Data from: Community assembly of a euryhaline fish microbiome during salinity acclimation

Microbiomes play a critical role in promoting a range of host functions. Microbiome function, in turn, is dependent on its community composition. Yet, how microbiome taxa are assembled from their regional species pool remains unclear. Many possible drivers have been hypothesized, including deterministic processes of competition, stochastic processes of colonization and migration, and physiological 'host-effect' habitat filters. The contribution of each to assembly in nascent or perturbed microbiomes is important for understanding host–microbe interactions and host health. In this study, we characterized the bacterial communities in a euryhaline fish and the surrounding tank water during salinity acclimation. To assess the relative influence of stochastic versus deterministic processes in fish microbiome assembly, we manipulated the bacterial species pool around each fish by changing the salinity of aquarium water. Our results show a complete and repeatable turnover of dominant bacterial taxa in the microbiomes from individuals of the same species after acclimation to the same salinity. We show that changes in fish microbiomes are not correlated with corresponding changes to abundant taxa in tank water communities and that the dominant taxa in fish microbiomes are rare in the aquatic surroundings, and vice versa. Our results suggest that bacterial taxa best able to compete within the unique host environment at a given salinity appropriate the most niche space, independent of their relative abundance in tank water communities. In this experiment, deterministic processes appear to drive fish microbiome assembly, with little evidence for stochastic colonization.

微生物组（microbiomes）在促进宿主多项生理功能方面发挥关键作用。而微生物组的功能反过来又依赖于其群落组成。然而，微生物类群如何从区域物种库（species pool）中组装形成，目前仍未明确。已有诸多潜在驱动因素被提出假说，包括介导竞争的确定性过程（deterministic processes）、涉及定植（colonization）与迁移的随机过程（stochastic processes），以及生理性‘宿主效应’生境过滤（habitat filters）。解析各类因素在新生或受扰动微生物组组装过程中的贡献，对于理解宿主-微生物互作（host–microbe interactions）与宿主健康具有重要意义。本研究针对盐度驯化过程中的广盐性鱼类（euryhaline fish）及其周边水箱水体的细菌群落进行了表征。为评估随机过程与确定性过程对鱼类微生物组组装的相对影响，我们通过改变水族箱水体的盐度，调控每条鱼类周围的细菌物种库。研究结果显示，同一物种的个体在适应相同盐度后，其微生物组内的优势细菌类群会发生完全且可重复的更替。研究发现，鱼类微生物组的变化与水箱水体群落中优势类群的相应变化并无相关性，且鱼类微生物组中的优势类群在水生环境中丰度极低，反之亦然。本研究结果显示，在特定盐度条件下，最能在独特宿主环境中完成竞争的细菌类群占据了最多的生态位空间（niche space），这一过程不受其在水箱水体群落中相对丰度的影响。本实验结果表明，确定性过程主导了鱼类微生物组的组装，几乎无证据显示随机定植发挥了作用。