Charting the Complexity of the Marine Microbiome through Single-Cell Genomics
Charting the Complexity of the Marine Microbiome through Single-Cell Genomics
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DOI：
10.1016/j.cell.2019.11.017
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发表时间：
2019-12-12
期刊：
影响因子：
64.5
通讯作者：
Stepanauskas, Ramunas
中科院分区：
文献类型：
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作者：
Pachiadaki, Maria G.;Brown, Julia M.;Stepanauskas, Ramunas
海洋细菌和古菌在全球海洋地球化学中起着重要作用。为了提高我们对这种复杂微生物组的理解，我们采用单细胞基因组学和随机的，假设不可知的细胞选择策略，从热带和亚热带真光海洋中恢复了12，715个部分基因组。从一个单一的，0.4毫升的海洋样品，这表明，基因组信息有效地分散在整个地球仪已知的原核浮游生物编码潜力的一个很大的部分被回收。然而，我们发现每个基因组都是独特的，这意味着原核浮游生物种群中的克隆性有限。光收集和次级代谢物生物合成途径在整个谱系中有很多，突出了单细胞基因组学的价值，以促进未培养微生物群体的生态作用和生物技术潜力的鉴定。该基因组集合使来自热带和亚热带表面海洋的>80%的个体宏基因组读数的功能注释和属级分类学分配成为可能，从而提供了改进复杂微生物组的参考基因组数据库的模型。
Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.