, B.A., Miller, C.S., Sharon, I., Thomas, B.C., Baker, R., Morowitz, M.J., Banfield, J.F. (2014) Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. Microbiome, 2, Article Number: UNSP 1, DOI: 10.1186/2049-2618-2-1


Sharon, I., Hug, L.A., Kantor, R.S., Thomas, B.C., Wrighton, K.C., Handley, K.M., Banfield, J.F. (2014) Time-Series Metagenomics Reveal Complex Dynamics of Groundwater Sediment Microbial Communities in Response to Geochemical Transitions. Abstracts of the General Meeting of the American Society for Microbiology, 114, 1317


Kantor, R.S., van Wyk, N., van Zyl, A., Thomas, B.C., Singh, A., van Hille, R., Harrison, S.T.L., Banfield, J.F. (2014) Metagenomic Analysis of Bioreactor-based Thiocyanate and Cyanide Degradation. Abstracts of the General Meeting of the American Society for Microbiology, 114, 1385


Raveh, T., Firek, B., Sharon, I., Baker, R., Costello, E.K., Brown, C.T., Thomas, B.C., Relman, D.A., Morowitz, M.J., Banfield, J.F. (2014) Genotype-Resolved Metagenomic Analysis of the Colonization of the GI Tract in Premature Infants Reveals Widespread Differences in Genomes Recovered from Co-Hospitalized Babies. Abstracts of the General Meeting of the American Society for Microbiology, 114, 2743


Di Rienzi, S.C., Sharon, I., Wrighton, K.C., Koren, O., Hug, L.A., Thomas, B.C., Goodrich, J.K., Bell, J.T., Spector, T.D., Banfield, J.F. (2013) The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife, 2, Article Number: e01102, DOI: 10.7554/eLife.01102


Goltsman, D.S.A., Dasari, M., Thomas, B.C., Shah, M.B., VerBerkmoes, N.C., Hettich, R.L., Banfield, J.F. (2013) New Group in the Leptospirillum Clade: Cultivation-Independent Community Genomics, Proteomics, and Transcriptomics of the New Species "Leptospirillum Group IV UBA BS". Applied and Environmental Biology, 17, 5384-5393, DOI: 10.1128/AEM.00202-13


Castelle, C.J., Hug, L.A., Wrighton, K.C., Thomas, B.C., Williams, K.H., Wu, D.Y., Tringe, S.G., Singer, S.W., Eisen, J.A., Banfield, J.F. (2013) Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications, 4, Article Number: 2120, DOI: 10.1038/ncomms3120


Fischer, C.R., Bowen, B.P., Pan, C.L., Northen, T.R., Banfield, J.F. (2013) Stable-Isotope Probing Reveals That Hydrogen Isotope Fractionation in Proteins and Lipids in a Microbial Community Are Different and Species-Specific. ACS Chemical Biology, 8, 1755-1763, DOI: 10.1021/cb400210q


Podell, S., Ugalde, J.A., Narasingarao, P., Banfield, J.F., Heidelberg, K.B., Allen, E.E. (2013)Assembly- Driven Community Genomics of a Hypersaline Microbial Ecosystem. PLoS One 8(4)e61692, DOI: 10.1371/journal.pone.0061692.


Yelton, A.P., Williams, K.H., Fournelle, J. Wrighton, K.C., Handley, K.M., Banfield, J.F. (2013) Vanadate and Acetate Biostimulation of Contaminated Sediments Decreases Diversity, Selects for Specific Taxa, and Decreases Aqueous V5+ Concentration. Environmental Science & Technology, 47(12), 6500-6509, DOI: 10.1021/es4006674.


Castelle, C.J., Hug, L.A., Wrighton, K.C., Thomas, B.C., Williams, K.H., Wu, D., Tringe, S.G., Singer, S.W., Eisen, J.A., and Banfield, J.F., (2013). Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications, 4:2120 DOI:10.1038/ncomm3120.


Yelton, A.P., Comolli, L.R., Justice, N., Castelle, C., Denef, V.J., Thomas, B.C., and Banfield, J.F. (2013) Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. BMC Genomics, 14, 485 (15p), DOI: 10.1186/1471-2164-14-485


Hug, L.A., Castelle, C.J., Wrighton, K.C., Thomas, B.C., Sharon, I., Frischkorn, K.R., Williams, K.H., Tringe, S.G., and Banfield, J.F. (2013) Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome, 1:22 DOI:10.1186/2049-2618-1-22


Emerson, J., Thomas, B.C., Andrade, K., Heidelberg, K., and Banfield, J.F. (2013) Characterizing the diversity and dynamics of natural viral assemblages, as demonstrated in a hypersaline lake system. Applied and Environmental Microbiology, in press.


