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Items: 1 to 50 of 266

1.

Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants.

Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown MR, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, Yang Y, Deng Y, Tu Q, Wang A; Global Water Microbiome Consortium, Zhang T, He Z, Keller J, Nielsen PH, Alvarez PJJ, Criddle CS, Wagner M, Tiedje JM, He Q, Curtis TP, Stahl DA, Alvarez-Cohen L, Rittmann BE, Wen X, Zhou J.

Nat Microbiol. 2019 Dec;4(12):2579. doi: 10.1038/s41564-019-0617-0.

PMID:
31728072
2.

Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons.

Wang B, Qin W, Ren Y, Zhou X, Jung MY, Han P, Eloe-Fadrosh EA, Li M, Zheng Y, Lu L, Yan X, Ji J, Liu Y, Liu L, Heiner C, Hall R, Martens-Habbena W, Herbold CW, Rhee SK, Bartlett DH, Huang L, Ingalls AE, Wagner M, Stahl DA, Jia Z.

ISME J. 2019 Dec;13(12):3067-3079. doi: 10.1038/s41396-019-0493-x. Epub 2019 Aug 28.

3.

Nitrous oxide emissions associated with ammonia-oxidizing bacteria abundance in fields of switchgrass with and without intercropped alfalfa.

Pannu MW, Meinhardt KA, Bertagnolli A, Fransen SC, Stahl DA, Strand SE.

Environ Microbiol Rep. 2019 Oct;11(5):727-735. doi: 10.1111/1758-2229.12790. Epub 2019 Sep 1.

PMID:
31430046
4.

Kinetic implication of moving warm side-stream Anaerobic ammonium oxidizing bacteria to cold mainstream wastewater.

Straka L, Summers A, Stahl DA, Winkler MKH.

Bioresour Technol. 2019 Sep;288:121534. doi: 10.1016/j.biortech.2019.121534. Epub 2019 May 22.

PMID:
31155313
5.

Global diversity and biogeography of bacterial communities in wastewater treatment plants.

Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown MR, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, Yang Y, Deng Y, Tu Q, Wang A; Global Water Microbiome Consortium, Zhang T, He Z, Keller J, Nielsen PH, Alvarez PJJ, Criddle CS, Wagner M, Tiedje JM, He Q, Curtis TP, Stahl DA, Alvarez-Cohen L, Rittmann BE, Wen X, Zhou J.

Nat Microbiol. 2019 Jul;4(7):1183-1195. doi: 10.1038/s41564-019-0426-5. Epub 2019 May 13. Erratum in: Nat Microbiol. 2019 Dec;4(12):2579.

6.

Affinity informs environmental cooperation between ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (Anammox) bacteria.

Straka LL, Meinhardt KA, Bollmann A, Stahl DA, Winkler MH.

ISME J. 2019 Aug;13(8):1997-2004. doi: 10.1038/s41396-019-0408-x. Epub 2019 Apr 1.

PMID:
30936420
7.

Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium.

Vuono DC, Read RW, Hemp J, Sullivan BW, Arnone JA 3rd, Neveux I, Blank RR, Loney E, Miceli D, Winkler MH, Chakraborty R, Stahl DA, Grzymski JJ.

Front Microbiol. 2019 Jan 22;10:3. doi: 10.3389/fmicb.2019.00003. eCollection 2019.

8.

Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle.

Ge X, Vaccaro BJ, Thorgersen MP, Poole FL 2nd, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, Hazen TC, Adams MWW.

Environ Microbiol. 2019 Jan;21(1):152-163. doi: 10.1111/1462-2920.14435. Epub 2018 Nov 21.

9.

Accumulation of NO2 -cobalamin in nutrient-stressed ammonia-oxidizing archaea and in the oxygen deficient zone of the eastern tropical North Pacific.

Heal KR, Qin W, Amin SA, Devol AH, Moffett JW, Armbrust EV, Stahl DA, Ingalls AE.

Environ Microbiol Rep. 2018 Aug;10(4):453-457. doi: 10.1111/1758-2229.12664. Epub 2018 Aug 8.

PMID:
30022612
10.

Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins.

Li PN, Herrmann J, Tolar BB, Poitevin F, Ramdasi R, Bargar JR, Stahl DA, Jensen GJ, Francis CA, Wakatsuki S, van den Bedem H.

ISME J. 2018 Oct;12(10):2389-2402. doi: 10.1038/s41396-018-0191-0. Epub 2018 Jun 13.

11.

Ammonia-oxidizing bacteria are the primary N2 O producers in an ammonia-oxidizing archaea dominated alkaline agricultural soil.

Meinhardt KA, Stopnisek N, Pannu MW, Strand SE, Fransen SC, Casciotti KL, Stahl DA.

