DNA and RNA Stable Isotope Probing of Methylotrophic Methanogenic Archaea

  • Xiuran Yin
  • Ajinkya C. Kulkarni
  • Michael W. FriedrichEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2046)


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.

Key words

Methylotrophic methanogens Stable isotope probing (SIP) Labeling strategy Dissolved inorganic carbon Methanol 


  1. 1.
    Ferry JG, Lessner DJ (2008) Methanogenesis in marine sediments. Ann N Y Acad Sci 1125:147–157CrossRefGoogle Scholar
  2. 2.
    Liu Y, Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 1125:171–189CrossRefGoogle Scholar
  3. 3.
    Lu Y, Conrad R (2005) In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309:1088–1090CrossRefGoogle Scholar
  4. 4.
    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 9:223–237CrossRefGoogle Scholar
  5. 5.
    Liu F, Conrad R (2010) Thermoanaerobacteriaceae oxidize acetate in methanogenic rice field soil at 50 degrees C. Environ Microbiol 12:2341–2354PubMedGoogle Scholar
  6. 6.
    Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649CrossRefGoogle Scholar
  7. 7.
    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 16:2179–2183CrossRefGoogle Scholar
  8. 8.
    Dumont MG, Murrell JC (2005) Stable isotope probing—linking microbial identity to function. Nat Rev Microbiol 3(6):499–504CrossRefGoogle Scholar
  9. 9.
    Chistoserdova L, Kalyuzhnaya MG, Lidstrom ME (2009) The expanding world of methylotrophic metabolism. Annu Rev Microbiol 63:477–499CrossRefGoogle Scholar
  10. 10.
    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):480–491CrossRefGoogle Scholar
  11. 11.
    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):4007–4018CrossRefGoogle Scholar
  12. 12.
    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):1012–1035CrossRefGoogle Scholar
  13. 13.
    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):653–663CrossRefGoogle Scholar
  14. 14.
    Weimer PJ, Zeikus JG (1978) One carbon metabolism in methanogenic bacteria. Arch Microbiol 119:49–57CrossRefGoogle Scholar
  15. 15.
    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):1164–1176CrossRefGoogle Scholar
  16. 16.
    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. Scholar
  17. 17.
    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 14:665–670CrossRefGoogle Scholar
  18. 18.
    Dunford EA, Neufeld JD (2010) DNA stable-isotope probing (DNA-SIP). J Vis Exp (42):e2027.
  19. 19.
    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):135–141CrossRefGoogle Scholar
  20. 20.
    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):960–969PubMedPubMedCentralGoogle Scholar
  21. 21.
    Lueders T, Friedrich M (2000) Archaeal population dynamics during sequential reduction processes in rice field soil. Appl Environ Microbiol 66(7):2732–2742CrossRefGoogle Scholar
  22. 22.
    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–e02917CrossRefGoogle Scholar
  23. 23.
    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 9:2574CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Xiuran Yin
    • 1
    • 2
    • 3
  • Ajinkya C. Kulkarni
    • 1
    • 2
    • 3
  • Michael W. Friedrich
    • 1
    • 2
    Email author
  1. 1.Microbial Ecophysiology Group, Faculty of Biology/ChemistryUniversity of BremenBremenGermany
  2. 2.MARUM—Center for Marine Environmental SciencesUniversity of BremenBremenGermany
  3. 3.International Max Planck Research School for Marine MicrobiologyMax Planck Institute for Marine MicrobiologyBremenGermany

Personalised recommendations