An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant

Abstract

To study the metaproteome of a biogas-producing microbial community, fermentation samples were taken from an agricultural biogas plant for microbial cell and protein extraction and corresponding metagenome analyses. Based on metagenome sequence data, taxonomic community profiling was performed to elucidate the composition of bacterial and archaeal sub-communities. The community's cytosolic metaproteome was represented in a 2D-PAGE approach. Metaproteome databases for protein identification were compiled based on the assembled metagenome sequence dataset for the biogas plant analyzed and non-corresponding biogas metagenomes. Protein identification results revealed that the corresponding biogas protein database facilitated the highest identification rate followed by other biogas-specific databases, whereas common public databases yielded insufficient identification rates. Proteins of the biogas microbiome identified as highly abundant were assigned to the pathways involved in methanogenesis, transport and carbon metabolism. Moreover, the integrated metagenome/-proteome approach enabled the examination of genetic-context information for genes encoding identified proteins by studying neighboring genes on the corresponding contig. Exemplarily, this approach led to the identification of a Methanoculleus sp. contig encoding 16 methanogenesis-related gene products, three of which were also detected as abundant proteins within the community's metaproteome. Thus, metagenome contigs provide additional information on the genetic environment of identified abundant proteins.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

“…Compilation of protein databases specific for biogas communities essentially improved protein identification in metaproteome analyses (Heyer et al 2016 ; Ortseifen et al 2016 ). Metagenome sequences representing biogas-producing microbial communities were assembled to deduce encoded gene products for compilation of biogas-specific protein databases.…”

Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter

“…In general, little is known about the in situ transcriptional activity of single archaeal strains in biogas fermenters. However, it was shown for microbial communities in biogas fermenters, that archaeal genes involved in energy metabolism and methanogenesis were among the highest transcribed genes [43] and corresponding gene products are highly expressed [44][45][46]. The second most TPM (97,901) belong to category O ('post-translational modification, protein turnover, and chaperones').…”

The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production

“…In the past four years, hundreds of genomes belonging to the microbes involved in biogas production process have been sequenced. To improve the understanding of the highly diverse and interconnected network of the AD microbiome, several studies focused on the characterization of microbial communities from the full-scale biogas plants [14–17] trying to connect the microbial composition to differences in process parameters [7,18]. Other studies were focused on the identification of the functional roles of some microbial species [19–22].…”