Environ Microbiol. 2018 Jun;20(6):2195-2206. doi: 10.1111/1462-2920.14246. Epub 2018 Jun 1.

PMID:
29687586
12.

Constraint-based modelling captures the metabolic versatility of Desulfovibrio vulgaris.

Flowers JJ, Richards MA, Baliga N, Meyer B, Stahl DA.

Environ Microbiol Rep. 2018 Apr;10(2):190-201. doi: 10.1111/1758-2229.12619. Epub 2018 Feb 19.

PMID:
29377633
13.

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris.

Zhou A, Lau R, Baran R, Ma J, von Netzer F, Shi W, Gorman-Lewis D, Kempher ML, He Z, Qin Y, Shi Z, Zane GM, Wu L, Bowen BP, Northen TR, Hillesland KL, Stahl DA, Wall JD, Arkin AP, Zhou J.

MBio. 2017 Nov 14;8(6). pii: e01780-17. doi: 10.1128/mBio.01780-17.

14.

Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations.

Qin W, Amin SA, Lundeen RA, Heal KR, Martens-Habbena W, Turkarslan S, Urakawa H, Costa KC, Hendrickson EL, Wang T, Beck DA, Tiquia-Arashiro SM, Taub F, Holmes AD, Vajrala N, Berube PM, Lowe TM, Moffett JW, Devol AH, Baliga NS, Arp DJ, Sayavedra-Soto LA, Hackett M, Armbrust EV, Ingalls AE, Stahl DA.

ISME J. 2018 Feb;12(2):508-519. doi: 10.1038/ismej.2017.186. Epub 2017 Oct 20.

15.

Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota.

Qin W, Heal KR, Ramdasi R, Kobelt JN, Martens-Habbena W, Bertagnolli AD, Amin SA, Walker CB, Urakawa H, Könneke M, Devol AH, Moffett JW, Armbrust EV, Jensen GJ, Ingalls AE, Stahl DA.

Int J Syst Evol Microbiol. 2017 Dec;67(12):5067-5079. doi: 10.1099/ijsem.0.002416. Epub 2017 Oct 16.

PMID:
29034851
16.

Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough.

Zeng L, Wooton E, Stahl DA, Walian PJ.

J Bacteriol. 2017 Oct 31;199(23). pii: e00286-17. doi: 10.1128/JB.00286-17. Print 2017 Dec 1.

17.

Robustness of a model microbial community emerges from population structure among single cells of a clonal population.

Thompson AW, Turkarslan S, Arens CE, López García de Lomana A, Raman AV, Stahl DA, Baliga NS.

Environ Microbiol. 2017 Aug;19(8):3059-3069. doi: 10.1111/1462-2920.13764. Epub 2017 May 29.

PMID:
28419704
18.

Mechanism for microbial population collapse in a fluctuating resource environment.

Turkarslan S, Raman AV, Thompson AW, Arens CE, Gillespie MA, von Netzer F, Hillesland KL, Stolyar S, López García de Lomana A, Reiss DJ, Gorman-Lewis D, Zane GM, Ranish JA, Wall JD, Stahl DA, Baliga NS.

Mol Syst Biol. 2017 Mar 20;13(3):919. doi: 10.15252/msb.20167058.

19.

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer.

Zhang P, He Z, Van Nostrand JD, Qin Y, Deng Y, Wu L, Tu Q, Wang J, Schadt CW, W Fields M, Hazen TC, Arkin AP, Stahl DA, Zhou J.

Environ Sci Technol. 2017 Apr 4;51(7):3609-3620. doi: 10.1021/acs.est.6b02980. Epub 2017 Mar 16.

PMID:
28300407
20.

Influence of oxygen availability on the activities of ammonia-oxidizing archaea.

Qin W, Meinhardt KA, Moffett JW, Devol AH, Virginia Armbrust E, Ingalls AE, Stahl DA.

Environ Microbiol Rep. 2017 Jun;9(3):250-256. doi: 10.1111/1758-2229.12525. Epub 2017 Mar 13.

PMID:
28211189
21.

Two distinct pools of B12 analogs reveal community interdependencies in the ocean.

Heal KR, Qin W, Ribalet F, Bertagnolli AD, Coyote-Maestas W, Hmelo LR, Moffett JW, Devol AH, Armbrust EV, Stahl DA, Ingalls AE.

Proc Natl Acad Sci U S A. 2017 Jan 10;114(2):364-369. doi: 10.1073/pnas.1608462114. Epub 2016 Dec 27.

22.

A Purple Cupredoxin from Nitrosopumilus maritimus Containing a Mononuclear Type 1 Copper Center with an Open Binding Site.

Hosseinzadeh P, Tian S, Marshall NM, Hemp J, Mullen T, Nilges MJ, Gao YG, Robinson H, Stahl DA, Gennis RB, Lu Y.

