Metagenomics of the svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci

Pope, Phillip B., Mackenzie, Alasdair K., Gregor, Ivan, Smith, Wendy, Sundset, Monica A., McHardy, Alice C., Morrison, Mark and Eijsink, Vincent G.H. (2012) Metagenomics of the svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. PLoS ONE, 7 6: e38571.1-e38571.10. doi:10.1371/journal.pone.0038571


Author Pope, Phillip B.
Mackenzie, Alasdair K.
Gregor, Ivan
Smith, Wendy
Sundset, Monica A.
McHardy, Alice C.
Morrison, Mark
Eijsink, Vincent G.H.
Title Metagenomics of the svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci
Journal name PLoS ONE   Check publisher's open access policy
ISSN 1932-6203
Publication date 2012-06-06
Year available 2012
Sub-type Article (original research)
DOI 10.1371/journal.pone.0038571
Open Access Status DOI
Volume 7
Issue 6
Start page e38571.1
End page e38571.10
Total pages 10
Place of publication San Francisco United States
Publisher Public Library of Science (PLoS)
Language eng
Formatted abstract
Lignocellulosic biomass remains a largely untapped source of renewable energy predominantly due to its recalcitrance and an incomplete understanding of how this is overcome in nature. We present here a compositional and comparative analysis of metagenomic data pertaining to a natural biomass-converting ecosystem adapted to austere arctic nutritional conditions, namely the rumen microbiome of Svalbard reindeer (Rangifer tarandus platyrhynchus). Community analysis showed that deeply-branched cellulolytic lineages affiliated to the Bacteroidetes and Firmicutes are dominant, whilst sequence binning methods facilitated the assemblage of metagenomic sequence for a dominant and novel Bacteroidales clade (SRM-1). Analysis of unassembled metagenomic sequence as well as metabolic reconstruction of SRM-1 revealed the presence of multiple polysaccharide utilization loci-like systems (PULs) as well as members of more than 20 glycoside hydrolase and other carbohydrate-active enzyme families targeting various polysaccharides including cellulose, xylan and pectin. Functional screening of cloned metagenome fragments revealed high cellulolytic activity and an abundance of PULs that are rich in endoglucanases (GH5) but devoid of other common enzymes thought to be involved in cellulose degradation. Combining these results with known and partly re-evaluated metagenomic data strongly indicates that much like the human distal gut, the digestive system of herbivores harbours high numbers of deeply branched and as-yet uncultured members of the Bacteroidetes that depend on PUL-like systems for plant biomass degradation.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: UQ Diamantina Institute Publications
 
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