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Items: 1 to 50 of 56

1.

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.

Brewer TE, Aronson EL, Arogyaswamy K, Billings SA, Botthoff JK, Campbell AN, Dove NC, Fairbanks D, Gallery RE, Hart SC, Kaye J, King G, Logan G, Lohse KA, Maltz MR, Mayorga E, O'Neill C, Owens SM, Packman A, Pett-Ridge J, Plante AF, Richter DD, Silver WL, Yang WH, Fierer N.

MBio. 2019 Oct 1;10(5). pii: e01318-19. doi: 10.1128/mBio.01318-19.

2.

Manganese co-localizes with calcium and phosphorus in Chlamydomonas acidocalcisomes and is mobilized in Mn-deficient conditions.

Tsednee M, Castruita M, Salomé PA, Sharma A, Lewis BE, Schmollinger SR, Strenkert D, Holbrook K, Otegui MS, Khatua K, Das S, Datta A, Chen S, Ramon C, Ralle M, Weber PK, Stemmler TL, Pett-Ridge J, Hoffman BM, Merchant SS.

J Biol Chem. 2019 Sep 16. pii: jbc.RA119.009130. doi: 10.1074/jbc.RA119.009130. [Epub ahead of print]

3.

Reply to Krishna et al.: Resolving age-related changes in nitrogen fixation and mineral weathering by Alnus tree species.

Perakis SS, Pett-Ridge JC.

Proc Natl Acad Sci U S A. 2019 Oct 1;116(40):19789-19790. doi: 10.1073/pnas.1911688116. Epub 2019 Aug 29. No abstract available.

PMID:
31467170
4.

Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS.

Mayali X, Weber PK, Nuccio E, Lietard J, Somoza M, Blazewicz SJ, Pett-Ridge J.

Methods Mol Biol. 2019;2046:71-87. doi: 10.1007/978-1-4939-9721-3_6.

PMID:
31407297
5.

EcoFABs: advancing microbiome science through standardized fabricated ecosystems.

Zengler K, Hofmockel K, Baliga NS, Behie SW, Bernstein HC, Brown JB, Dinneny JR, Floge SA, Forry SP, Hess M, Jackson SA, Jansson C, Lindemann SR, Pett-Ridge J, Maranas C, Venturelli OS, Wallenstein MD, Shank EA, Northen TR.

Nat Methods. 2019 Jul;16(7):567-571. doi: 10.1038/s41592-019-0465-0. No abstract available.

6.

Evolutionary history constrains microbial traits across environmental variation.

Morrissey EM, Mau RL, Hayer M, Liu XA, Schwartz E, Dijkstra P, Koch BJ, Allen K, Blazewicz SJ, Hofmockel K, Pett-Ridge J, Hungate BA.

Nat Ecol Evol. 2019 Jul;3(7):1064-1069. doi: 10.1038/s41559-019-0918-y. Epub 2019 Jun 17.

PMID:
31209289
7.

Reply to Lambers et al.: How does nitrogen-fixing red alder eat rocks?

Perakis SS, Pett-Ridge JC.

Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11577-11578. doi: 10.1073/pnas.1906596116. Epub 2019 Jun 4. No abstract available.

PMID:
31164426
8.

System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris.

Navid A, Jiao Y, Wong SE, Pett-Ridge J.

BMC Bioinformatics. 2019 May 9;20(1):233. doi: 10.1186/s12859-019-2844-z.

9.

Predictive genomic traits for bacterial growth in culture versus actual growth in soil.

Li J, Mau RL, Dijkstra P, Koch BJ, Schwartz E, Liu XA, Morrissey EM, Blazewicz SJ, Pett-Ridge J, Stone BW, Hayer M, Hungate BA.

ISME J. 2019 Sep;13(9):2162-2172. doi: 10.1038/s41396-019-0422-z. Epub 2019 May 3.

PMID:
31053828
10.

Underlying lithology controls trace metal mobilization during redox fluctuations.

King EK, Thompson A, Pett-Ridge JC.

Sci Total Environ. 2019 May 15;665:1147-1157. doi: 10.1016/j.scitotenv.2019.02.192. Epub 2019 Feb 14.

PMID:
30893746
11.

Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle.

Ceja-Navarro JA, Karaoz U, Bill M, Hao Z, White RA 3rd, Arellano A, Ramanculova L, Filley TR, Berry TD, Conrad ME, Blackwell M, Nicora CD, Kim YM, Reardon PN, Lipton MS, Adkins JN, Pett-Ridge J, Brodie EL.

