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Items: 1 to 50 of 66

1.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6.

PMID:
31399723
2.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. No abstract available. Erratum in: Nat Biotechnol. 2019 Sep;37(9):1091.

PMID:
31341288
3.

Deciphering Biosignatures in Planetary Contexts.

Chan MA, Hinman NW, Potter-McIntyre SL, Schubert KE, Gillams RJ, Awramik SM, Boston PJ, Bower DM, Des Marais DJ, Farmer JD, Jia TZ, King PL, Hazen RM, Léveillé RJ, Papineau D, Rempfert KR, Sánchez-Román M, Spear JR, Southam G, Stern JC, Cleaves HJ.

Astrobiology. 2019 Sep;19(9):1075-1102. doi: 10.1089/ast.2018.1903. Epub 2019 Jul 22.

4.

Probing the geological source and biological fate of hydrogen in Yellowstone hot springs.

Lindsay MR, Colman DR, Amenabar MJ, Fristad KE, Fecteau KM, Debes RV 2nd, Spear JR, Shock EL, Hoehler TM, Boyd ES.

Environ Microbiol. 2019 Oct;21(10):3816-3830. doi: 10.1111/1462-2920.14730. Epub 2019 Jul 25.

PMID:
31276280
5.

Corrigendum: Exploring, Mapping, and Data Management Integration of Habitable Environments in Astrobiology.

Chan MA, Bowen BB, Corsetti FA, Farrand WH, Law ES, Newsom HE, Perl SM, Spear JR, Thompson DR.

Front Microbiol. 2019 May 29;10:1190. doi: 10.3389/fmicb.2019.01190. eCollection 2019.

6.

Exploring, Mapping, and Data Management Integration of Habitable Environments in Astrobiology.

Chan MA, Bowen BB, Corsetti FA, Farrand WH, Law ES, Newsom HE, Spear JR, Thompson DR.

Front Microbiol. 2019 Mar 5;10:147. doi: 10.3389/fmicb.2019.00147. eCollection 2019. Erratum in: Front Microbiol. 2019 May 29;10:1190.

7.

Physiological adaptations to serpentinization in the Samail Ophiolite, Oman.

Fones EM, Colman DR, Kraus EA, Nothaft DB, Poudel S, Rempfert KR, Spear JR, Templeton AS, Boyd ES.

ISME J. 2019 Jul;13(7):1750-1762. doi: 10.1038/s41396-019-0391-2. Epub 2019 Mar 12.

8.

Evidence for Biotic Perchlorate Reduction in Naturally Perchlorate-Rich Sediments of Pilot Valley Basin, Utah.

Lynch KL, Jackson WA, Rey K, Spear JR, Rosenzweig F, Munakata-Marr J.

Astrobiology. 2019 May;19(5):629-641. doi: 10.1089/ast.2018.1864. Epub 2019 Mar 1.

PMID:
30822097
9.

Draft Genome Sequence of Picocystis sp. Strain ML, Cultivated from Mono Lake, California.

Junkins EN, Stamps BW, Corsetti FA, Oremland RS, Spear JR, Stevenson BS.

Microbiol Resour Announc. 2019 Jan 24;8(4). pii: e01353-18. doi: 10.1128/MRA.01353-18. eCollection 2019 Jan.

10.

Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA.

Honeyman AS, Day ML, Spear JR.

PeerJ. 2018 Nov 21;6:e5961. doi: 10.7717/peerj.5961. eCollection 2018.

11.

Characterization of the Microbiome at the World's Largest Potable Water Reuse Facility.

Stamps BW, Leddy MB, Plumlee MH, Hasan NA, Colwell RR, Spear JR.

Front Microbiol. 2018 Oct 26;9:2435. doi: 10.3389/fmicb.2018.02435. eCollection 2018.

12.

Metabolic Capability and Phylogenetic Diversity of Mono Lake during a Bloom of the Eukaryotic Phototroph Picocystis sp. Strain ML.

Stamps BW, Nunn HS, Petryshyn VA, Oremland RS, Miller LG, Rosen MR, Bauer KW, Thompson KJ, Tookmanian EM, Waldeck AR, Loyd SJ, Johnson HA, Stevenson BS, Berelson WM, Corsetti FA, Spear JR.

Appl Environ Microbiol. 2018 Oct 17;84(21). pii: e01171-18. doi: 10.1128/AEM.01171-18. Print 2018 Nov 1.

13.

Low-Temperature Sulfidic-Ice Microbial Communities, Borup Fiord Pass, Canadian High Arctic.

