Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that can provide insights into adaptation to divergent ecological niches. While patterns of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is relatively rare. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Differences in nitrogen and sulfur physiology between the two dominant symbiont groups, Ca. Ruthia and Ca. Vesicomyosocius, have been hypothesized to influence niche exploitation, which likely affects gene content evolution in these symbionts. However, genomic data are currently limited to confirm this assumption. In the present study we sequenced and compared 11 vesicomyid symbiont genomes with existing assemblies for Ca. Vesicomyosocius okutanii and Ca. Ruthia magnifica. Our analyses indicate that the two vesicomyid symbiont groups have a common core genome related to chemosynthetic metabolism, but differ in their potential for nitrate respiration and flexibility to environmental sulfide concentrations. Moreover, Ca. Vesicomyosocius and Ca. Ruthia have different enzymatic requirements for cobalamin and nickel and show contrasting capacities to acquire foreign genetic material. Tests for site-specific positive selection in metabolic candidate genes imply that the observed physiological differences are adaptive and thus likely correspond to ecological niches available to each symbiont group. These findings highlight the role of niche differentiation in creating divergent paths of reductive genome evolution in vertically transmitted symbionts.

中文翻译：

---

辅助因子，氧气和硫的需求量差异影响深海囊泡蛤共生酶的生态位适应性

细菌内共生菌的垂直传播伴随着几乎不可逆的基因损失，可以为适应不同的生态位提供见识。尽管在某些陆地共生中已经很好地描述了基因组减少的模式，但在垂直传播相对罕见的海洋系统中却鲜为人知。深海类囊蛤与化学合成的γ-变形细菌之间的联系是海洋中母亲遗传的共生体的一个例子。两个主要共生体群Ca和N的生理差异。Ruthia和Ca。假单胞菌被认为会影响利基开发，这可能会影响这些共生体的基因含量演变。但是，基因组数据目前仅限于确认这一假设。在本研究中，我们对11个囊藻共生体基因组进行了测序，并将其与现有的Ca装配进行了比较。Vesicomyosocius okutanii和Ca。番木瓜。我们的分析表明，两个囊藻共生体组具有与化学合成代谢相关的共同核心基因组，但是它们在硝酸盐呼吸和对环境硫化物浓度的适应性方面存在差异。此外，钙。Vesicomyosocius和Ca。钌对钴胺素和镍具有不同的酶促要求，并且在获取外来遗传物质方面显示出不同的能力。对代谢候选基因中位点特异性阳性选择的测试表明，观察到的生理差异是适应性的，因此可能对应于每个共生体群体可利用的生态位。