Nat Microbiol. 2019 May;4(5):864-875. doi: 10.1038/s41564-019-0384-y. Epub 2019 Mar 11.

12.

Nitrogen-fixing red alder trees tap rock-derived nutrients.

Perakis SS, Pett-Ridge JC.

Proc Natl Acad Sci U S A. 2019 Mar 12;116(11):5009-5014. doi: 10.1073/pnas.1814782116. Epub 2019 Feb 25.

13.

Redox Fluctuations Control the Coupled Cycling of Iron and Carbon in Tropical Forest Soils.

Bhattacharyya A, Campbell AN, Tfaily MM, Lin Y, Kukkadapu RK, Silver WL, Nico PS, Pett-Ridge J.

Environ Sci Technol. 2018 Dec 18;52(24):14129-14139. doi: 10.1021/acs.est.8b03408. Epub 2018 Dec 7.

PMID:
30451506
14.

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat.

Lee JZ, Everroad RC, Karaoz U, Detweiler AM, Pett-Ridge J, Weber PK, Prufert-Bebout L, Bebout BM.

PLoS One. 2018 Sep 11;13(9):e0202792. doi: 10.1371/journal.pone.0202792. eCollection 2018.

15.

Microbial community assembly differs across minerals in a rhizosphere microcosm.

Whitman T, Neurath R, Perera A, Chu-Jacoby I, Ning D, Zhou J, Nico P, Pett-Ridge J, Firestone M.

Environ Microbiol. 2018 Dec;20(12):4444-4460. doi: 10.1111/1462-2920.14366. Epub 2018 Sep 10.

16.

Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions.

Samo TJ, Kimbrel JA, Nilson DJ, Pett-Ridge J, Weber PK, Mayali X.

Environ Microbiol. 2018 Dec;20(12):4385-4400. doi: 10.1111/1462-2920.14357. Epub 2018 Oct 24.

PMID:
30022580
17.

Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease.

Ackerman CM, Weber PK, Xiao T, Thai B, Kuo TJ, Zhang E, Pett-Ridge J, Chang CJ.

Metallomics. 2018 Mar 1;10(3):474-485. doi: 10.1039/c7mt00349h. Epub 2018 Mar 6.

18.

Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate.

D'haeseleer P, Lee JZ, Prufert-Bebout L, Burow LC, Detweiler AM, Weber PK, Karaoz U, Brodie EL, Glavina Del Rio T, Tringe SG, Bebout BM, Pett-Ridge J.

Stand Genomic Sci. 2017 Nov 15;12:67. doi: 10.1186/s40793-017-0279-6. eCollection 2017.

19.

Phylogenetically conserved resource partitioning in the coastal microbial loop.

Bryson S, Li Z, Chavez F, Weber PK, Pett-Ridge J, Hettich RL, Pan C, Mayali X, Mueller RS.

ISME J. 2017 Dec;11(12):2781-2792. doi: 10.1038/ismej.2017.128. Epub 2017 Aug 11.

20.

Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota.

Warren MJ, Lin X, Gaby JC, Kretz CB, Kolton M, Morton PL, Pett-Ridge J, Weston DJ, Schadt CW, Kostka JE, Glass JB.

Appl Environ Microbiol. 2017 Aug 17;83(17). pii: e01174-17. doi: 10.1128/AEM.01174-17. Print 2017 Sep 1.

21.

Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton.

Bryson S, Li Z, Pett-Ridge J, Hettich RL, Mayali X, Pan C, Mueller RS.

mSystems. 2016 Apr 26;1(2). pii: e00027-15. eCollection 2016 Mar-Apr.

22.

Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria.

Everroad RC, Stuart RK, Bebout BM, Detweiler AM, Lee JZ, Woebken D, Prufert-Bebout L, Pett-Ridge J.

Stand Genomic Sci. 2016 Aug 24;11(1):53. doi: 10.1186/s40793-016-0174-6. eCollection 2016.

23.

Tracking microbial interactions with NanoSIMS.

Musat N, Musat F, Weber PK, Pett-Ridge J.

Curr Opin Biotechnol. 2016 Oct;41:114-121. doi: 10.1016/j.copbio.2016.06.007. Epub 2016 Jul 12. Review.

PMID:
27419912
24.

Light Regimes Shape Utilization of Extracellular Organic C and N in a Cyanobacterial Biofilm.

