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单氨基酸变体揭示了塑造全球 SAR11 亚群生物地理学的进化过程。

Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade.

机构信息

Department of Medicine, The University of Chicago, Chicago, United States.

Graduate Program in Biophysical Sciences, University of Chicago, Chicago, United States.

出版信息

Elife. 2019 Sep 3;8:e46497. doi: 10.7554/eLife.46497.

DOI:10.7554/eLife.46497
PMID:31478833
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6721796/
Abstract

Members of the SAR11 order Pelagibacterales dominate the surface oceans. Their extensive diversity challenges emerging operational boundaries defined for microbial 'species' and complicates efforts of population genetics to study their evolution. Here, we employed single-amino acid variants (SAAVs) to investigate ecological and evolutionary forces that maintain the genomic heterogeneity within ubiquitous SAR11 populations we accessed through metagenomic read recruitment using a single isolate genome. Integrating amino acid and protein biochemistry with metagenomics revealed that systematic purifying selection against deleterious variants governs non-synonymous variation among very closely related populations of SAR11. SAAVs partitioned metagenomes into two main groups matching large-scale oceanic current temperatures, and six finer proteotypes that connect distant oceanic regions. These findings suggest that environmentally-mediated selection plays a critical role in the journey of cosmopolitan surface ocean microbial populations, and the idea 'everything is everywhere but the environment selects' has credence even at the finest resolutions.

摘要

SAR11 目浮游杆菌纲的成员主导着海洋表面。它们广泛的多样性挑战了新兴的微生物“种”的操作界限，并使种群遗传学研究其进化的努力复杂化。在这里，我们采用单氨基酸变体（SAAV）来研究维持我们通过使用单个分离株基因组招募宏基因组读数来获取的普遍 SAR11 种群内基因组异质性的生态和进化力量。将氨基酸和蛋白质生物化学与宏基因组学相结合，揭示了系统的纯化选择对有害变体的选择，从而控制了 SAR11 的非常密切相关的种群中的非同义变异。SAAV 将宏基因组分为与大规模海洋洋流温度匹配的两个主要组，以及连接遥远海洋区域的六个更精细的蛋白质型。这些发现表明，环境介导的选择在世界性海洋表面微生物种群的迁徙中起着至关重要的作用，即使在最细微的分辨率下，“一切都在任何地方，但环境选择”的观点也有其可信度。

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