Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific

Supplementary material for 'Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific', as described in Microbial Genomics.<br>Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with sampling site, sediment type and depth. Inferring functional patterns provided insights into pos- sible ecological roles of the main microbial taxa. These included <i>Chloroflexota</i>, the most abundant phylum across all samples, whereby the classes <i>Dehalococcoida </i>and <i>Anaerolineae </i>dominated deep-subsurface and most shallow coastal sediments, respectively. <i>Thermoproteota </i>and <i>Asgardarchaeota </i>were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. <i>Tangaroaeota </i>phyl. nov. (former RBG-13-66-14), <i>Ryujiniota </i>phyl. nov. (former UBA6262) and <i>Spongiisociota </i>phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitro- gen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.

刊载于《Microbial Genomics》的《西太平洋浅海海岸与深海海底沉积物的分类与功能模式宏基因组学解析》补充材料。海洋沉积物是广袤且尚未被充分探索的生境，同时也是地球上最大的碳储库之一。微生物群落驱动着沉积物中的营养元素循环，但我们对其分类学与代谢多样性的完整范围仍有待探索。本研究针对西太平洋区域采集的浅海海岸与深海海底沉积物岩芯展开分析，采样深度范围为海底以下0.01米至近600米。通过宏基因组学（metagenomics）分析，我们在所有样本中鉴定出多个分类学聚类簇，这些聚类簇主要与采样位点、沉积物类型及采样深度相匹配。通过推断功能模式，我们得以解析主要微生物类群的潜在生态功能。其中包括绿弯菌门（Chloroflexota），它是所有样本中丰度最高的菌门；其下的脱卤球菌纲（Dehalococcoida）与厌氧绳菌纲（Anaerolineae）分别主导了深地下沉积物与多数浅海海岸沉积物。热原体门（Thermoproteota）与阿斯加德古菌门（Asgardarchaeota）是古菌域中丰度最高的两个菌门，在部分样本中古菌的相对丰度可达50%以上。我们为所有主要原核生物谱系获得了高质量的宏基因组组装基因组（metagenome-assembled genomes），并为三个菌门提出了新名称：即唐加罗古菌门（Tangaroaeota）phyl. nov.（原分类单元编号RBG-13-66-14）、流球古菌门（Ryujiniota）phyl. nov.（原分类单元编号UBA6262）与海绵共生菌门（Spongiisociota）phyl. nov.（原分类单元编号UBA8248）。所有样本的代谢功能谱涵盖从最浅层沉积物中的有氧呼吸与光合作用，到深层缺氧沉积物中的异养碳利用、硫酸盐还原与产甲烷作用。此外，我们还鉴定出潜在参与氮循环、硫循环及异养碳利用的微生物类群。综上，本研究有助于增进我们对西太平洋区域海洋沉积物中底栖原核生物群落分类学与功能多样性的认知。