Additional file 1 of Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer
Creators: name: Ohana Y. A. Costa
name: Hollander, Mattias De
name: Pijl, Agata
name: Binbin Liu
name: Kuramae, Eiko E.
Publisher: name: figshare
Year: 2020
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 1 Supplementary Figure S1: Taxonomic composition and relative abundance of microbial groups at phylum level in SIP metagenome treatments based on a) SSU rRNA gene sequence classification (&gt;2.2 % abundance) b) ORF taxonomic classification (&gt;0.1% abundance). Average abundances of 4 replicates. Unc: unclassified. No EPS – incubation without WH15EPS. Unlab EPS-incubation containing 12C-WH15EPS. Heavy – ‘heavy fraction’ of incubations containing 13C-WH15EPS; Supplementary Figure S2: Biplot of the Redundancy analysis (RDA) based on normalized and Hellinger-transformed abundances of a) SSU rRNA gene taxonomy classification and b) ORF taxonomic classification. Only the best 20 fitting groups are displayed. Unc: unclassified. No EPS – incubation without WH15EPS. Unlab EPS-incubation containing 12C-WH15EPS. Heavy – ‘heavy fraction’ of incubations containing 13C-WH15EPS; Supplementary Figure S3: Box-plot comparisons of alpha-diversity assessment by richness estimators (number of observed OTUs, Chao1, ACE) and diversity indices (Shannon, Inverse Simpson) for SIP 16S rRNA gene samples. ‘Heavy fraction’ values are significantly lower in comparison with both controls for all comparisons (p-value &lt; 0.05). Comparisons performed across treatments using ANOVA test and Tukey`s HSD post-hoc test. Data rarefied to the minimum sampling depth. Unlab. EPS-incubation containing 12C-WH15EPS. Heavy – ‘heavy fraction’ of incubations containing 13C-WH15EPS; Supplementary Figure S4: Relative abundance distribution of the most abundant functional categories in TPM-normalized metagenome sequencing data from the SIP metagenome. a) COG annotation (all categories); b) KEGG annotation (above 0.1 % abundance); c) dbCAN annotation (above 1% abundance). E-Amino acid transport and metabolism; G- Carbohydrate transport and metabolism; H-Coenzyme transport and metabolism; C-Energy production and conversion; I-Lipid transport and metabolism; F-Nucleotide transport and metabolism; Q- Secondary metabolites; D-Cell acycle; N-Cell motility; M-Cell wall/membrane/envelope biogenesis; V-Defence mechanisms; P-Inorganic ion transport and metabolism; U-Intracellular trafficking; O-Post translational modification; T-Signal transduction mechanisms; L-Replication, recombination and repair; K-Transcription; J-Translation; S-Function unknown; R-General function and prediction; X-Mobilome.; Supplementary Figure S5: Principal Coordinate Analysis (PCoA) clustering of normalized and Hellinger-transformed SIP metagenome sequencing data based on Bray-Curtis distances of a) COG annotation, b) KEGG annotation and c) dbCAN annotation. No EPS – incubation without WH15EPS. Unlabeled EPS-incubation containing 12C-WH15EPS. Heavy – ‘heavy fraction’ of incubations containing 13C-WH15EPS; Supplementary Figure S6: Taxonomic composition and relative abundance of microbial groups at a) kingdom and b) phylum level in samples from the metagenome shotgun of cultivated microrganims based SSU rRNA gene taxonomic classification. Average from 2 replicates per plate of culture medium.; Supplementary Figure S7: Venn diagram depicting the number of common and unique glycoside hydrolase (GH) families observed in SIP metagenome and metagenome of cultivate microorganisms` datasets; Supplementary Figure S8: Distribution of the 20 most abundant CAZyme families in a) SIP metagenome samples (relative abundance, average of 4 replicates); b) metagenome of cultivated microorganisms (relative abundance, average of 2 replicates); c) Metagenome-Assembled Genomes (MAGs) (number of genes), and most abundant glycosyl hydrolases (GH) in d) SIP metagenome samples (relative abundance, average of 4 replicates), e) metagenome of cultivated microorganisms (relative abundance, average of 2 replicates) and f) Metagenome-Assembled Genomes (MAGs) (number of genes); Supplementary Figure S9: CO2 emission. CO2 production during total incubation period. Control: control without EPS; EPS: control containing 12C-EPS; Labeled: incubation with 13C-EPS; Labeled CO2 percentage: 13CO2 emitted during 13C-EPS sample incubation; water: days when samples were hydrated; air: days when samples were aired. Supplementary Table S1: COG functions that significantly segregated across treatments selected by Boruta random forests algorithm based on 1000 permutations in the SIP metagenome treatment comparisons; Supplementary Table S2: KEGG orthologs that significantly segregated across treatments selected by Boruta random forests algorithm based on 1000 permutations in the SIP metagenome treatment comparisons; Supplementary Table S3:CAZyme families that significantly segregated across treatments selected by Boruta random forests algorithm based on 1000 permutations in the SIP metagenome treatment comparisons; Supplementary Table S4: Most abundant CAZyme families (above 1% abundance) and most abundant KEGG orthologs (above 0.2% abundance) in the shotgun metagenome of cultivated microorganisms; Supplementary Table S5: MAGs coverage in all samples; Supplementary Table S6: Most abundant KEGG orthologs in MAGs and their associated functions. A selection of the top 10 most abundant KEGG orthologs in each genome is displayed. Annotation performed using eggNOG database.; Supplementary Table S7: Sugar transporters in MAG1 annotated with eggNOG database; Supplementary Table S8: Sugar transporters in MAG2 annotated with eggNOG database; Supplementary Table S9: General type transporters in MAG3 annotated with eggNOG database; Supplementary Table S10: Sugar transporters in MAG4 annotated with eggNOG database; Supplementary Table S11: Families of CAZymes observed in the MAGs, number of ORFs and associated functions; Supplementary Table S12: Coordinates of the sampling sites; Supplementary Table S13: Physicochemical properties of topsoil-litter samples.