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

Abstract

BackgroundTo 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.ResultsNovel 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 T3/55T, Herbinix luporum SD1DT, Clostridium bornimense M2/40T, Proteiniphilum saccharofermentans M3/6T, Fermentimonas caenicola ING2-E5BT, and Petrimonas mucosa ING2-E5AT. 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.ConclusionsIsolation 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.Electronic supplementary materialThe online version of this article (10.1186/s13068-017-0947-1) contains supplementary material, which is available to authorized users.

Characterization of Core Microbiomes and Functional Profiles of Mesophilic Anaerobic Digesters Fed With Chlorella vulgaris Green Microalgae and Maize Silage

“…Default parameter sets were fixed at absolute read count threshold: 100, with the persistence Venn diagram type (additional settings: between group relative abundance: 0.8, samples in group relative: 0.8) (Wang Y. et al, 2016). The functional profiles of the reactors, fed with the various feedstocks, were investigated using metagenomics data and EMBL-EBI InterPro database (Schlüter et al, 2008;Wirth et al, 2012;Campanaro et al, 2016Campanaro et al, , 2018aStolze et al, 2016;Finn et al, 2017;Maus et al, 2017).…”

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

“…For this propose, the integration of different -omics approaches (integrated or poly-omics), as example, the combination of metagenome with metatranscriptome datasets, is indispensable to distinguish between metabolically active and less active microbial species. Genomecentered biogas microbiome analyses already disclosed and prospectively will disclose further functionalities and interactions of keystone microbiome members [14][15][16][17][18][19][20][21].…”

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

“…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]. More frequently, laboratory-scale reactors were studied, since they offer the unique opportunity to implement different configurations, modulate individual process parameters, or explore different feedstock compositions and inocula [23–30].…”