Publications

Up-to-date List

2018 Lear G, Dickie I, Banks J, Boyer S, Buckley HL, Buckley TR, Cruickshank R, Dopheide A, Handley KM, Hermans S, Kamke J, Lee CK, MacDiarmid R, Morales SE, Orlovich DA, Smissen R, Wood J, Holdaway R. Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. New Zealand Journal of Ecology 42: 10-50A.

2017 Handley KM, Piceno YM, Hu P, Tom LM, Mason OU, Andersen GL, Jansson JK, Gilbert JA. Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill. The ISME Journal 11: 2569-83.

2017 Lear G, Lau K, Perchec A-M, Buckley HL, Case BS, Neale M, Fierer N, Leff JW, Handley KM, Lewis G. Following Rapoport’s Rule: The geographic range and genome size of bacterial taxa decline at warmer latitudes. Environmental Microbiology 19: 3152-62.

2017 Marshall CW, Ross DE, Handley KM, Weisenhorn PB, Edirisinghe JN, Henry CS, Gilbert JA, May HD, Norman RS. Metabolic reconstruction and modeling microbial electrosynthesis. Scientific Reports 7: 8391.

2017 Lax S, Sangwan N, Smith D, Larsen P, Handley KM, Richardson M, Guyton K, Krezalek M, Shogan BD, Defazio J, Flemming I, Shakhsheer B, Weber S, Landon E, Garcia-Houchins S, Siegel J, Alverdy JC, Knight R, Stephens B, Gilbert JA. Colonization and Succession of Hospital-Associated Bacteria. Science Translational Medicine 345: 1048-52.

2017 Thompson LR, Sanders JG, McDonald D, …, Earth Microbiome Project Consortium (2017) A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551: 457-63.

2016 Brewer T, Handley KM, Carini P, Gilbert JA, Noah F. Genome reduction in an abundant and ubiquitous soil bacterial lineage. Nature Microbiology. Article number: 16198.

2016 Paez-Espino D, Chen I-MA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang, Markowitz VM, Nielsen T, Huntemann M, Reddy TBK, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu W-T, Rivers AR, Ivanova NN, Kyrpides NC. IMG/VR: A database of cultured and uncultured DNA Viruses and Retroviruses. Nucleic Acids Research 45: D457-D65.

2016 Joye SB, Kleindienst S, Gilbert JA, Handley KM, Weisenhorn P, Overholt WA, Kostka JE. The response of microbial communities to hydrocarbon exposure. Oceanography. 29: 136–149.

2016 Britstein M, Devescovi G, Handley KM, Malik A, Haber M, Saurav K, Teta R, Costantino V, Burgsdorf I, Gilbert JA, Sher N, Venturi V and Steindler L. A New N-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella Swinhoei. Applied and Environmental Microbiology 82: 1274-1285.

2015 Burgsdorf I, Slaby BM, Handley KM, Haber M, Blom J, Marshall CW, Gilbert JA, Hentschel U, Steindler L. Lifestyle evolution in cyanobacterial symbionts of sponges. mBio 6: e00391-15.

2015 Lin X, Handley KM, Gilbert JA, Kostka J. Metabolic potential of fatty acid oxidation and anaerobic respiration by members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. The ISME Journal 9: 2740-2744.

2015 Handley KM, Wrighton KC, Miller CS, Wilkins MJ, Kantor RS, Williams KH, Gilbert JA, Long PE, Banfield JF. Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points. Environmental Microbiology 17: 622-636.

2015 Campbell KA, Lynne BY, Handley KM, Jordan S, Farmer JD, Guido DM, Foucher F, Turner S, Perry RS. Tracing biosignature preservation of geothermally silicified microbial textures into the geological record. Astrobiology 15: 858-882.

2015 Long PE, Williams KH, Davis JA, Fox PM, Wilkins MJ, Yabusaki SB, Fang Y, Waichler SR, Berman ESF, Gupta M, Chandler DP, Murray C, … Handley KM, et al. Bicarbonate impact on U(VI) bioreduction in a shallow alluvial aquifer. Geochimica et Cosmochimica Acta 150: 106-124.

