Banfield Laboratory

University of California, Berkeley

Publications

2017

 

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

 

2016

 

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.

 

 

2014-2015

 

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

 

 

Nanogeoscience

 

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

 

 

Bioinformatics

 

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

 

 

Reviews

 

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: 6.7.2017

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