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Items: 1 to 50 of 92

1.

Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi.

Mellbye BL, Giguere AT, Murthy GS, Bottomley PJ, Sayavedra-Soto LA, Chaplen FWR.

mSystems. 2018 Mar 13;3(3). pii: e00170-17. doi: 10.1128/mSystems.00170-17. eCollection 2018 May-Jun.

2.

Nitrite-oxidizing activity responds to nitrite accumulation in soil.

Giguere AT, Taylor AE, Myrold DD, Mellbye BL, Sayavedra-Soto LA, Bottomley PJ.

FEMS Microbiol Ecol. 2018 Mar 1;94(3). doi: 10.1093/femsec/fiy008.

PMID:
29360963
3.

Contrasting growth properties of Nocardioides JS614 on threedifferent vinyl halides.

Taylor AE, Bottomley PJ, Semprini L.

Appl Microbiol Biotechnol. 2018 Feb;102(4):1859-1867. doi: 10.1007/s00253-017-8723-5. Epub 2018 Jan 3.

PMID:
29297101
4.

Acyl-Homoserine Lactone Production in Nitrifying Bacteria of the Genera Nitrosospira, Nitrobacter, and Nitrospira Identified via a Survey of Putative Quorum-Sensing Genes.

Mellbye BL, Spieck E, Bottomley PJ, Sayavedra-Soto LA.

Appl Environ Microbiol. 2017 Oct 31;83(22). pii: e01540-17. doi: 10.1128/AEM.01540-17. Print 2017 Nov 15.

5.

Draft Genome Sequence of Nitrobacter vulgaris Strain Ab1, a Nitrite-Oxidizing Bacterium.

Mellbye BL, Davis EW 2nd, Spieck E, Chang JH, Bottomley PJ, Sayavedra-Soto LA.

Genome Announc. 2017 May 4;5(18). pii: e00290-17. doi: 10.1128/genomeA.00290-17.

6.

Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria.

Taylor AE, Giguere AT, Zoebelein CM, Myrold DD, Bottomley PJ.

ISME J. 2017 Apr;11(4):896-908. doi: 10.1038/ismej.2016.179. Epub 2016 Dec 20.

7.

Quorum Quenching of Nitrobacter winogradskyi Suggests that Quorum Sensing Regulates Fluxes of Nitrogen Oxide(s) during Nitrification.

Mellbye BL, Giguere AT, Bottomley PJ, Sayavedra-Soto LA.

MBio. 2016 Oct 25;7(5). pii: e01753-16. doi: 10.1128/mBio.01753-16.

8.

Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil.

Rice MC, Norton JM, Valois F, Bollmann A, Bottomley PJ, Klotz MG, Laanbroek HJ, Suwa Y, Stein LY, Sayavedra-Soto L, Woyke T, Shapiro N, Goodwin LA, Huntemann M, Clum A, Pillay M, Kyrpides N, Varghese N, Mikhailova N, Markowitz V, Palaniappan K, Ivanova N, Stamatis D, Reddy TB, Ngan CY, Daum C.

Stand Genomic Sci. 2016 Jul 28;11:46. doi: 10.1186/s40793-016-0168-4. eCollection 2016.

9.

Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea.

Mellbye BL, Giguere A, Chaplen F, Bottomley PJ, Sayavedra-Soto LA.

Appl Environ Microbiol. 2016 May 16;82(11):3310-3318. doi: 10.1128/AEM.00294-16. Print 2016 Jun 1.

10.

Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N-Acyl-Homoserine Lactone Autoinducers.

Mellbye BL, Bottomley PJ, Sayavedra-Soto LA.

Appl Environ Microbiol. 2015 Sep 1;81(17):5917-26. doi: 10.1128/AEM.01103-15. Epub 2015 Jun 19.

11.

Inhibitory effects of C2 to C10 1-alkynes on ammonia oxidation in two Nitrososphaera species.

Taylor AE, Taylor K, Tennigkeit B, Palatinszky M, Stieglmeier M, Myrold DD, Schleper C, Wagner M, Bottomley PJ.

Appl Environ Microbiol. 2015 Mar;81(6):1942-8. doi: 10.1128/AEM.03688-14. Epub 2015 Jan 9.

12.

Interactions of Nitrosomonas europaea and Nitrobacter winogradskyi grown in co-culture.

PĂ©rez J, Buchanan A, Mellbye B, Ferrell R, Chang JH, Chaplen F, Bottomley PJ, Arp DJ, Sayavedra-Soto LA.

Arch Microbiol. 2015 Jan;197(1):79-89. doi: 10.1007/s00203-014-1056-1. Epub 2014 Nov 2.

PMID:
25362506
13.

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.

14.

Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales.

Zeglin LH, Bottomley PJ, Jumpponen A, Rice CW, Arango M, Lindsley A, McGowan A, Mfombep P, Myrold DD.

Ecology. 2013 Oct;94(10):2334-45.

PMID:
24358718
15.

