Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci.
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.
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. phil.pope@umb.no
Phillip B
PB
Pope
Alasdair K
AK
Mackenzie
Ivan
I
Gregor
Wendy
W
Smith
Monica A
MA
Sundset
Alice C
AC
McHardy
Mark
M
Morrison
Vincent G H
VG
Eijsink
D000818:Animals; D001110:Arctic Regions; D041963:Bacteroidetes / Q000235:genetics*; D001483:Base Sequence; D002482:Cellulose / Q000378:metabolism; D003001:Cloning, Molecular; D017931:DNA Primers / Q000235:genetics; D005260:Female; D056426:Genetic Loci / Q000235:genetics; D006094:Gram-Positive Bacteria / Q000235:genetics* / Q000378:metabolism; D016013:Likelihood Functions; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics / Q000379:methods; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009664:Norway; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012053:Reindeer / Q000382:microbiology*; D012417:Rumen / Q000382:microbiology*; D017422:Sequence Analysis, DNA
D017931:DNA Primers; D012336:RNA, Ribosomal, 16S; D002482:Cellulose