Comparative population genomics of Pacific deep-sea tubeworms and their bacterial endosymbionts: cryptic diversity and host-symbiont specificity

太平洋深海管虫及其细菌内共生体的比较群体基因组学：隐秘多样性和宿主共生体特异性

• 批准号: 320317443
• 负责人: Dr. Corinna Breusing
• 金额: --
• 依托单位: Southhampton Oceanography Centre
• 依托单位国家: 德国
• 项目类别: Research Fellowships
• 财政年份: 2016
• 资助国家: 德国
• 起止时间: 2015-12-31 至 2017-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/320317443?language=en
• 关键词: Comparative; population; genomics; Pacific; deep

Vestimentiferan tubeworms are dominant taxa in vent and seep habitats worldwide. Lacking a digestive system as adults, they are nutritionally dependent on their sulfur-oxidizing bacterial endosymbionts, which are acquired from the local environment. Although horizontal transmission should allow uptake of various symbiotic microbes, traditional 16S rRNA sequence analyses suggest that every tubeworm harbors a clonal population of only one bacterial phylotype. The same studies have shown that different host taxa from the same location can be infected by the same symbiotic phylotype, indicating that there is no exclusive association (specificity) between a particular symbiont and a host species. However, evidence for multiple infections and subtype variation from multi-gene analyses has recently challenged the finding of genetic homogeneity in the tubeworm endosymbionts, implying that their diversity has so far been largely underestimated. Should these assumptions hold true, it is likely that also patterns of host-symbiont specificity have been overlooked due to limited variability of the investigated marker genes and insufficient information on the genetic variation in both partners. My hypotheses are that (1) tubeworms are infected by a heterogeneous mixture of bacterial types and that (2) hosts and symbionts are specific to each other, both at the species and genotype level. To test these hypotheses, I propose to analyze symbiotic associations in geographically widespread populations of the tubeworm species Lamellibrachia barhami and Escarpia spicata, which co-occur at cold seep systems in the eastern Pacific Ocean. By combining high-throughput restriction-site associated DNA sequencing with metagenomics, I will identify single-nucleotide polymorphisms (SNP) in hosts and symbionts to get an estimate of the genomic diversity and population structure in both partners. The genotypic data from different SNP subsets will then be used in multivariate and correlative statistics to determine the degree of host-symbiont specificity. I expect that my study will advance our understanding of symbioses between animals and bacteria in the deep sea and provide a basis for future research on how host-symbiont interactions influence ecological adaptation, genetic population differentiation and evolutionary diversification of both partners.

Vestimentiferan管虫是世界范围内喷口和渗漏栖息地的优势类群。由于缺乏消化系统，它们在营养上依赖于从当地环境中获得的硫氧化细菌内共生体。虽然水平传播应该允许吸收各种共生微生物，传统的16 S rRNA序列分析表明，每一个管虫窝藏只有一个细菌的克隆种群的细菌的类型。同样的研究表明，来自同一地点的不同宿主分类群可以被相同的共生菌感染，这表明在特定的共生体和宿主物种之间没有排他性的关联（特异性）。然而，多基因分析的多重感染和亚型变异的证据最近对管虫内共生体的遗传同质性的发现提出了挑战，这意味着它们的多样性到目前为止在很大程度上被低估了。如果这些假设成立，它是可能的，也模式的主机共生体的特异性已被忽视，由于有限的变异性的研究标记基因和不充分的信息，在双方的遗传变异。我的假设是：（1）管虫是由细菌类型的异质混合物感染的;（2）宿主和共生体在物种和基因型水平上都是相互特异的。为了验证这些假设，我建议分析共生协会在地理上广泛分布的种群的管虫种Lamellibrachia barhami和Escarpia spicata，共同发生在冷渗漏系统在东太平洋。通过将高通量限制性位点相关DNA测序与宏基因组学相结合，我将鉴定宿主和共生体中的单核苷酸多态性（SNP），以估计双方的基因组多样性和种群结构。然后将来自不同SNP子集的基因型数据用于多变量和相关统计以确定宿主-共生体特异性的程度。我希望我的研究将促进我们对深海动物和细菌之间共生关系的理解，并为未来研究宿主-共生体相互作用如何影响双方的生态适应、遗传种群分化和进化多样性提供基础。

项目成果

Intra-host symbiont diversity in eastern Pacific cold seep tubeworms identified by the 16S-V6 region, but undetected by the 16S-V4 region

• DOI: 10.1371/journal.pone.0227053
• 发表时间: 2020-01-15
• 期刊: PLOS ONE
• 影响因子: 3.7
• 作者: Breusing, Corinna;Franke, Maximilian;Young, Curtis Robert
• 通讯作者: Young, Curtis Robert