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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.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-016-0534-x) contains supplementary material, which is available to authorized users.

biotechnology for biofuels

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