Abstract
Methylotrophic methanogenic archaea are an integral part of the carbon cycle in various anaerobic environments. Different from methylotrophic bacteria, methylotrophic methanogens assimilate both, the methyl compound and dissolved inorganic carbon. Here, we present DNA- and RNA-stable isotope probing (SIP) methods involving an effective labeling strategy using 13C-labeled dissolved inorganic carbon (DIC) as carbon source along with methanol as dissimilatory substrate.
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References
Ferry JG, Lessner DJ (2008) Methanogenesis in marine sediments. Ann N Y Acad Sci 1125:147–157
Liu Y, Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 1125:171–189
Lu Y, Conrad R (2005) In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309:1088–1090
Schwarz JI, Lueders T, Eckert W, Conrad R (2007) Identification of acetate-utilizing bacteria and archaea in methanogenic profundal sediments of Lake Kinneret (Israel) by stable isotope probing of rRNA. Environ Microbiol 9:223–237
Liu F, Conrad R (2010) Thermoanaerobacteriaceae oxidize acetate in methanogenic rice field soil at 50 degrees C. Environ Microbiol 12:2341–2354
Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649
Manefield M, Whiteley AS, Ostle N, Ineson P, Bailey MJ (2002) Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function. Rapid Commun Mass Spectrom 16:2179–2183
Dumont MG, Murrell JC (2005) Stable isotope probing—linking microbial identity to function. Nat Rev Microbiol 3(6):499–504
Chistoserdova L, Kalyuzhnaya MG, Lidstrom ME (2009) The expanding world of methylotrophic metabolism. Annu Rev Microbiol 63:477–499
Neufeld JD, Schafer H, Cox MJ, Boden R, McDonald IR, Murrell JC (2007) Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism. ISME J 1(6):480–491
Grob C, Taubert M, Howat AM, Burns OJ, Dixon JL, Richnow HH et al (2015) Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph. Environ Microbiol 17(10):4007–4018
Allen MA, Lauro FM, Williams TJ, Burg D, Siddiqui KS, De Francisci D et al (2009) The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation. ISME J 3(9):1012–1035
Williams TJ, Burg D, Ertan H, Raftery MJ, Poljak A, Guilhaus M et al (2010) Global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon Methanococcoides burtonii. Part II: the effect of different methylated growth substrates. J Proteome Res 9(2):653–663
Weimer PJ, Zeikus JG (1978) One carbon metabolism in methanogenic bacteria. Arch Microbiol 119:49–57
Goodchild A, Raftery MJ, Saunders NFW, Guilhaus M, Cavicchioli R (2004) Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry. J Proteome Res 3(6):1164–1176
Yin X, Wu W, Maeke M, Richter-Heitmann T, Kulkarni AC, Oni OE, Wendt J, Elvert M, Friedrich MW (2019) CO2 conversion to methane and biomass in obligate methylotrophic methanogens in marine sediments. ISME J. https://doi.org/10.1038/s41396-019-0425-9
van Rensburg MJ, Botha A, Ntsasa NG, Tshilongo J, Leshabane N (2009) Towards the simultaneous detection of the low nmol/mol range of CO, CH4 and CO2 in nitrogen using GC-FID. Accred Qual Assur 14:665–670
Dunford EA, Neufeld JD (2010) DNA stable-isotope probing (DNA-SIP). J Vis Exp (42):e2027. https://doi.org/10.3791/2027
Yao H, Conrad R (2000) Effect of temperature on reduction of iron and production of carbon dioxide and methane in anoxic wetland rice soils. Biol Fertil Soils 32(2):135–141
Grosskopf R, Janssen PH, Liesack W (1998) Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 64(3):960–969
Lueders T, Friedrich M (2000) Archaeal population dynamics during sequential reduction processes in rice field soil. Appl Environ Microbiol 66(7):2732–2742
Fortney NW, He S, Kulkarni A, Friedrich MW et al (2018) Stable isotope probing for microbial iron reduction in chocolate pots hot spring, Yellowstone National Park. Appl Environ Microbiol 84(11):e02894–e02917
Aromokeye DA, Richter-Heitmann T, Oni OE, Kulkarni A, Yin X, Kasten S, Friedrich MW (2018) Temperature controls crystalline iron oxide utilization by microbial communities in methanic ferruginous marine sediment incubations. Front Microbiol 9:2574
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Yin, X., Kulkarni, A.C., Friedrich, M.W. (2019). DNA and RNA Stable Isotope Probing of Methylotrophic Methanogenic Archaea. In: Dumont, M., Hernández García, M. (eds) Stable Isotope Probing. Methods in Molecular Biology, vol 2046. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9721-3_15
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DOI: https://doi.org/10.1007/978-1-4939-9721-3_15
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