Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation

PeerJ

Volumn 2015, Issue 2, 2015, Pages

  Hernandez, Maria E ^a,b   Beck, David A C ^a   Lidstrom, Mary E ^a   Chistoserdova, Ludmila ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b National Institute of Ecology   (Mexico)

Author keywords

Lake Washington; Methanotroph; Methylobacter; Methylophilaceae; Methylophilus; Methylosarcina; Methylotenera; Methylotrophy

Indexed keywords

HYDROGENASE; METHANE; NITRATE REDUCTASE; NITRIC OXIDE REDUCTASE; OXYGEN; RNA 16S;

ARTICLE; BIOENERGY; BIOINFORMATICS; EURYARCHAEOTA; GENE SEQUENCE; LAKE SEDIMENT; METHANOSARCINA; METHANOTROPH; METHYLOBACTER; METHYLOCOCCACEAE; METHYLOPHILACEAE; METHYLOPHILUS; METHYLOTENERA; MICROBIAL COMMUNITY; MICROCOSM; NITROGEN FIXATION; NONHUMAN; OXIDATION; OXYGEN TENSION; RNF COMPLEX;

METHYLOBACTER; METHYLOCOCCACEAE; METHYLOPHILACEAE; METHYLOPHILUS; METHYLOSARCINA; METHYLOTENERA;

EID: 84926429468     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.801     Document Type: Article

References (29)

