State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Genomics Proteomics Bioinformatics. 2024 Jul 3;22(2). doi: 10.1093/gpbjnl/qzad006.
Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.
深海冷泉与能源勘探以及全球气候变化密切相关。以烷烃为主导的化学能源驱动模型使冷泉成为深海生命的绿洲，展示了无与伦比的微生物遗传多样性库。在这里，通过分析从全球 5 种冷泉类型的 14 个地点收集的 113 个宏基因组，我们展示了一个全面的深海冷泉微生物组数据库 (CSMD)，用于存档冷泉微生物组的基因组和功能多样性。CSMD 包含超过 4900 万个非冗余基因和 3175 个宏基因组组装基因组，代表跨越 105 个门的 1895 个物种。此外，β多样性分析表明，采样地点和冷泉类型都对原核微生物组群落组成有重大影响。异养和厌氧代谢在微生物群落中普遍存在，同时伴随着相当数量的混合营养体和兼性厌氧菌，突出了冷泉中多样化的代谢潜力。此外，次生代谢基因簇分析表明，至少 98.81%的序列可能编码新的天然产物，其中核糖体合成和翻译后修饰肽是广泛分布在古菌和细菌中的主要类型。总体而言，CSMD 是一个有价值的资源，将增强对全球深海冷泉微生物组的理解和利用。
