Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts’ microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.

中文翻译：

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从山脊到礁石的生态系统微生物普查揭示了动植物微生物群落的环境储库

微生物几乎存在于地球上的每个栖息地和生物体中，它们对宿主的健康、健身和新陈代谢至关重要。在大多数生物体中，很少有微生物是在出生时遗传的；相反，获取微生物组通常涉及环境、宿主和共生体之间复杂的相互作用。尽管获取微生物组很关键，但我们对宿主微生物在不在感兴趣的宿主体内或宿主上的位置知之甚少。由于微生物跨越了一个连续体，从与多个宿主和栖息地相关的多面手到宿主范围较窄的专家，识别可能有助于无关宿主微生物组的微生物多样性的潜在来源是我们对微生物组组装理解的空白。微生物扩散随距离衰减，因此，识别来源和汇点需要来自微生物组的数据，这些数据是当代的并且足够接近潜在的微生物传播。在这里，我们描述了整个流域中相邻的陆地和水生宿主和栖息地的微生物群落，表明物种最贫乏的微生物群落是物种最丰富的微生物群落的部分子集，并且植物和动物的微生物群落嵌套在它们环境中的微生物群落中。此外，我们表明，单一生态系统中微生物的宿主和栖息地范围可以预测其全球分布，这与全球微生物组装过程的影响有关。因此，微生物占据多个栖息地和不相关宿主的趋势使得微生物组能够持久存在，即使宿主种群是分离的。