BACKGROUND Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and abiotic factors, complicating the study design. We tackled this issue in the northern part of the Jordan River system, in which a few fish species geographically overlap, across steep gradients of water temperature and salinity. RESULTS Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy. To better characterise the indigenous skin community, we excluded bacteria that were equally abundant in the skin samples and in the water samples, from our analysis of the skin samples. With this in mind, we found alpha diversity of the skin communities to be stable across sites, but higher in benthic loaches, compared to other fish. Beta diversity was found to be different among sites and to weakly covary with the dissolved oxygen, when treated skin communities were considered. In contrast, water temperature and conductivity were strong factors explaining beta diversity in the untreated skin communities. Beta diversity differences between co-occurring fish species emerged only for the treated skin communities. Metagenomics predictions highlighted the microbiome functional implications of excluding the water community contamination from the fish skin communities. Finally, we found that human-induced eutrophication promotes dysbiosis of the fish skin community, with signatures relating to fish health. CONCLUSIONS Consideration of the background water microbiome when studying fish skin microbiomes, across varying fish species and water properties, exposes patterns otherwise undetected and highlight among-fish-species differences. We suggest that sporadic nutrient pollution events, otherwise undetected, drive fish skin communities to dysbiosis. This finding is in line with a recent study, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring. Video abstract.

中文翻译：

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在异质内陆水系统中剖析影响鱼皮微生物群的因素。

背景技术尽管鱼皮微生物群对鱼类健康和生态具有重要意义，但在内陆水域系统中很少对其进行研究。这主要是因为鱼类种类的分布经常与其他生物和非生物因素共变，从而使研究设计复杂化。我们在约旦河系统的北部解决了这个问题，在约旦河系统的水温和盐分陡峭梯度中，一些鱼类在地理上重叠。结果使用16S rRNA元条形码，我们研究了塑造皮肤细菌群落及其与鱼类分类学相互作用的水质。为了更好地表征本地皮肤群落，我们从皮肤样品的分析中排除了皮肤样品和水样品中同样丰富的细菌。考虑到这一点，我们发现，与其他鱼类相比，皮肤群落的α多样性在各个地点都稳定，但在底栖泥higher中较高。当考虑到处理过的皮肤群落时，发现各部位之间的Beta多样性不同，并且与溶解氧的共价关系较弱。相反，水温和电导率是解释未经处理的皮肤群落中β多样性的重要因素。共生鱼类之间的β多样性差异仅在经过处理的皮肤群落中出现。元基因组学的预测突出了从鱼皮群落中排除水群落污染的微生物组功能含义。最后，我们发现人为的富营养化促进了鱼皮群落的营养不良，并具有与鱼类健康有关的特征。结论研究鱼类皮肤微生物组时，在不同鱼类和水性质之间的背景水微生物组考虑因素会暴露出原本未被发现的模式，并突显了鱼类之间的差异。我们建议零星的养分污染事件（否则未被发现）会促使鱼皮群落发生菌丝异常。这一发现与最近的一项研究相吻合，该研究表明生物膜捕获了零星的污染事件，而散布的水监测无法检测到这些事件。录像摘要。表明生物膜捕获了零星的污染事件，这在散布的水监测中无法检测到。录像摘要。表明生物膜捕获了零星的污染事件，这在散布的水监测中无法检测到。录像摘要。