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Items: 1 to 50 of 57

1.

Uncovering the Diversity and Activity of Methylotrophic Methanogens in Freshwater Wetland Soils.

Narrowe AB, Borton MA, Hoyt DW, Smith GJ, Daly RA, Angle JC, Eder EK, Wong AR, Wolfe RA, Pappas A, Bohrer G, Miller CS, Wrighton KC.

mSystems. 2019 Dec 3;4(6). pii: e00320-19. doi: 10.1128/mSystems.00320-19.

2.

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes.

Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA.

Nat Microbiol. 2019 Nov;4(11):1895-1906. doi: 10.1038/s41564-019-0510-x. Epub 2019 Jul 22.

3.

Metagenomic Approaches Unearth Methanotroph Phylogenetic and Metabolic Diversity.

Smith GJ, Wrighton KC.

Curr Issues Mol Biol. 2019 Jun 5;33:57-84. doi: 10.21775/cimb.033.057. [Epub ahead of print]

4.

Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp.

Booker AE, Hoyt DW, Meulia T, Eder E, Nicora CD, Purvine SO, Daly RA, Moore JD, Wunch K, Pfiffner SM, Lipton MS, Mouser PJ, Wrighton KC, Wilkins MJ.

Appl Environ Microbiol. 2019 May 30;85(12). pii: e00018-19. doi: 10.1128/AEM.00018-19. Print 2019 Jun 15.

5.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.

Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17.

6.

Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing.

Daly RA, Roux S, Borton MA, Morgan DM, Johnston MD, Booker AE, Hoyt DW, Meulia T, Wolfe RA, Hanson AJ, Mouser PJ, Moore JD, Wunch K, Sullivan MB, Wrighton KC, Wilkins MJ.

Nat Microbiol. 2019 Feb;4(2):352-361. doi: 10.1038/s41564-018-0312-6. Epub 2018 Dec 3.

7.

Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin.

Evans MV, Panescu J, Hanson AJ, Welch SA, Sheets JM, Nastasi N, Daly RA, Cole DR, Darrah TH, Wilkins MJ, Wrighton KC, Mouser PJ.

Front Microbiol. 2018 Nov 15;9:2646. doi: 10.3389/fmicb.2018.02646. eCollection 2018.

8.

Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland.

Smith GJ, Angle JC, Solden LM, Borton MA, Morin TH, Daly RA, Johnston MD, Stefanik KC, Wolfe R, Gil B, Wrighton KC.

MBio. 2018 Nov 6;9(6). pii: e00815-18. doi: 10.1128/mBio.00815-18.

9.

Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale.

Borton MA, Daly RA, O'Banion B, Hoyt DW, Marcus DN, Welch S, Hastings SS, Meulia T, Wolfe RA, Booker AE, Sharma S, Cole DR, Wunch K, Moore JD, Darrah TH, Wilkins MJ, Wrighton KC.

Environ Microbiol. 2018 Dec;20(12):4596-4611. doi: 10.1111/1462-2920.14467.

PMID:
30394652
10.

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem.

Solden LM, Naas AE, Roux S, Daly RA, Collins WB, Nicora CD, Purvine SO, Hoyt DW, Schückel J, Jørgensen B, Willats W, Spalinger DE, Firkins JL, Lipton MS, Sullivan MB, Pope PB, Wrighton KC.

Nat Microbiol. 2018 Nov;3(11):1274-1284. doi: 10.1038/s41564-018-0225-4. Epub 2018 Oct 24.

11.

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.

Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, Solden L, Ellenbogen J, Runyon AT, Bolduc B, Woodcroft BJ, Saleska SR, Tyson GW, Wrighton KC, Sullivan MB, Rich VI.

mSystems. 2018 Oct 2;3(5). pii: e00076-18. doi: 10.1128/mSystems.00076-18. eCollection 2018 Sep-Oct.

12.

Characterizing the Deep Terrestrial Subsurface Microbiome.