Wilkins, M.J., Wrighton, K.C., Nicora, C.D., Williams, K.H., McCue, L.A., Handley, K.M., Miller, C.S., Gilotaux, L., Montgomery, A.P., Lovley, D.R., Banfield, J.F., Long, P.E., Lipton, M.S. (2103) Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface. PLoS One, 8, DOI: 10.1371/journal.pone.0057819


Schoenknecht, G., Chen W-H., Ternes, C.M., Barbier, G.C., Guillaume, G., Shrestha, R.P., Stanke, M., Brautigam, A., Baker, B.J., Banfield, J.F., Garavito, R., Carr, K., Wilkerson, C. Rensing, S.A., Gagneul, D., Dickenson, N.E., Oesterhelt, C., Lercher, M.J., Weber, A.P.M. (2013) Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote. Science, 339, 1207-1210, DOI: 10.1126/science.1231707.


Fischer C., Bowen, B., Pan, C., Northen, T., Banfield, J.F. (2013) Stable-isotope probing reveals hydrogen isotope fractionation in proteins and lipids in a microbial community are different and species-specific. ACS Chemical Biology, in press. DOI: 10.1021/cb400210q


Goltsman-Aliaga et al. (2013) A new group in the Leptospirillum clade: cultivation-independent community genomics, proteomics and transcriptomics of the new species Leptospirillum group IV UBA BS, Applied and Environmental Microbiology, in press. DOI: 10.1128/AEM.00202-13


Paez-Espino, D., Morovic, W., Sun, C.L., Thomas, B.C., Ueda, K., Stahl, B., Barrangou, R., and Banfield, J.F. (2013). Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nature Communications, 4, Article Number: 1430 DOI: 10.1038/ncomms2440


Mosier, A.C., Justice, N.B., Bowen, B.P., Baran, R., Thomas, B.C., Northen, T.R., Banfield, J.F. (2013) Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable isotope enabled metabolomics. mBio, in press. DOI: 10.1128/mBio.00484-12


Miller, C.S., Handley, K.M., Wrighton, K.C., Firschkorn, K., Thomas, B.C., and Banfield, J.F. (2013) Short-read assembly of full-length 16S amplicons to uncover bacterial diversity in subsurface sediments. PLoS One, e56018 DOI: 10.1371/journal.pone.0056018


Sharon, I. Morowitz, M.J., Thomas, B.C., Costello, E.K., Relman, D.A., and Banfield J.F. (2012) Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Research, DOI: 10.1101/gr.142315.112


Justice, N.B., Pan, C., Mueller, R., Spaulding, S.E., Shah, V., Sun, C.L., Yelton, A.P., Miller, C.S., Thomas, B.C., Shah, M., VerBerkmoes, N., Hettich, R., and Banfield, J.F. (2012) Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities. Applied and Environmental Microbiology, DOI: 10.1128/AEM.01938-12


Handley, K.M., VerBerkmoes, N.C., Steefel, C.I., Williams, K.H., Sharon, I., Miller, C.S., Frischkorn, K.R., Chourey, K., Thomas, B.C., Shah, M.B., Long, P.E., Hettich, R.L., and Banfield, J.F. (2012) Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. ISME Journal, Hardcopy (2013) 7, 800-816, DOI: 10.1038/ismej.2012.148


Cruz-MartÃnez, K., Rosling, A., Zhang, Y., Song, M., Andersen, G.L., Banfield, J.F. (2012) Effect of rainfall-induced soil geochemistry dynamics on grassland soil microbial communities. Applied Environmental Microbiology. 78(21):7587. DOI: 10.1128/AEwiM.00203-12


Young, J., Dill, B.D., Pan, C., Hettich, R.L., Banfield, J.F., Shah, M., Fremaux, C., Horvath, P., Barrangou, R., Verberkmoes, N.C. (2012) Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophiles. PLoS One, 7, DOI: 10.1371/journal.pone.0038077


Wrighton, K.C., Thomas, B.C., Sharon, I., Miller, C.S., Castelle, C.J., VerBerkmoes, N.C., Wilkins, M.J., Hettich, R.L., Lipton, M.S., Williams, K.H. Long, P.E., Banfield, J.F. (2012) Fermentation, hydrogen and sulfur metabolism in multiple uncultivated bacterial phyla. Science. 337:1661-1665, DOI: 10.1126/science.1224041


Emerson, J.B., Thomas, B.C., Andrade, K., Allen, E.E., Heidelberg, K.B., and Banfield, J.F. (2012) Dynamic Viral populations in hypersaline systems as revealed by metagenomic assembly. Applied and Environmental Microbiology, 78, 6309-6320, DOI: 10.1128/AEM.01212-12.


