Kent Alyssa G, Dupont Chris L, Yooseph Shibu, Martiny Adam C
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA.
ISME J. 2016 Aug;10(8):1856-65. doi: 10.1038/ismej.2015.265. Epub 2016 Feb 2.
Prochlorococcus, the smallest known photosynthetic bacterium, is abundant in the ocean's surface layer despite large variation in environmental conditions. There are several genetically divergent lineages within Prochlorococcus and superimposed on this phylogenetic diversity is extensive gene gain and loss. The environmental role in shaping the global ocean distribution of genome diversity in Prochlorococcus is largely unknown, particularly in a framework that considers the vertical and lateral mechanisms of evolution. Here we show that Prochlorococcus field populations from a global circumnavigation harbor extensive genome diversity across the surface ocean, but this diversity is not randomly distributed. We observed a significant correspondence between phylogenetic and gene content diversity, including regional differences in both phylogenetic composition and gene content that were related to environmental factors. Several gene families were strongly associated with specific regions and environmental factors, including the identification of a set of genes related to lower nutrient and temperature regions. Metagenomic assemblies of natural Prochlorococcus genomes reinforced this association by providing linkage of genes across genomic backbones. Overall, our results show that the phylogeography in Prochlorococcus taxonomy is echoed in its genome content. Thus environmental variation shapes the functional capabilities and associated ecosystem role of the globally abundant Prochlorococcus.
原绿球藻是已知最小的光合细菌，尽管环境条件差异很大，但它在海洋表层中数量丰富。原绿球藻内有几个基因不同的谱系，在这种系统发育多样性之上叠加着广泛的基因得失。环境在塑造原绿球藻基因组多样性的全球海洋分布中的作用在很大程度上尚不清楚，尤其是在一个考虑垂直和横向进化机制的框架中。在这里，我们表明，来自全球环航的原绿球藻野外种群在表层海洋中具有广泛的基因组多样性，但这种多样性并非随机分布。我们观察到系统发育和基因内容多样性之间存在显著对应关系，包括系统发育组成和基因内容的区域差异与环境因素有关。几个基因家族与特定区域和环境因素密切相关，包括鉴定出一组与较低营养和温度区域相关的基因。天然原绿球藻基因组的宏基因组组装通过提供跨基因组骨架的基因联系加强了这种关联。总体而言，我们的结果表明，原绿球藻分类学中的系统地理学在其基因组内容中得到了体现。因此，环境变异塑造了全球丰富的原绿球藻的功能能力及其相关的生态系统作用。
