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Items: 1 to 50 of 83

1.

A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria.

Sedlacek CJ, McGowan B, Suwa Y, Sayavedra-Soto L, Laanbroek HJ, Stein LY, Norton JM, Klotz MG, Bollmann A.

Microb Ecol. 2019 Apr 11. doi: 10.1007/s00248-019-01378-8. [Epub ahead of print]

PMID:
30976841
2.

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.

3.

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
4.

Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.

Herbold CW, Lehtovirta-Morley LE, Jung MY, Jehmlich N, Hausmann B, Han P, Loy A, Pester M, Sayavedra-Soto LA, Rhee SK, Prosser JI, Nicol GW, Wagner M, Gubry-Rangin C.

Environ Microbiol. 2017 Dec;19(12):4939-4952. doi: 10.1111/1462-2920.13971. Epub 2017 Dec 4.

5.

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.

6.

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.

7.

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.

8.

Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters.

Rice MC, Norton JM, Stein LY, Kozlowski J, Bollmann A, Klotz MG, Sayavedra-Soto L, Shapiro N, Goodwin LA, Huntemann M, Clum A, Pillay M, Varghese N, Mikhailova N, Palaniappan K, Ivanova N, Mukherjee S, Reddy TB, Yee Ngan C, Daum C, Kyrpides N, Woyke T.

Genome Announc. 2017 Mar 16;5(11). pii: e00011-17. doi: 10.1128/genomeA.00011-17.

9.

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.

10.

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.

11.

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.

12.

Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon "Candidatus Nitrosotalea devanaterra".

Lehtovirta-Morley LE, Sayavedra-Soto LA, Gallois N, Schouten S, Stein LY, Prosser JI, Nicol GW.

Appl Environ Microbiol. 2016 Apr 18;82(9):2608-2619. doi: 10.1128/AEM.04031-15. Print 2016 May.

13.

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.

14.

Nitrobacter winogradskyi transcriptomic response to low and high ammonium concentrations.

Sayavedra-Soto L, Ferrell R, Dobie M, Mellbye B, Chaplen F, Buchanan A, Chang J, Bottomley P, Arp D.

FEMS Microbiol Lett. 2015 Jan;362(3):1-7. doi: 10.1093/femsle/fnu040. Epub 2014 Dec 4.

15.

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

Pérez 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
16.

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.

17.

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations.

Bollmann A, Sedlacek CJ, Norton J, Laanbroek HJ, Suwa Y, Stein LY, Klotz MG, Arp D, Sayavedra-Soto L, Lu M, Bruce D, Detter C, Tapia R, Han J, Woyke T, Lucas SM, Pitluck S, Pennacchio L, Nolan M, Land ML, Huntemann M, Deshpande S, Han C, Chen A, Kyrpides N, Mavromatis K, Markowitz V, Szeto E, Ivanova N, Mikhailova N, Pagani I, Pati A, Peters L, Ovchinnikova G, Goodwin LA.

Stand Genomic Sci. 2013 Feb 25;7(3):469-82. doi: 10.4056/sigs.3517166. eCollection 2013.

18.

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.

19.

Characterization of a nitrite reductase involved in nitrifier denitrification.

Lawton TJ, Bowen KE, Sayavedra-Soto LA, Arp DJ, Rosenzweig AC.

J Biol Chem. 2013 Aug 30;288(35):25575-83. doi: 10.1074/jbc.M113.484543. Epub 2013 Jul 15.

20.

The Draft Genome Sequence of Nocardioides sp. Strain CF8 Reveals the Scope of Its Metabolic Capabilities.

Kimbrel JA, Chang J, Arp DJ, Sayavedra-Soto LA.

Genome Announc. 2013 Jul 5;1(4). pii: e00439-13. doi: 10.1128/genomeA.00439-13.

21.

Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments.

