2018

Dalcin Martins P, Danczak RE, Roux S, Frank J, Borton MA, Wolfe RA, Burris MN, and Wilkins MJ (2018) Viral and Metabolic Controls on High Rates of Microbial Sulfur and Carbon Cycling in Wetland Ecosystems. Microbiome. doi: 10.1186/s40168-018-0522-4

Danczak RE, Johnston MD, Kenah C, Slattery M, and Wilkins MJ (2018) Microbial community cohesion mediates community turnover in unperturbed aquifers. mSystems. doi: 10.1128/mSystems.00066-18

Borton MA, Hoyt DW, Roux S, Daly RA, Welch SA, Nicora CD, Purvine S, Eder EK, Hanson AJ, Sheets JM, Morgan DM, Sharma S, Carr TR, Cole DR, Mouser PJ, Lipton MS, Wilkins MJ, and Wrighton KC (2018) Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1800155115

Stegen JC, Johnson T, Fredrickson JF, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Fansler SJ, Kennedy DW, Resch CT, Tfaily MM, and Zachara J (2018) Influences of Organic-C Speciation on Hyporheic Corridor Biogeochemistry and Microbial Ecology Nature Communications. doi:10.1038/s41467-018-02922-9

Grottoli AG, Dalcin Martins P, Wilkins MJ, Johnston MD, Warner ME, Cai WJ, Melman TF, Hoadley KD, Pettay DT, Hu X, Levas S, and Schoepf V (2018) In the face of global change, coral with stable microbiomes are also physiologically stable PLoS One, doi:10.1371/journal.pone.0191156.

2017

Danczak RE, Johnston MD, Kenah C, Slattery M, Wrighton KC, and Wilkins MJ (2017) Members of the Candidate Phyla Radiation are functionally differentiated by carbon and nitrogen cycling capabilitiesMicrobiome, doi: 10.1186/s40168-017-0331-1

Booker AE, Johnston MD, Daly RA, Wrighton KC, and Wilkins MJ (2017) Draft genome sequences of multiple Frackibacter strains isolated from hydraulically fractured shale environmentsASM Genome Announcements. 5:32 e00608-17. doi: 10.1128/genomeA.00608-17

Booker AE, Borton MA, Daly RA, Welch S, Nicora CD, Hoyt DW, Wilson T, Purvine SO, Sharma S, Mouser PJ, Cole DR, Lipton MS, Wrighton KC, and Wilkins MJ (2017) Sulfide Generation by Dominant Colonizing Halanaerobium Microorganisms in Hydraulically Fractured ShalesmSphere, 10.1128/mSphereDirect.00257-17.

Yabusaki SB, Wilkins MJ, Fang Y, Williams KH, Arora B, Bargar J, Beller HR, Bouskill NJ, Brodie EL, Christensen JN, Conrad MJ, Danczak RE, King E, Spycher NF, Steefel CI, Tokunaga T, Versteeg R, Waichler SR, and Wainright HM (2017) Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated FloodplainEnvironmental Science and Technology, doi: 10.1021/acs.est.6b04873.

Saup CM, Williams KH, Rodriguez-Freire L, Cerrato JM, Johnston MD, and Wilkins MJ (2017) Anoxia stimulates microbially catalyzed metal release from Animas River sedimentsEnvironmental Science: Processes and Impacts. doi: 10.1039/C7EM00036G.

Dalcin Martins P, Hoyt DW, Bansal S, Mills CT, Tfaily M, Tangen BA, Finocchiaro RG, Johnston MD, McAdams BC, Solensky MJ, Smith GJ, Chin Y-P, and Wilkins MJ (2017) Unprecedented Methane Fluxes and Sulfate Reduction Rates in Prairie Pothole WetlandsGlobal Change Biology. doi: 10.1111/gcb.13633

2016

Danczak RE, Sawyer AH, Williams KH, Stegen JC, Hobson C, and Wilkins MJ (2016) Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sedimentsJGR – Biogeosciences. doi: 10.1002/2016JG003527

Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, and Banfield JF (2016) Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer systemNature Communications, 7, 13219. doi:10.1038/ncomms13219

Daly RA, Borton MA, Wilkins MJ, Hoyt DW, Wolfe R, Kountz DJ, Welch SA, Marcus DN, Trexler RV, McRae J, Krzycki JA, Cole DR, Mouser PJ, and Wrighton KC (2016) Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales Nature Microbiology. 1:16146 doi:10.1038/nmicrobiol.2016.146

Danczak RE, Yabusaki SB, Williams KH, Fang Y, Hobson C, and Wilkins MJ (2016) Snowmelt induced hydrologic perturbations drive dynamic microbiological and geochemical behaviors across a shallow riparian aquiferFrontiers in Earth Sciences. 4:57. doi: 10.3389/feart.2016.00057

Stegen JC, Fredrickson JF, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Danczak RE, Fansler SJ, Kennedy DW, Resch CT, and Tfaily M (2016) Coupled Microbiome-Biogeochemical Responses to Groundwater-Surface Water MixingNature Communications. doi:10.1038/ncomms11237.

