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

Abstract

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

Long‐term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis

“…They are known as typical colonizers of biogas plants and competitors in the anaerobic degradation of organic material. The ratio of Firmicutes versus Bacteroidetes was in the range of 1.7:1 and 6.1:1, which is comparable to previously described observations in biogas plants (Güllert et al ., ). In other plant biomass degrading habitats, like cow rumen or elephant intestine, significantly lower ratios of Firmicutes versus Bacteroidetes are typically observed as part of the healthy gut flora (Güllert et al ., ).…”

“…The ratio of Firmicutes versus Bacteroidetes was in the range of 1.7:1 and 6.1:1, which is comparable to previously described observations in biogas plants (Güllert et al ., ). In other plant biomass degrading habitats, like cow rumen or elephant intestine, significantly lower ratios of Firmicutes versus Bacteroidetes are typically observed as part of the healthy gut flora (Güllert et al ., ). In the above‐mentioned habitats, as well as in the biogas reactor, Firmicutes and Bacteroidetes are involved in the degradation of biomass during the hydrolysis, acidogenesis and acetogenesis (Wirth et al ., ; Güllert et al ., ).…”

“…In other plant biomass degrading habitats, like cow rumen or elephant intestine, significantly lower ratios of Firmicutes versus Bacteroidetes are typically observed as part of the healthy gut flora (Güllert et al ., ). In the above‐mentioned habitats, as well as in the biogas reactor, Firmicutes and Bacteroidetes are involved in the degradation of biomass during the hydrolysis, acidogenesis and acetogenesis (Wirth et al ., ; Güllert et al ., ). During the raising NH 4 + –N concentrations in the studied biogas plant, clostridial sequences increased from 52% at the start of the observations up to 65% at the peak observed NH 4 + –N concentration (day 226, BGR07).…”

“…In a recent publication, Güllert et al . () investigated the cellulolytic potential of the very same biogas reactor by an in depth metagenomic study. Within this study, several high‐quality metagenomic bins were generated and taxonomically annotated in detail for one selected time point (BGR03).…”

Metagenomic and metaproteomic analyses of a corn stover-adapted microbial consortium EMSD5 reveal its taxonomic and enzymatic basis for degrading lignocellulose

“…The prevalence of Proteobacteria was also found in a sugarcane bagasse microbial community, although it has a much smaller proportion of Firmicutes [9]. The metagenomic and 16S rRNA amplicon data sets showed that microbial communities in biogas reactors were frequently affiliated with the phylum Firmicutes , which played a significant role in the anaerobic digestion process [12, 23, 24]. Like biogas reactors, the submerged fermentation under static culture conditions in this study provided a relatively anaerobic environment in favor of the growth of anaerobic bacteria such as Firmicutes .…”