Data_Sheet_7_Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World’s Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus).PDF

The symbiosis between a host and its microbiome is essential for host fitness, and this association is a consequence of the host’s physiology and habitat. Sinocyclocheilus, the largest cavefish diversification of the world, an emerging multi-species model system for evolutionary novelty, provides an excellent opportunity for examining correlates of host evolutionary history, habitat, and gut-microbial community diversity. From the diversification-scale patterns of habitat occupation, major phylogenetic clades (A–D), geographic distribution, and knowledge from captive-maintained Sinocyclocheilus populations, we hypothesize habitat to be the major determinant of microbiome diversity, with phylogeny playing a lesser role. For this, we subject environmental water samples and fecal samples (representative of gut-microbiome) from 24 Sinocyclocheilus species, both from the wild and after being in captivity for 6 months, to bacterial 16S rRNA gene profiling using Illumina sequencing. We see significant differences in the gut microbiota structure of Sinocyclocheilus, reflective of the three habitat types; gut microbiomes too, were influenced by host-related factors. There is no significant association between the gut microbiomes and host phylogeny. However, there is some microbiome related structure at the clade level, with the most geographically distant clades (A and D) being the most distinct, and the two overlapping clades (B and C) showing similarities. Microbes inhabiting water were not a cause for significant differences in fish-gut microbiota, but water quality parameters were. Transferring from wild to captivity, the fish microbiomes changed significantly and became homogenized, signifying plastic changes and highlighting the importance of environmental factors (habitat) in microbiome community assembly. The core microbiome of this group, at higher taxonomic scale, resembled that of other teleost fishes. Our results suggest that divergent natural environments giving rise to evolutionary novelties underlying host adaptations, also includes the microbiome of these fishes.

宿主与其微生物组之间的共生关系对宿主适合度至关重要，而这种关联是宿主生理特征与栖息环境共同作用的结果。金线鲃属（Sinocyclocheilus）作为全球物种多样性最丰富的洞穴鱼类类群，同时也是研究演化新奇性的新兴多物种模型系统，为探究宿主演化历史、栖息环境与肠道微生物组群落多样性之间的关联提供了绝佳契机。基于栖息地占据的演化尺度模式、主要系统发育分支（A-D）、地理分布数据，以及人工饲养金线鲃种群的相关研究基础，我们提出假说：栖息环境是微生物组多样性的主要决定因素，而宿主系统发育的影响相对较弱。为此，我们针对24种金线鲃的环境水样与粪便样本（作为肠道微生物组的代表）开展了基于Illumina测序技术的细菌16S rRNA基因谱分析，这些样本分别采自野生种群以及人工饲养6个月后的个体。研究发现，金线鲃的肠道菌群结构存在显著差异，且该差异与三种栖息环境类型相对应；同时肠道微生物组也受到宿主相关因素的影响。尽管肠道微生物组与宿主系统发育之间未呈现显著关联，但在分支水平上仍存在一定的微生物组结构特征：地理分布差异最大的分支A与分支D的菌群结构差异最为显著，而两个分布重叠的分支B与分支C则表现出相似的菌群组成。栖息于水环境中的微生物并非鱼类肠道菌群差异的主要成因，而水环境的水质参数才是关键影响因素。从野生环境转入人工饲养环境后，鱼类的肠道微生物组发生了显著变化并趋于同质化，这表明菌群存在可塑性改变，同时也凸显了环境因素（栖息环境）在微生物组群落构建中的重要作用。本类群的核心微生物组在更高分类阶元尺度上与其他硬骨鱼类的核心微生物组具有相似性。本研究结果表明，催生宿主适应性演化新奇性的多样自然环境，同样也塑造了这类鱼类的微生物组。