Trivedi CB, Lau GE, Grasby SE, Templeton AS, Spear JR.

Front Microbiol. 2018 Jul 24;9:1622. doi: 10.3389/fmicb.2018.01622. eCollection 2018.

14.

Environmental and Biological Influences on Carbonate Precipitation Within Hot Spring Microbial Mats in Little Hot Creek, CA.

Wilmeth DT, Johnson HA, Stamps BW, Berelson WM, Stevenson BS, Nunn HS, Grim SL, Dillon ML, Paradis O, Corsetti FA, Spear JR.

Front Microbiol. 2018 Jul 13;9:1464. doi: 10.3389/fmicb.2018.01464. eCollection 2018.

15.

Microscale Biosignatures and Abiotic Mineral Authigenesis in Little Hot Creek, California.

Kraus EA, Beeler SR, Mors RA, Floyd JG; GeoBiology 2016, Stamps BW, Nunn HS, Stevenson BS, Johnson HA, Shapiro RS, Loyd SJ, Spear JR, Corsetti FA.

Front Microbiol. 2018 May 25;9:997. doi: 10.3389/fmicb.2018.00997. eCollection 2018.

16.

Carbonate-rich dendrolitic cones: insights into a modern analog for incipient microbialite formation, Little Hot Creek, Long Valley Caldera, California.

Bradley JA, Daille LK, Trivedi CB, Bojanowski CL, Stamps BW, Stevenson BS, Nunn HS, Johnson HA, Loyd SJ, Berelson WM, Corsetti FA, Spear JR.

NPJ Biofilms Microbiomes. 2017 Nov 21;3:32. doi: 10.1038/s41522-017-0041-2. eCollection 2017.

17.

Temporal characterization and statistical analysis of flowback and produced waters and their potential for reuse.

Oetjen K, Chan KE, Gulmark K, Christensen JH, Blotevogel J, Borch T, Spear JR, Cath TY, Higgins CP.

Sci Total Environ. 2018 Apr 1;619-620:654-664. doi: 10.1016/j.scitotenv.2017.11.078. Epub 2017 Nov 29.

PMID:
29156284
18.

The deep, hot biosphere: Twenty-five years of retrospection.

Colman DR, Poudel S, Stamps BW, Boyd ES, Spear JR.

Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):6895-6903. doi: 10.1073/pnas.1701266114.

19.

Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs across a Methanogenic Gradient.

Shelton JL, Akob DM, McIntosh JC, Fierer N, Spear JR, Warwick PD, McCray JE.

Front Microbiol. 2016 Sep 28;7:1535. eCollection 2016.

20.

Microbialite response to an anthropogenic salinity gradient in Great Salt Lake, Utah.

Lindsay MR, Anderson C, Fox N, Scofield G, Allen J, Anderson E, Bueter L, Poudel S, Sutherland K, Munson-McGee JH, Van Nostrand JD, Zhou J, Spear JR, Baxter BK, Lageson DR, Boyd ES.

Geobiology. 2017 Jan;15(1):131-145. doi: 10.1111/gbi.12201. Epub 2016 Jul 14.

21.

Sacrificing power for more cost-effective treatment: A techno-economic approach for engineering microbial fuel cells.

Stoll ZA, Ma Z, Trivedi CB, Spear JR, Xu P.

Chemosphere. 2016 Oct;161:10-18. doi: 10.1016/j.chemosphere.2016.06.072. Epub 2016 Jul 7.

PMID:
27395791
22.

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA.

Stanish LF, Hull NM, Robertson CE, Harris JK, Stevens MJ, Spear JR, Pace NR.

PLoS One. 2016 Jun 30;11(6):e0157966. doi: 10.1371/journal.pone.0157966. eCollection 2016.

23.

Using geochemical indicators to distinguish high biogeochemical activity in floodplain soils and sediments.

Kenwell A, Navarre-Sitchler A, Prugue R, Spear JR, Hering AS, Maxwell RM, Carroll RW, Williams KH.

Sci Total Environ. 2016 Sep 1;563-564:386-95. doi: 10.1016/j.scitotenv.2016.04.014. Epub 2016 May 1.

PMID:
27145490
24.

Antimicrobial activity and biologic potential of silver-substituted calcium phosphate constructs produced with self-propagating high-temperature synthesis.

Vollmer NL, Spear JR, Ayers RA.

J Mater Sci Mater Med. 2016 Jun;27(6):104. doi: 10.1007/s10856-016-5715-4. Epub 2016 Apr 19.

