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Fig. 1 Alpha diversity of zebrafish and carp RAS- and fish-associated microbiota. A) Chao1 index (ASV richness) of alpha diversity per sample type. Each dot corresponds to one sequenced sample, with bars indicating median values. Significance of species and sample type in the systems was tested using a two-way ANOVA. Sample type had a significant effect on Chao1 diversity index values (F (3, 29) = 23.84, p < 0.001). B) Shannon diversity index (ASV richness and evenness) of alpha diversity per sample type. Each dot corresponds to one sequenced sample, with bars indicating median values. Significance of the species and sample type was tested using a two-way ANOVA followed by multiple comparison testing. Sample type had a significant effect on the Shannon diversity index (F (3, 29) = 5.683, p = 0.0035), with an additional interaction effect observed between sample type and species (F (3, 29) = 112.0, p < 0.001). Carp and zebrafish samples were tested separately. Significant differences between sample types are indicated using different letters, with upper-case letters used for carp samples and lower-case letters for zebrafish samples.