Abstract
The relationship between the internal microbiome of an individual organism and that of its external environment has been little investigated in freshwater ecosystems. Thus, this is an area of interest in freshwater fish biology. Along with the genotype of the fish host, external environment plays an important role in determining the composition of the internal microbiome. Here, we characterized the variability of the microbiome of wild Crucian carp (Carassius auratus), along with those of their surrounding environments (water and mud). We found that each environment had distinct bacterial communities, with varying composition and structure. The primary bacterial phyla identified in the Crucian carp gut were Fusobacteria and Proteobacteria (90% of all bacterial phyla identified); the primary genera identified were Cetobacterium, Aeromonas, and Plesiomonas (85% of all bacterial phyla identified). We identified 1,739 operational taxonomic units (OTUs) in the Crucian carp gut, 1,703 in water, and 5,322 in mud. Each environment had unique OTUs, but the fewest unique OTUs (97) were found in the Crucian carp gut. There were significant differences in the relative abundances of different bacterial phyla in the different environments. It may be that only bacterial phyla vital for efficient fish function (e.g., immune response or metabolism), such as Fusobacteria and Proteobacteria, are retained in the Crucian carp gut.