PMID:
27094319
25.

Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica.

Carr SA, Orcutt BN, Mandernack KW, Spear JR.

Front Microbiol. 2015 Aug 26;6:872. doi: 10.3389/fmicb.2015.00872. eCollection 2015.

26.

Low bone mineral density and risk of incident fracture in HIV-infected adults.

Battalora L, Buchacz K, Armon C, Overton ET, Hammer J, Patel P, Chmiel JS, Wood K, Bush TJ, Spear JR, Brooks JT, Young B; HIV Outpatient Study (HOPS) and SUN Study Investigators.

Antivir Ther. 2016;21(1):45-54. doi: 10.3851/IMP2979. Epub 2015 Jul 21.

PMID:
26194468
27.

Microbially influenced corrosion communities associated with fuel-grade ethanol environments.

Williamson CH, Jain LA, Mishra B, Olson DL, Spear JR.

Appl Microbiol Biotechnol. 2015 Aug;99(16):6945-57. doi: 10.1007/s00253-015-6729-4. Epub 2015 Jun 20.

28.

Disturbance opens recruitment sites for bacterial colonization in activated sludge.

Vuono DC, Munakata-Marr J, Spear JR, Drewes JE.

Environ Microbiol. 2016 Jan;18(1):87-99. doi: 10.1111/1462-2920.12824. Epub 2015 Apr 15.

PMID:
25727891
29.

Draft genome of a novel chlorobi member assembled by tetranucleotide binning of a hot spring metagenome.

Stamps BW, Corsetti FA, Spear JR, Stevenson BS.

Genome Announc. 2014 Sep 11;2(5). pii: e00897-14. doi: 10.1128/genomeA.00897-14.

30.

Disturbance and temporal partitioning of the activated sludge metacommunity.

Vuono DC, Benecke J, Henkel J, Navidi WC, Cath TY, Munakata-Marr J, Spear JR, Drewes JE.

ISME J. 2015 Feb;9(2):425-35. doi: 10.1038/ismej.2014.139. Epub 2014 Aug 15.

31.

Microbial response to single-cell protein production and brewery wastewater treatment.

Lee JZ, Logan A, Terry S, Spear JR.

Microb Biotechnol. 2015 Jan;8(1):65-76. doi: 10.1111/1751-7915.12128. Epub 2014 May 16.

32.

Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche.

Ricci JN, Coleman ML, Welander PV, Sessions AL, Summons RE, Spear JR, Newman DK.

ISME J. 2014 Mar;8(3):675-84. doi: 10.1038/ismej.2013.191. Epub 2013 Oct 24.

33.

Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry.

Inskeep WP, Jay ZJ, Herrgard MJ, Kozubal MA, Rusch DB, Tringe SG, Macur RE, Jennings Rd, Boyd ES, Spear JR, Roberto FF.

Front Microbiol. 2013 May 15;4:95. doi: 10.3389/fmicb.2013.00095. eCollection 2013.

34.

Bacterial abundance and composition in marine sediments beneath the Ross Ice Shelf, Antarctica.

Carr SA, Vogel SW, Dunbar RB, Brandes J, Spear JR, Levy R, Naish TR, Powell RD, Wakeham SG, Mandernack KW.

Geobiology. 2013 Jul;11(4):377-95. doi: 10.1111/gbi.12042. Epub 2013 May 20.

PMID:
23682649
35.

Metagenomic evidence for sulfur lithotrophy by Epsilonproteobacteria as the major energy source for primary productivity in a sub-aerial arctic glacial deposit, Borup Fiord Pass.

Wright KE, Williamson C, Grasby SE, Spear JR, Templeton AS.

Front Microbiol. 2013 Apr 22;4:63. doi: 10.3389/fmicb.2013.00063. eCollection 2013.

36.

Contrasting patterns of community assembly in the stratified water column of Great Salt Lake, Utah.

Meuser JE, Baxter BK, Spear JR, Peters JW, Posewitz MC, Boyd ES.

Microb Ecol. 2013 Aug;66(2):268-80. doi: 10.1007/s00248-013-0180-9. Epub 2013 Jan 25.

PMID:
23354179
37.

Surface orientation affects the direction of cone growth by Leptolyngbya sp. strain C1, a likely architect of coniform structures Octopus Spring (Yellowstone National Park).

Reyes K, Gonzalez NI 3rd, Stewart J, Ospino F, Nguyen D, Cho DT, Ghahremani N, Spear JR, Johnson HA.

