Water microbiome dynamics of Pacific white shrimp Penaeus vannamei infected with Vibrio parahaemolyticus strains responsible for acute hepatopancreatic necrosis disease

Acute hepatopancreatic necrosis disease (AHPND) is an emerging shrimp disease caused by pathogenic Vibrio parahaemolyticus (Vp) specific strains hosting the plasmid-related pirABvp toxin gene, but the changes on the water microbiome of have not been studied. Juvenile Penaeus vannamei were inoculated with a moderate virulent strain, M0607, and a highly virulent strain, M0904, and water samples collected from the bottom of the experimental units were analysed using shotgun metagenomics. There were variations in the water microbiota community structure between strains of Vp, depending on the degree of virulence and time along the experiment. A significant marked reduction was observed in the reads assigned to Neptuniibacter spp. after the inoculation of both strains, particularly with M0904. The consistent depletion of reads assigned to the Neptuniibacter complex suggests that the type VI secretion system 1 (T6SS1) of Vp strains might have a dual function, kill surrounding bacteria and damage the hepatopancreas during intoxication by AHPND. In addition, we found a relationship between the copy numbers of the virulent plasmid and the bacterial density. This study allows for the understanding of the bacterial interactions that could happen in shrimp farms.