Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system

Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy

Yaron Krotman; Timur M. Yergaliyev; Rivka Alexander Shani; Yosef Avrahami; Amir Szitenberg

2020

Scholarcy highlights

  • The importance of the cutaneous mucus in fish is well established
  • The species most co-occurring with C. damascina was Oxynoemacheilus insignis, which was found in three H sites, one S site and one J site
  • Key bacterial amplicon sequence variants in the fish skin microbiome The bacterial classes recovered from raw swab communities, having the highest median relative abundances, belonged to Alphaproteobacteria, Actinobacteria, Gammaproteobacteria, Bacilli
  • As for the alpha diversity, we evaluated how assumptions of linearity may bias the results, by comparing the linear and radial basis function kernels in a kernel principal component analysis framework, followed by support vector regression with linear or RBF kernel
  • We have investigated freshwater fish and identified Alphaproteobacteria as having the highest median relative abundance, highlighting their dominance as a possible feature of some freshwater fish skin microbiomes, compared to marine fish
  • Site-related factors shaping the fish skin microbiome Based on alpha and beta diversity analyses, the raw swab communities of some of the sites are clearly different from the water communities in the same location, when water temperature is low
  • This finding is in line with a recent study, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring

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