Wrighton KC, Castelle CJ, Varaljay V, Satagopan S, Brown CT, Wilkins MJ, Thomas BC, Williams KH, Tabita FR, and Banfield JF (2016) RubisCO of a nucleotide pathway from Archaea is central to the metabolism of diverse uncultivated bacteriaISME Journal. doi: 10.1038/ismej.2016.53.

2015

Wilkins MJ and Fredrickson JK (2015) Terrestrial Subsurface Ecosystem. In Erlich’s Geomicrobiology, 6th Edition. Eds: Erlich HL, Newman DK, Kappler A. CRC Press.

Harvey OR, Qafoku NP, Cantrell KJ, Wilkins MJ, and Brown CF (2015) Methanogenesis-induced pH-Eh shifts drives aqueous metal(loid) mobility in sulfide mineral systems under CO2-enriched conditionsGeochimica et Cosmochimica Acta, 173, 232-245

Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, Wilkins MJ, Wrighton KC, Williams KH, and Banfield JF (2015)  Unusual biology across a group comprising more than 15% of domain Bacteria. Nature. doi:10.1038/nature14486

Hug LA, Thomas BC, Sharon I, Brown CT, Sharma R, Hettich RL, Wilkins MJ, Williams KH, Singh A, and Banfield JF (2015) Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages Environmental Microbiology, DOI:10.1111/1462-2920.12930

Kieft TL, Onstott TC, Ahonen L, Aloisi V, Colwell FS, Engelen B, Fendrihan S, Gaidos E, Harms U, Head I, Kallmeyer J, Kiel Reese B, Lin L-H, Long PE, Moser DP, Mills H, Sar P, Schulze-Makuch D, Stan-Lotter H, Wagner D, Wang P-L, Westall F, and Wilkins MJ (2015) Workshop to develop deep-life continental scientific drilling projectsScientific Drilling, 3, 1-11

Long PE, Williams KH, Davis JA, Fox PM, Wilkins MJ, Yabusaki SB, Fang Y, Waichler SR, Berman ESF, Gupta M, Chandler DP, Murray C, Peacock AD, Giloteaux L, Handley KM, Lovley DR, and Banfield JF (2015) Bicarbonate Impact on U(VI) Bioreduction in a Shallow Alluvial AquiferGeochimica et Cosmochimica Acta, 150, 106-124

Grate JW, Kai-For M, Shin Y, Vasdekis A, Warner M, Kelly R, Orr G, Hu D, Dehoff K, Brockman F, and Wilkins MJ (2015) Alexa Fluor-labeled Fluorescent Cellulose Nanocrystals for Bioimaging Solid Cellulose in Spatially-Structured MicroenvironmentsBioconjugate Chemistry, 10.1021/acs.bioconjchem.5b00048

Merkley E, Wrighton KC, Castelle CJ, Anderson, B, Wilkins MJ, Shah V, Arbour T, Brown J, Singer S, Smith R, and Lipton, MS (2015) Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensisJournal of Proteome Research14, 1361–1375

Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe SG, Singh A, Markillie LM, Taylor RC, Williams KH, and Banfield JF (2015) Genomic expansion of Domain Archaea highlights roles for organisms from new phyla in subsurface anaerobic carbon cyclingCurrent Biology, 25, 690-701

McGuinness LR, Wilkins MJ, Williams KH, Long PE, and Kerkhof L (2015) Active bacteria using uranium as a terminal electron acceptor at the Rifle, CO, Integrated Field Research SitePLoS One, doi: 10.1371/journal.pone.0137270

2014

Wilkins MJ, Daly R, Mouser PJ, Trexler R, Sharma S, Cole DR, Wrighton KC, Biddle JF, Denis EH, Fredrickson JK, Kieft TL, Onstott TC, Petersen L, Pfiffner SM, Phelps TJ, and Schrenk MO (2014) Trends and future challenges in sampling the deep terrestrial biosphere Frontiers in Microbiology: Frontiers in Systems Microbiology, doi: 10.3389/fmicb.2014.00481

Wilkins MJ, Hoyt DW, Marshall MJ, Alderson PA, Plymale AE, Markilli LM, Tucker AE, Walter ED, Linggi BE, Dohnalkova AC, and Taylor RC (2014) CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain HildenboroughFrontiers in Microbiology: Frontiers in Extreme Microbiology, doi: 10.3389/fmicb.2014.00507

