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Items: 1 to 50 of 71

1.

Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata.

Kits KD, Jung MY, Vierheilig J, Pjevac P, Sedlacek CJ, Liu S, Herbold C, Stein LY, Richter A, Wissel H, Brüggemann N, Wagner M, Daims H.

Nat Commun. 2019 Apr 23;10(1):1836. doi: 10.1038/s41467-019-09790-x.

2.

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
3.

Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels.

Orata FD, Meier-Kolthoff JP, Sauvageau D, Stein LY.

Front Microbiol. 2018 Dec 19;9:3162. doi: 10.3389/fmicb.2018.03162. eCollection 2018.

4.

Combined Effects of Carbon and Nitrogen Source to Optimize Growth of Proteobacterial Methanotrophs.

Tays C, Guarnieri MT, Sauvageau D, Stein LY.

Front Microbiol. 2018 Sep 25;9:2239. doi: 10.3389/fmicb.2018.02239. eCollection 2018.

5.

Insights into the physiology of ammonia-oxidizing microorganisms.

Stein LY.

Curr Opin Chem Biol. 2019 Apr;49:9-15. doi: 10.1016/j.cbpa.2018.09.003. Epub 2018 Sep 17. Review.

PMID:
30236860
6.

Eukaryotic Evolution: An Ancient Breath of Nitrate.

Stein LY.

Curr Biol. 2018 Aug 20;28(16):R875-R877. doi: 10.1016/j.cub.2018.06.029.

PMID:
30130507
7.

Defining Nutrient Combinations for Optimal Growth and Polyhydroxybutyrate Production by Methylosinus trichosporium OB3b Using Response Surface Methodology.

Zaldívar Carrillo JA, Stein LY, Sauvageau D.

Front Microbiol. 2018 Jul 18;9:1513. doi: 10.3389/fmicb.2018.01513. eCollection 2018.

8.

Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria.

Zorz JK, Kozlowski JA, Stein LY, Strous M, Kleiner M.

Front Microbiol. 2018 May 14;9:938. doi: 10.3389/fmicb.2018.00938. eCollection 2018.

9.
10.

Resolving N2 O respiration pathways: a tale of two NosZ clades.

Stein LY.

Environ Microbiol. 2017 Dec;19(12):4806-4807. doi: 10.1111/1462-2920.13969. Epub 2017 Nov 21. No abstract available.

PMID:
29076635
11.

Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle.

Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, Daebeler A, Romano S, Albertsen M, Stein LY, Daims H, Wagner M.

Nature. 2017 Sep 14;549(7671):269-272. doi: 10.1038/nature23679. Epub 2017 Aug 23.

12.

Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems.

Frindte K, Kalyuzhnaya MG, Bringel F, Dunfield PF, Jetten MSM, Khmelenina VN, Klotz MG, Murrell JC, Op den Camp HJM, Sakai Y, Semrau JD, Shapiro N, DiSpirito AA, Stein LY, Svenning MM, Trotsenko YA, Vuilleumier S, Woyke T, Knief C.

Genome Announc. 2017 Aug 17;5(33). pii: e00526-17. doi: 10.1128/genomeA.00526-17.

13.

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.

14.

Methylamine: a vital nitrogen (and carbon) source for marine microbes.

Stein LY.

Environ Microbiol. 2017 Jun;19(6):2117-2118. doi: 10.1111/1462-2920.13716. Epub 2017 Apr 3. No abstract available.

PMID:
28256063
15.

Accessories make the microbe.

Stein LY.

Environ Microbiol Rep. 2017 Feb;9(1):21-22. doi: 10.1111/1758-2229.12492. Epub 2016 Dec 6. No abstract available.

PMID:
27775875
16.

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.

17.

Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria.

Kozlowski JA, Kits KD, Stein LY.

Front Microbiol. 2016 Jul 12;7:1090. doi: 10.3389/fmicb.2016.01090. eCollection 2016.

18.

Complete Genome Sequence of Nitrosomonas ureae Strain Nm10, an Oligotrophic Group 6a Nitrosomonad.

Kozlowski JA, Kits KD, Stein LY.

Genome Announc. 2016 Mar 10;4(2). pii: e00094-16. doi: 10.1128/genomeA.00094-16.

19.

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.

20.

Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota.

Kozlowski JA, Stieglmeier M, Schleper C, Klotz MG, Stein LY.

ISME J. 2016 Aug;10(8):1836-45. doi: 10.1038/ismej.2016.2. Epub 2016 Feb 16.

21.

The nitrogen cycle.

Stein LY, Klotz MG.

Curr Biol. 2016 Feb 8;26(3):R94-8. doi: 10.1016/j.cub.2015.12.021.

22.

Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems.

Flynn JD, Hirayama H, Sakai Y, Dunfield PF, Klotz MG, Knief C, Op den Camp HJ, Jetten MS, Khmelenina VN, Trotsenko YA, Murrell JC, Semrau JD, Svenning MM, Stein LY, Kyrpides N, Shapiro N, Woyke T, Bringel F, Vuilleumier S, DiSpirito AA, Kalyuzhnaya MG.

