An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.
To study the metaproteome of a biogas-producing microbial community, fermentation samples were taken from an agricultural biogas plant for microbial cell and protein extraction and corresponding metagenome analyses. Based on metagenome sequence data, taxonomic community profiling was performed to elucidate the composition of bacterial and archaeal sub-communities. The community's cytosolic metaproteome was represented in a 2D-PAGE approach. Metaproteome databases for protein identification were compiled based on the assembled metagenome sequence dataset for the biogas plant analyzed and non-corresponding biogas metagenomes. Protein identification results revealed that the corresponding biogas protein database facilitated the highest identification rate followed by other biogas-specific databases, whereas common public databases yielded insufficient identification rates. Proteins of the biogas microbiome identified as highly abundant were assigned to the pathways involved in methanogenesis, transport and carbon metabolism. Moreover, the integrated metagenome/-proteome approach enabled the examination of genetic-context information for genes encoding identified proteins by studying neighboring genes on the corresponding contig. Exemplarily, this approach led to the identification of a Methanoculleus sp. contig encoding 16 methanogenesis-related gene products, three of which were also detected as abundant proteins within the community's metaproteome. Thus, metagenome contigs provide additional information on the genetic environment of identified abundant proteins.
Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
Vera
V
Ortseifen
Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
Yvonne
Y
Stolze
Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
Irena
I
Maus
Computational Metagenomics, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
Alexander
A
Sczyrba
Computational Metagenomics, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
Andreas
A
Bremges
Bioinformatics Resource Facility, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
Stefan P
SP
Albaum
Bioinformatics and Systems Biology, Justus Liebig University, 35392 Giessen, Germany.
Sebastian
S
Jaenicke
Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Strasse, D-35394 Giessen, Germany.
Jochen
J
Fracowiak
Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
Alfred
A
Pühler
Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany. Electronic address: aschluet@CeBiTec.Uni-Bielefeld.de.
Andreas
A
Schlüter
D056804:Biofuels / Q000382:microbiology*; D019149:Bioreactors / Q000382:microbiology*; D030562:Databases, Protein; D015180:Electrophoresis, Gel, Two-Dimensional; D054892:Metagenome / Q000235:genetics*; D059013:Microbial Consortia / Q000235:genetics*; D020543:Proteome / Q000032:analysis* / Q000235:genetics
D056804:Biofuels; D020543:Proteome
Biogas microbial community; Contig context information; Database impact on protein identification; Integrated metagenome/-proteome study; Taxonomic profile