Bacterial Communities From Two Freshwater Aquaculture Systems in Northern Germany

The microbial communities in aquaculture systems are primarily affected by changes in water quality, fish metabolism, feeding strategies and fish disease prevention treatments. Monitoring changes in aquatic microbiomes related to aquaculture activities is necessary to improve management strategies and reduce the environmental impact of aquaculture water discharge. This study assessed the effects of activities within two fish farms on water microbiome composition by analysing the water entering and leaving both systems. Additionally, pathogenic bacterial species associated with common fish diseases were identified. The abundance, diversity and identity of microorganisms were evaluated using 16S rRNA hypervariable gene region amplicon sequencing. Proteobacteria (38.2%) and Bacteroidetes (31.3%) were the most abundant phyla in all water samples. Changes in microbiome composition after passage through the fish tanks were observed in several taxa, such as Nitrospirae, Chloroflexi, Deferribacteres and Cyanobacteria. Flavobacterium sp. and Pseudomonas sp. were the predominant potential pathogens and heterotrophic bacteria detected in both farms. Several chemolithotrophic bacteria and archaea were found in the natural reservoir used for aquaculture activities, while water microbiomes in the aquaculture systems were generally dominated by heterotrophic organisms.