J Am Chem Soc. 2016 May 25;138(20):6324-7. doi: 10.1021/jacs.5b13128. Epub 2016 May 12.

PMID:
27120678
23.

Agricultural land usage transforms nitrifier population ecology.

Bertagnolli AD, McCalmont D, Meinhardt KA, Fransen SC, Strand S, Brown S, Stahl DA.

Environ Microbiol. 2016 Jun;18(6):1918-29. doi: 10.1111/1462-2920.13114. Epub 2016 Jan 21.

PMID:
26526405
24.

Confounding effects of oxygen and temperature on the TEX86 signature of marine Thaumarchaeota.

Qin W, Carlson LT, Armbrust EV, Devol AH, Moffett JW, Stahl DA, Ingalls AE.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):10979-84. doi: 10.1073/pnas.1501568112. Epub 2015 Aug 17.

25.

A method to analyze, sort, and retain viability of obligate anaerobic microorganisms from complex microbial communities.

Thompson AW, Crow MJ, Wadey B, Arens C, Turkarslan S, Stolyar S, Elliott N, Petersen TW, van den Engh G, Stahl DA, Baliga NS.

J Microbiol Methods. 2015 Oct;117:74-7. doi: 10.1016/j.mimet.2015.07.009. Epub 2015 Jul 14.

26.

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.

27.

Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria.

Meinhardt KA, Bertagnolli A, Pannu MW, Strand SE, Brown SL, Stahl DA.

Environ Microbiol Rep. 2015 Apr;7(2):354-63. doi: 10.1111/1758-2229.12259. Epub 2015 Feb 12.

PMID:
25534249
28.

Influence of edaphic and management factors on the diversity and abundance of ammonia-oxidizing thaumarchaeota and bacteria in soils of bioenergy crop cultivars.

Bertagnolli AD, Meinhardt KA, Pannu M, Brown S, Strand S, Fransen SC, Stahl DA.

Environ Microbiol Rep. 2015 Apr;7(2):312-20. doi: 10.1111/1758-2229.12250. Epub 2015 Feb 26.

PMID:
25504683
29.

The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger.

Martens-Habbena W, Qin W, Horak RE, Urakawa H, Schauer AJ, Moffett JW, Armbrust EV, Ingalls AE, Devol AH, Stahl DA.

Environ Microbiol. 2015 Jul;17(7):2261-74. doi: 10.1111/1462-2920.12677. Epub 2015 Jan 27.

PMID:
25420929
30.

Earthworm symbiont Verminephrobacter eiseniae mediates natural transformation within host egg capsules using type IV pili.

Davidson SK, Dulla GF, Go RA, Stahl DA, Pinel N.

Front Microbiol. 2014 Oct 29;5:546. doi: 10.3389/fmicb.2014.00546. eCollection 2014.

31.

Nitrosospira lacus sp. nov., a psychrotolerant, ammonia-oxidizing bacterium from sandy lake sediment.

Urakawa H, Garcia JC, Nielsen JL, Le VQ, Kozlowski JA, Stein LY, Lim CK, Pommerening-Röser A, Martens-Habbena W, Stahl DA, Klotz MG.

Int J Syst Evol Microbiol. 2015 Jan;65(Pt 1):242-50. doi: 10.1099/ijs.0.070789-0. Epub 2014 Oct 21.

PMID:
25336720
32.

Determination of four forms of vitamin B12 and other B vitamins in seawater by liquid chromatography/tandem mass spectrometry.

Heal KR, Carlson LT, Devol AH, Armbrust EV, Moffett JW, Stahl DA, Ingalls AE.

Rapid Commun Mass Spectrom. 2014 Nov 30;28(22):2398-404. doi: 10.1002/rcm.7040.

PMID:
25303468
33.

Erosion of functional independence early in the evolution of a microbial mutualism.

Hillesland KL, Lim S, Flowers JJ, Turkarslan S, Pinel N, Zane GM, Elliott N, Qin Y, Wu L, Baliga NS, Zhou J, Wall JD, Stahl DA.

Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14822-7. doi: 10.1073/pnas.1407986111. Epub 2014 Sep 29.

34.

Analysis of the xplAB-containing gene cluster involved in the bacterial degradation of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine.

Chong CS, Sabir DK, Lorenz A, Bontemps C, Andeer P, Stahl DA, Strand SE, Rylott EL, Bruce NC.

Appl Environ Microbiol. 2014 Nov;80(21):6601-10. doi: 10.1128/AEM.01818-14. Epub 2014 Aug 15.

35.

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation.

Qin W, Amin SA, Martens-Habbena W, Walker CB, Urakawa H, Devol AH, Ingalls AE, Moffett JW, Armbrust EV, Stahl DA.

Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12504-9. doi: 10.1073/pnas.1324115111. Epub 2014 Aug 11.

36.

Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation.

Könneke M, Schubert DM, Brown PC, Hügler M, Standfest S, Schwander T, Schada von Borzyskowski L, Erb TJ, Stahl DA, Berg IA.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8239-44. doi: 10.1073/pnas.1402028111. Epub 2014 May 19.

37.

Cycloheximide prevents the de novo polypeptide synthesis required to recover from acetylene inhibition in Nitrosopumilus maritimus.

Vajrala N, Bottomley PJ, Stahl DA, Arp DJ, Sayavedra-Soto LA.

FEMS Microbiol Ecol. 2014 Jun;88(3):495-502. doi: 10.1111/1574-6941.12316. Epub 2014 Mar 24.

38.

Thermodynamic characterization of proton-ionizable functional groups on the cell surfaces of ammonia-oxidizing bacteria and archaea.

Gorman-Lewis D, Martens-Habbena W, Stahl DA.

Geobiology. 2014 Mar;12(2):157-71. doi: 10.1111/gbi.12075. Epub 2014 Jan 20.

PMID:
24589203
39.

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem.

Zhou J, Deng Y, Zhang P, Xue K, Liang Y, Van Nostrand JD, Yang Y, He Z, Wu L, Stahl DA, Hazen TC, Tiedje JM, Arkin AP.

Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):E836-45. doi: 10.1073/pnas.1324044111. Epub 2014 Feb 18.

40.

The energy-conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf.

Meyer B, Kuehl JV, Price MN, Ray J, Deutschbauer AM, Arkin AP, Stahl DA.

Environ Microbiol. 2014 Nov;16(11):3463-86. doi: 10.1111/1462-2920.12405. Epub 2014 Mar 5.

PMID:
24447568
41.

Transcriptional response of the archaeal ammonia oxidizer Nitrosopumilus maritimus to low and environmentally relevant ammonia concentrations.

Nakagawa T, Stahl DA.

Appl Environ Microbiol. 2013 Nov;79(22):6911-6. doi: 10.1128/AEM.02028-13. Epub 2013 Aug 30.

42.

Mapping of active replication origins in vivo in thaum- and euryarchaeal replicons.

Pelve EA, Martens-Habbena W, Stahl DA, Bernander R.

Mol Microbiol. 2013 Nov;90(3):538-50. doi: 10.1111/mmi.12382. Epub 2013 Sep 16.

43.

Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes.

Meyer B, Kuehl JV, Deutschbauer AM, Arkin AP, Stahl DA.

J Bacteriol. 2013 Nov;195(21):4900-14. doi: 10.1128/JB.00504-13. Epub 2013 Aug 23.

44.

Identification of microbial populations assimilating nitrogen from RDX in munitions contaminated military training range soils by high sensitivity stable isotope probing.

Andeer P, Stahl DA, Lillis L, Strand SE.

Environ Sci Technol. 2013 Sep 17;47(18):10356-63. doi: 10.1021/es401729c. Epub 2013 Sep 4.

PMID:
23909596
45.

Membrane protein complex of APS reductase and Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis.

Krumholz LR, Wang L, Beck DA, Wang T, Hackett M, Mooney B, Juba TR, McInerney MJ, Meyer B, Wall JD, Stahl DA.

Microbiology. 2013 Oct;159(Pt 10):2162-8. doi: 10.1099/mic.0.063818-0. Epub 2013 Jul 10.

PMID:
23842468
46.

Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments.

Kang S, Van Nostrand JD, Gough HL, He Z, Hazen TC, Stahl DA, Zhou J.

FEMS Microbiol Ecol. 2013 Nov;86(2):200-14. doi: 10.1111/1574-6941.12152. Epub 2013 Jul 9.

47.

Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea.

Horak RE, Qin W, Schauer AJ, Armbrust EV, Ingalls AE, Moffett JW, Stahl DA, Devol AH.

ISME J. 2013 Oct;7(10):2023-33. doi: 10.1038/ismej.2013.75. Epub 2013 May 9.

48.

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution.

Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, Joachimiak MP, Xie M, Song R, Arkin AP, Hazen TC, Keasling JD, Wall JD, Stahl DA, Zhou J.

ISME J. 2013 Sep;7(9):1790-802. doi: 10.1038/ismej.2013.60. Epub 2013 Apr 11.

49.

Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea.

Vajrala N, Martens-Habbena W, Sayavedra-Soto LA, Schauer A, Bottomley PJ, Stahl DA, Arp DJ.

Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):1006-11. doi: 10.1073/pnas.1214272110. Epub 2012 Dec 31.

50.

Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth.

Meyer B, Kuehl J, Deutschbauer AM, Price MN, Arkin AP, Stahl DA.

J Bacteriol. 2013 Mar;195(5):990-1004. doi: 10.1128/JB.01959-12. Epub 2012 Dec 21.

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