1. Auman AJ, Stolyar S, Costello AM, LidstromME. 2000. Molecular characterization of methanotrophic isolates from freshwater lake sediment. Applied and Environmental Microbiology 66:5259-5266 DOI 10.1128/AEM.66.12.5259-5266.2000.
2. Beck DAC, Kalyuzhnaya MG, Malfatti S, Tringe SG, Glavina del Rio T, Ivanova N, LidstromME, Chistoserdova L. 2013. A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PeerJ 1:e23 DOI 10.7717/peerj.23.
3. Beck DAC, McTaggart TL, Setboonsarng U, Vorobev A, Kalyuzhnaya MG, Ivanova N, Goodwin L, Woyke T, LidstromME, Chistoserdova L. 2014. The expanded diversity of Methylophilaceae from Lake Washington through cultivation and genomic sequencing of novel ecotypes. PLoS ONE 9:e102458 DOI 10.1371/journal.pone.0102458.
4. Chistoserdova L, LidstromME. 2013. Aerobic methylotrophic prokaryotes. In: Rosenberg E, DeLong EF, Thompson F, Lory S, Stackebrandt E, eds. The prokaryotes. Fourth edition. Berlin: Springer-Verlag Berlin Heidelberg, 267-285.
5. Dedysh SN, Dunfield PF. 2014. Cultivation of methanotrophs. In: McGenity T, Timmis K, Nogales B, eds. Hydrocarbon and lipid microbiology protocols, Springer protocols handbooks. Berlin: Springer-Ferlag.
6. Dubinsky EA, Conrad ME, Chakraborty R, Bill M, Borglin SE, Hollibaugh JT, Mason OU, Piceno MY, Reid FC, StringfellowWT, TomLM, Hazen TC, Andersen GL. 2013. Succession of hydrocarbon-degrading bacteria in the aftermath of the deepwater horizon oil spill in the Gulf of Mexico. Environmental Science Technology 47:10860-10867 DOI 10.1021/es401676y.
7. Dunfield PF, Liesack W, Henckel T, Knowles R, Conrad R. 1999. High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph. Applied Environmental Microbiology 65:1009-1014.
8. Edgar RC. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10:996-998 DOI 10.1038/nmeth.2604.
9. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194-2200 DOI 10.1093/bioinformatics/btr381.
10. He R, Wooller MJ, Pohlman JW, Catranis C, Quensen J, Tiedje JM, Leigh MB. 2012. Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing. Environmental Microbiology 14:1403-1419 DOI 10.1111/j.1462-2920.2012.02725.x.
11. Jensen S, Neufeld JD, Birkeland NK, Hovland M, Murrell JC. 2008. High diversity of microplancton surrounds deep-water coral reef sediment off the coast of Norway. FEMS Microbiology Ecology 66:320-330 DOI 10.1111/j.1574-6941.2008.00575.x.
12. Joergensen L. 1985. The methane mono-oxygenase reaction system studied in vivo by membrane-inlet mass spectrometry. Biochemical Journal 225:441-448.
13. Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E, Levine SR, Barry K, Green-Tringe S, Grigoriev I, Markowitz V, Rigoutsos I, Richardson PM, LidstromME, Chistoserdova L. 2008. High resolution metagenomics targets major functional types in complex microbial communities. Nature Biotechnology 26:1029-1034 DOI 10.1038/nbt.1488.
14. Kalyuzhnaya MG, Stolyar SM, Auman AJ, Lara JC, LidstromME, Chistoserdova L. 2005. Methylosarcina lacus sp. nov., a methanotroph from Lake Washington, Seattle, USA, and emended description of the genus Methylosarcina. International Journal of Systematic and Evolutionary Microbiology 55:2345-2350 DOI 10.1099/ijs.0.63405-0.
15. Kits KD, Klotz MG, Stein LY. 2015. Methane oxidation coupled to nitrate reduction under hypoxia by the Gammaproteobacterium Methylomonas denitrificans, sp. nov. Type Strain FJG1. Environmental Microbiology DOI 10.1111/1462-2920.12772.
16. McTaggart TL, Benuska G, Shapiro N, Woyke T, Chistoserdova L. 2015. Draft genomes of five new strains of Methylophilaceae isolated from Lake Washington sediment. Genome Announcements 3:e01511-14 DOI 10.1128/genomeA.01511-14.
17. Mustakhimov I, Kalyuzhnaya MG, Lidstrom MW, Chistoserdova L. 2013. Insights into denitrification in Methylotenera mobilis from denitrification pathway and methanol metabolism mutants. Journal of Bacteriology 195:2207-2211 DOI 10.1128/JB.00069-13.
18. Nisbet EG, Dlugokencky EJ, Bousquet P. 2014. Atmospheric science. Methane on the rise-again. Science 343:493-495 DOI 10.1126/science.1247828.
19. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H. 2014. Vegan: community ecology package.
20. Oshkin I, Beck DACB, Lamb AE, Tchesnokova V, Benuska G, McTaggart TL, Kalyuzhnaya MG, Dedysh S, LidstromME, Chistoserdova L. 2014. Methane fed microcosms show differential community dynamics and pinpoint specific taxa involved in communal response. The ISME Journal DOI 10.1038/ismej.2014.203.
21. Redmond MC, Valentine DL, Sessions AL. 2010. Identification of novel methane-, ethane-, and propane-oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing. Applied Environmental Microbiology 76:6412-6422 DOI 10.1128/AEM.00271-10.
22. Rivers AR, Sharma S, Tringe SG, Martin J, Joye SB, Moran MA. 2013. Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. The ISME Journal 7:2315-2329 DOI 10.1038/ismej.2013.129.
23. Schmehl M, Jahn A, Meyer zu Vilsendorf A, Hennecke S, Masepohl B, Schuppler M, Marxer M, Oelze J, Klipp W. 1993. Identification of a new class of nitrogen fixation genes in Rhodobacter capsulatus: a putative membrane complex involved in electron transport to nitrogenase. Molecular and General Genetics 241:602-615 DOI 10.1007/BF00279903.
24. Singh BK, Bardgett RD, Smith P, Reay DS. 2010. Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nature Reviews Microbiology 8:779-790 DOI 10.1038/nrmicro2439.
25. Tavormina PL, Orphan VJ, Kalyuzhnaya MG, Jetten MS, Klotz MG. 2011. A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs. Environmental Microbiology Reports 3:91-100 DOI 10.1111/j.1758-2229.2010.00192.x.
26. Trotsenko YA, Murrell JC. 2008. Metabolic aspects of aerobic obligate methanotrophy. Advancements in Applied Microbiology 6:183-229 DOI 10.1016/S0065-2164(07)00005-6.
27. Van der Ha D, Vanwonterghem I, Hoefman S, De Vos P, Boon N. 2013. Selection of associated heterotrophs by methane-oxidizing bacteria at different copper concentrations. Antonie Van Leeuwenhoek 103:527-537 DOI 10.1007/s10482-012-9835-7.
28. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73:5261-5267 DOI 10.1128/AEM.00062-07.
29. Wartiainen I, Hestnes AG, McDonald IR, Svenning MM. 2006. Methylobacter tundripaludum sp. nov., a methane-oxidizing bacterium from Arctic wetland soil on the Svalbard islands, Norway (78 degrees N). International Journal of Systematic and Evolutionary Microbiology 56:109-113 DOI 10.1099/ijs.0.63728-0.