title: Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates.
abstract: BACKGROUND
  One 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.
  
  
  RESULTS
  The 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 Clostridium thermocellum 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.
  
  
  CONCLUSIONS
  Obtained 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.
authors.affiliation: Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany.
authors.forename: Irena
authors.initials: I
authors.lastname: Maus
authors.affiliation: Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany.
authors.forename: Daniela E
authors.initials: DE
authors.lastname: Koeck
authors.affiliation: Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany.
authors.forename: Katharina G
authors.initials: KG
authors.lastname: Cibis
authors.affiliation: Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany.
authors.forename: Sarah
authors.initials: S
authors.lastname: Hahnke
authors.affiliation: Faculty Life Sciences/Research Center ''Biomass Utilization Hamburg', University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany.
authors.forename: Yong S
authors.initials: YS
authors.lastname: Kim
authors.affiliation: Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Langer
authors.affiliation: Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Kreubel
authors.affiliation: RIPAC-LABOR GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany.
authors.forename: Marcel
authors.initials: M
authors.lastname: Erhard
authors.affiliation: Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany ; Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Bremges
authors.affiliation: Faculty Life Sciences/Research Center ''Biomass Utilization Hamburg', University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany.
authors.forename: Sandra
authors.initials: S
authors.lastname: Off
authors.affiliation: Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Stolze
authors.affiliation: Department of Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Jaenicke
authors.affiliation: Department of Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.affiliation: Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany ; Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Sczyrba
authors.affiliation: Faculty Life Sciences/Research Center ''Biomass Utilization Hamburg', University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany.
authors.forename: Paul
authors.initials: P
authors.lastname: Scherer
authors.affiliation: Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany.
authors.forename: Helmut
authors.initials: H
authors.lastname: König
authors.affiliation: Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany.
authors.forename: Wolfgang H
authors.initials: WH
authors.lastname: Schwarz
authors.affiliation: Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany.
authors.forename: Vladimir V
authors.initials: VV
authors.lastname: Zverlov
authors.affiliation: Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Liebl
authors.affiliation: Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany.
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.affiliation: Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schlüter
authors.affiliation: Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Klocke
keywords: Acetogenic Bacteria; Acidogenic Bacteria; Anaerobic digestion; Biomethanation; Cellulolytic Bacteria; Culturomics; Fragment recruitment; Methanogenic Archaea; Microbial community structure; Polyphasic characterization