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Items: 1 to 50 of 79

1.

Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments.

Smith HJ, Zelaya AJ, De León KB, Chakraborty R, Elias DA, Hazen TC, Arkin AP, Cunningham AB, Fields MW.

FEMS Microbiol Ecol. 2018 Dec 1;94(12). doi: 10.1093/femsec/fiy191.

2.

Microbial community changes during a toxic cyanobacterial bloom in an alkaline Hungarian lake.

Bell TAS, Sen-Kilic E, Felföldi T, Vasas G, Fields MW, Peyton BM.

Antonie Van Leeuwenhoek. 2018 Dec;111(12):2425-2440. doi: 10.1007/s10482-018-1132-7. Epub 2018 Aug 1.

PMID:
30069722
3.

Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia.

Carlson RP, Beck AE, Phalak P, Fields MW, Gedeon T, Hanley L, Harcombe WR, Henson MA, Heys JJ.

Biochem Soc Trans. 2018 Apr 17;46(2):269-284. doi: 10.1042/BST20170242. Epub 2018 Feb 22. Review.

PMID:
29472366
4.

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, Elias DA, Watson DB, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin AP, Zhou J.

MBio. 2018 Feb 20;9(1). pii: e02435-17. doi: 10.1128/mBio.02435-17.

5.

Cr(VI) reduction and physiological toxicity are impacted by resource ratio in Desulfovibrio vulgaris.

Franco LC, Steinbeisser S, Zane GM, Wall JD, Fields MW.

Appl Microbiol Biotechnol. 2018 Mar;102(6):2839-2850. doi: 10.1007/s00253-017-8724-4. Epub 2018 Feb 10.

6.

Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough.

De León KB, Zane GM, Trotter VV, Krantz GP, Arkin AP, Butland GP, Walian PJ, Fields MW, Wall JD.

MBio. 2017 Oct 17;8(5). pii: e01696-17. doi: 10.1128/mBio.01696-17.

7.

Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments.

McKay LJ, Hatzenpichler R, Inskeep WP, Fields MW.

Sci Rep. 2017 Aug 3;7(1):7252. doi: 10.1038/s41598-017-07354-x.

8.

Systems biology guided by XCMS Online metabolomics.

Huan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G.

Nat Methods. 2017 Apr 27;14(5):461-462. doi: 10.1038/nmeth.4260. No abstract available.

9.

Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds.

Hwang C, Copeland A, Lucas S, Lapidus A, Barry K, Detter JC, Glavina Del Rio T, Hammon N, Israni S, Dalin E, Tice H, Pitluck S, Chertkov O, Brettin T, Bruce D, Han C, Schmutz J, Larimer F, Land ML, Hauser L, Kyrpides N, Mikhailova N, Ye Q, Zhou J, Richardson P, Fields MW.

Genome Announc. 2016 Nov 3;4(6). pii: e01226-16. doi: 10.1128/genomeA.01226-16.

10.

Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses.

Montenegro-Burke JR, Phommavongsay T, Aisporna AE, Huan T, Rinehart D, Forsberg E, Poole FL, Thorgersen MP, Adams MW, Krantz G, Fields MW, Northen TR, Robbins PD, Niedernhofer LJ, Lairson L, Benton HP, Siuzdak G.

Anal Chem. 2016 Oct 4;88(19):9753-9758. Epub 2016 Sep 15.

11.

Engineering microbial consortia for controllable outputs.

Lindemann SR, Bernstein HC, Song HS, Fredrickson JK, Fields MW, Shou W, Johnson DR, Beliaev AS.

ISME J. 2016 Sep;10(9):2077-84. doi: 10.1038/ismej.2016.26. Epub 2016 Mar 11.

12.

A Lipid-Accumulating Alga Maintains Growth in Outdoor, Alkaliphilic Raceway Pond with Mixed Microbial Communities.

Bell TA, Prithiviraj B, Wahlen BD, Fields MW, Peyton BM.

Front Microbiol. 2016 Jan 7;6:1480. doi: 10.3389/fmicb.2015.01480. eCollection 2015.

13.

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.

Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JD, Wu L, He Z, Chain PS, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, Arkin AP, Zhou J.

Front Microbiol. 2015 Oct 31;6:1205. doi: 10.3389/fmicb.2015.01205. eCollection 2015.

14.

Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum.

De León KB, Utturkar SM, Camilleri LB, Elias DA, Arkin AP, Fields MW, Brown SD, Wall JD.

Genome Announc. 2015 Sep 24;3(5). pii: e01090-15. doi: 10.1128/genomeA.01090-15.

