Independent Ichthyologist, Be'er Tuvia, Israel.
Dead Sea and Arava Science Center, Dead Sea Branch, 8693500, Masada, Israel.
Microbiome. 2020 Jan 31;8(1):9. doi: 10.1186/s40168-020-0784-5.
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.
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.
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.
尽管鱼类皮肤微生物组对鱼类健康和生态具有重要意义，但它们在内陆水系中却很少被研究。这主要是因为鱼类的物种分布通常与其他生物和非生物因素相关，这使得研究设计变得复杂。我们在约旦河系统的北部解决了这个问题，该地区的一些鱼类物种在地理上重叠，横跨水温和盐度的陡峭梯度。
我们使用 16S rRNA 宏条形码技术研究了影响鱼类皮肤细菌群落形成的水特性，以及它们与鱼类分类学的相互作用。为了更好地描述本土皮肤群落，我们从皮肤样本的分析中排除了在皮肤样本和水样中同样丰富的细菌。有鉴于此，我们发现皮肤群落的 alpha 多样性在各个地点都很稳定，但在底栖泥鳅中比其他鱼类更高。当处理过的皮肤群落被考虑时，beta 多样性被发现存在于不同的地点之间，并与溶解氧弱相关。相比之下，当处理过的皮肤群落被考虑时，水温和电导率是解释未处理皮肤群落 beta 多样性的重要因素。仅在处理过的皮肤群落中才出现共同出现的鱼类物种之间的 beta 多样性差异。宏基因组预测强调了从鱼类皮肤群落中排除水污染对微生物组功能的影响。最后，我们发现人为富营养化促进了鱼类皮肤群落的失调，其特征与鱼类健康有关。
在研究不同鱼类物种和水特性的鱼类皮肤微生物组时，考虑背景水微生物组会揭示出否则无法检测到的模式，并突出鱼类之间的差异。我们认为，否则无法检测到的零星营养污染事件会导致鱼类皮肤群落失调。这一发现与最近的一项研究一致，该研究表明生物膜捕获了不可检测的零星污染事件。视频摘要。
