A novel fingerprint method to assess the diversity of methanogens in microbial systems

FEMS Microbiology Letters

Volumn 325, Issue 2, 2011, Pages 115-122

  Gagnon, Nathalie ^a   Barret, Maialen ^a   Topp, Edward ^b   Kalmokoff, Martin ^c   Massé, Daniel ^a   Masse, Lucie ^a   Talbot, Guylaine ^a  

^a SHERBROOKE RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^b AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^c Agriculture and Agri Food Canada Kentville   (Canada)

Author keywords

Amplicon length heterogeneity; Methanogenic Archaea; Methyl coenzyme M reductase

Indexed keywords

METHANE; METHYL COENZYME M REDUCTASE ALPHA; MICROBIAL ENZYME; PLASMID DNA; UNCLASSIFIED DRUG;

AMPLICON; ARTICLE; BIOREACTOR; CONTROLLED STUDY; DNA FINGERPRINTING; DNA SEQUENCE; ENVIRONMENT; GENE; GENE LIBRARY; MANURE; MCRA GENE; METHANOBREVIBACTER; METHANOCORPUSCULUM; METHANOCULLEUS; METHANOGEN; METHANOGENIUM; METHANOSARCINACEAE; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; POPULATION ABUNDANCE; PRIORITY JOURNAL; VALIDATION PROCESS;

ANIMALS; BIOREACTORS; CATTLE; DNA FINGERPRINTING; DNA, ARCHAEAL; EURYARCHAEOTA; GENE LIBRARY; MANURE; OXIDOREDUCTASES; PHYLOGENY; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SWINE;

EID: 81855192779     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2011.02418.x     Document Type: Article

References (24)

1. Boyd VL, Moody KI, Karger AE, Livak KJ, Zon G & Burns JW (2006) Methylation-dependent fragment separation: direct detection of DNA methylation by capillary electrophoresis of PCR products from bisulfite-converted genomic DNA. Anal Biochem 354: 266-273.
2. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
3. Fellenstein J (1986) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
4. Freitag TE & Prosser JI (2009) Correlation of methane production and functional gene transcriptional activity in a peat soil. Appl Environ Microbiol 75: 6679-6687.
5. Galtier N, Gouy M & Gautier C (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12: 543-548.
6. Griffiths RI, Witheley AS, O'Donnell AG & Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA and rRNA-based microbial community composition. Appl Environ Microbiol 66: 5488-5491.
7. Hallam SJ, Girguis PR, Preston CM, Richardson PM & DeLong EF (2003) Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl Environ Microbiol 69: 5483-5491.
8. Intergovernmental Panel on Climate Change (IPCC) (1996) Climate Change 1995: The Science of Climate Change. Contribution of Working Group I to the Second Assessment Report of the Intergovernmental Panel on Climate Change (Houghton JT, Meiro Fihlo LG, Callander BA, Harris N, Kattenberg A & Maskell K, eds), pp. 540. Cambridge University Press, New York, NY.
9. Jukes TH & Cantor SR (1969) Evolution of protein molecules. Mammalian Protein Metabolism (Munro H, ed), pp. 81-132. Academic Press, New York, NY.
10. Lehmacher A & Klenk HP (1994) Characterization and phylogeny of mcrII, a gene cluster encoding an isoenzyme of methyl coenzyme M reductase from hyperthermophilic Methanothermus fervidus. Mol Gen Genet 243: 198-206.
11. Lettinga G (1995) Anaerobic digestion and wastewater treatment systems. Antonie Van Leewenhoek 67: 3-28.
12. Ludwig W, Strunk O, Westram R et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
13. Lueders T & Friedrich MW (2003) Evaluation of PCR amplification bias by terminal restriction length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69: 320-326.
14. Lueders T, Chin KJ, Conrad R & Friedrich M (2001) Molecular analyses of methyl-coenzyme M reductase α-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ Microbiol 3: 194-204.
15. Luton PE, Wayne JM, Sharp RJ & Riley PW (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148: 3521-3530.
16. Mills DK, Fitzgerald K, Litchfield CD & Gillevet PM (2003) A comparison of DNA profiling techniques for monitoring nutrient impact on microbial community composition during bioremediation of petroleum-contaminated soils. J Microbiol Methods 54: 57-74.
17. Roy CS, Talbot G, Topp E, Beaulieu C, Palin MF & Massé DI (2009) Bacterial community dynamics in an anaerobic plug-flow type bioreactor treating swine manure. Water Res 43: 21-32.
18. Schink B & Stams AJM (2006) Syntrophism among prokaryotes. The Prokaryotes, 3rd edn, Vol. 2 (Dworkin M, Falkow S, Rosenberg E, Schleifer KH & Stackebrandt E, eds), pp. 309-335. Springer, New York, NY, USA.
19. Suzuki M, Rappé MS & Giovannoni SJ (1998) Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl Environ Microbiol 64: 4522-4529.
20. Talbot G, Topp E, Palin MF & Massé DI (2008) Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors. Water Res 42: 513-537.
21. Talbot G, Roy CS, Topp E, Beaulieu C, Palin MF & Massé DI (2009) Multivariate statistical analyses of rDNA and rRNA fingerprint data to differentiate microbial communities in swine manure. FEMS Microbiol Ecol 70: 540-552.
22. Talbot G, Roy CS, Topp E, Kalmokoff ML, Brooks SPJ, Beaulieu C, Palin MF & Massé DI (2010) Spatial distribution of some microbial trophic groups in a plug-flow type anaerobic bioreactor treating swine manure. Water Sci Technol 61: 1147-1155.
23. Thauer RK (1998) Biochemistry of methanogenesis: a tribute to Marjory Stephenson: 1998 Marjory Stephenson Prize Lecture. Microbiology 144: 2377-2406.
24. Whitford MF, Teather RM & Forster RJ (2001) Phylogenetic analysis of methanogens from the bovine rumen. BMC Microbiol 1: 1-5.