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Identification of metabolically active proteobacterial and archaeal communities in the rumen by DNA ‐ and RNA ‐derived 16 S rRNA gene
Author(s) -
Kang S.H.,
Evans P.,
Morrison M.,
McSweeney C.
Publication year - 2013
Publication title -
journal of applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.889
H-Index - 156
eISSN - 1365-2672
pISSN - 1364-5072
DOI - 10.1111/jam.12270
Subject(s) - biology , methanogen , rumen , library , ribosomal rna , 16s ribosomal rna , proteobacteria , gene , temperature gradient gel electrophoresis , population , dna , genomic dna , microbiology and biotechnology , bacteria , genetics , biochemistry , demography , sociology , fermentation
Aims To gain new insights into the metabolic contribution of bacterial group in the rumen. Methods and Results Both DNA ‐ and RNA ‐derived bacterial 16 S ribosomal materials from bovine rumen contents were used as the template for bacterial community and analyse microbiota by three methods namely custom phylogenetic microarray, quantitative real‐time PCR and denaturing gradient gel electrophoresis techniques. Bacterial analysis showed that genera affiliating with the P roteobacteria apparently made a greater metabolic contribution to rumen function than their population sizes indicated. Analysis of another rumen microbial group, the methanogens, using clone libraries for the expressed methyl coenzyme reductase subunit A ( mcr A ) revealed that an uncultivated methanogen clade contributes one‐third of RNA ‐derived mcr A sequences based on a limited number of clones analysed. These uncultivated methanogen species were not observed in the mcr A gene library based on the DNA ‐derived sequences. Conclusions The comparison of results obtained from DNA ‐ and RNA ‐derived materials suggests that some of the Proteobacteria and novel methanogen species appeared to be low in abundance in the rumen maintained on grain‐based diets might play a greater role in rumen metabolism. Significance and Impact of the Study These studies provide the first report to compare high‐throughput analysis of bacterial 16 S rRNA genes from DNA ‐ and RNA ‐derived materials to indicate differences that species make to community structure and metabolic activity.