Holmes DE, Giloteaux L, Chaurasia A, Williams KH, Luef B, Wilkins MJ, Wrighton KC, Thompson C, Comolli LR, and Lovley DR (2014) Evidence of Geobacter-associated phage in a uranium contaminated aquiferISME Journal, DOI:10.1038/ismej.2014.128

Vasdekis AE, Wilkins MJ, Grate JW, Kelly RT, Konopka AE, Xantheas SS and Chang TM (2014) Solvent immersion imprint lithographyLab On A Chip, 14, 2072-2080

Wilkins MJ, Kennedy DW, Castelle CJ, Field EK, Stepanauskas R, Fredrickson JK and Konopka A (2014) Single cell genomics reveal metabolic strategies for microbial growth and survival in an oligotrophic aquiferMicrobiology, 160: 362-372

Wrighton KC, Castelle CJ, Wilkins MJ, Hug, LA, Sharon I, Thomas BC, Handley KM, Mullin SW, Nicora CD, Singh A, Lipton MS, Long PE, Williams KH and Banfield JF (2014) Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquiferISME Journal, 8, 1452–1463;  doi:10.1038/ismej.2013.249

Handley KM, Wrighton KC, Miller CS, Wilkins MJ, Kantor RS, Thomas BC, Williams KH, Gilbert JA, Long PE and Banfield JF (2014) Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting pointsEnvironmental Microbiology, DOI: 10.1111/1462-2920.12467

2013

Wilkins MJ, Wrighton KC, Nicora, CD, Williams KH, McCue LA, Handley KM, Miller CS, Giloteaux L, Montgomery AP, Lovley DR, Banfield JF, Long PE and Lipton MS (2013) Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurfacePLoS One, 8(3): e57819

Holmes DE, Giloteaux L, Barlett M, Chavan MA, Smith JA, Williams KH, Wilkins MJ, Long PE and Lovley DR (2013) Molecular analysis of the in situ growth rate of subsurface Geobacter speciesApplied and Environmental Microbiology, 79: 1646-1653

Holmes DE, Giloteaux L, Williams KH, Wrighton KC, Wilkins MJ, Thompson CA, Roper TJ, Long PE and Lovley DR (2013) Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwaterISME Journal, 7: 1286-1298

Giloteaux L, Holmes DE, Williams KH, Wrighton KW, Wilkins MJ, Montgomery AP, Smith JA, Orellana R, Thompson CA, Roper TJ, Long PE and Lovley DR (2013) Characterization and transcription of arsenic respiration and resistance genes during in situ uranium bioremediationISME Journal, 7: 370-83

Williams KH, Wilkins MJ, N’Guessan AL, Arey B, Dodova E, Dohnalkova A, Holmes D, Yang L, Lovley DR, Banfield JF and Long PE (2013) Field evidence of selenium bioreduction in a uranium contaminated aquiferEnvironmental Microbiology Reports, 5: 444-452

2012

Fang Y, Wilkins MJ, Yabusaki SB, Lipton MS and Long PE (2012) Evaluation of a genome-scale in silico metabolic model of Geobacter metallireducens using proteomic data from a field biostimulation experiment Applied and Environmental Microbiology, 78:8735-8742

Luef B, Fakra SC, Csencsits R, Wrighton KC, Williams KH, Wilkins MJ, Downing KH, Long PE, Comolli LR and Banfield JF (2012) Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growthISME Journal, 7: 338-350

Webb-Robertson BJM, Bailey VL, Fansler SJ, Wilkins MJ and Hess NJ (2012) Spectral signatures for the classification of microbial species using Raman spectraAnalytical and Bioanalytical Chemistry. 404: 563-572.

Pearce CI, Wilkins MJ, Zhang C, Heald S, Fredrickson JK and Zachara JF (2012) Pore-scale imaging and characterization of biogeochemical controls on iron and uranium speciation under flow conditionsEnvironmental Science and Technology, 46: 7992-8000

Konopka A and Wilkins MJ (2012) Application of meta-transcriptomics and -proteomics to analysis of in situ physiological stateFrontiers in Microbiotechnology, 3:184

Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, Long PE and Banfield JF (2012) Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phylaScience, 337: 1661

Handley KM, Wrighton KC, Piceno YM, Andersen GL, DeSantis TZ, Williams KH, Wilkins MJ, N’Guessan LA, Peacock A, Bargar J, Long PE and Banfield JF (2012) High‐ Density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendmentFEMS Microbiology Ecology, 81: 188-204.

