Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates

Abstract

BackgroundOne of the most promising technologies to sustainably produce energy and to mitigate greenhouse gas emissions from combustion of fossil energy carriers is the anaerobic digestion and biomethanation of organic raw material and waste towards biogas by highly diverse microbial consortia. In this context, the microbial systems ecology of thermophilic industrial-scale biogas plants is poorly understood.ResultsThe microbial community structure of an exemplary thermophilic biogas plant was analyzed by a comprehensive approach comprising the analysis of the microbial metagenome and metatranscriptome complemented by the cultivation of hydrolytic and acido-/acetogenic Bacteria as well as methanogenic Archaea. Analysis of metagenome-derived 16S rRNA gene sequences revealed that the bacterial genera Defluviitoga (5.5 %), Halocella (3.5 %), Clostridium sensu stricto (1.9 %), Clostridium cluster III (1.5 %), and Tepidimicrobium (0.7 %) were most abundant. Among the Archaea, Methanoculleus (2.8 %) and Methanothermobacter (0.8 %) were predominant. As revealed by a metatranscriptomic 16S rRNA analysis, Defluviitoga (9.2 %), Clostridium cluster III (4.8 %), and Tepidanaerobacter (1.1 %) as well as Methanoculleus (5.7 %) mainly contributed to these sequence tags indicating their metabolic activity, whereas Hallocella (1.8 %), Tepidimicrobium (0.5 %), and Methanothermobacter (<0.1 %) were transcriptionally less active. By applying 11 different cultivation strategies, 52 taxonomically different microbial isolates representing the classes Clostridia, Bacilli, Thermotogae, Methanomicrobia and Methanobacteria were obtained. Genome analyses of isolates support the finding that, besides Clostridiumthermocellum and Clostridium stercorarium,Defluviitoga tunisiensis participated in the hydrolysis of hemicellulose producing ethanol, acetate, and H2/CO2. The latter three metabolites are substrates for hydrogentrophic and acetoclastic archaeal methanogenesis.ConclusionsObtained results showed that high abundance of microorganisms as deduced from metagenome analysis does not necessarily indicate high transcriptional or metabolic activity, and vice versa. Additionally, it appeared that the microbiome of the investigated thermophilic biogas plant comprised a huge number of up to now unknown and insufficiently characterized species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0581-3) contains supplementary material, which is available to authorized users.

Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants

“…Figure modified according to Maus et al . (). Carbohydrates are labelled in light orange ovals, transporters in blue and corresponding genes in yellow rectangles.…”

“…Alternatively, lactate could be used for pyruvate production. Hydrogen and acetate production is known for D. tunisiensis L3 and was previously discussed as hint for a syntrophic lifestyle with aceticlastic or hydrogenotrophic Archaea (Maus et al ., ; Stolze et al ., ). This assumption is further supported by the presence and partially high transcriptional activities of genes encoding enzymes associated with syntrophy (Worm et al ., ).…”

“…The previous taxonomic and genetic analyses of the Thermotogae genome bin showed that it represents a species closely related to the thermophilic bacterium Defluviitoga tunisiensis L3 (Maus et al ., , ), or may even indicate another strain of this species. It is presumably able to utilize a wide variety of mono‐, di‐ and polysaccharides and was predicted to produce acetate, hydrogen and carbon dioxide as end‐products (Stolze et al ., ).…”

Microbial rRNA gene expression and co‐occurrence profiles associate with biokinetics and elemental composition in full‐scale anaerobic digesters

“…Defluviitoga spp. have been detected at high levels in other thermophilic digesters (Maus et al ., 2016b) indicating its potential significance to methane production at high temperatures. Notably, genera harbouring known syntrophic acetate‐oxidizing (SAO) bacteria of Tepidanaerobacter and Syntrophaceticus (Westerholm et al ., , ) were detected at higher rRNA and rRNA gene fractions in the codigesters compared to SS digesters, again with the exception of the thermophilic SS2T digester (Fig.…”

Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis

“…Depending on the process conditions, such as temperature and fed substrates, differences in the community profiles were identified [39][40][41]. For example, the bacterial phyla Actinobacteria, Deltaproteobacteria, and Spirochaetes were frequently found in mesophilic bioreactors [42], whereas members of the phylum Thermotogae (42%) were observed to be a predominant taxon under thermophilic conditions [1,43,44]. Comparison of the four biogas communities analyzed in this study revealed that the genera Defluviitoga and Halocella were highly abundant in the thermophilic BGP4.…”