15.

Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea.

Barnhart EP, McClure MA, Johnson K, Cleveland S, Hunt KA, Fields MW.

Sci Rep. 2015 Aug 3;5:12498. doi: 10.1038/srep12498.

16.

Natural bacterial communities serve as quantitative geochemical biosensors.

Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA Jr, Preheim SP, Sanders MC, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC.

MBio. 2015 May 12;6(3):e00326-15. doi: 10.1128/mBio.00326-15.

17.

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris.

Zhou A, Hillesland KL, He Z, Schackwitz W, Tu Q, Zane GM, Ma Q, Qu Y, Stahl DA, Wall JD, Hazen TC, Fields MW, Arkin AP, Zhou J.

ISME J. 2015 Nov;9(11):2360-72. doi: 10.1038/ismej.2015.45. Epub 2015 Apr 7.

18.

A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction.

Zhang P, Van Nostrand JD, He Z, Chakraborty R, Deng Y, Curtis D, Fields MW, Hazen TC, Arkin AP, Zhou J.

Environ Sci Technol. 2015 Nov 3;49(21):12922-31. doi: 10.1021/acs.est.5b00024. Epub 2015 Oct 23.

PMID:
25835088
19.

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.

Ramsay BD, Hwang C, Woo HL, Carroll SL, Lucas S, Han J, Lapidus AL, Cheng JF, Goodwin LA, Pitluck S, Peters L, Chertkov O, Held B, Detter JC, Han CS, Tapia R, Land ML, Hauser LJ, Kyrpides NC, Ivanova NN, Mikhailova N, Pagani I, Woyke T, Arkin AP, Dehal P, Chivian D, Criddle CS, Wu W, Chakraborty R, Hazen TC, Fields MW.

Genome Announc. 2015 Mar 12;3(2). pii: e00092-15. doi: 10.1128/genomeA.00092-15.

20.

Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment.

Hwang C, Copeland A, Lucas S, Lapidus A, Barry K, Glavina Del Rio T, Dalin E, Tice H, Pitluck S, Sims D, Brettin T, Bruce DC, Detter JC, Han CS, Schmutz J, Larimer FW, Land ML, Hauser LJ, Kyrpides N, Lykidis A, Richardson P, Belieav A, Sanford RA, Löeffler FE, Fields MW.

Genome Announc. 2015 Jan 22;3(1). pii: e01449-14. doi: 10.1128/genomeA.01449-14.

21.

Comprehensive bioimaging with fluorinated nanoparticles using breathable liquids.

Kurczy ME, Zhu ZJ, Ivanisevic J, Schuyler AM, Lalwani K, Santidrian AF, David JM, Giddabasappa A, Roberts AJ, Olivos HJ, O'Brien PJ, Franco L, Fields MW, Paris LP, Friedlander M, Johnson CH, Epstein AA, Gendelman HE, Wood MR, Felding BH, Patti GJ, Spilker ME, Siuzdak G.

Nat Commun. 2015 Jan 20;6:5998. doi: 10.1038/ncomms6998.

22.

Biofilm growth mode promotes maximum carrying capacity and community stability during product inhibition syntrophy.

Brileya KA, Camilleri LB, Zane GM, Wall JD, Fields MW.

Front Microbiol. 2014 Dec 15;5:693. doi: 10.3389/fmicb.2014.00693. eCollection 2014.

23.

Autonomous metabolomics for rapid metabolite identification in global profiling.

Benton HP, Ivanisevic J, Mahieu NG, Kurczy ME, Johnson CH, Franco L, Rinehart D, Valentine E, Gowda H, Ubhi BK, Tautenhahn R, Gieschen A, Fields MW, Patti GJ, Siuzdak G.

Anal Chem. 2015 Jan 20;87(2):884-91. doi: 10.1021/ac5025649. Epub 2014 Dec 26.

24.

Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium.

Rajeev L, Luning EG, Altenburg S, Zane GM, Baidoo EE, Catena M, Keasling JD, Wall JD, Fields MW, Mukhopadhyay A.

Front Microbiol. 2014 Jul 29;5:382. doi: 10.3389/fmicb.2014.00382. eCollection 2014.

25.

3D-fluorescence in situ hybridization of intact, anaerobic biofilm.

Brileya KA, Camilleri LB, Fields MW.

Methods Mol Biol. 2014;1151:189-97. doi: 10.1007/978-1-4939-0554-6_13.

PMID:
24838887
26.

Correction: Strong inter-population cooperation leads to partner intermixing in microbial communities.

