Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies.
BACKGROUND
The diverse microbial communities in agricultural biogas fermenters are assumed to be well adapted for the anaerobic transformation of plant biomass to methane. Compared to natural systems, biogas reactors are limited in their hydrolytic potential. The reasons for this are not understood.


RESULTS
In this paper, we show that a typical industrial biogas reactor fed with maize silage, cow manure, and chicken manure has relatively lower hydrolysis rates compared to feces samples from herbivores. We provide evidence that on average, 2.5 genes encoding cellulolytic GHs/Mbp were identified in the biogas fermenter compared to 3.8 in the elephant feces and 3.2 in the cow rumen data sets. The ratio of genes coding for cellulolytic GH enzymes affiliated with the Firmicutes versus the Bacteroidetes was 2.8:1 in the biogas fermenter compared to 1:1 in the elephant feces and 1.4:1 in the cow rumen sample. Furthermore, RNA-Seq data indicated that highly transcribed cellulases in the biogas fermenter were four times more often affiliated with the Firmicutes compared to the Bacteroidetes, while an equal distribution of these enzymes was observed in the elephant feces sample.


CONCLUSIONS
Our data indicate that a relatively lower abundance of bacteria affiliated with the phylum of Bacteroidetes and, to some extent, Fibrobacteres is associated with a decreased richness of predicted lignocellulolytic enzymes in biogas fermenters. This difference can be attributed to a partial lack of genes coding for cellulolytic GH enzymes derived from bacteria which are affiliated with the Fibrobacteres and, especially, the Bacteroidetes. The partial deficiency of these genes implies a potentially important limitation in the biogas fermenter with regard to the initial hydrolysis of biomass. Based on these findings, we speculate that increasing the members of Bacteroidetes and Fibrobacteres in biogas fermenters will most likely result in an increased hydrolytic performance.
Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany.
Simon
S
Güllert
Institute for General Microbiology, Christian Albrecht University Kiel, Kiel, Germany.
Martin A
MA
Fischer
CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria.
Dmitrij
D
Turaev
CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria.
Britta
B
Noebauer
Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany.
Nele
N
Ilmberger
Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, Germany.
Bernd
B
Wemheuer
Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Martinistr. 52, Hamburg, Germany ; Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, Hamburg, Germany.
Malik
M
Alawi
CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria.
Thomas
T
Rattei
Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, Germany.
Rolf
R
Daniel
Institute for General Microbiology, Christian Albrecht University Kiel, Kiel, Germany.
Ruth A
RA
Schmitz
Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, Hamburg, Germany.
Adam
A
Grundhoff
Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany.
Wolfgang R
WR
Streit
Anaerobic digestion; Biofuels; Biogas; Biorefinery; Cellulases; Lignocellulosic biomass; Metagenomics; Microbial communities; PULs