Data from: Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents

Background: Chemolithoautotrophic primary production sustains dense invertebrate communities at deep-sea hydrothermal vents and hydrocarbon seeps. Symbiotic bacteria that oxidize dissolved sulfur, methane, and hydrogen gases nourish bathymodiolin mussels that thrive in these environments worldwide. The mussel symbionts are newly acquired in each generation via infection by free-living forms. This study examined geographical subdivision of the thiotrophic endosymbionts hosted by Bathymodiolus mussels living along the eastern Pacific hydrothermal vents. High-throughput sequencing data of 16S ribosomal RNA encoding gene and fragments of six protein-coding genes of symbionts were examined in the samples collected from nine vent localities at the East Pacific Rise, Galápagos Rift, and Pacific-Antarctic Ridge.
Results: Both of the parapatric sister-species, B. thermophilus and B. antarcticus, hosted the same numerically dominant phylotype of thiotrophic Gammaproteobacteria. However, sequences from six protein-coding genes revealed highly divergent symbiont lineages living north and south of the Easter Microplate and hosted by these two Bathymodiolus mussel species. High heterogeneity of symbiont haplotypes among host individuals sampled from the same location suggested that stochasticity associated with initial infections was amplified as symbionts proliferated within the host individuals. The mussel species presently contact one another and hybridize along the Easter Microplate, but the northern and southern symbionts appear to be completely isolated. Vicariance associated with orogeny of the Easter Microplate region, 2.5-5.3 million years ago, may have initiated isolation of the symbiont and host populations. Estimates of synonymous substitution rates for the protein-coding
bacterial genes examined in this study were 0.77-1.62%/nucleotide/million years.
Conclusions: Our present study reports the most comprehensive population genetic analyses of the chemosynthetic endosymbiotic bacteria based on high-throughput genetic data and extensive geographical sampling to date, and demonstrates the role of the geographical features, the Easter Microplate and geographical distance, in the intraspecific divergence of this bacterial species along the mid-ocean ridge axes in the eastern Pacific. Altogether, our results provide insights into extrinsic and intrinsic factors affecting the dispersal and evolution of chemosynthetic symbiotic partners in the hydrothermal vents along the eastern Pacific Ocean.

背景：化能自养初级生产（Chemolithoautotrophic primary production）支撑着深海热液喷口（deep-sea hydrothermal vents）与烃类渗漏区（hydrocarbon seeps）处高密度的无脊椎动物群落。氧化溶解态硫、甲烷与氢气的共生细菌，为全球范围内在这类环境中繁盛生存的偏顶蛤属（Bathymodiolus）贻贝提供营养。这类贻贝的共生菌在每一世代中均通过自由生活态菌体的侵染实现代际间的重新获取。本研究针对东太平洋热液喷口区域栖息的偏顶蛤所宿主的硫氧化型内共生菌（thiotrophic endosymbionts）的地理分化情况展开了考察。研究人员对采自东太平洋海隆（East Pacific Rise）、加拉帕戈斯裂谷（Galápagos Rift）与太平洋-南极海岭（Pacific-Antarctic Ridge）共9处喷口位点的样本，开展了共生菌16S核糖体RNA编码基因（16S ribosomal RNA encoding gene）与6个蛋白质编码基因片段的高通量测序（high-throughput sequencing）数据分析。
结果：两种邻域分布的姊妹物种——热泉偏顶蛤（B. thermophilus）与南极偏顶蛤（B. antarcticus）——均宿主有丰度占优的同一类硫氧化型γ-变形菌门（Gammaproteobacteria）系统发育型。但6个蛋白质编码基因的序列分析显示，栖息于复活微板块（Easter Microplate）南北两侧、分别由这两种偏顶蛤宿主的共生菌演化支系存在显著分化。同一位点采集的宿主个体间共生菌单倍型（haplotype）存在高度异质性，这表明初始侵染过程中的随机性会随着共生菌在宿主个体内增殖而被放大。目前这两种贻贝在复活微板块区域存在接触并发生杂交，但南北两侧的共生菌似乎已完全隔离。距今250万至530万年前复活微板块区域造山运动所引发的地理隔离事件，可能启动了共生菌与宿主种群的分化隔离过程。本研究涉及的细菌蛋白质编码基因的同义替换速率估算值为0.77~1.62%/核苷酸/百万年。
结论：本研究基于高通量遗传数据与大范围地理采样，完成了迄今为止最为全面的化能合成内共生菌种群遗传学分析，并证实了地理特征（复活微板块）与地理距离在东太平洋洋中脊轴带该细菌物种种内分化过程中的作用。综上，本研究结果为解析东太平洋热液喷口区域化能合成共生伙伴的扩散与演化过程中的外在与内在影响因素提供了新的认知。