Berhe, A.A., Suttle, K.B., Burton, S.D., and Banfield, J.F. (2012) Contingency in the direction and mechanics of soil organic matter responses to increased rainfall. Plant and Soil 358 (1-2): 371-3383. DOI:10.1007/s11104-012-1156-0.


Weinberger, A.D., Sun, C.L., Pluciński, M.M., Denef, V.J., Thomas, B.C., Horvath, P., Barrangou, R., Gilmore, M.S., Getz, W.M., and Banfield, J.F. (2012) Persisting Low-Abundance Viral Sequences Shape Microbial CRISPR-based Immunity. PLoS Computational Biology, DOI: 10.1371/journal.pcbi.1002475


Handley, K., Wrighton, K., Piceno, Y., Andersen, G. DeSantis, T., Williams, KH, Wilkins, M., N'Guessan, L., Peacock, A., Bargar, J., Long, P. Banfield, J.F. (2012) High-Density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment. FEMS Microbiology Ecology, 81, 188-204. DOI: 10.1111/j.1574-6941.2012.01363.x


Narasingarao, P., Podell, S., Ugalde, J.A., Brochier-Armanet, C., Emerson, J.B., Brocks, J.J., Heidelberg, K.B., Banfield, J.F., and Allen, E.E. (2012) De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME Journal, 6, 81-93. DOI: 10.1038/ismej.2011.78


Fujishima, K., Sugahara. J., Miller, C.S., Baker, B.J., Di Giulio, M., Takesue, K., Sato, A., Tomita, M., Banfield, J.F., and Kanai, A. (2012) A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Research, 39, 9695-9704. DOI: 10.1093/nar/gkr692


Comolli, L.R., Duarte, R., Baum, D., Luef, B., Downing, K.H., Larsen, D.M., Csencsits, R., Banfield, J.F. (2012) A portable cryo-plunger for on-site intact cryogenic microscopy sample preparation in natural environments. Microscopy Research and Technique,75, 829-836. DOI:10.1002/jemt.22001


Fischer, C.R., Wilmes, P., Bowen, B.P., Northen T.R., and Banfield J.F. (2011) Deuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities. Metabolomics. 8, 566-578. DOI:10.1007/s11306-011-0344-x


Mueller, R.S., Dill, B.D., Pan, C., Belnap, C.P., Thomas, B.C., VerBerkmoes, N.C., Hettich, R.L., and Banfield, J.F. (2011) Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community. Environmental Microbiology, 13, 2279-2292. DOI:10.1111/j.1462-2920.2011.02486.x


Pride, D.T., Sun, C.L., Salzman, J., Rao, N., Loomer, P., Armitage, G.C., Banfield, J.F., and Relman, D.A. (2011) Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Research, 21, 126-136. DOI: 10.1101/gr.111732.110


Belnap, C.P., Pan, C. Denef, V.J., Samatova, N.F., Hettich, R.L., and Banfield, J.F. (2011) Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions. ISME Journal, 1-10. DOI: 10.1038/ismej.2010.200


Pan, C., Fischer, C.R., Hyatt, D. Bowen, B.P., Hettich, R.L., and Banfield, J.F. (2011) Quantitative tracking of isotope flows in proteomes of microbial communities. Molecular and Cellular Proteomics, 10, 006049. DOI: 10.1074/mcp.M110.006049


Morowitz, M.J., Denef, V.J., Costello, E.K., Thomas, B.C., Poroyko, V., Relman, D.A. and Banfield, J.F. (2010) Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proceedings of the National Academy of Science, DOI: 10.1073/pnas.1010992108


Callister, S.J., Wilkins, M.J., Nicora, C.D., Williams, K.H., Banfield, J.F., VerBerkmoes, N.C., Hettich, R.L., NaCuessan, L., Mouser, P.J., Elifantz, H., Smith, R.D., Lovley, D.R., Lipton, M.S., Long, P.E. (2010) Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles. Environmental Science and Technology, 44, 9907-8903. DOI: 10.1021/es101029f