Daly RA, Wrighton KC, Wilkins MJ.

Methods Mol Biol. 2018;1849:1-15. doi: 10.1007/978-1-4939-8728-3_1.

PMID:
30298244
13.

Host-linked soil viral ecology along a permafrost thaw gradient.

Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, Singleton CM, Solden LM, Naas AE, Boyd JA, Hodgkins SB, Wilson RM, Trubl G, Li C, Frolking S, Pope PB, Wrighton KC, Crill PM, Chanton JP, Saleska SR, Tyson GW, Rich VI, Sullivan MB.

Nat Microbiol. 2018 Aug;3(8):870-880. doi: 10.1038/s41564-018-0190-y. Epub 2018 Jul 16.

14.

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.

Borton MA, Hoyt DW, Roux S, Daly RA, Welch SA, Nicora CD, Purvine S, Eder EK, Hanson AJ, Sheets JM, Morgan DM, Wolfe RA, Sharma S, Carr TR, Cole DR, Mouser PJ, Lipton MS, Wilkins MJ, Wrighton KC.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):E6585-E6594. doi: 10.1073/pnas.1800155115. Epub 2018 Jun 25.

15.

Draft Genome Sequences of Two Chemosynthetic Arcobacter Strains Isolated from Hydraulically Fractured Wells in Marcellus and Utica Shales.

Panescu J, Daly RA, Wrighton KC, Mouser PJ.

Genome Announc. 2018 May 17;6(20). pii: e00159-18. doi: 10.1128/genomeA.00159-18.

16.

Draft Genome Sequences of Marinobacter Strains Recovered from Utica Shale-Produced Fluids.

Tummings S, Panescu J, Daly RA, Wrighton KC, Mouser PJ.

Genome Announc. 2018 Apr 5;6(14). pii: e00155-18. doi: 10.1128/genomeA.00155-18.

17.

"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system.

Naas AE, Solden LM, Norbeck AD, Brewer H, Hagen LH, Heggenes IM, McHardy AC, Mackie RI, Paša-Tolić L, Arntzen MØ, Eijsink VGH, Koropatkin NM, Hess M, Wrighton KC, Pope PB.

Microbiome. 2018 Mar 1;6(1):44. doi: 10.1186/s40168-018-0421-8.

18.

Salmonella-Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut.

Wu J, Sabag-Daigle A, Borton MA, Kop LFM, Szkoda BE, Deatherage Kaiser BL, Lindemann SR, Renslow RS, Wei S, Nicora CD, Weitz KK, Kim YM, Adkins JN, Metz TO, Boyaka P, Gopalan V, Wrighton KC, Wysocki VH, Ahmer BMM.

Infect Immun. 2018 Apr 23;86(5). pii: e00945-17. doi: 10.1128/IAI.00945-17. Print 2018 May.

19.

Identification of Bacterial Species That Can Utilize Fructose-Asparagine.

Sabag-Daigle A, Wu J, Borton MA, Sengupta A, Gopalan V, Wrighton KC, Wysocki VH, Ahmer BMM.

Appl Environ Microbiol. 2018 Feb 14;84(5). pii: e01957-17. doi: 10.1128/AEM.01957-17. Print 2018 Mar 1.

20.

Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions.

Angle JC, Morin TH, Solden LM, Narrowe AB, Smith GJ, Borton MA, Rey-Sanchez C, Daly RA, Mirfenderesgi G, Hoyt DW, Riley WJ, Miller CS, Bohrer G, Wrighton KC.

Nat Commun. 2017 Nov 16;8(1):1567. doi: 10.1038/s41467-017-01753-4.

21.

Finding life's missing pieces.

Solden LM, Wrighton KC.

Nat Microbiol. 2017 Nov;2(11):1458-1459. doi: 10.1038/s41564-017-0048-8. No abstract available.

PMID:
29070823
22.

Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities.

