Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR.
ISME J. 2024 Jan 8;18(1). doi: 10.1093/ismejo/wrae163.
Marine eukaryotic phytoplankton are fundamental to the marine food web, yet the lack of reference genomes or just a single genome representing a taxon has led to an underestimation of their taxonomic, adaptive, and functional diversity. Here, we integrated strain isolation with metagenomic binning to recover genomes from the cosmopolitan picophytoplankton genus Bathycoccus, traditionally considered monospecific. Our recovery and analysis of 37 Bathycoccus genomes delineated their global genomic diversity and established four evolutionary clades (BI, BII, BIII, BIV). Our metagenomic abundance survey revealed well-differentiated ecological niches and distinct biogeographic distributions for each clade, predominantly shaped by temperature, salinity, and nutrient availability. Comparative genomics analyses further revealed clade-specific genomic traits that underpin niche adaptation and contribute to the global prevalence of Bathycoccus. Our findings underscore temperature as a major driver of genome diversification in this genus, with clade divergences coinciding with major paleoclimatic events that influenced their contemporary thermal niches. Moreover, the unique enrichment of C2H2 zinc finger and ankyrin repeat gene families in polar-adapted clades suggests previously unrecognized cold-adaptation mechanisms in marine eukaryotic phytoplankton. Our study offers a comprehensive genomic landscape of this crucial eukaryotic picophytoplankton, providing insights into their microdiversity and adaptive evolution in response to changing environments.
海洋真核浮游植物是海洋食物网的基础，但由于缺乏参考基因组或仅代表一个分类群的单个基因组，导致对其分类、适应性和功能多样性的低估。在这里，我们将菌株分离与宏基因组分箱相结合，从传统上被认为是单种的世界性微微浮游植物属巴氏球菌中回收基因组。我们对 37 个巴氏球菌基因组的回收和分析描绘了它们的全球基因组多样性，并建立了四个进化枝（BI、BII、BIII、BIV）。我们的宏基因组丰度调查揭示了每个进化枝的分化良好的生态位和独特的生物地理分布，主要由温度、盐度和养分可用性塑造。比较基因组学分析进一步揭示了支持生态位适应的特定于进化枝的基因组特征，并有助于巴氏球菌的全球流行。我们的研究结果强调了温度是该属基因组多样化的主要驱动因素，进化枝的分歧与影响其当代热生态位的主要古气候事件相吻合。此外，极地适应进化枝中 C2H2 锌指和锚蛋白重复基因家族的独特富集表明，海洋真核浮游植物中存在以前未被认识到的冷适应机制。我们的研究提供了这个关键的真核微微浮游植物的综合基因组景观，深入了解了它们在应对环境变化时的微观多样性和适应性进化。
