Microbiota and Microsatellite genotypes of Pacific oysters stemming from three oyster bed in the Northern Wadden Sea

Background: Studies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity however remains underexplored and unexplained, although environmental conditions and host genetics have been implicated. We used 454 next generation 16S rRNA amplicon sequencing of individually tagged PCR reactions to explore the diversity of bacterial communities in gill tissue of the invasive Pacific oyster Crassostrea gigas stemming from genetically differentiated beds under ambient outdoor conditions and after a multifaceted disturbance treatment imposing stress on the host.
Results: While the gill associated microbial communities in oysters were dominated by few abundant taxa (i.e. Sphingomonas, Mycoplasma) the distribution of rare bacterial groups correlated to relatedness between the hosts under ambient conditions. Exposing the host to disturbance broke apart this relationship by removing rare phylotypes thereby reducing overall microbial diversity. Shifts in the microbiome composition in response to stress did not result in a net increase in genera known to contain potentially pathogenic strains.
Conclusion: The decrease in microbial diversity and the disassociation between population genetic structure of the hosts and their associated microbiome suggest that disturbance (i.e. stress) may play a significant role for the assembly of the natural microbiome. Such community shifts may in turn also feed back on the course of disease and the occurrence of mass mortality events in oyster populations.

研究背景：针对牡蛎微生物组的相关研究表明，包括病原体在内的有限微生物类群，可在宿主鳃、肠道等组织的微生物群落中占据主导地位。尽管已有研究将环境条件与宿主遗传学纳入细菌多样性未被充分阐释的关联因素，但绝大多数细菌多样性仍未得到充分探索与解析。本研究通过对带个体标签的聚合酶链式反应（PCR）开展454高通量16S rRNA扩增子测序，旨在探究入侵种太平洋牡蛎（Crassostrea gigas）鳃组织的细菌群落多样性；实验样本采自遗传分化的野外栖息床，分别设置自然室外环境与多维度宿主胁迫干扰处理两组实验条件。

研究结果：尽管牡蛎鳃附着微生物群落被少数丰富类群（即鞘氨醇单胞菌属（Sphingomonas）、支原体属（Mycoplasma））主导，但在自然环境条件下，稀有细菌类群的分布与宿主亲缘关系呈显著相关。对宿主施加干扰处理后，该关联被打破：稀有系统型（phylotype）被移除，整体微生物多样性随之降低。响应胁迫的微生物组组成转变，并未导致已知含潜在致病菌株的菌属出现净增长。

研究结论：微生物多样性的下降，以及宿主种群遗传结构与其附着微生物组之间的关联解离，表明干扰（即胁迫）可能在自然微生物组的组装过程中发挥关键作用。此类群落结构转变反过来也可能对牡蛎种群的疾病进程与大规模死亡事件的发生产生反馈影响。