Natural water bodies contain physically interconnected habitats suitable for microbes, such as different water layers and substrates for biofilms. Yet, little is known on the extent to which microbial communities are shared between such habitats and whether differences and similarities are consistent between sites. Here we explicitly tested hypotheses on similarities between aquatic bacterial communities found floating in water, in association with daphnids and with copepods, within bottom sediments, and on littoral stones of a lake. Through high-throughput 16S rDNA amplicon sequencing, distinguishable patterns were retrieved between habitats. In particular, community composition was more similar between the two zooplankton taxa, between the two water depths, and was rather different in sediments, where a large fraction of the total diversity was present. Most bacterial taxa were restricted to one or few habitats, whereas only few were found as generalists on different habitats. Our results indicate a limited role of source–sink dynamics between habitats for aquatic bacteria. Similarly to patterns of diversity in larger organisms, community composition was different between habitats, potentially because of specific mechanisms creating and maintaining habitat filtering.

中文翻译：

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湖港内的不同底物连接但专门的微生物群落

天然水体包含适合微生物的物理互连栖息地，例如不同的水层和生物膜基质。然而，关于微生物群落在这些栖息地之间共享的程度以及不同地点之间的差异和相似之处是否一致，我们知之甚少。在这里，我们明确测试了关于漂浮在水中的水生细菌群落之间的相似性的假设，这些细菌群落与水蚤和桡足类动物、底部沉积物内和湖边的石头上有关。通过高通量 16S rDNA 扩增子测序，在栖息地之间检索到可区分的模式。尤其是两个浮游动物类群之间、两个水深之间的群落组成更加相似，沉积物差异较大，其中存在总多样性的很大一部分。大多数细菌分类群仅限于一个或几个栖息地，而只有少数被发现是不同栖息地的通才。我们的结果表明，水生细菌栖息地之间的源-汇动力学作用有限。与较大生物体的多样性模式类似，栖息地之间的群落组成不同，这可能是因为创建和维持栖息地过滤的特定机制。