Stuart RK, Mayali X, Boaro AA, Zemla A, Everroad RC, Nilson D, Weber PK, Lipton M, Bebout BM, Pett-Ridge J, Thelen MP.

MBio. 2016 Jun 28;7(3). pii: e00650-16. doi: 10.1128/mBio.00650-16.

25.

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass.

Nuccio EE, Anderson-Furgeson J, Estera KY, Pett-Ridge J, De Valpine P, Brodie EL, Firestone MK.

Ecology. 2016 May;97(5):1307-18.

26.

Nitrogen enrichment regulates calcium sources in forests.

Hynicka JD, Pett-Ridge JC, Perakis SS.

Glob Chang Biol. 2016 Dec;22(12):4067-4079. doi: 10.1111/gcb.13335. Epub 2016 Jun 21.

PMID:
27135298
27.

Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer.

Moyes AB, Kueppers LM, Pett-Ridge J, Carper DL, Vandehey N, O'Neil J, Frank AC.

New Phytol. 2016 Apr;210(2):657-68. doi: 10.1111/nph.13850. Epub 2016 Feb 1.

28.

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.

Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP, Dekas AE, Grasby SE, Brady AL, Dong H, Briggs BR, Li WJ, Goudeau D, Malmstrom R, Pati A, Pett-Ridge J, Rubin EM, Woyke T, Kyrpides NC, Ivanova NN.

Nat Commun. 2016 Jan 27;7:10476. doi: 10.1038/ncomms10476.

29.

Cyanobacterial reuse of extracellular organic carbon in microbial mats.

Stuart RK, Mayali X, Lee JZ, Craig Everroad R, Hwang M, Bebout BM, Weber PK, Pett-Ridge J, Thelen MP.

ISME J. 2016 May;10(5):1240-51. doi: 10.1038/ismej.2015.180. Epub 2015 Oct 23.

30.

Long-term litter decomposition controlled by manganese redox cycling.

Keiluweit M, Nico P, Harmon ME, Mao J, Pett-Ridge J, Kleber M.

Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):E5253-60. doi: 10.1073/pnas.1508945112. Epub 2015 Sep 8.

31.

Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons.

Shi S, Nuccio E, Herman DJ, Rijkers R, Estera K, Li J, da Rocha UN, He Z, Pett-Ridge J, Brodie EL, Zhou J, Firestone M.

MBio. 2015 Aug 4;6(4):e00746. doi: 10.1128/mBio.00746-15.

32.

Metagenome sequencing of a coastal marine microbial community from monterey bay, california.

Mueller RS, Bryson S, Kieft B, Li Z, Pett-Ridge J, Chavez F, Hettich RL, Pan C, Mayali X.

Genome Announc. 2015 Apr 30;3(2). pii: e00341-15. doi: 10.1128/genomeA.00341-15.

33.

Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas.

Hong-Hermesdorf A, Miethke M, Gallaher SD, Kropat J, Dodani SC, Chan J, Barupala D, Domaille DW, Shirasaki DI, Loo JA, Weber PK, Pett-Ridge J, Stemmler TL, Chang CJ, Merchant SS.

Nat Chem Biol. 2015 Mar;11(3):235. doi: 10.1038/nchembio0315-235c. No abstract available.

34.

Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas.

Hong-Hermesdorf A, Miethke M, Gallaher SD, Kropat J, Dodani SC, Chan J, Barupala D, Domaille DW, Shirasaki DI, Loo JA, Weber PK, Pett-Ridge J, Stemmler TL, Chang CJ, Merchant SS.

Nat Chem Biol. 2014 Dec;10(12):1034-42. doi: 10.1038/nchembio.1662. Epub 2014 Oct 26. Erratum in: Nat Chem Biol. 2015 Mar;11(3):235.

35.

Revisiting N₂ fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach.

Woebken D, Burow LC, Behnam F, Mayali X, Schintlmeister A, Fleming ED, Prufert-Bebout L, Singer SW, Cortés AL, Hoehler TM, Pett-Ridge J, Spormann AM, Wagner M, Weber PK, Bebout BM.

ISME J. 2015 Feb;9(2):485-96. doi: 10.1038/ismej.2014.144. Epub 2014 Oct 10.

36.

Phylogenetic patterns in the microbial response to resource availability: amino acid incorporation in San Francisco Bay.

Mayali X, Weber PK, Mabery S, Pett-Ridge J.

PLoS One. 2014 Apr 21;9(4):e95842. doi: 10.1371/journal.pone.0095842. eCollection 2014.