Appl Environ Microbiol. 2013 Feb;79(4):1302-8. doi: 10.1128/AEM.03008-12. Epub 2012 Dec 14.

38.

Secondary metabolites produced by fungi derived from a microbial mat encountered in an iron-rich natural spring.

Gerea AL, Branscum KM, King JB, You J, Powell DR, Miller AN, Spear JR, Cichewicz RH.

Tetrahedron Lett. 2012 Aug 8;53(32):4202-4205. Epub 2012 Jun 8.

39.

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

Harris JK, Caporaso JG, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR.

ISME J. 2013 Jan;7(1):50-60. doi: 10.1038/ismej.2012.79. Epub 2012 Jul 26.

40.

Cyanobacterial construction of hot spring siliceous stromatolites in Yellowstone National Park.

Pepe-Ranney C, Berelson WM, Corsetti FA, Treants M, Spear JR.

Environ Microbiol. 2012 May;14(5):1182-97. doi: 10.1111/j.1462-2920.2012.02698.x. Epub 2012 Feb 22.

PMID:
22356555
41.

Phototrophic phylotypes dominate mesothermal microbial mats associated with hot springs in Yellowstone National Park.

Ross KA, Feazel LM, Robertson CE, Fathepure BZ, Wright KE, Turk-Macleod RM, Chan MM, Held NL, Spear JR, Pace NR.

Microb Ecol. 2012 Jul;64(1):162-70. doi: 10.1007/s00248-012-0012-3. Epub 2012 Feb 11.

PMID:
22327269
42.

Hot spring siliceous stromatolites from Yellowstone National Park: assessing growth rate and laminae formation.

Berelson WM, Corsetti FA, Pepe-Ranney C, Hammond DE, Beaumont W, Spear JR.

Geobiology. 2011 Sep;9(5):411-24. doi: 10.1111/j.1472-4669.2011.00288.x. Epub 2011 Jul 20.

PMID:
21777367
43.

Differences in lateral gene transfer in hypersaline versus thermal environments.

Rhodes ME, Spear JR, Oren A, House CH.

BMC Evol Biol. 2011 Jul 8;11:199. doi: 10.1186/1471-2148-11-199.

44.

Low temperature S(0) biomineralization at a supraglacial spring system in the Canadian High Arctic.

Gleeson DF, Williamson C, Grasby SE, Pappalardo RT, Spear JR, Templeton AS.

Geobiology. 2011 Jul;9(4):360-75. doi: 10.1111/j.1472-4669.2011.00283.x. Epub 2011 May 19.

PMID:
21592302
45.

A comparative molecular analysis of water-filled limestone sinkholes in north-eastern Mexico.

Sahl JW, Gary MO, Harris JK, Spear JR.

Environ Microbiol. 2011 Jan;13(1):226-240. doi: 10.1111/j.1462-2920.2010.02324.x. Epub 2010 Aug 25.

PMID:
20738374
46.

[FeFe]-hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism.

Boyd ES, Hamilton TL, Spear JR, Lavin M, Peters JW.

ISME J. 2010 Dec;4(12):1485-95. doi: 10.1038/ismej.2010.76. Epub 2010 Jun 10.

PMID:
20535223
47.

Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing.

Harris JK, Sahl JW, Castoe TA, Wagner BD, Pollock DD, Spear JR.

Appl Environ Microbiol. 2010 Jun;76(12):3863-8. doi: 10.1128/AEM.02585-09. Epub 2010 Apr 23.

48.

Novel microbial diversity retrieved by autonomous robotic exploration of the world's deepest vertical phreatic sinkhole.

Sahl JW, Fairfield N, Harris JK, Wettergreen D, Stone WC, Spear JR.

Astrobiology. 2010 Mar;10(2):201-13. doi: 10.1089/ast.2009.0378.

PMID:
20298146
49.

Microbial species richness and metabolic activities in hypersaline microbial mats: insight into biosignature formation through lithification.

Baumgartner LK, Dupraz C, Buckley DH, Spear JR, Pace NR, Visscher PT.

Astrobiology. 2009 Nov;9(9):861-74. doi: 10.1089/ast.2008.0329.

PMID:
19968463
50.

Microbial diversity in modern marine stromatolites, Highborne Cay, Bahamas.

Baumgartner LK, Spear JR, Buckley DH, Pace NR, Reid RP, Dupraz C, Visscher PT.

Environ Microbiol. 2009 Oct;11(10):2710-9. doi: 10.1111/j.1462-2920.2009.01998.x. Epub 2009 Jul 6.

PMID:
19601956

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