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（microbiome）在促进宿主一系列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，微生物组类群如何从其区域物种库中组装形成，目前仍不明确。学界已提出多种潜在驱动假说，包括竞争的确定性过程、定殖与迁移的随机性过程，以及生理层面的‘宿主效应’生境过滤作用。厘清各类过程在新生或受扰动微生物组组装中的相对贡献，对于理解宿主-微生物互作及宿主健康至关重要。本研究针对盐度驯化过程中的广盐性鱼类及其周围水族箱水体的细菌群落展开表征分析。为评估随机性与确定性过程在鱼类微生物组组装中的相对影响，本研究通过改变水族箱水体盐度，调控每条鱼类周围的细菌物种库。研究结果显示，同物种个体的微生物组在适应相同盐度后，其优势细菌类群发生了完全且可重复的更替。研究发现，鱼类微生物组的变化与水族箱水体群落中优势类群的相应变化并无关联，且鱼类微生物组中的优势类群在水生环境中较为稀有，反之亦然。研究结果表明，在特定盐度下，最能在宿主独特环境中竞争的细菌类群占据了最多的生态位空间，这与其在水族箱水体群落中的相对丰度无关。本实验结果表明，确定性过程似乎主导了鱼类微生物组的组装，几乎没有证据支持随机性定殖的作用。