Denef, V.J., and Banfield, J.F. (2012) In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science, 336, 462-466. DOI: 10.1126/science.1218389


Wilmes, P., Benjamin P. Bowen, B.P. Brian C. Thomas, B.C., Mueller, R.S., Denef, V.J., VerBerkmoes, N.C., Hettich, R.L., Northen, T.R., and Banfield, J.F. (2010)Metabolome-Proteome Differentiation Coupled to Microbial Divergence. MBIO, 1(5), e00246. DOI: 10.1128/mBio.00246-10


Mueller, R., Denef, V.J., Kalnejais, L., Suttle, B., Thomas, B.C., Wilmes, P., Smith, R., Nordstrom, D.K., McCleskey, B., Shah, M., VerBerkmoes, N., Banfield, J.F. (2010) Ecological distribution and population physiology defined by proteomics in a natural microbial community. Molecular Systems Biology, 6, 4819-4828. DOI: 10.1038/msb.2010.30


Baker, B.J., Comolli, L., Dick, G., Hauser, L., Hyatt, D., Dill, B.D., Land, M., VerBerkmoes, N.C., Hettich, R.L., Banfield, J.F. (2010) Enigmatic, ultra-small uncultivated Archaea. Proc. Nat. Acad. Sci., 107, 8806 - 8811. DOI: 10.1073/pnas.0914470107


Denef V.J., Kalnejais, L.H., Mueller, R.S., Wilmes, P., Baker, B.J., Thomas, B.C., VerBerkmoes, N.C., Hettich, R.L., Banfield, J.F. (2009) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Nat. Acad. Sci., 107, 2383-2390. DOI: 10.1073/pnas.0907041107


Belnap, C.P., Pan, C., VerBerkmoes, N.C., Power, M.E., Samatova, N.F., Carver, R.L., Hettich, R.L., Banfield J.F. Cultivation and quantitative proteomic analyses of acidophilic microbial communities. ISME Journal, 4, 520-530. DOI: 10.1038/ismej.2009.139


Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10: R85. DOI: 10.1186/gb-2009-10-8-r85


Wilkins, M.J., N.C. Verberkmoes, K.H. Williams, S.J. Callister, P.J. Mouser, H. Elifantz, A.L. N'Guessan, B.C. Thomas, C.D. Nicora, M.B. Shah, P. Abraham, M.S. Lipton, D.R. Lovley, R.L. Hettich, P.E. Long, and J.F. Banfield. (2009) Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Applied Environmental Microbioliology 75:6591-6599. DOI: 10.1128/AEM.01064-09


Goltsman, D.S.A, Denef, V.J., Singer, S.W., VerBerkmoes, N.C., Lefsrud, M., Mueller, R.S., Dick, G.J., Sun, C.L., Wheeler, K.E., Zemla, A., Baker, B.J., Hauser, L., Land, M., Shah, M.B., Thelen, M.P., Hettich, R.L., Banfield, J.F. (2009) Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms. Applied and Environmental Microbiology, 75, 4599-4615. DOI: 10.1128/AEM.02943-08


Cruz-Martinez, K., Suttle, K.B., Brodie, E.L., Power, M.E., Andersen, G.L., and Banfield, J.F. (2009) Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME Journal, 1-7. DOI: 10.1038/ismej.2009.16


Baker, B., Tyson, G., and Banfield, J.F. (2009) Insights into the diversity eukaryotes in acid mine drainage biofilm communities. Applied and Enviornmental Microbiology, 75, 2192-2199. DOI: 10.1128/AEM.02500-08


Denef, V., VerBerkmoes, N.C., Shah, M.B., Abraham, P., Lefsud, M., Hettich, R.L., and Banfield, J.F. (2009) Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environmental Microbiology, 11, 313-325. DOI: 10.1111/j.1462-2920.2008.01769.x


Wilmes, P., Andersson, A.F., Lefsrud, M.G., Wexler, M., Shah, M., Zhang, B., Hettich, R.L., VerBerkmoes, N.C. and Banfield, J.F. (2008) Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME Journal, DOI: 10.1038/ismej.2008.38


Andersson, A. and Banfield J.F. (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science, 230, 1047-1050. DOI: 10.1126/science.1157358


Simmons S.L., DiBartolo, G., Denef, V.J., Aliaga Goltsman, D., Thelen, M.P., and Banfield J.F. (2008) Population genomic analysis of strain variation in Leptospirillum Group II bacteria involved in acid mine drainage formation. PLoS Biology, 6, e177, 1427- 1442. DOI: 10.1371/journal.pbio.0060177