Use of aliphatic n-alkynes to discriminate soil nitrification activities of ammonia-oxidizing thaumarchaea and bacteria.

Taylor AE, Vajrala N, Giguere AT, Gitelman AI, Arp DJ, Myrold DD, Sayavedra-Soto L, Bottomley PJ.

Appl Environ Microbiol. 2013 Nov;79(21):6544-51. doi: 10.1128/AEM.01928-13. Epub 2013 Aug 16.

16.

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.

17.

A consideration of the relative contributions of different microbial subpopulations to the soil N cycle.

Bottomley PJ, Taylor AE, Myrold DD.

Front Microbiol. 2012 Oct 23;3:373. doi: 10.3389/fmicb.2012.00373. eCollection 2012.

18.

Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials.

Taylor AE, Zeglin LH, Wanzek TA, Myrold DD, Bottomley PJ.

ISME J. 2012 Nov;6(11):2024-32. doi: 10.1038/ismej.2012.51. Epub 2012 Jun 14.

19.

Global analysis of the Nitrosomonas europaea iron starvation stimulon.

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

Arch Microbiol. 2012 Apr;194(4):305-13. doi: 10.1007/s00203-011-0778-6. Epub 2011 Dec 16.

PMID:
22173827
20.

Bacterial and archaeal amoA gene distribution covaries with soil nitrification properties across a range of land uses.

Zeglin LH, Taylor AE, Myrold DD, Bottomley PJ.

Environ Microbiol Rep. 2011 Dec;3(6):717-26. doi: 10.1111/j.1758-2229.2011.00290.x. Epub 2011 Sep 29.

PMID:
23761362
21.

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
22.

Role of a Fur homolog in iron metabolism in Nitrosomonas europaea.

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

BMC Microbiol. 2011 Feb 21;11:37. doi: 10.1186/1471-2180-11-37.

23.

Evidence for different contributions of archaea and bacteria to the ammonia-oxidizing potential of diverse Oregon soils.

Taylor AE, Zeglin LH, Dooley S, Myrold DD, Bottomley PJ.

Appl Environ Microbiol. 2010 Dec;76(23):7691-8. doi: 10.1128/AEM.01324-10. Epub 2010 Oct 1.

24.

Role of Nitrosomonas europaea NitABC iron transporter in the uptake of Fe3+-siderophore complexes.

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

Arch Microbiol. 2010 Nov;192(11):899-908. doi: 10.1007/s00203-010-0620-6. Epub 2010 Aug 25.

PMID:
20737137
25.

Extending the alkene substrate range of vinyl chloride utilizing Nocardioides sp. strain JS614 with ethene oxide.

Taylor AE, Arp DJ, Bottomley PJ, Semprini L.

Appl Microbiol Biotechnol. 2010 Aug;87(6):2293-302. doi: 10.1007/s00253-010-2719-8. Epub 2010 Jun 27.

PMID:
20582588
26.

Soil microbial communities associated with Douglas-fir and red alder stands at high- and low-productivity forest sites in Oregon, USA.

Yarwood SA, Bottomley PJ, Myrold DD.

Microb Ecol. 2010 Oct;60(3):606-17. doi: 10.1007/s00248-010-9675-9. Epub 2010 May 7.

PMID:
20449582
27.

Nitrification and degradation of halogenated hydrocarbons--a tenuous balance for ammonia-oxidizing bacteria.

Sayavedra-Soto LA, Gvakharia B, Bottomley PJ, Arp DJ, Dolan ME.

Appl Microbiol Biotechnol. 2010 Mar;86(2):435-44. doi: 10.1007/s00253-010-2454-1. Epub 2010 Feb 10. Review.

PMID:
20146060
28.

Growth of a non-methanotroph on natural gas: ignoring the obvious to focus on the obscure.

Cooley RB, Bottomley PJ, Arp DJ.

Environ Microbiol Rep. 2009 Oct;1(5):408-13. doi: 10.1111/j.1758-2229.2009.00060.x. Epub 2009 Aug 13.

PMID:
23765894
29.

Thauera butanivorans sp. nov., a C2-C9 alkane-oxidizing bacterium previously referred to as 'Pseudomonas butanovora'.

Dubbels BL, Sayavedra-Soto LA, Bottomley PJ, Arp DJ.

Int J Syst Evol Microbiol. 2009 Jul;59(Pt 7):1576-8. doi: 10.1099/ijs.0.000638-0. Epub 2009 Jun 15.

30.

Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly 'Pseudomonas butanovora'.

Cooley RB, Dubbels BL, Sayavedra-Soto LA, Bottomley PJ, Arp DJ.

Microbiology. 2009 Jun;155(Pt 6):2086-96. doi: 10.1099/mic.0.028175-0. Epub 2009 Apr 21.

31.

Construction of recombinant Nitrosomonas europaea expressing green fluorescent protein in response to co-oxidation of chloroform.

Gvakharia BO, Bottomley PJ, Arp DJ, Sayavedra-Soto LA.