2011

Campbell KM, Davis JA, Bargar J, Giammar D, Bernier-Latmani R, Kukkadapu R, Williams KH, Varamani H, Ulrich KU, Stubbs J, Yabusaki S, Figueroa L, Lesher E, Wilkins MJ, Peacock A and Long PE (2011) Composition, stability, and measurement of reduced uranium phases for groundwater bioremediation at Old Rifle, COApplied Geochemistry, 26: S167-169

Wilkins MJ, Callister SJ, Miletto M, Williams KH, Nicora CD, Lovley DR, Long PE and Lipton MS (2011) Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI) Microbial Biotechnology, 4: 55-63

Williams KH, Long PE, Davis JA, Wilkins MJ, N’Guessan AL, Yang L, Newcomer D, Spane FA, McGuinness L, Kerkhof LJ, Dayvault R and Lovley DR (2011) Acetate availability and its influence on sustainable bioremediation of uranium-contaminated groundwaterGeomicrobiology Journal, 28: 519-539

2010

Callister SJ, Wilkins MJ, Lipton MS, Nicora CD, Williams KH, Banfield JF, VerBerkmoes NC, Hettich RL, N’Guessan AL, Mouser PJ, Elifantz H, Lovley DR and Long PE (2010) Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles Environmental Science & Technology, 44: 8897-8903.

Elifantz H, N’Guessan AL, Mouser PJ, Williams KH, Wilkins MJ, Risso C, Holmes DE, Long PE and Lovley DR (2010) Expression of acetate permease-like (apl) genes in subsurface communities of Geobacterspecies under fluctuating acetate concentrations FEMS Microbiology Ecology, 73: 441-449

N’Guessan AL, Elifantz H, Nevin KP, Mouser PJ, Methe B, Woodward TL, Manley K, Williams KH, Wilkins MJ, Larsen JT, Long PE and Lovley DR (2010) Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquiferISME Journal, 4: 253-266

Wilkins MJ, Livens FR, Vaughan DJ, Beadle I, Small J and Lloyd JR (2010) Fe(III) reduction in the subsurface at a low-level radioactive waste disposal siteGeomicrobiology Journal, 27: 231-239.

2009

Wilkins MJ, VerBerkmoes NC, Williams KH, Callister SJ, Hettich RL, Lipton MS, Mouser PJ, Elifantz H, N’Guessan AL, Lovley DR, Long PE and Banfield JF (2009) Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation Applied and Environmental Microbiology, 75: 6591-6599

Li L, Steefel CI, Williams KH, Wilkins MJ and Hubbard SS (2009) Mineral transformations and biomass accumulation during uranium bioremediation at Rifle, ColoradoEnvironmental Science & Technology, 43: 5429-5435

Williams KH, Kemna A, Wilkins MJ, Druhan J, Arntzen E, N’Guessan AL, Long PE, Hubbard SS and Banfield JF (2009) Geophysical monitoring of microbial activity during stimulated subsurface bioremediation Environmental Science & Technology, 43: 6717-6723

Mouser PJ, N’Guessan AL, Elifantz H, Holmes DE, Williams KH, Wilkins MJ, Long PE and Lovley DR (2009) Impact of heterogeneous ammonium availability on community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater Environmental Science & Technology, 43: 4386-4392

2008

Melton SJ, Yu H, Ali MF, Williams KH, Wilkins MJ, Long PE and Blake DA (2008) Detection of hexavalent uranium with inline and field portable immunosensorsIn Uranium, Mining, and Hydrogeology; Merkel, B. J.; Hasche-Berger, A., Eds. Springer-Verlag; Berlin.

Hand VL, Lloyd JR, Vaughan DJ, Wilkins MJ and Boult S (2008) Experimental studies of the influence of grain size, oxygen availability and organic carbon availability on bioclogging in porous media Environmental Science & Technology, 42: 1485-1491

2007

Wilkins MJ, Livens FR, Vaughan DJ, Beadle I and Lloyd JR (2007) The influence of microbial redox cycling on radionuclide mobility in the subsurface at a low-level radioactive waste storage siteGeobiology, 5: 293-301

Wilkins MJ, Wincott PL, Livens FR, Vaughan DJ and Lloyd JR (2007) Growth of Geobacter sulfurreducens on poorly crystalline Fe(III) oxyhydroxide coatingsGeomicrobiology Journal, 24: 199-204

2006

Wilkins MJ, Livens FR, Vaughan DJ and Lloyd JR (2006)  The impact of Fe(III)-reducing bacteria on uranium mobilityBiogeochemistry, 78: 125-150

Davis JA, Curtis GP, Wilkins MJ, Kohler M, Fox P, Naftz DL and Lloyd JR (2006) Processes affecting transport of uranium in a suboxic aquiferPhysics and Chemistry of the Earth, 31: 548-555