Eppley, J. M., Tyson, G.W., Getz, W.M. and Banfield J.F. (2007) Genetic exchange across a species boundary in the archaeal genus Ferroplasma. Genetics, 177, 407-416. DOI: 10.1534/genetics.107.072892


Tyson, G.W. and Banfield, J.F. (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environmental Microbiology, 10, 200-207. DOI: 10.1111/j.1462-2920.2007.01444.x


Denef V.D., Shah, M.B., VerBerkmoes, N.C., Hettich, R.L., and Banfield J.F. (2007) Implications of strain- and species-level divergence for community and isolate shotgun proteomic analysis. Journal of Proteome Research, 6, 3152 -3161. DOI: 10.1021/pr0701005


Lo, I., Denef V.D., VerBerkmoes N.C., Shah M. B., Goltsman D., DiBartolo, G., Tyson G. W., Allen E. E., Ram, R. J., Detter, J. C., Richardson, P., Thelen, M. P. Hettich R. L., and Banfield J. F. (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 446 (7135), 537-541. DOI: 10.1038/nature05624


Baker, B.J., Tyson, G.W., Webb, R.I., Flanagan, J., Hugenholtz, P., Allen, P., Allen, E.E., and Banfield, J.F., (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314, 1933-1935. DOI: 10.1126/science.1132690


Allen, E.E., Tyson, G.W., Whitaker, R.J., Detter, J.C., Richardson, P.M., and Banfield J.F. (2007) Genome dynamics in a natural archaeal population. Proceedings of the National Academy of Science, 104, 1883-1888. DOI: 10.1073/pnas.0604851104





Brown, C.T., Hug, L.A., Thomas, B.C., Banfield, J.F. (2014) Extensive Sampling of 16S rRNA Genes from OD1 and OP11 Bacteria Reveals Large, Possibly Self-Splicing, Insertion Sequences and Provides a New View of These Phyla. Abstracts of the General Meeting of the American Society for Microbiology, 114, 2348


Justice, N.B., Norman, A., Brown, C.T., Singh, A., Thomas, B.C., Banfield, J.F. (2014) Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics.DOI: 10.1186/1471-2164-15-1107


Sharon, I., Banfield, J.F. (2013) Genomes for Metagenomics. Science, 342, 1057-1058, DOI: 10.1126/science.1247023


Acuna, L.G., Cardenas, J.P., Covarrubias, P.C., Haristoy, J.J., Flores, R., Nunez, H., Riadi, G., Shmaryahu, A., Valdes, J., Dopson, M., Rawlings, D.E., Banfield, J.F., Holmes, D.S., Quatrini, R. (2013) Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus. PLoS One, 8, Article Number: e78237, DOI: 10.1371/journal.pone.0078237


Emerson, J.B., Thomas, B.C., Andrade, K., Heidelberg, K.B., Banfield, J.F. (2013) New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake. Applied and Environmental Microbiology, 79, 6755-6764, DOI: 10.1128/AEM.01946-13


Yelton, A.P., Comolli, L.R., Justice, N.B., Castelle, C., Denef, V.J., Thomas, B.C., Banfield, J.F. (2013) Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. BMC Genomics, 14, Article Number: 485, DOI: 10.1186/1471-2164-14-485


Yelton, A.P., Thomas, B.C., Simmons, S.L., Wilmes, P., Zemla, A., Thelen, M.P., Justice, N., and Banfield, J.F. (2011) A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes. PLoS Computational Biology, 7, e1002230 (12 pages). DOI: 10.1371/journal.pcbi.1002230


Bowen, B.P., Fischer, C., Baran, R. Banfield, J.F. and Northen, T. (2011) Improved genome annotation through untargeted detection of pathway-specific metabolites. BMC Genomics, 12, 1471-2164/12/S1/S6. DOI: 10.1186/1471-2164-12-S1-S6


Miller C.S., Baker, B.J., Thomas B.C., Singer, S.W., and Banfield, J.F. (2011) EMIRGE: Reconstruction of full length ribosomal genes from microbial community short read sequencing data. Genome Biology, 12:R44 DOI:10.1186/gb-2011-12-5-r44


Eppley, J. M., Tyson, G.W., Getz, W.M. and Banfield J.F. (2007) Strainer: Software for analysis of population variation in community genomic datasets. BMC Bioinformatics, 8, 398m, DOI: 10.1186/1471-2105-8-398.