2014 Alessi DS, Lezama-Pacheco JS, Janot N, Suvorova EI, Cerrato JM, Giammar DE, Davis JA, Fox PM, Williams KH, Long PE, Handley KM, Bernier-Latmani R, Bargar JR. Speciation and reactivity of uranium products formed during in situ bioremediation in a shallow alluvial aquifer. Environmental Science & Technology 48: 12842-12850.

2014 Lax S, Smith DP, Hampton-Marcell J, Owens S, Handley KM, Scott N, Gibbons S, Larsen P, Shogan BD, Weiss S, Metcalf J, Ursell LK, Vázquez-Baeza Y, et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345: 1048-1052.

2014 Handley KM, Bartels D, O’Loughlin EJ, Williams KH, Trimble W, Skinner K, Gilbert JA, Desai N, Glass EM, Paczian T, Wilke A, Antonopoulos D, Kemner KM, et al. The complete genome sequence for putative H2– and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome. Environmental Microbiology 16: 3443-3462.

2014 Wrighton KC, Castelle CJ, Wilkins MJ, Hug LA, Sharon I, Thomas BC, Handley KM, Mullin S, Singh A, Lipton MS, Long PE, Williams KH, Banfield JF. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in a subsurface aquifer. The ISME Journal 8: 1452-1463.

2013 Kantor RS, Wrighton KC, Handley KM, Hug LA, Sharon I, Castelle CJ, Thomas BC, Banfield JF. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. mBio 4: e00708-13.

2013 Yelton AP, Williams KH, Fournelle J, Wrighton KC, Handley KM, Banfield JF. Vanadate and acetate biostimulation of contaminated sediments decreases diversity, selects for specific taxa and decreases aqueous V5+ concentration. Environmental Science & Technology 47: 6500-6509.

2013 Handley KM, VerBerkmoes NC, Steefel CI, Williams KH, Sharon I, Miller CS, Frischkorn KR, Chourey K, Thomas BC, Shah MB, Long PE, Hettich R, Banfield JF. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. The ISME Journal 7: 800-816.

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

2013 Miller CS, Handley KM, Wrighton KC, Frischkorn KR, Thomas BC, Banfield JF. Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments. PLoS ONE 8: e56018.

2013 Handley KM, McBeth J, Charnock JM, Wincott PL, Vaughan DJ, Polya DA, Lloyd JR. Effect of iron redox transformations on arsenic solid-phase associations in an arsenic-rich, ferruginous hydrothermal sediment. Geochimica et Cosmochimica Acta 102: 124-142.

2013 Handley KM, Lloyd JR. Biogeochemical implications of the ubiquitous colonization of marine habitats and redox gradients by Marinobacter species. Frontiers in Microbiology 4: 136.

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

2010 Müller M, Handley KM, Lloyd J, Pancost RD, Mills RA. Biogeochemical controls on microbial diversity in seafloor sulphidic sediments. Geobiology 8: 309-326.

2010 Handley KM, Boothman C, Pancost RD, Mills RA, Lloyd JR. Functional diversity of bacteria in a ferruginous hydrothermal sediment. The ISME Journal 4: 1193-1205.

2009 Handley KM, Héry M, Lloyd JR. Redox cycling of arsenic by the hydrothermal marine bacterium Marinobacter santoriniensis. Environmental Microbiology 11: 1601-1611.

2009 Handley KM, Héry M, Lloyd JR. Marinobacter santoriniensis sp. nov., an arsenate-respiring and arsenite-oxidizing bacterium isolated from hydrothermal sediment. International Journal of Systematic and Evolutionary Microbiology 59: 886-892.

2008 Handley KM, Turner SJ, Campbell KA, Mountain BW. Silicifying biofilm exopolymers on a hot spring microstromatolite: templating nanometer-thick laminae. Astrobiology 8: 747-770.

2007 Burnett P-GG, Handley KM, Peak D, Daughney CJ. Divalent metal adsorption by the thermophile Anoxybacillus flavithermus in single and multi-metal systems. Chemical Geology 244: 493-506.

2005 Handley KM, Campbell KA, Mountain BW, Browne PRL. Abiotic-biotic controls on the origin and development of spicular sinter: In situ growth experiments, Champagne Pool, Waiotapu, New Zealand. Geobiology 3: 93-114.