Additional file 3 of Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge
Creators: name: Pan, Jie
name: Xu, Wei
name: Zhou, Zhichao
name: Shao, Zongze
name: Dong, Chunming
name: Liu, Lirui
name: Luo, Zhuhua
name: Li, Meng
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 2: Fig. S1 Bathymetric map of the southern Mid-Atlantic Ocean and the location of the Deyin-1 hydrothermal field. Fig. S2 Phylogenetic tree and relative abundance of 16S rRNA genes in the current study. The maximum likelihood phylogenetic tree was constructed based on 16S rRNA gene sequences from the assembled scaffolds. The scale bar represents 0.1 nucleotide substitutions per sequence position. The bar plots are based on the relative abundance of each sequence, and the color of the bars represents the samples that each sequence was obtained from. The full phylogenetic tree is available in Supplementary Data 3. Fig. S3 Ribosomal protein tree of the MAGs in the current study. The maximum likelihood phylogenetic tree was constructed based on 16 ribosomal protein sequences. The scale bar represents 0.1 amino acid substitutions per sequence position. The colors represent the taxonomy of the MAG. The full phylogenetic tree is available in Supplementary Data 4. Fig. S4 Phylogenetic tree, relative abundance, and functional potentials of Alphaproteobacteria MAGs. The maximum likelihood phylogenetic tree was constructed based on 16 concatenated ribosomal protein sequences. The scale bar represents 0.1 amino acid substitutions per sequence position. RPKM value is the relative abundance of each MAG, calculated by number of mapped reads / (sequence length × metagenomic size). Fig. S5 Phylogenetic tree, relative abundance, and functional potentials of Gammaproteobacteria MAGs. The maximum likelihood phylogenetic tree was constructed based on 16 concatenated ribosomal protein sequences. The scale bar represents 0.1 amino acid substitutions per sequence position. RPKM value is the relative abundance of each MAG, calculated by number of mapped reads / (sequence length × metagenomic size). Fig. S6 Phylogenetic tree, relative abundance, and functional potentials of Bacteroidetes MAGs. The maximum likelihood phylogenetic tree was constructed based on 16 concatenated ribosomal protein sequences. The scale bar represents 0.1 amino acid substitutions per sequence position. RPKM value is the relative abundance of each MAG, calculated by number of mapped reads / (sequence length × metagenomic size). Fig. S7 Venn diagram of OTUs clustered with 16S rRNA gene sequences in this study (a) and MDS analysis of the taxonomic compositions with reference active and inactive chimney data (b). The taxonomic details of reference samples were available in Table S5. Fig. S8 Rarefaction curves based on the 16S rRNA gene coverages in all samples. (a) Observed OTU number. (b) Chao1 index. Fig. S9 Relative abundance of functional genes encoded by the taxa in each sample. The details of gene abundance are available in Table S3. Fig. S10 Relative abundance of carbohydrate-active enzymes (CAZymes) encoded by the taxa in each sample. The purple triangle indicates CAZymes with a potential secretion signal. The details of CAZymes abundance are available in Table S4. Fig. S11 Phylogenetic tree based on 120 bacterial marker genes (a) and the percentages of conserved proteins (b) with the reference Nitrospirae genomes and the MAG SZUA-77. Fig. S12 Command parameters of twelve binning methods using MetaBAT (a) and the evaluation of each result comparing to the final result optimized by using DAS_Tool. Fig. S13 Phylogenetic tree of dsrA and rdsrA amino acid sequences from the MAGs. The scale bar of the phylogenetic trees represents 0.1 amino acid substitutions per sequence position. The bar plots are based on the average abundance of the sequences. The stars represent the existence of dsrD gene in the same MAG.