Science and Policy


Dunphy Guzman, K., Taylor, M.R., Banfield, J.F. (2006) Environmental Risks of Nanotechnology: National Nanotechnology Initiative Funding, 2000-2004. Environmental Science and Technology, 40, 1401-1407. DOI: 10.1021/es0515708



Proteomics, biochemistry (collaborative studies led by other labs)


Hanke, A., Hamann, E., Sharma, R., Geelhoed, J.S., Hargesheimer, T., Kraft, B., Meyer, V., Lenk, S., Osmers, H., Wu, r., Makinwa, K., Hettich, R.L., Banfield, J.F., Tegetmeyer, H.E., Strous, M. (2014) Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Frontiers in Microbiology, 5, Article Number: 231, DOI: 10.3389/fmicb.2014.00231


Wheeler, K.E., Zemla, A., Jiao, Y., Aliaga Goltsman, D., Singer, S.W., Banfield, J.F., and Thelen, M.P (2010) Functional insights from computational modeling of orphan proteins expressed in a natural microbial community. Journal of Proteomics and Bioinformatics, in press.


Singer, S.W., Erickson, B.K., VerBerkmoes, N.C., Hwant, M., Shah, M.B., Hettich, R.L., Banfield, J.F., and Thelen, M.P. Post-translational modification and sequence variation of redox-active proteins correlate with biofilm lifecycle in a natural microbial community. ISME Journal, in press. DOI: 10.1038/ismej.2010.64


Erickson, B.K., Mueller, R.S., VerBerkmoes, N.C., Shah, M., Singer, S.W. Thelen, M.P., Banfield, J.F., and Hettich, R.L. (2010) Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community. J. Proteome Research, 9, 2148 - 2159. DOI: 10.1021/pr900877a


Jiao, Y., D'haeseleer, P., Dill, B. D., Shah, M., Verberkmoes, N.C., Hettich, R.L., J. F. Banfield, J.F., Thelen, M. P. (2010) Characterization of Extracellular Polymeric Substances from Acidophilic Microbial Biofilms, 76, 2916-2922. DOI: 10.1128/AEM.02289-09


Pan, C., Park, B.N., McDonald, W.H., Carey, P., Banfield, J.F., VerBerkmoes, N.C., Hettich, R.L., and Samatova, N.F. (2010) High-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. BMC Bioinformatics, 11, article 18. DOI: 10.1186/1471-2105-11-118


Singer, S.W., Chan, C.S., Zemla, A., VerBerkmoes, N.C., Hwang, M., Hettich, R.L., Banfield, J.F., and Thelen, M.P. (2008) Characterization of cytochrome 579, and unusual cytochrome isolated from an iron oxidizing microbial community. Applied and Environmental Microbiology, 74, 4454-4462. DOI: 10.1128/AEM.02799-07


Jeans C., Singer, S.W., Chan, C.S., VerBerkoes, N.C., Shah, M., Hettich, R.L., Banfield, J.F., and Thelen, M.P. (2008) Cytochrome 572 is a conspicuous membrane protein withiron oxidation activity purified directly from a natural acidophilic microbial community. ISME Journal, DOI:10.1038/ismej.2008.1





Banfield, J.F. and Young, M. (2009) Variety - the splice of life in microbial communities. Science, 326, 1198-1199. DOI: 10.1126/science.1181501


Denef, V.J., Mueller, R.S., and Banfield J.F. (2010) AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME Journal, 1-12. DOI: 10.1038/ismej.2009.158


Brocks J. J., and Banfield J.F. (2009) Unravelling ancient microbial history with community proteogenomics and lipid geochemistry. Nature Reviews Microbiology 7, 601. DOI: 10.1038/nrmicro2167


VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF (2009) Functional analysis of natural microbial consortia using community proteomics. Nature Reviews Microbiology, 7: 196-205. DOI: 10.1038/nrmicro2080


Wilmes, P., Simmons, S.L., Denef, V.J., and Banfield, J.F. (2008) The dynamic genetic repertoire of microbial communities. FEMS Microbiology Review, 33, 1-24. DOI: 10.1111/j.1574-6976.2008.00144.x


Whitaker, R.J. and Banfield J.F. (2006) Population genomics in natural microbial communities. Trends in Ecology and Evolution, 21, 508-516. DOI: 10.1016/j.tree.2006.07.001


  Last updated: 4.11.2019