PDF(Pubmed)
Abstract：
The within-species diversity of symbiotic bacteria represents an important genetic resource for their environmental adaptation, especially for horizontally transmitted endosymbionts. Although strain-level intraspecies variation has recently been detected in many deep-sea endosymbionts, their ecological role in environmental adaptation, their genome evolution pattern under heterogeneous geochemical environments, and the underlying molecular forces remain unclear.
Here, we conducted a fine-scale metagenomic analysis of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont collected from distinct habitats: hydrothermal vent and methane seep. Endosymbiont genomes were assembled using a pipeline that distinguishes within-species variation and revealed highly heterogeneous compositions in mussels from different habitats. Phylogenetic analysis separated the assemblies into three distinct environment-linked clades. Their functional differentiation follows a mosaic evolutionary pattern. Core genes, essential for central metabolic function and symbiosis, were conserved across all clades. Clade-specific genes associated with heavy metal resistance, pH homeostasis, and nitrate utilization exhibited signals of accelerated evolution. Notably, transposable elements and plasmids contributed to the genetic reshuffling of the symbiont genomes and likely accelerated adaptive evolution through pseudogenization and the introduction of new genes.
The current study uncovers the environment-driven evolution of deep-sea symbionts mediated by mobile genetic elements. Its findings highlight a potentially common and critical role of within-species diversity in animal-microbiome symbioses. Video Abstract.
Here, we conducted a fine-scale metagenomic analysis of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont collected from distinct habitats: hydrothermal vent and methane seep. Endosymbiont genomes were assembled using a pipeline that distinguishes within-species variation and revealed highly heterogeneous compositions in mussels from different habitats. Phylogenetic analysis separated the assemblies into three distinct environment-linked clades. Their functional differentiation follows a mosaic evolutionary pattern. Core genes, essential for central metabolic function and symbiosis, were conserved across all clades. Clade-specific genes associated with heavy metal resistance, pH homeostasis, and nitrate utilization exhibited signals of accelerated evolution. Notably, transposable elements and plasmids contributed to the genetic reshuffling of the symbiont genomes and likely accelerated adaptive evolution through pseudogenization and the introduction of new genes.
The current study uncovers the environment-driven evolution of deep-sea symbionts mediated by mobile genetic elements. Its findings highlight a potentially common and critical role of within-species diversity in animal-microbiome symbioses. Video Abstract.
摘要：
背景：共生细菌的种内多样性代表了其环境适应的重要遗传资源，特别是水平传播的内共生体。尽管最近在许多深海内共生体中发现了应变水平的物种内变化，它们在环境适应中的生态作用，它们在异质地球化学环境下的基因组进化模式，和潜在的分子力仍不清楚。
结果：这里，我们对从不同栖息地收集的深海贻贝Gigantidasplatifrons细菌内共生体进行了精细的宏基因组分析：热液喷口和甲烷渗漏。内共生体基因组是使用管道组装的，该管道可以区分种内变异，并揭示了来自不同栖息地的贻贝中高度异质的组成。系统发育分析将装配体分为三个不同的与环境相关的进化枝。它们的功能分化遵循马赛克进化模式。核心基因,对于中枢代谢功能和共生至关重要，保存在所有分支中。与重金属抗性相关的分支特异性基因，pH稳态，硝酸盐利用表现出加速进化的信号。值得注意的是,转座因子和质粒有助于共生体基因组的遗传改组，并可能通过假基因化和引入新基因来加速适应性进化。
结论：当前的研究揭示了由可移动遗传元件介导的深海共生体的环境驱动进化。其发现强调了物种内多样性在动物-微生物组共生中的潜在共同和关键作用。视频摘要。
结果：这里，我们对从不同栖息地收集的深海贻贝Gigantidasplatifrons细菌内共生体进行了精细的宏基因组分析：热液喷口和甲烷渗漏。内共生体基因组是使用管道组装的，该管道可以区分种内变异，并揭示了来自不同栖息地的贻贝中高度异质的组成。系统发育分析将装配体分为三个不同的与环境相关的进化枝。它们的功能分化遵循马赛克进化模式。核心基因,对于中枢代谢功能和共生至关重要，保存在所有分支中。与重金属抗性相关的分支特异性基因，pH稳态，硝酸盐利用表现出加速进化的信号。值得注意的是,转座因子和质粒有助于共生体基因组的遗传改组，并可能通过假基因化和引入新基因来加速适应性进化。
结论：当前的研究揭示了由可移动遗传元件介导的深海共生体的环境驱动进化。其发现强调了物种内多样性在动物-微生物组共生中的潜在共同和关键作用。视频摘要。
