Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

Irena Maus, Andreas Bremges, Yvonne Stolze, Sarah Hahnke, Katharina G. Cibis, Daniela E. Koeck, Yong S. Kim, Jana Kreubel, Julia Hassa, Daniel Wibberg, Aaron Weimann, Sandra Off, Robbin Stantscheff, Vladimir V. Zverlov, Wolfgang H. Schwarz, Helmut König, Wolfgang Liebl, Paul Scherer, Alice C. McHardy, Alexander Sczyrba, Michael Klocke, Alfred Pühler, Andreas Schlüter

To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Unfortunately, generated data can only partialy be interpreted rudimentary since databases lack reference sequences. Novel cellulolytic, hydrolytic, and acidogenic/acetogenic Bacteria as well as methanogenic Archaea originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production. Some of the analyzed bacterial strains were recently described as new species and even genera, namely Herbinix hemicellulosilytica T3/55(T), Herbinix luporum SD1D(T), Clostridium bornimense M2/40(T), Proteiniphilum saccharofermentans M3/6(T), Fermentimonas caenicola ING2-E5B(T), and Petrimonas mucosa ING2-E5A(T). High-throughput genome sequencing of 22 anaerobic digestion isolates enabled functional genome interpretation, metabolic reconstruction, and prediction of microbial traits regarding their abilities to utilize complex bio-polymers and to perform specific fermentation pathways. To determine the prevalence of the isolates included in this study in different biogas systems, corresponding metagenome fragment mappings were done. Methanoculleus bourgensis was found to be abundant in three mesophilic biogas plants studied and slightly less abundant in a thermophilic biogas plant, whereas Defluviitoga tunisiensis was only prominent in the thermophilic system. Moreover, several of the analyzed species were clearly detectable in the mesophilic biogas plants, but appeared to be only moderately abundant. Among the species for which genome sequence information was publicly available prior to this study, only the species Amphibacillus xylanus, Clostridium clariflavum, and Lactobacillus acidophilus are of importance for the biogas microbiomes analyzed, but did not reach the level of abundance as determined for M. bourgensis and D. tunisiensis. Isolation of key anaerobic digestion microorganisms and their functional interpretation was achieved by application of elaborated cultivation techniques and subsequent genome analyses. New isolates and their genome information extend the repository covering anaerobic digestion community members.