Momeni B, Brileya KA, Fields MW, Shou W.

Elife. 2014 Apr 16;3:e02945. doi: 10.7554/eLife.02945. No abstract available.

27.

Sources and resources: importance of nutrients, resource allocation, and ecology in microalgal cultivation for lipid accumulation.

Fields MW, Hise A, Lohman EJ, Bell T, Gardner RD, Corredor L, Moll K, Peyton BM, Characklis GW, Gerlach R.

Appl Microbiol Biotechnol. 2014 Jun;98(11):4805-16. doi: 10.1007/s00253-014-5694-7. Epub 2014 Apr 3. Review.

28.

Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park.

Bowen De León K, Gerlach R, Peyton BM, Fields MW.

Front Microbiol. 2013 Nov 12;4:330. doi: 10.3389/fmicb.2013.00330. eCollection 2013.

29.

Taxis toward hydrogen gas by Methanococcus maripaludis.

Brileya KA, Connolly JM, Downey C, Gerlach R, Fields MW.

Sci Rep. 2013 Nov 5;3:3140. doi: 10.1038/srep03140. Erratum in: Sci Rep. 2014;4:3690.

30.

Nutrient resupplementation arrests bio-oil accumulation in Phaeodactylum tricornutum.

Valenzuela J, Carlson RP, Gerlach R, Cooksey K, Peyton BM, Bothner B, Fields MW.

Appl Microbiol Biotechnol. 2013 Aug;97(15):7049-59. doi: 10.1007/s00253-013-5010-y. Epub 2013 Jun 15.

31.

Physiological and molecular analysis of carbon source supplementation and pH stress-induced lipid accumulation in the marine diatom Phaeodactylum tricornutum.

Mus F, Toussaint JP, Cooksey KE, Fields MW, Gerlach R, Peyton BM, Carlson RP.

Appl Microbiol Biotechnol. 2013 Apr;97(8):3625-42. doi: 10.1007/s00253-013-4747-7. Epub 2013 Mar 6.

PMID:
23463245
32.

Strong inter-population cooperation leads to partner intermixing in microbial communities.

Momeni B, Brileya KA, Fields MW, Shou W.

Elife. 2013 Jan 22;2:e00230. doi: 10.7554/eLife.00230. Erratum in: Elife. 2014;3:e02945.

33.

Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction.

Bowen De León K, Young ML, Camilleri LB, Brown SD, Skerker JM, Deutschbauer AM, Arkin AP, Fields MW.

J Bacteriol. 2012 Oct;194(19):5456-7. doi: 10.1128/JB.01224-12.

34.

Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum.

Valenzuela J, Mazurie A, Carlson RP, Gerlach R, Cooksey KE, Peyton BM, Fields MW.

Biotechnol Biofuels. 2012 Jun 6;5(1):40.

35.

Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.

Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou JZ, Arkin AP, Mukhopadhyay A, Fields MW.

BMC Genomics. 2012 Apr 16;13:138. doi: 10.1186/1471-2164-13-138.

36.

Quality-score refinement of SSU rRNA gene pyrosequencing differs across gene region for environmental samples.

Bowen De León K, Ramsay BD, Fields MW.

Microb Ecol. 2012 Aug;64(2):499-508. doi: 10.1007/s00248-012-0043-9. Epub 2012 Apr 5.

37.

Evaluation and remediation of bulk soap dispensers for biofilm.

Lorenz LA, Ramsay BD, Goeres DM, Fields MW, Zapka CA, Macinga DR.

Biofouling. 2012;28(1):99-109. doi: 10.1080/08927014.2011.653637.

PMID:
22257312
38.

Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough.

Zhou A, Chen YI, Zane GM, He Z, Hemme CL, Joachimiak MP, Baumohl JK, He Q, Fields MW, Arkin AP, Wall JD, Hazen TC, Zhou J.

Appl Environ Microbiol. 2012 Feb;78(4):1168-77. doi: 10.1128/AEM.05666-11. Epub 2011 Dec 9.

39.

Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields.

Hemme CL, Fields MW, He Q, Deng Y, Lin L, Tu Q, Mouttaki H, Zhou A, Feng X, Zuo Z, Ramsay BD, He Z, Wu L, Van Nostrand J, Xu J, Tang YJ, Wiegel J, Phelps TJ, Zhou J.

Appl Environ Microbiol. 2011 Nov;77(22):7998-8008. doi: 10.1128/AEM.05677-11. Epub 2011 Sep 23.

40.

Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth.

Sundararajan A, Kurowski J, Yan T, Klingeman DM, Joachimiak MP, Zhou J, Naranjo B, Gralnick JA, Fields MW.