37.

Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community.

Burow LC, Woebken D, Marshall IP, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Bebout BM, Weber PK, Hoehler TM.

Geobiology. 2014 May;12(3):221-30. doi: 10.1111/gbi.12080.

PMID:
24730641
38.

Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats.

Lee JZ, Burow LC, Woebken D, Everroad RC, Kubo MD, Spormann AM, Weber PK, Pett-Ridge J, Bebout BM, Hoehler TM.

Front Microbiol. 2014 Feb 26;5:61. doi: 10.3389/fmicb.2014.00061. eCollection 2014.

39.

Correlated SEM, FIB-SEM, TEM, and NanoSIMS imaging of microbes from the hindgut of a lower termite: methods for in situ functional and ecological studies of uncultivable microbes.

Carpenter KJ, Weber PK, Davisson ML, Pett-Ridge J, Haverty MI, Keeling PJ.

Microsc Microanal. 2013 Dec;19(6):1490-501. doi: 10.1017/S1431927613013482. Epub 2013 Oct 11.

PMID:
24119340
40.

Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus.

Ceja-Navarro JA, Nguyen NH, Karaoz U, Gross SR, Herman DJ, Andersen GL, Bruns TD, Pett-Ridge J, Blackwell M, Brodie EL.

ISME J. 2014 Jan;8(1):6-18. doi: 10.1038/ismej.2013.134. Epub 2013 Aug 29.

41.

Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1.

Everroad RC, Woebken D, Singer SW, Burow LC, Kyrpides N, Woyke T, Goodwin L, Detweiler A, Prufert-Bebout L, Pett-Ridge J.

Genome Announc. 2013 Aug 1;1(4). pii: e00527-13. doi: 10.1128/genomeA.00527-13.

42.

Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil.

Pett-Ridge J, Petersen DG, Nuccio E, Firestone MK.

FEMS Microbiol Ecol. 2013 Jul;85(1):179-94. doi: 10.1111/1574-6941.12111. Epub 2013 Apr 4.

43.

An arbuscular mycorrhizal fungus significantly modifies the soil bacterial community and nitrogen cycling during litter decomposition.

Nuccio EE, Hodge A, Pett-Ridge J, Herman DJ, Weber PK, Firestone MK.

Environ Microbiol. 2013 Jun;15(6):1870-81. doi: 10.1111/1462-2920.12081. Epub 2013 Jan 30.

PMID:
23360621
44.

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics.

Burow LC, Woebken D, Marshall IP, Lindquist EA, Bebout BM, Prufert-Bebout L, Hoehler TM, Tringe SG, Pett-Ridge J, Weber PK, Spormann AM, Singer SW.

ISME J. 2013 Apr;7(4):817-29. doi: 10.1038/ismej.2012.150. Epub 2012 Nov 29.

45.

Taxon-specific C/N relative use efficiency for amino acids in an estuarine community.

Mayali X, Weber PK, Pett-Ridge J.

FEMS Microbiol Ecol. 2013 Feb;83(2):402-12. doi: 10.1111/j.1574-6941.12000.x. Epub 2012 Sep 20.

46.

NanoSIP: NanoSIMS applications for microbial biology.

Pett-Ridge J, Weber PK.

Methods Mol Biol. 2012;881:375-408. doi: 10.1007/978-1-61779-827-6_13.

PMID:
22639220
47.

Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis.

Woebken D, Burow LC, Prufert-Bebout L, Bebout BM, Hoehler TM, Pett-Ridge J, Spormann AM, Weber PK, Singer SW.

ISME J. 2012 Jul;6(7):1427-39. doi: 10.1038/ismej.2011.200. Epub 2012 Jan 12.

48.

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use.

Mayali X, Weber PK, Brodie EL, Mabery S, Hoeprich PD, Pett-Ridge J.

ISME J. 2012 Jun;6(6):1210-21. doi: 10.1038/ismej.2011.175. Epub 2011 Dec 8.

49.

Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay.

Burow LC, Woebken D, Bebout BM, McMurdie PJ, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Weber PK, Hoehler TM.

ISME J. 2012 Apr;6(4):863-74. doi: 10.1038/ismej.2011.142. Epub 2011 Oct 20.

50.

Nitrogen mineralization and assimilation at millimeter scales.

Myrold DD, Pett-Ridge J, Bottomley PJ.

Methods Enzymol. 2011;496:91-114. doi: 10.1016/B978-0-12-386489-5.00004-X. Review.

PMID:
21514461

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