Danczak RE, Johnston MD, Kenah C, Slattery M, Wrighton KC, Wilkins MJ.

Microbiome. 2017 Sep 2;5(1):112. doi: 10.1186/s40168-017-0331-1.

23.

Draft Genome Sequences of Multiple Frackibacter Strains Isolated from Hydraulically Fractured Shale Environments.

Booker AE, Johnston MD, Daly RA, Wrighton KC, Wilkins MJ.

Genome Announc. 2017 Aug 10;5(32). pii: e00608-17. doi: 10.1128/genomeA.00608-17.

24.

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales.

Booker AE, Borton MA, Daly RA, Welch SA, Nicora CD, Hoyt DW, Wilson T, Purvine SO, Wolfe RA, Sharma S, Mouser PJ, Cole DR, Lipton MS, Wrighton KC, Wilkins MJ.

mSphere. 2017 Jul 5;2(4). pii: e00257-17. doi: 10.1128/mSphereDirect.00257-17. eCollection 2017 Jul-Aug.

25.

Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome.

Borton MA, Sabag-Daigle A, Wu J, Solden LM, O'Banion BS, Daly RA, Wolfe RA, Gonzalez JF, Wysocki VH, Ahmer BMM, Wrighton KC.

Microbiome. 2017 Apr 27;5(1):47. doi: 10.1186/s40168-017-0264-8.

26.

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils.

Narrowe AB, Angle JC, Daly RA, Stefanik KC, Wrighton KC, Miller CS.

Environ Microbiol. 2017 Jun;19(6):2192-2209. doi: 10.1111/1462-2920.13703. Epub 2017 Mar 28.

PMID:
28217877
27.

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11.

Solden LM, Hoyt DW, Collins WB, Plank JE, Daly RA, Hildebrand E, Beavers TJ, Wolfe R, Nicora CD, Purvine SO, Carstensen M, Lipton MS, Spalinger DE, Firkins JL, Wolfe BA, Wrighton KC.

ISME J. 2017 Mar;11(3):691-703. doi: 10.1038/ismej.2016.150. Epub 2016 Dec 13.

28.

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria.

Wrighton KC, Castelle CJ, Varaljay VA, Satagopan S, Brown CT, Wilkins MJ, Thomas BC, Sharon I, Williams KH, Tabita FR, Banfield JF.

ISME J. 2016 Nov;10(11):2702-2714. doi: 10.1038/ismej.2016.53. Epub 2016 May 3.

29.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales.

Daly RA, Borton MA, Wilkins MJ, Hoyt DW, Kountz DJ, Wolfe RA, Welch SA, Marcus DN, Trexler RV, MacRae JD, Krzycki JA, Cole DR, Mouser PJ, Wrighton KC.

Nat Microbiol. 2016 Sep 5;1:16146. doi: 10.1038/nmicrobiol.2016.146.

PMID:
27595198
30.

Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface.

Mouser PJ, Borton M, Darrah TH, Hartsock A, Wrighton KC.

FEMS Microbiol Ecol. 2016 Nov;92(11). pii: fiw166. doi: 10.1093/femsec/fiw166. Epub 2016 Aug 8. Review.

PMID:
27507739
31.

Functional metagenomic selection of ribulose 1, 5-bisphosphate carboxylase/oxygenase from uncultivated bacteria.

Varaljay VA, Satagopan S, North JA, Witte B, Dourado MN, Anantharaman K, Arbing MA, Hoeft McCann S, Oremland RS, Banfield JF, Wrighton KC, Tabita FR.

Environ Microbiol. 2016 Apr;18(4):1187-99. doi: 10.1111/1462-2920.13138. Epub 2016 Jan 21.

32.

Unusual biology across a group comprising more than 15% of domain Bacteria.

Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, Wilkins MJ, Wrighton KC, Williams KH, Banfield JF.

Nature. 2015 Jul 9;523(7559):208-11. doi: 10.1038/nature14486. Epub 2015 Jun 15.