Appl Microbiol Biotechnol. 2009 Apr;82(6):1179-85. doi: 10.1007/s00253-009-1914-y. Epub 2009 Feb 27.

PMID:
19247648
32.

Expression of a putative nitrite reductase and the reversible inhibition of nitrite-dependent respiration by nitric oxide in Nitrobacter winogradskyi Nb-255.

Starkenburg SR, Arp DJ, Bottomley PJ.

Environ Microbiol. 2008 Nov;10(11):3036-42. doi: 10.1111/j.1462-2920.2008.01763.x.

PMID:
18973623
33.

D-Lactate metabolism and the obligate requirement for CO2 during growth on nitrite by the facultative lithoautotroph Nitrobacter hamburgensis.

Starkenburg SR, Arp DJ, Bottomley PJ.

Microbiology. 2008 Aug;154(Pt 8):2473-81. doi: 10.1099/mic.0.2008/018085-0.

PMID:
18667580
34.

Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon.

Boyle-Yarwood SA, Bottomley PJ, Myrold DD.

Environ Microbiol. 2008 Nov;10(11):2956-65. doi: 10.1111/j.1462-2920.2008.01600.x. Epub 2008 Apr 3.

PMID:
18393992
35.

Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment.

Norton JM, Klotz MG, Stein LY, Arp DJ, Bottomley PJ, Chain PS, Hauser LJ, Land ML, Larimer FW, Shin MW, Starkenburg SR.

Appl Environ Microbiol. 2008 Jun;74(11):3559-72. doi: 10.1128/AEM.02722-07. Epub 2008 Apr 4.

36.

Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter.

Starkenburg SR, Larimer FW, Stein LY, Klotz MG, Chain PS, Sayavedra-Soto LA, Poret-Peterson AT, Gentry ME, Arp DJ, Ward B, Bottomley PJ.

Appl Environ Microbiol. 2008 May;74(9):2852-63. doi: 10.1128/AEM.02311-07. Epub 2008 Mar 7.

37.

Evidence for involvement of copper ions and redox state in regulation of butane monooxygenase in Pseudomonas butanovora.

Doughty DM, Kurth EG, Sayavedra-Soto LA, Arp DJ, Bottomley PJ.

J Bacteriol. 2008 Apr;190(8):2933-8. doi: 10.1128/JB.01409-07. Epub 2008 Feb 15.

38.

Involvement of BmoR and BmoG in n-alkane metabolism in 'Pseudomonas butanovora'.

Kurth EG, Doughty DM, Bottomley PJ, Arp DJ, Sayavedra-Soto LA.

Microbiology. 2008 Jan;154(Pt 1):139-47. doi: 10.1099/mic.0.2007/012724-0.

PMID:
18174133
39.

Propionate inactivation of butane monooxygenase activity in 'Pseudomonas butanovora': biochemical and physiological implications.

Doughty DM, Halsey KH, Vieville CJ, Sayavedra-Soto LA, Arp DJ, Bottomley PJ.

Microbiology. 2007 Nov;153(Pt 11):3722-9.

PMID:
17975080
40.

Utilization of fluoroethene as a surrogate for aerobic vinyl chloride transformation.

Taylor AE, Dolan ME, Bottomley PJ, Semprini L.

Environ Sci Technol. 2007 Sep 15;41(18):6378-83.

PMID:
17948782
41.
42.

Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane.

Gvakharia BO, Permina EA, Gelfand MS, Bottomley PJ, Sayavedra-Soto LA, Arp DJ.

Appl Environ Microbiol. 2007 May;73(10):3440-5. Epub 2007 Mar 16.

44.

Product repression of alkane monooxygenase expression in Pseudomonas butanovora.

Doughty DM, Sayavedra-Soto LA, Arp DJ, Bottomley PJ.

J Bacteriol. 2006 Apr;188(7):2586-92.

45.

Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255.

Starkenburg SR, Chain PS, Sayavedra-Soto LA, Hauser L, Land ML, Larimer FW, Malfatti SA, Klotz MG, Bottomley PJ, Arp DJ, Hickey WJ.

Appl Environ Microbiol. 2006 Mar;72(3):2050-63.

46.

Effects of Soil on Ammonia, Ethylene, Chloroethane, and 1,1,1-Trichloroethane Oxidation by Nitrosomonas europaea.

Hommes NG, Russell SA, Bottomley PJ, Arp DJ.

Appl Environ Microbiol. 1998 Apr;64(4):1372-8.

47.
48.
49.

Product and product-independent induction of butane oxidation in Pseudomonas butanovora.

Sayavedra-Soto LA, Doughty DM, Kurth EG, Bottomley PJ, Arp DJ.

FEMS Microbiol Lett. 2005 Sep 1;250(1):111-6.

50.

Trichloroethylene degradation by butane-oxidizing bacteria causes a spectrum of toxic effects.

Halsey KH, Sayavedra-Soto LA, Bottomley PJ, Arp DJ.

Appl Microbiol Biotechnol. 2005 Oct;68(6):794-801. Epub 2005 Oct 13.

PMID:
15754184

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