Genome Announc. 2016 Jan 21;4(1). pii: e01629-15. doi: 10.1128/genomeA.01629-15.

23.

Genome Sequence of Nitrosomonas communis Strain Nm2, a Mesophilic Ammonia-Oxidizing Bacterium Isolated from Mediterranean Soil.

Kozlowski JA, Kits KD, Stein LY.

Genome Announc. 2016 Jan 14;4(1). pii: e01541-15. doi: 10.1128/genomeA.01541-15.

24.

Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8.

Kits KD, Campbell DJ, Rosana AR, Stein LY.

Front Microbiol. 2015 Oct 6;6:1072. doi: 10.3389/fmicb.2015.01072. eCollection 2015.

25.

Microbiology: Cyanate fuels the nitrogen cycle.

Stein LY.

Nature. 2015 Aug 6;524(7563):43-4. doi: 10.1038/nature14639. Epub 2015 Jul 29. No abstract available.

PMID:
26222024
26.

Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems.

Hamilton R, Kits KD, Ramonovskaya VA, Rozova ON, Yurimoto H, Iguchi H, Khmelenina VN, Sakai Y, Dunfield PF, Klotz MG, Knief C, Op den Camp HJ, Jetten MS, Bringel F, Vuilleumier S, Svenning MM, Shapiro N, Woyke T, Trotsenko YA, Stein LY, Kalyuzhnaya MG.

Genome Announc. 2015 Jun 4;3(3). pii: e00515-15. doi: 10.1128/genomeA.00515-15.

27.

Methane oxidation coupled to nitrate reduction under hypoxia by the Gammaproteobacterium Methylomonas denitrificans, sp. nov. type strain FJG1.

Kits KD, Klotz MG, Stein LY.

Environ Microbiol. 2015 Sep;17(9):3219-32. doi: 10.1111/1462-2920.12772. Epub 2015 Mar 10.

PMID:
25580993
28.

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
29.

Characterization of denitrifying activity by the alphaproteobacterium, Sphingomonas wittichii RW1.

Cua LS, Stein LY.

Front Microbiol. 2014 Aug 6;5:404. doi: 10.3389/fmicb.2014.00404. eCollection 2014.

30.

Revision of N2O-producing pathways in the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC 19718.

Kozlowski JA, Price J, Stein LY.

Appl Environ Microbiol. 2014 Aug;80(16):4930-5. doi: 10.1128/AEM.01061-14. Epub 2014 Jun 6.

31.

Draft Genome Sequence of Nitrosospira sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment.

Garcia JC, Urakawa H, Le VQ, Stein LY, Klotz MG, Nielsen JL.

Genome Announc. 2013 Nov 7;1(6). pii: e00930-13. doi: 10.1128/genomeA.00930-13.

32.

Energy-mediated vs. ammonium-regulated gene expression in the obligate ammonia-oxidizing bacterium, Nitrosococcus oceani.

Stein LY, Campbell MA, Klotz MG.

Front Microbiol. 2013 Sep 13;4:277. doi: 10.3389/fmicb.2013.00277. eCollection 2013.

33.

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.

34.

Draft Genome Sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium.

Khmelenina VN, Beck DA, Munk C, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Lo CC, Scholz M, Teshima H, Xu Y, Chain P, Bringel F, Vuilleumier S, Dispirito A, Dunfield P, Jetten MS, Klotz MG, Knief C, Murrell JC, Op den Camp HJ, Sakai Y, Semrau J, Svenning M, Stein LY, Trotsenko YA, Kalyuzhnaya MG.

Genome Announc. 2013 Jun 27;1(4). pii: e00053-13. doi: 10.1128/genomeA.00053-13.

35.

Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8.

Kits KD, Kalyuzhnaya MG, Klotz MG, Jetten MS, Op den Camp HJ, Vuilleumier S, Bringel F, Dispirito AA, Murrell JC, Bruce D, Cheng JF, Copeland A, Goodwin L, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T, Zeytun A, Stein LY.

Genome Announc. 2013 Apr 11;1(2):e0017013. doi: 10.1128/genomeA.00170-13.

36.

Global Molecular Analyses of Methane Metabolism in Methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: Transcriptomic Study.

Matsen JB, Yang S, Stein LY, Beck D, Kalyuzhnaya MG.

Front Microbiol. 2013 Apr 3;4:40. doi: 10.3389/fmicb.2013.00040. eCollection 2013.

37.

Enhancing nitrification at low temperature with zeolite in a mining operations retention pond.

Miazga-Rodriguez M, Han S, Yakiwchuk B, Wei K, English C, Bourn S, Bohnert S, Stein LY.

Front Microbiol. 2012 Jul 30;3:271. doi: 10.3389/fmicb.2012.00271. eCollection 2012.

38.

Draft genome sequence of the volcano-inhabiting thermoacidophilic methanotroph Methylacidiphilum fumariolicum strain SolV.