33.

Diverse uncultivated ultra-small bacterial cells in groundwater.

Luef B, Frischkorn KR, Wrighton KC, Holman HY, Birarda G, Thomas BC, Singh A, Williams KH, Siegerist CE, Tringe SG, Downing KH, Comolli LR, Banfield JF.

Nat Commun. 2015 Feb 27;6:6372. doi: 10.1038/ncomms7372.

PMID:
25721682
34.

Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.

Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe SG, Singh A, Markillie LM, Taylor RC, Williams KH, Banfield JF.

Curr Biol. 2015 Mar 16;25(6):690-701. doi: 10.1016/j.cub.2015.01.014. Epub 2015 Feb 19.

35.

Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis.

Merkley ED, Wrighton KC, Castelle CJ, Anderson BJ, Wilkins MJ, Shah V, Arbour T, Brown JN, Singer SW, Smith RD, Lipton MS.

J Proteome Res. 2015 Mar 6;14(3):1361-75. doi: 10.1021/pr500983v. Epub 2015 Feb 3.

PMID:
25496566
36.

Trends and future challenges in sampling the deep terrestrial biosphere.

Wilkins MJ, Daly RA, Mouser PJ, Trexler R, Sharma S, Cole DR, Wrighton KC, Biddle JF, Denis EH, Fredrickson JK, Kieft TL, Onstott TC, Peterson L, Pfiffner SM, Phelps TJ, Schrenk MO.

Front Microbiol. 2014 Sep 12;5:481. doi: 10.3389/fmicb.2014.00481. eCollection 2014.

37.

Evidence of Geobacter-associated phage in a uranium-contaminated aquifer.

Holmes DE, Giloteaux L, Chaurasia AK, Williams KH, Luef B, Wilkins MJ, Wrighton KC, Thompson CA, Comolli LR, Lovley DR.

ISME J. 2015 Feb;9(2):333-46. doi: 10.1038/ismej.2014.128. Epub 2014 Aug 1.

38.

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
39.

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.

40.

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling.

Hug LA, Castelle CJ, Wrighton KC, Thomas BC, Sharon I, Frischkorn KR, Williams KH, Tringe SG, Banfield JF.

Microbiome. 2013 Aug 5;1(1):22. doi: 10.1186/2049-2618-1-22.

41.

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.

42.

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria.

Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield JF, Ley RE.

Elife. 2013 Oct 1;2:e01102. doi: 10.7554/eLife.01102.

43.

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment.

Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF.

Nat Commun. 2013;4:2120. doi: 10.1038/ncomms3120.

44.

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
45.

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.

46.

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater.

Holmes DE, Giloteaux L, Williams KH, Wrighton KC, Wilkins MJ, Thompson CA, Roper TJ, Long PE, Lovley DR.

ISME J. 2013 Jul;7(7):1286-98. doi: 10.1038/ismej.2013.20. Epub 2013 Feb 28.

47.

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.

48.

Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth.

Luef B, Fakra SC, Csencsits R, Wrighton KC, Williams KH, Wilkins MJ, Downing KH, Long PE, Comolli LR, Banfield JF.

ISME J. 2013 Feb;7(2):338-50. doi: 10.1038/ismej.2012.103. Epub 2012 Oct 4.

49.

Characterization and transcription of arsenic respiration and resistance genes during in situ uranium bioremediation.

Giloteaux L, Holmes DE, Williams KH, Wrighton KC, Wilkins MJ, Montgomery AP, Smith JA, Orellana R, Thompson CA, Roper TJ, Long PE, Lovley DR.

ISME J. 2013 Feb;7(2):370-83. doi: 10.1038/ismej.2012.109. Epub 2012 Oct 4.

50.

Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla.

Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, Long PE, Banfield JF.

Science. 2012 Sep 28;337(6102):1661-5. Erratum in: Science. 2012 Nov 9;338(6108):742.

PMID:
23019650

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