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.
Highlights
To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important
Selection of a set of microbial isolates from different biogas‐producing communities Limited availability of genome sequence information in public databases for Anaerobic digestion (AD) community members generally constrains the interpretation of metagenomic and metatranscriptomic data of such communities leading to large amounts of non-classifiable metagenome sequences from AD habitats [15,16,17,18, 46, 47]. Parallel application of both traditional culturomics [48] as well as molecular analysis combined with HT sequencing techniques is necessary for detailed studies of complex microbial biogas consortia
Two archaeal members, namely M. bourgensis MS2T [49] and M. formicicum MFT [50], were obtained from the DSMZ and included in this study as the reference strains for methanogenic Archaea since they were isolated from AD communities
Summary
To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Quantitative ‘real-time’ polymerase chain reaction (qPCR), e.g., [1,2,3,4,5], terminal restriction fragment length polymorphism (TRFLP) [6,7,8], and the 16S rRNA gene amplicon [9, 10] as well as metagenome sequencing approaches [9, 11,12,13,14] applying high-throughput (HT) technologies are the most commonly used methods In these studies, bacterial members belonging to the classes Clostridia and Bacteroidia were identified to dominate the biogas microbial communities, followed by Proteobacteria, Bacilli, Flavobacteria, Spirochaetes, and Erysipelotrichi. Within the domain Archaea, members from the orders Methanomicrobiales, Methanosarcinales, and Methanobacteriales were described to be abundant in biogas systems
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