Additional file 2 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

Additional file 2: Table S1. Sample metadata including location, year, research vessel, number of metagenome reads and accession numbers. Table S2. MAG genome properties, accession numbers and taxonomic classifications. Taxonomy was assigned using GTDB-Tk, and mis-classified MAGs were taxonomically re-assigned at the phylum level (Bacteria) and class level (Archaea) using curated archaeal and bacterial phylogenetic trees. Genome quality statistics are based on completion and contamination (high quality, >90% completion, <5% contamination; medium quality, ≥50% completion, ≤10% contamination). Average contamination was 4.02%. Table S3. Average amino acid identity (AAI) matrices for the (A) Bacteria and (B) Archaea. Matrices are grouped by GTDB taxonomy and include MAGs that could not be assigned to a known genus by GTDB-Tk. Details are provided which recently identified MAGs were from Brothers volcano hydrothermal deposits. Table S4. Relative abundance of GTDB taxa by site, based on read coverage of MAGs normalized to 100M reads per sample. MAG coverage for each site was summed and expressed as a percent. Table S5. METABOLIC-G results for JALSQH01 (3 MAGs) and JALWCF01 (13 MAGs). In the summary rows for JALSQH01 and JALWCF01, functions and modules are listed as “present” if identified in ≥50% of all MAGs, “partially present” if found in <50% of the MAGs, and “absent” if undetected in the MAGs. Table S6. Selected functional genes found in Patescibacteria MAGs, based on annotation with GhostKOALA. KEGG module numbers are shown in parentheses. Table S7. Functional genes identified in selected > 80%-completeness MAGs from the Chloroflexota. (A) Genes are marked as present (1; green highlight) or not detected (0) in individual MAGs. (B) The proportion of > 80%-completeness MAGs in six GTDB orders that encode functional genes is also shown, with proportions ≥50% highlighted in green. Table S8. Identification and distribution of functional genes in this study. (A) The HMMs, MEROPS peptidases, and CAZymes used to identify functional genes. Gene call numbers were calculated using the component (C) or accumulative (A) methods described in the methods. Genes requiring manual validation (M) are indicated. (B) Functional gene abundance, calculated as described in the methods. Table S9. Percentage of MAGs in phylogenetic clusters that encode core metabolic genes. Unless otherwise indicated, Archaea are shown at the class level, and Bacteria are shown at the phylum level. Genes were detected using METABOLIC, with additional validation steps for oxidative and reductive Dsr, Sdo, PmoA and McrA. Table S10. Comparative (A) relative abundance and (B) functional gene abundance for the Gammaproteobacteria and Campylobacteria, used to generate Fig. 10.

附加文件2：表S1。包含采样地点、年份、科考船信息、宏基因组读段数量及登录号的样本元数据。
表S2。宏基因组组装基因组（Metagenome-Assembled Genome, MAG）的基因组属性、登录号与分类学注释。分类学分配通过GTDB-Tk（Genome Taxonomy Database Toolkit）完成，对于错分的MAG，基于整理后的古菌与细菌系统发育树，分别在门水平（细菌）和纲水平（古菌）进行重新分类学注释。基因组质量统计基于完整率与污染率：高质量（完整率＞90%，污染率＜5%）；中等质量（完整率≥50%，污染率≤10%）。平均污染率为4.02%。
表S3。（A）细菌与（B）古菌的平均氨基酸同一性（Average Amino Acid Identity, AAI）矩阵。矩阵按GTDB分类学分组，包含无法通过GTDB-Tk分配到已知属的MAG。同时附注了近期从布罗瑟斯火山热液沉积区获取的MAG相关细节。
表S4。基于将MAG读段覆盖度标准化至每样本1亿读段后得到的各采样位点GTDB分类群相对丰度。各采样位点的MAG覆盖度经求和后以百分比形式呈现。
表S5。针对JALSQH01（3个MAG）与JALWCF01（13个MAG）的METABOLIC-G分析结果。在JALSQH01与JALWCF01的汇总行中，若功能与模块在≥50%的MAG中被检出，则标记为“存在”；若在<50%的MAG中被检出，则标记为“部分存在”；若未在任何MAG中检出，则标记为“缺失”。
表S6。基于GhostKOALA注释得到的帕茨斯科特菌门（Patescibacteria）MAG中筛选出的功能基因，括号内标注KEGG模块编号。
表S7。在筛选自绿弯菌门（Chloroflexota）、完整率＞80%的MAG中鉴定到的功能基因。（A）在单个MAG中，功能基因以“存在（1；绿色高亮）”或“未检出（0）”标记。（B）同时展示了6个GTDB目级分类群中，携带功能基因的完整率＞80%的MAG占比，其中占比≥50%的结果以绿色高亮标注。
表S8。本研究中功能基因的鉴定与分布情况。（A）用于鉴定功能基因的隐马尔可夫模型（Hidden Markov Model, HMM）、MEROPS肽酶及碳水化合物活性酶（Carbohydrate-Active enZymes, CAZymes）。基因计数采用方法部分描述的组分法（C）或累积法（A）进行计算。需手动验证的基因（M）已标注。（B）按方法部分描述计算得到的功能基因丰度。
表S9。系统发育簇中携带核心代谢基因的MAG占比。除非另有说明，古菌按纲水平展示，细菌按门水平展示。核心代谢基因通过METABOLIC进行检出，并针对氧化性与还原性Dsr、Sdo、PmoA及McrA增设了验证步骤。
表S10。用于生成图10的γ-变形菌纲（Gammaproteobacteria）与弯曲菌纲（Campylobacteria）的（A）相对丰度与（B）功能基因丰度比较分析结果。