Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants

Abstract

BackgroundBiofuel production from conversion of biomass is indispensable in the portfolio of renewable energies. Complex microbial communities are involved in the anaerobic digestion process of plant material, agricultural residual products and food wastes. Analysis of the genetic potential and microbiology of communities degrading biomass to biofuels is considered to be the key to develop process optimisation strategies. Hence, due to the still incomplete taxonomic and functional characterisation of corresponding communities, new and unknown species are of special interest.ResultsThree mesophilic and one thermophilic production-scale biogas plants (BGPs) were taxonomically profiled using high-throughput 16S rRNA gene amplicon sequencing. All BGPs shared a core microbiome with the thermophilic BGP featuring the lowest diversity. However, the phyla Cloacimonetes and Spirochaetes were unique to BGPs 2 and 3, Fusobacteria were only found in BGP3 and members of the phylum Thermotogae were present only in the thermophilic BGP4. Taxonomic analyses revealed that these distinctive taxa mostly represent so far unknown species. The only exception is the dominant Thermotogae OTU featuring 16S rRNA gene sequence identity to Defluviitoga tunisiensis L3, a sequenced and characterised strain. To further investigate the genetic potential of the biogas communities, corresponding metagenomes were sequenced in a deepness of 347.5 Gbp in total. A combined assembly comprised 80.3 % of all reads and resulted in the prediction of 1.59 million genes on assembled contigs. Genome binning yielded genome bins comprising the prevalent distinctive phyla Cloacimonetes, Spirochaetes, Fusobacteria and Thermotogae. Comparative genome analyses between the most dominant Thermotogae bin and the very closely related Defluviitogatunisiensis L3 genome originating from the same BGP revealed high genetic similarity. This finding confirmed applicability and reliability of the binning approach. The four highly covered genome bins of the other three distinct phyla showed low or very low genetic similarities to their closest phylogenetic relatives, and therefore indicated their novelty.ConclusionsIn this study, the 16S rRNA gene sequencing approach and a combined metagenome assembly and binning approach were used for the first time on different production-scale biogas plants and revealed insights into the genetic potential and functional role of so far unknown species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0565-3) contains supplementary material, which is available to authorized users.

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

“…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 ., ).…”

“…In this approach, species genomes are reconstructed from metagenome data sets representing a microbial community, enabling the reconstruction of their metabolic potential and abundance determination by mapping back metagenome reads on the respective genome bins (Mande et al, 2012;Sharpton, 2014;Sangwan et al, 2016). Binning has previously been used on biogas communities from laboratory-and production-scale biogas production reactors, resulting in reconstruction of unknown species Stolze et al, 2016;Treu et al, 2016;Xia et al, 2016;Kougias et al, 2017). Still, a study on the actual role within the community and these species' in situ metabolic transcriptional activity within their respective habitats is missing.…”

“…The four genome bins, of which three are novel and uncharacterized, represent species of the bacterial phyla Thermotogae, Fusobacteria, Spirochaetes and Cloacimonetes (WWE1) respectively. They have been previously selected due to their taxonomic affiliation and genomically characterized (Stolze et al, 2016). Analyses on the four species represented by the genome bins gave insights into their actual transcriptional activities and showed their respective metabolism and role within their habitats.…”

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

“…Two mesophilic biogas plants, namely BGP2 and BGP3, and the thermophilic BGP4 were operated by applying the general continuous wet fermentation technology, with the addition of pig manure instead of cow manure in the case of BGP3 and BGP4. The description of the BGPs analyzed in this study was recently published [6,16,17]. Table 1 summarizes the process parameters, feeding details, process temperature, biogas yield, and methane content of the sampling time point for the different BGPs, as was recorded in the log sheets by the corresponding plant operators and by individual interviews.…”

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

“…A combined assembly generally results in a higher number of well-characterized contigs, leading to a better taxonomic and functional annotation of sequence data. For example, a combination of combined assembly and genome binning of high-throughput metagenome sequences of microbial communities (from GOLD study Gs0095506) led to the identification of previously unknown bacterial species from biogas plants in Germany (40). The previous version of GOLD supported combined assemblies among metagenome projects only.…”