The Structure of the Natural Microbiome of Sturgeons

Abstract

In order to determine the structure of the natural microbiome of sturgeons grown in a recirculating aquaculture system, samples from the surfaces of the fish body and systems of organs that have the most frequent contacts with external environment (surface of the skin, respiratory and digestive organs of fish) were studied. Pieces of fins, fragments of gill filaments and contents of the intestine were taken from ten conditionally healthy spiny sturgeons (Acipenser nudiventris) kept in two nursery pools and were used as the material for research. To conduct the study of the metagenome of sturgeon fish, the following was performed: extraction of DNA samples in accordance with the kit manufacturer instructions; analysis of the nucleotide sequence of the fragments; processing of the obtained sequences using conventional methods. The level of community diversity was assessed using the following environmental indicators: the Simpson (evenness), Chao (richness) and Shannon coefficients. Сluster analysis was used to assess diversity between communities (beta diversity). The Dice coincidence index, which accounts only for the presence or absence of a taxon, was used as a similarity measure. It was found that the highest values for all three estimates were characteristic of communities obtained from the surface of the gills and the lowest values were observed in communities obtained from intestinal scrapings. The results of cluster analysis with the use of the principal component method showed that the intestinal microbiomes of the two pools had the greatest difference and the microbiomes of the fin surfaces had the smallest difference. Thus, the dependence of the degree of differences between microbiomes on the pool they were obtained from increased in the following order: fin surface communities – gill surface communities – intestinal communities. Microbiomes obtained from the surface organs of fish were more similar to each other and intestinal microbiomes were less.