MOESM1 of Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates
Creators: name: Maus, Irena
name: Koeck, Daniela
name: Cibis, Katharina
name: Hahnke, Sarah
name: Kim, Yong
name: Langer, Thomas
name: Kreubel, Jana
name: Erhard, Marcel
name: Bremges, Andreas
name: Off, Sandra
name: Stolze, Yvonne
name: Jaenicke, Sebastian
name: Goesmann, Alexander
name: Sczyrba, Alexander
name: Scherer, Paul
name: König, Helmut
name: Schwarz, Wolfgang
name: Zverlov, Vladimir
name: Liebl, Wolfgang
name: Pühler, Alfred
name: Schlüter, Andreas
name: Klocke, Michael
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: Additional file 1. Additional information is available at Biotechnology for Biofuels journal’s website as pdf document, Maus_et_al_v2016-08-03_additional_file_1.pdf. This file contains Additional information on methods as well as additional figures and tables as follows: (i) Additional information on methods for extraction of total microbial RNA. (ii) Additional information on methods for identification of isolates. (iii) Table S1. Statistics of quality-controlled metagenomes sequences data for the microbial community of the thermophilic production-scale biogas plant. (iv) Table S2. Statistics of taxonomically classified sequences obtained from the metagenome and metatranscriptome datasets. (v) Table S3. Number of 16S rRNA sequences and corresponding percentages of bacterial and archaeal genera within the analyzed metagenome and metatranscriptome datasets. The number of metatranscriptome-derived 16S rRNA sequences, i.e. 532,381, was normalized to the number of metagenome-derived sequences, i.e. 18,817. Only genera with at least 10 (normalized) sequences in one of the datasets were considered. ND = no sequences were determined in the dataset. (vi) Figure S1. Exemplary work-flow illustration of the different strategies for the isolation of cellulolytic bacteria. Isolation strategy (3): direct enrichment and isolation using different media. Isolation strategy (4): serial dilution (i.e. dilution to extinction) in liquid medium. Isolation strategy (5): direct plating on solid medium without previous enrichment in liquid culture. (vii) Figure S2. Relative abundance of the 25 most abundant families within the biogas microbial community of the thermophilic biogas plant as deduced from 16S rRNA gene sequences of combined metagenome datasets (&gt;= 0.05 % of the sequences in the metagenome). Taxonomic assignments of the 16S rRNA gene sequences were obtained applying BLASTN against the RDP database applying MGX. (viii) Figure S3. Relative abundance of the 25 most abundant families within the biogas microbial community of the thermophilic biogas plant as deduced from 16S rRNA sequences of the metatranscriptome datasets (&gt;= 0.05 % of the sequences in the metatranscriptome). Taxonomic assignments of the 16S rRNA sequences were obtained applying BLASTN against the RDP database applying MGX. (ix) Figure S4. Cultivable microbial species applying the isolation strategies (1)–(2) and corresponding cell counts in samples of substrate (swine manure), fermenter content (main fermenter), and digestate (second fermenter). The cultivation temperature was 37 or 50 °C (*), respectively. (x) Figure S5. Light- (a) and fluorescent (b) microscopic picture of Methanothermobacter marburgensis isolated from the thermophilic biogas plant. (xi) Figure S6. Phylogenetic tree of selected archaeal (a) and bacterial (b) isolates in relation to corresponding type species. The 16S rRNA gene sequences from closely related type species were obtained from the SILVA database [47]. The isolate T3/55T represents the type strain for a novel genus and species, namely Herbinix hemicellulosilytica, which was recently described by [35]. (xii) Figure S7. Fragment recruitment of metagenome sequences derived from the microbial community of the analyzed thermophilic biogas plant to the genomes of the strains Clostridium cellulosi str. DG5 (a), Herbinix hemicellulosilytica str. T3/55T (b) and Defluviitoga tunisiensis str. L3 (c). Only metagenome sequence reads with more than 75 % sequence identity (y-axis) to the corresponding genome were mapped. Percent identity (y-axis) of a mapped metagenome read was plotted against the mapping position on the genome sequence (x-axis) of H. hemicellulosilytica str. T3/55T or D. tunisiensis str. L3. The x-axis represents the extension (scale) of the C. cellulosi str. DG5, H. hemicellulosilytica str. T3/55T or D. tunisiensis str. L3 genome. Sequence coverage is visualized by gray scale intensity (right margin). Matching sequence read length is indicated by the diameter of the circle representing the mapping position (scale is given on the top right).