Appl Environ Microbiol. 2011 Jul;77(13):4647-56. doi: 10.1128/AEM.03003-10. Epub 2011 May 20.

41.

Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production.

Hemme CL, Mouttaki H, Lee YJ, Zhang G, Goodwin L, Lucas S, Copeland A, Lapidus A, Glavina del Rio T, Tice H, Saunders E, Brettin T, Detter JC, Han CS, Pitluck S, Land ML, Hauser LJ, Kyrpides N, Mikhailova N, He Z, Wu L, Van Nostrand JD, Henrissat B, He Q, Lawson PA, Tanner RS, Lynd LR, Wiegel J, Fields MW, Arkin AP, Schadt CW, Stevenson BS, McInerney MJ, Yang Y, Dong H, Xing D, Ren N, Wang A, Huhnke RL, Mielenz JR, Ding SY, Himmel ME, Taghavi S, van der Lelie D, Rubin EM, Zhou J.

J Bacteriol. 2010 Dec;192(24):6494-6. doi: 10.1128/JB.01064-10. Epub 2010 Oct 1.

42.

Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough.

Zhou A, He Z, Redding-Johanson AM, Mukhopadhyay A, Hemme CL, Joachimiak MP, Luo F, Deng Y, Bender KS, He Q, Keasling JD, Stahl DA, Fields MW, Hazen TC, Arkin AP, Wall JD, Zhou J.

Environ Microbiol. 2010 Oct;12(10):2645-57. doi: 10.1111/j.1462-2920.2010.02234.x.

PMID:
20482586
43.

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community.

Hemme CL, Deng Y, Gentry TJ, Fields MW, Wu L, Barua S, Barry K, Tringe SG, Watson DB, He Z, Hazen TC, Tiedje JM, Rubin EM, Zhou J.

ISME J. 2010 May;4(5):660-72. doi: 10.1038/ismej.2009.154. Epub 2010 Feb 25.

PMID:
20182523
44.

Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation.

He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, Phan R, Mukhopadhyay A, Hemme CL, Huang K, Alm EJ, Fields MW, Wall J, Stahl D, Hazen TC, Keasling JD, Arkin AP, Zhou J.

Appl Environ Microbiol. 2010 Mar;76(5):1574-86. doi: 10.1128/AEM.02141-09. Epub 2009 Dec 28.

45.

Real-time molecular monitoring of chemical environment in obligate anaerobes during oxygen adaptive response.

Holman HY, Wozei E, Lin Z, Comolli LR, Ball DA, Borglin S, Fields MW, Hazen TC, Downing KH.

Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12599-604. doi: 10.1073/pnas.0902070106. Epub 2009 Jun 16.

46.

Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation.

Elias DA, Mukhopadhyay A, Joachimiak MP, Drury EC, Redding AM, Yen HC, Fields MW, Hazen TC, Arkin AP, Keasling JD, Wall JD.

Nucleic Acids Res. 2009 May;37(9):2926-39. doi: 10.1093/nar/gkp164. Epub 2009 Mar 17.

47.

Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths.

Hwang C, Wu W, Gentry TJ, Carley J, Corbin GA, Carroll SL, Watson DB, Jardine PM, Zhou J, Criddle CS, Fields MW.

ISME J. 2009 Jan;3(1):47-64. doi: 10.1038/ismej.2008.77. Epub 2008 Sep 4. Erratum in: ISME J. 2009 Jan;3(1):137.

PMID:
18769457
48.

Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness.

Wu L, Liu X, Fields MW, Thompson DK, Bagwell CE, Tiedje JM, Hazen TC, Zhou J.

ISME J. 2008 Jun;2(6):642-55. doi: 10.1038/ismej.2008.23. Epub 2008 Feb 28.

PMID:
18309358
49.

Hexavalent chromium reduction in Desulfovibrio vulgaris Hildenborough causes transitory inhibition of sulfate reduction and cell growth.

Klonowska A, Clark ME, Thieman SB, Giles BJ, Wall JD, Fields MW.

Appl Microbiol Biotechnol. 2008 Apr;78(6):1007-16. doi: 10.1007/s00253-008-1381-x. Epub 2008 Feb 12.

PMID:
18265973
50.

Biofilm formation in Desulfovibrio vulgaris Hildenborough is dependent upon protein filaments.

Clark ME, Edelmann RE, Duley ML, Wall JD, Fields MW.

Environ Microbiol. 2007 Nov;9(11):2844-54.

PMID:
17922767

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