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Items: 32

1.

Determining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom Barriers.

Handley KM.

mSystems. 2019 Jun 4;4(3). pii: e00153-19. doi: 10.1128/mSystems.00153-19.

2.

Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont.

Burgsdorf I, Handley KM, Bar-Shalom R, Erwin PM, Steindler L.

mSystems. 2019 May 7;4(4). pii: e00057-19. doi: 10.1128/mSystems.00057-19. eCollection 2019 Jul-Aug.

3.

Metabolic Reconstruction and Modeling Microbial Electrosynthesis.

Marshall CW, Ross DE, Handley KM, Weisenhorn PB, Edirisinghe JN, Henry CS, Gilbert JA, May HD, Norman RS.

Sci Rep. 2017 Aug 21;7(1):8391. doi: 10.1038/s41598-017-08877-z.

4.

Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill.

Handley KM, Piceno YM, Hu P, Tom LM, Mason OU, Andersen GL, Jansson JK, Gilbert JA.

ISME J. 2017 Nov;11(11):2569-2583. doi: 10.1038/ismej.2017.110. Epub 2017 Aug 4.

5.

Bacterial colonization and succession in a newly opened hospital.

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 J, Knight R, Stephens B, Gilbert JA.

Sci Transl Med. 2017 May 24;9(391). pii: eaah6500. doi: 10.1126/scitranslmed.aah6500.

6.

Following Rapoport's Rule: the geographic range and genome size of bacterial taxa decline at warmer latitudes.

Lear G, Lau K, Perchec AM, Buckley HL, Case BS, Neale M, Fierer N, Leff JW, Handley KM, Lewis G.

Environ Microbiol. 2017 Aug;19(8):3152-3162. doi: 10.1111/1462-2920.13797. Epub 2017 Jun 27.

PMID:
28504344
7.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, 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 WT, Rivers AR, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30.

8.

Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'.

Brewer TE, Handley KM, Carini P, Gilbert JA, Fierer N.

Nat Microbiol. 2016 Oct 31;2:16198. doi: 10.1038/nmicrobiol.2016.198.

PMID:
27798560
9.

A New N-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella swinhoei.

Britstein M, Devescovi G, Handley KM, Malik A, Haber M, Saurav K, Teta R, Costantino V, Burgsdorf I, Gilbert JA, Sher N, Venturi V, Steindler L.

Appl Environ Microbiol. 2015 Dec 11;82(4):1274-1285. doi: 10.1128/AEM.03111-15. Print 2016 Feb 15.

10.

Tracing Biosignature Preservation of Geothermally Silicified Microbial Textures into the Geological Record.

Campbell KA, Lynne BY, Handley KM, Jordan S, Farmer JD, Guido DM, Foucher F, Turner S, Perry RS.

Astrobiology. 2015 Oct;15(10):858-82. doi: 10.1089/ast.2015.1307.

PMID:
26496526
11.

Lifestyle evolution in cyanobacterial symbionts of sponges.

Burgsdorf I, Slaby BM, Handley KM, Haber M, Blom J, Marshall CW, Gilbert JA, Hentschel U, Steindler L.

MBio. 2015 Jun 2;6(3):e00391-15. doi: 10.1128/mBio.00391-15.

12.

Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat.

Lin X, Handley KM, Gilbert JA, Kostka JE.

ISME J. 2015 Dec;9(12):2740-4. doi: 10.1038/ismej.2015.77. Epub 2015 May 22.

13.

Speciation and reactivity of uranium products formed during in situ bioremediation in a shallow alluvial aquifer.

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.

Environ Sci Technol. 2014 Nov 4;48(21):12842-50. doi: 10.1021/es502701u. Epub 2014 Oct 27.

14.

Longitudinal analysis of microbial interaction between humans and the indoor environment.

Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA.

Science. 2014 Aug 29;345(6200):1048-52. doi: 10.1126/science.1254529.

15.

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.

Handley KM, Wrighton KC, Miller CS, Wilkins MJ, Kantor RS, Thomas BC, Williams KH, Gilbert JA, Long PE, Banfield JF.

Environ Microbiol. 2015 Mar;17(3):622-36. doi: 10.1111/1462-2920.12467. Epub 2014 Apr 18.

PMID:
24674078
16.

The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome.

Handley KM, Bartels D, O'Loughlin EJ, Williams KH, Trimble WL, Skinner K, Gilbert JA, Desai N, Glass EM, Paczian T, Wilke A, Antonopoulos D, Kemner KM, Meyer F.

Environ Microbiol. 2014 Nov;16(11):3443-62. doi: 10.1111/1462-2920.12453. Epub 2014 Apr 21.

PMID:
24628880
17.

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer.

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, Banfield JF.

