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

Abstract

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism’s genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.Electronic supplementary materialThe online version of this article (10.1007/s00253-018-8976-7) contains supplementary material, which is available to authorized users.

Using meta‐omics of contaminated sediments to monitor changes in pathways relevant to climate regulation

“…While gene abundance (DNA) data give a good insight into the functional potential of a community, transcriptional (RNA) data provide a direct measurement of function and thus enable the understanding of a community's role in ecosystem function (Aguiar-Pulido et al, 2016;Singer et al, 2017;Hassa et al, 2018). Transcriptional data have been found to include gene sequences that are not present in corresponding gene abundance data (Shi et al, 2011).…”

Different response of bacteria, archaea and fungi to process parameters in nine full‐scale anaerobic digesters

“…Comparative studies of compositions of bacterial and archaeal communities in several (n ≥ 7) full-scale anaerobic digesters were done based on extracted genomic DNA (Riviere et al, 2009;Sundberg et al, 2013;Abendroth et al, 2015;Li et al, 2015;Rui et al, 2015;Luo et al, 2016). In recent years, much more attention was paid to transcriptomic and proteomic approaches (for reviews see Heyer et al, 2016;Hassa et al, 2018). However, studies targeting the 16S rRNA of bacteria, archaea and 28S rRNA of fungi, respectively, are rare for anaerobic reactors (Lebuhn et al, 2014;De Vrieze et al, 2016;Dollhofer et al, 2017).…”

“…Therefore, RNA-based community screening can give more reliable information on actually active community members and to identify key species that determine the AD process Ziels et al, 2018). Same is true for studies dealing with metatranscriptomic approaches to investigate microbial community responses with respect to altered process conditions (Zakrzewski et al, 2012;Bremges et al, 2015;G€ ullert et al, 2016;Maus et al, 2016;Hassa et al, 2018).…”

The Future Agricultural Biogas Plant in Germany: A Vision

“…Intensive research has provided new insights into the digestion process microbiology during the last two decades, still knowledge on the biogas microbiome is rather limited. Most of the microbiome members and even more their functions and ecological roles in the biogas process are still unknown [32][33][34][35][36][37].…”