Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.
Appl Environ Microbiol. 2020 Apr 1;86(8). doi: 10.1128/AEM.02549-19.
The deep-sea hydrothermal vent shrimp largely depends on a dense epibiotic chemoautotrophic bacterial community within its enlarged cephalothoracic chamber. However, our understanding of shrimp-bacterium interactions is limited. In this report, we focused on the deltaproteobacterial epibiont of from the relatively unexplored South Mid-Atlantic Ridge. A nearly complete genome of a epibiont was binned from the assembled metagenome. Whole-genome phylogenetic analysis reveals that it is affiliated with the genus , representing a potential novel species for which the name " Desulfobulbus rimicarensis" is proposed. Genomic and transcriptomic analyses reveal that this bacterium utilizes the Wood-Ljungdahl pathway for carbon assimilation and harvests energy via sulfur disproportionation, which is significantly different from other shrimp epibionts. Additionally, this epibiont has putative nitrogen fixation activity, but it is extremely active in directly taking up ammonia and urea from the host or vent environments. Moreover, the epibiont could be distinguished from its free-living relatives by various features, such as the lack of chemotaxis and motility traits, a dramatic reduction in biosynthesis genes for capsular and extracellular polysaccharides, enrichment of genes required for carbon fixation and sulfur metabolism, and resistance to environmental toxins. Our study highlights the unique role and symbiotic adaptation of in deep-sea hydrothermal vent shrimps. The shrimp represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. are ubiquitous in epibiotic communities of , and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe " Desulfobulbus rimicarensis," an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of , this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the host.
深海热液喷口虾主要依赖于其扩大的头胸甲腔内密集的共生化能自养细菌群落。然而，我们对虾-细菌相互作用的理解有限。在本报告中，我们专注于来自相对未开发的南大西洋中脊的 虾的δ变形菌共生体。从组装的宏基因组中分拣出一个 共生体的近乎完整基因组。全基因组系统发育分析表明，它与属有关，代表一种潜在的新物种，建议命名为“Desulfobulbus rimicarensis”。基因组和转录组分析表明，这种细菌利用 Wood-Ljungdahl 途径进行碳同化，并通过硫歧化作用获取能量，这与其他虾共生体明显不同。此外，这种共生体具有固氮活性，但它非常活跃地直接从宿主或喷口环境中吸收氨和尿素。此外，这种共生体可以通过各种特征与自由生活的近亲区分开来，例如缺乏趋化性和运动特征、用于荚膜和细胞外多糖生物合成的基因急剧减少、需要碳固定和硫代谢的基因丰富，以及对环境毒素的抗性。我们的研究强调了 在深海热液喷口虾中的独特作用和共生适应。虾 是中大西洋脊沿线许多深海热液喷口生态系统中占主导地位的动物生物量。该生物在其扩大的头胸甲腔内容纳密集的细菌共生体，在营养方面发挥重要作用。 在 的附生群落中普遍存在，它们作为附生体的功能作用仅基于功能基因的存在。在这里，我们描述了“Desulfobulbus rimicarensis”，一种未培养的δ变形菌附生体。与 的弯曲杆菌和γ变形菌附生体相比，这种细菌具有独特的代谢途径，例如 Wood-Ljungdahl 途径以及硫歧化和固氮途径。此外，与密切相关的自由生活的 菌株相比，这种附生体可以通过其减少的遗传含量和潜在的功能丧失来区分，这表明对虾宿主的独特适应。本研究是对一种δ变形菌附生体的基因组和转录组分析，极大地扩展了对其代谢和对 宿主适应的理解。