Khadem AF, Wieczorek AS, Pol A, Vuilleumier S, Harhangi HR, Dunfield PF, Kalyuzhnaya MG, Murrell JC, Francoijs KJ, Stunnenberg HG, Stein LY, DiSpirito AA, Semrau JD, Lajus A, Médigue C, Klotz MG, Jetten MS, Op den Camp HJ.

J Bacteriol. 2012 Jul;194(14):3729-30. doi: 10.1128/JB.00501-12.

39.

Effects of nitrogen dioxide and anoxia on global gene and protein expression in long-term continuous cultures of Nitrosomonas eutropha C91.

Kartal B, Wessels HJ, van der Biezen E, Francoijs KJ, Jetten MS, Klotz MG, Stein LY.

Appl Environ Microbiol. 2012 Jul;78(14):4788-94. doi: 10.1128/AEM.00668-12. Epub 2012 May 4.

40.

Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z.

Vuilleumier S, Khmelenina VN, Bringel F, Reshetnikov AS, Lajus A, Mangenot S, Rouy Z, Op den Camp HJ, Jetten MS, Dispirito AA, Dunfield P, Klotz MG, Semrau JD, Stein LY, Barbe V, Médigue C, Trotsenko YA, Kalyuzhnaya MG.

J Bacteriol. 2012 Jan;194(2):551-2. doi: 10.1128/JB.06392-11.

41.

Nitrous oxide production by lithotrophic ammonia-oxidizing bacteria and implications for engineered nitrogen-removal systems.

Chandran K, Stein LY, Klotz MG, van Loosdrecht MC.

Biochem Soc Trans. 2011 Dec;39(6):1832-7. doi: 10.1042/BST20110717. Review.

PMID:
22103535
42.

Nitrifying and denitrifying pathways of methanotrophic bacteria.

Stein LY, Klotz MG.

Biochem Soc Trans. 2011 Dec;39(6):1826-31. doi: 10.1042/BST20110712. Review.

PMID:
22103534
43.

Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium sensitive to high levels of ammonia.

Suwa Y, Norton JM, Bollmann A, Klotz MG, Stein LY, Laanbroek HJ, Arp DJ, Goodwin LA, Chertkov O, Held B, Bruce D, Detter JC, Detter JC, Tapia R, Han CS.

J Bacteriol. 2011 Sep;193(18):5047-8. doi: 10.1128/JB.05521-11. Erratum in: J Bacteriol. 2011 Nov;193(21):6112. Yuichi, Suwa [corrected to Suwa, Yuichi].

44.

Grand challenges in terrestrial microbiology.

Stein LY, Nicol GW.

Front Microbiol. 2011 Jan 25;2:6. doi: 10.3389/fmicb.2011.00006. eCollection 2011. No abstract available.

45.

Genome sequence of the Arctic methanotroph Methylobacter tundripaludum SV96.

Svenning MM, Hestnes AG, Wartiainen I, Stein LY, Klotz MG, Kalyuzhnaya MG, Spang A, Bringel F, Vuilleumier S, Lajus A, Médigue C, Bruce DC, Cheng JF, Goodwin L, Ivanova N, Han J, Han CS, Hauser L, Held B, Land ML, Lapidus A, Lucas S, Nolan M, Pitluck S, Woyke T.

J Bacteriol. 2011 Nov;193(22):6418-9. doi: 10.1128/JB.05380-11. Epub 2011 Jul 1.

46.

Model of the molecular basis for hydroxylamine oxidation and nitrous oxide production in methanotrophic bacteria.

Campbell MA, Nyerges G, Kozlowski JA, Poret-Peterson AT, Stein LY, Klotz MG.

FEMS Microbiol Lett. 2011 Sep;322(1):82-9. doi: 10.1111/j.1574-6968.2011.02340.x. Epub 2011 Jul 13.

47.

Research on nitrification and related processes, Part B. Preface.

Stein LY, Klotz MG.

Methods Enzymol. 2011;496:xix-xx. doi: 10.1016/B978-0-12-386489-5.00027-0. No abstract available.

PMID:
21514457
48.

Effects of nitrite on ammonia-oxidizing activity and gene regulation in three ammonia-oxidizing bacteria.

Cua LS, Stein LY.

FEMS Microbiol Lett. 2011 Jun;319(2):169-75. doi: 10.1111/j.1574-6968.2011.02277.x. Epub 2011 Apr 20.

49.

Genome sequence of the methanotrophic alphaproteobacterium Methylocystis sp. strain Rockwell (ATCC 49242).

Stein LY, Bringel F, DiSpirito AA, Han S, Jetten MS, Kalyuzhnaya MG, Kits KD, Klotz MG, Op den Camp HJ, Semrau JD, Vuilleumier S, Bruce DC, Cheng JF, Davenport KW, Goodwin L, Han S, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T.

J Bacteriol. 2011 May;193(10):2668-9. doi: 10.1128/JB.00278-11. Epub 2011 Mar 25.

50.

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

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