Profiling the metabolically active community from a production scale biogas plant by means of high throughput metatranscriptome sequencing

Computational Genomics, Center for Biotechnology-CeBiTec, Bielefeld University, Bielefeld, Germany.
Journal of Biotechnology (Impact Factor: 2.88). 02/2012; 158(4):248-58. DOI: 10.1016/j.jbiotec.2012.01.020
Source: PubMed

ABSTRACT Structural composition and gene content of a biogas-producing microbial community from a production-scale biogas plant fed with renewable primary products was recently analyzed by means of a metagenome sequencing approach. To determine the transcriptionally active part of the same biogas community and to identify key transcripts for the biogas production process, the metatranscriptome of the microorganisms was sequenced for the first time. The metatranscriptome sequence dataset generated on the Genome Sequencer FLX platform is represented by 484,920 sequence reads. Taxonomic profiling of the active part of the community by classification of 16S ribosomal sequence tags revealed that members of the Euryarchaeota and Firmicutes account for the dominant phyla. Only smaller fractions of the 16S ribosomal sequence tags were assigned to the phyla Bacteroidetes, Actinobacteria and Synergistetes. Among the mRNA-derived sequence tags from the metatranscriptome dataset, transcripts encoding enzymes involved in substrate hydrolysis, acidogenesis, acetate formation and methanogenesis could be identified. Transcripts for enzymes functioning in methanogenesis are among the most abundant mRNA tags indicating that the corresponding pathway is very active in the methanogenic sub-community. As a frame of reference for evaluation of metatranscriptome sequence data, the 16S rDNA-based taxonomic profile of the community was analyzed by means of high-throughput 16S rDNA amplicon sequencing. Processing of the obtained amplicon reads resulted in 18,598 high-quality 16S rDNA sequences covering the V3-V4 hypervariable region of the 16S rRNA gene. Comparison of the taxonomic profiles deduced from 16S rDNA amplicon sequences and the metatranscriptome dataset indicates a high transcriptional activity of archaeal species. Overall, it was shown that the most abundant species dominating the community also contributed the majority of the transcripts. In the future, key transcripts for the biogas production process will provide valuable markers for evaluation of the performance of biogas-producing microbial communities with the objective to optimize the biotechnology of this process.

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Available from: Waleed Abu Al-Soud, Jul 29, 2015
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    • "Advances in high-throughput sequencing and bulk extraction of mRNA allow for RNA-based studies of organismal functioning in complex environments. Despite certain technological challenges, microbial metatranscriptomics has already helped elucidate microbial responses to oil spills and the resulting deep-sea hydrocarbon plumes, differences between anoxic and oxic paddy soils, and metabolic activity of methane-producing microbes, to name a few [31] [41] [47]. Similarly, metatranscriptomic approaches have been used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen [37] and in forest soils [6] [44]. "
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    • "Standard databases for protein identification are NCBInr (Acland et al., 2014), UniProtKB/Swiss-Prot or UniProtKB/TrEMBL (Consortium, 2012). With respect to metaproteomics, more specific databases or searches against metagenomes from the same or similar samples [e.g. for BGP samples (Schlüter et al., 2008; Rademacher et al., 2012; Wirth et al., 2012; Zakrzewski et al., 2012)] resulted in the identification of more proteins and are strongly recommended. "
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    • "Members of the phylum Bacteroidetes are frequently found in biogas reactors. Often they are the second most abundant group of the microbial community as indicated by cultivation-independent community analyses (Hanreich et al., 2013; Kröber et al., 2009; Rademacher et al., 2012; Schlüter et al., 2008; St-Pierre and Wright, 2014; Zakrzewski et al., 2012; Ziganshin et al., 2013). Bacteroidetes represent a metabolically heterogeneous group comprising species with a broad range of capabilities such as hydrolysis of polysaccharides and proteins, fermentation of sugars, and production of acids such as acetic, propionic, succinic and butyric acid (Krieg et al., 2011). "
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