Microbial communities associated with the gut and the skin are strongly influenced by environmental factors, and can rapidly adapt to change. Historical processes may also affect the microbiome. In particular, variation in microbial colonisation in early life has the potential to induce lasting effects on microbial assemblages. However, little is known about the relative extent of microbiome plasticity or the importance of historical colonisation effects following environmental change, especially for nonmammalian species. To investigate this we performed a reciprocal translocation of Atlantic salmon between artificial and semi-natural conditions. Wild and hatchery-reared fry were transferred to three common garden experimental environments for 6 weeks: standard hatchery conditions, hatchery conditions with an enriched diet, and simulated wild conditions. We characterized the faecal and skin microbiome of individual fish before and after the environmental translocation, using a BACI (before-after-control-impact) design. We found evidence of extensive microbiome plasticity for both the gut and skin, with the greatest changes in alpha and beta diversity associated with the largest changes in environment and diet. Microbiome richness and diversity were entirely determined by environment, with no detectable effects of fish origin, and there was also a near-complete turnover in microbiome structure. However, we also identified, for the first time in fish, evidence of historical colonisation effects reflecting early-life experience, including ASVs characteristic of captive rearing. These results have important implications for host adaptation to local selective pressures, and highlight how conditions experienced during early life can have a long-term influence on the microbiome and, potentially, host health.

中文翻译：

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大西洋鲑鱼微生物组的环境可塑性和定殖历史：易位实验。

与肠道和皮肤相关的微生物群落受到环境因素的强烈影响，并且可以迅速适应变化。历史过程也可能影响微生物组。特别是，早期生命中微生物定植的变化有可能诱导对微生物群落的持久影响。然而，人们对微生物组可塑性的相对程度或环境变化后历史殖民化影响的重要性知之甚少，特别是对于非哺乳动物物种而言。为了对此进行研究，我们在人工和半自然条件之间进行了大西洋鲑的倒易位。将野生和孵化场繁殖的鱼苗转移到三种常见的花园实验环境中进行6周：标准孵化场条件，富含饮食的孵化场条件，并模拟野生条件。我们使用BACI（控制前-影响后）设计对环境迁移前后鱼类的粪便和皮肤微生物组进行了表征。我们发现了肠道和皮肤都具有广泛的微生物组可塑性的证据，其中最大的α和β多样性变化与环境和饮食的最大变化有关。微生物组的丰富性和多样性完全由环境决定，没有鱼类起源的可察觉影响，微生物组结构也有接近完全的更新。但是，我们还首次在鱼类中发现了反映早期生活经验的历史殖民效应的证据，包括圈养动物的ASV特征。这些结果对于宿主适应局部选择压力具有重要意义，