ISME J. 2014 Jul;8(7):1452-63. doi: 10.1038/ismej.2013.249. Epub 2014 Mar 13.

18.

Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla.

Kantor RS, Wrighton KC, Handley KM, Sharon I, Hug LA, Castelle CJ, Thomas BC, Banfield JF.

MBio. 2013 Oct 22;4(5):e00708-13. doi: 10.1128/mBio.00708-13.

19.

Biogeochemical implications of the ubiquitous colonization of marine habitats and redox gradients by Marinobacter species.

Handley KM, Lloyd JR.

Front Microbiol. 2013 May 22;4:136. doi: 10.3389/fmicb.2013.00136. eCollection 2013.

20.

Vanadate and acetate biostimulation of contaminated sediments decreases diversity, selects for specific taxa, and decreases aqueous V5+ concentration.

Yelton AP, Williams KH, Fournelle J, Wrighton KC, Handley KM, Banfield JF.

Environ Sci Technol. 2013 Jun 18;47(12):6500-9. doi: 10.1021/es4006674. Epub 2013 Jun 10.

PMID:
23713472
21.

Genome Sequence of Hydrothermal Arsenic-Respiring Bacterium Marinobacter santoriniensis NKSG1T.

Handley KM, Upton M, Beatson SA, Héry M, Lloyd JR.

Genome Announc. 2013 May 9;1(3). pii: e00231-13. doi: 10.1128/genomeA.00231-13.

22.

Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface.

Wilkins MJ, Wrighton KC, Nicora CD, Williams KH, McCue LA, Handley KM, Miller CS, Giloteaux L, Montgomery AP, Lovley DR, Banfield JF, Long PE, Lipton MS.

PLoS One. 2013;8(3):e57819. doi: 10.1371/journal.pone.0057819. Epub 2013 Mar 5.

23.

Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments.

Miller CS, Handley KM, Wrighton KC, Frischkorn KR, Thomas BC, Banfield JF.

PLoS One. 2013;8(2):e56018. doi: 10.1371/journal.pone.0056018. Epub 2013 Feb 6.

24.

Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community.

Handley KM, VerBerkmoes NC, Steefel CI, Williams KH, Sharon I, Miller CS, Frischkorn KR, Chourey K, Thomas BC, Shah MB, Long PE, Hettich RL, Banfield JF.

ISME J. 2013 Apr;7(4):800-16. doi: 10.1038/ismej.2012.148. Epub 2012 Nov 29.

25.
26.

High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment.

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.

FEMS Microbiol Ecol. 2012 Jul;81(1):188-204. doi: 10.1111/j.1574-6941.2012.01363.x. Epub 2012 Apr 13.

27.

The nonfenestrated extracardiac Fontan procedure: a cohort of 145 patients.

O'Brien JE Jr, Marshall JA, Young AR, Handley KM, Lofland GK.

Ann Thorac Surg. 2010 Jun;89(6):1815-20. doi: 10.1016/j.athoracsur.2010.02.055.

PMID:
20494033
28.

Biogeochemical controls on microbial diversity in seafloor sulphidic sediments.

Müller M, Handley KM, Lloyd J, Pancost RD, Mills RA.

Geobiology. 2010 Sep;8(4):309-26. doi: 10.1111/j.1472-4669.2010.00242.x. Epub 2010 May 19.

PMID:
20491949
29.

Functional diversity of bacteria in a ferruginous hydrothermal sediment.

Handley KM, Boothman C, Mills RA, Pancost RD, Lloyd JR.

ISME J. 2010 Sep;4(9):1193-205. doi: 10.1038/ismej.2010.38. Epub 2010 Apr 22.

PMID:
20410934
30.

Marinobacter santoriniensis sp. nov., an arsenate-respiring and arsenite-oxidizing bacterium isolated from hydrothermal sediment.

Handley KM, Héry M, Lloyd JR.

Int J Syst Evol Microbiol. 2009 Apr;59(Pt 4):886-92. doi: 10.1099/ijs.0.003145-0. Erratum in: Int J Syst Evol Microbiol. 2009 Jul;59(Pt 7):1850.

PMID:
19329625
31.

Redox cycling of arsenic by the hydrothermal marine bacterium Marinobacter santoriniensis.

Handley KM, Héry M, Lloyd JR.

Environ Microbiol. 2009 Jun;11(6):1601-11. doi: 10.1111/j.1462-2920.2009.01890.x. Epub 2009 Feb 18.

PMID:
19226300
32.

Silicifying biofilm exopolymers on a hot-spring microstromatolite: templating nanometer-thick laminae.

Handley KM, Turner SJ, Campbell KA, Mountain BW.

Astrobiology. 2008 Aug;8(4):747-70. doi: 10.1089/ast.2007.0172.

PMID:
18781887

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