Additional file 2 of Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys

Additional file 2: Table S1 Measured concentrations of selected aqueous species and pH in replicate fluid samples from M-vent and L-vent. Table S2 General metagenomic and assembly characteristics of M- and L-vent chimney sample. Table S3 Taxonomic classification and relative abundance of full-length 16S rRNA genes recovered from L-vent sulfide chimney sample. Table S4 Taxonomic classification and relative abundance of full-length 16S rRNA genes recovered from M-vent sulfide chimney sample. Table S5 Completeness and contamination of 173 MAGs recovered from L- and M-vent chimney samples. Table S6: Metabolic potential of MAGs for the major microbial groups (> 1%) recovered from the L- and M-vent chimney. The specific method for estimating relative abundance/iRep are listed in the "Method and Materials" in the main text. The average iRep value of bacterial MAGs recovered from L- and M-vent sample are 1.42 and 1.51, respectively. The numbers in the metabolic pathway columns represent the percentage of the microbial taxa encoded the complete pathway (based on quantity of MAGs, e.g. 0.33 means 1 in 3 of the MAGs have the pathway). Table S7 Key genes of metabolic pathways for MAG annotation. The completeness of each metabolic pathway is classified into 3 level: 1- complete, 2 - uncomplete; 3- partial. The particular completeness classification standard for each pathway are listed in the following: Sulfide oxdation: complete-sqr or fccB; Sox pathway (thiosulfate oxidation): complete - sox A/B/X/Y/Z/C/D, uncomplete - soxB, partial: other Sox genes expect soxB/C/D; Dissimilatory sulfate reduction/oxidation: complete-sat/dsrAB/aprAB, uncomplete - two of sat/dsrAB/aprAB, partial - one of sat/dsrAB/aprAB. Subsequent dissimilatory nitrate reduction: complete-nirB or nrfA/H; uncomplete-one of nrfA/H. Subsequent denitrification: complete-nirS/K and norB/C and nosZ; uncomplete - two of nirS/K and norB/C and nosZ; partial - one of nirS/K and norB/C and nosZ. Nitrogen fixation: complete-nifK/D/H; uncomplete - two of nifD/H/K; partial - one of nifD/K/H. WL pathway: complete-cdhC or acsB and cdhE and cdhD and cooS; cdhC or acsB and one of cdhE/D and cooS; partial - two of cdhC/B and cdhE/D and cooS. CO oxidation: complete - coxM/L/S; uncomplete - coxL and one of coxS/M; partial - one of coxM/L/S. Acetate utilization/production: complete - ACSS or pta/ack. rTCA: complete - aclA/B; uncomplete - aclA or aclB. CBB pathway: complete - rbcL/S; uncomplete - rbcL or rbcS. Methanogenesis/aerobic methane oxidation: complete - mcrA/G/B; uncomplete: two of mcrA/B/G; partial - one of mcrA/G/B. Cytochrome c oxidase: complete - two Cox/Cyd/Qox genes or three cco/Cyo genes; uncomplete- one of Cox/Cyd/Qox genes or two of cco/Cyo genes; partial- one of cco/Cyo genes. Table S8 Sulfur metabolic pathways of Thermodesulfobacteria MAGs recovered. Table S9 Metabolic potential of Nitrospirae MAGs retrieved from this study and phylogenetically closed species. The red ID represented those Nitrospirae MAGs reconstructed from M-vent, the green ones represent those recovered from subseafloor massive sulfides [71] and the blue ones refer to those Nitrospirae retrieved from inactive sulfide chimneys [37]. Numbers in the form represent the completeness of specific pathways for each Nitrospirae genome/MAG, 1 indicates that complete key genes of the pathway were identified in the genomes/MAGs, other else the specific key genes were listed if the pathway is not complete. For sqr, cyctochrome C oxidase, multi-heme cyc and cyc2, numbers represent the quantity of specific genes identified in the genomes/MAGs. Table S10 Distribution and quantity of cytochrome c oxidase genes in 173 MAGs retrieved from M- and L-vent. Specific definition rules and types of cytochrome c oxidase genes could find in Table S7. Table S11 Summary of the activity, study method and microbial composition of deep-sea hydrothermal sulfide chimneys or in situ incubation experiments cited in this study.