Methanobrevibacter Phylotypes are the Dominant Methanogens in Sheep from Venezuela

Microbial Ecology - Tập 56 - Trang 390-394 - 2007
André-Denis G. Wright1,2, Xuanli Ma1,3, Nestor E. Obispo1,4
1CSIRO Livestock Industries, Centre for Environment and Life Sciences, Wembley, Australia
2CSIRO Livestock Industries, Queensland Bioscience Precinct, St. Lucia, Australia
3Faculty of Natural and Agricultural Sciences, University of Western Australia, Crawley, Australia
4Instituto Nacional de Investigaciones Agrícolas, Maracay, Venezuela

Tóm tắt

Rumen methanogens in sheep from Venezuela were examined using 16S rRNA gene libraries and denaturing gradient gel electrophoresis (DGGE) profiles prepared from pooled and individual PCR products from the rumen contents from 10 animals. A total of 104 clones were examined, revealing 14 different 16S rRNA gene sequences or phylotypes. Of the 14 phylotypes, 13 (99 of 104 clones) belonged to the genus Methanobrevibacter, indicating that the genus Methanobrevibacter is the most dominant component of methanogen populations in sheep in Venezuela. The largest group of clones (41 clones) was 97.9–98.5% similar to Methanobrevibacter gottschalkii. Two sequences were identified as possible new species, one belonging to the genus Methanobrevibacter and the other belonging to the genus Methanobacterium. DGGE analysis of the rumen contents from individual animals also revealed 14 different bands with a range of 4–9 bands per animal.

Tài liệu tham khảo

Christophersen CT, Wright A-DG, Vercoe PE (2004) Examining diversity of free living methanogens and those associated with protozoa in the rumen. J Anim Feed Sci 13:51–54 de Rijk P, de Wachter R (1993) DCSE, an interactive tool for sequence alignment and secondary structure research. Comput Appl Biosci 9:735–740 Felsenstein J (2004) PHYLIP (Phylogeny Inference Package) documentation files. Version 3.62c. Department of Genetics, University of Washington, Seattle, Washington Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317–2319 Irbis C, Ushida K (2004) Detection of methanogens and proteobacteria from a single cell of rumen ciliate protozoa. J Gen Appl Microbiol 50:203–212 Kimura M (1980) A simple method of estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 Miller TL, Wolin MJ (1986) Methanogens in human and animal digestive tracts. Syst Appl Microbiol 7:223–229 Primera Comunicación Nacional en Cambio Climático de Venezuela (2005) Caracas, Republica Bolivariana de Venezuela. 164 pp Saito N, Nei M (1987) The neighbor-joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 4:406–425 Sharp R, Ziemer CJ, Marshall DS, Stahl DA (1998) Taxon-specific associations between protozoal and methanogen populations in the rumen and a model system. FEMS Microbiol Ecol 26:71–78 Skillman LC, Evans PN, Strompl C, Joblin KN (2006) 16S rDNA directed PCR primers and detection of methanogens in the bovine rumen. Lett Appl Microbiol 42:222–228 Skillman LC, Evans PN, Naylor GE, Morvan B, Jarvis GN, Joblin KN (2004) 16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs. Anaerobe 10:277–285 Snell-Castro R, Godon JJ, Delgenes JP, Dabert P (2005) Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis. FEMS Microbiol Ecol 52:229–242 Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA:DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849 Tajima K, Nagamine T, Matsui H, Nakamura M, Rustam I, Aminov RI (2001) Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens. FEMS Microbiol Lett 200:67–72 Tokura M, Chagan I, Ushida K, Kojima Y (1999) Phylogenetic study of methanogens associated with rumen ciliates. Curr Microbiol 39:123–128 Whitford MF, Teather RM, Forster RJ (2001) Phylogenetic analysis of methanogens from the bovine rumen. BMC Microbiol 1:5 Wright A-DG, Pimm C (2003) Improved strategy for presumptive identification of methanogens using 16S riboprinting. J Microbiol Methods 55:337–349 Wright A-DG, Toovey AF, Pimm CL (2006) Molecular identification of methanogenic archaea from sheep in Queensland, Australia reveal more uncultured novel archaea. Anaerobe 12:134–139 Wright A-DG, Williams AJ, Winder B, Christophersen C, Rodgers S, Smith K (2004) Molecular diversity of rumen methanogens from sheep in Western Australia. Appl Environ Microbiol 70:1263–1270