Zhalnina K, de Quadros PD, Gano KA, Davis-Richardson A, Fagen JR, Brown CT, Giongo A, Drew JC, Sayavedra-Soto LA, Arp DJ, Camargo FA, Daroub SH, Clark IM, McGrath SP, Hirsch PR, Triplett EW.

Front Microbiol. 2013 May 1;4:104. doi: 10.3389/fmicb.2013.00104. eCollection 2013.

22.

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.

23.

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
24.

The membrane-associated monooxygenase in the butane-oxidizing Gram-positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family.

Sayavedra-Soto LA, Hamamura N, Liu CW, Kimbrel JA, Chang JH, Arp DJ.

Environ Microbiol Rep. 2011 Jun;3(3):390-6. doi: 10.1111/j.1758-2229.2010.00239.x. Epub 2011 Jan 26.

PMID:
23761285
25.

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.

26.

Dissecting iron uptake and homeostasis in Nitrosomonas europaea.

Sayavedra-Soto LA, Vajrala N, Arp DJ.

Methods Enzymol. 2011;486:403-28. doi: 10.1016/B978-0-12-381294-0.00018-3.

PMID:
21185446
27.

Genetic transformation of ammonia-oxidizing bacteria.

Sayavedra-Soto LA, Stein LY.

Methods Enzymol. 2011;486:389-402. doi: 10.1016/B978-0-12-381294-0.00017-1.

PMID:
21185445
28.

Computational prediction and transcriptional analysis of sRNAs in Nitrosomonas europaea.

Gvakharia BO, Tjaden B, Vajrala N, Sayavedra-Soto LA, Arp DJ.

FEMS Microbiol Lett. 2010 Nov;312(1):46-54. doi: 10.1111/j.1574-6968.2010.02095.x. Epub 2010 Sep 14.

29.

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
30.

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.

Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PS, Chan PP, Gollabgir A, Hemp J, Hügler M, Karr EA, Könneke M, Shin M, Lawton TJ, Lowe T, Martens-Habbena W, Sayavedra-Soto LA, Lang D, Sievert SM, Rosenzweig AC, Manning G, Stahl DA.

Proc Natl Acad Sci U S A. 2010 May 11;107(19):8818-23. doi: 10.1073/pnas.0913533107. Epub 2010 Apr 26.

31.

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
32.

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.

33.

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.

34.

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
35.

Crystal structure of a two-domain multicopper oxidase: implications for the evolution of multicopper blue proteins.

Lawton TJ, Sayavedra-Soto LA, Arp DJ, Rosenzweig AC.

J Biol Chem. 2009 Apr 10;284(15):10174-80. doi: 10.1074/jbc.M900179200. Epub 2009 Feb 17.

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.

Characterization of the ferrioxamine uptake system of Nitrosomonas europaea.

Wei X, Sayavedra-Soto LA, Arp DJ.

Microbiology. 2007 Dec;153(Pt 12):3963-72.

PMID:
18048911
40.

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
41.
42.
43.

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.

Alkane utilization by Rhodococcus strain NTU-1 alone and in its natural association with Bacillus fusiformis L-1 and Ochrobactrum sp.

Sayavedra-Soto LA, Chang WN, Lin TK, Ho CL, Liu HS.

Biotechnol Prog. 2006 Sep-Oct;22(5):1368-73.

PMID:
17022676
45.

Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea.

Wei X, Vajrala N, Hauser L, Sayavedra-Soto LA, Arp DJ.

Arch Microbiol. 2006 Aug;186(2):107-18. Epub 2006 Jun 21.

PMID:
16802173
47.

Transcript profiles of Nitrosomonas europaea during growth and upon deprivation of ammonia and carbonate.

Wei X, Yan T, Hommes NG, Liu X, Wu L, McAlvin C, Klotz MG, Sayavedra-Soto LA, Zhou J, Arp DJ.

FEMS Microbiol Lett. 2006 Apr;257(1):76-83.

48.

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.

49.

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.

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