Integration of metagenome and full-length 16S rRNA gene sequencing of the mariculture environmental bacterial community reveal potential pathogenic bacteria in broodstock breeding of the mud crab, Scylla paramamosain

High mortality associated with pathogenic bacteria is one of the huge obstacles to S. paramamosain aquaculture. Few studies have identified the effects of potentially pathogenic bacteria in water environment on the cultivation of ovigerous crabs. Herein, we gathered water samples (WH and JD) from different culture periods of ovigerous mud crabs and red plaque samples during mud crab disease outbreaks, and utilized Illumina metagenomic sequencing and full-length 16S rRNA sequencing to delve into the microbial composition in the mariculture environment and identify potentially pathogenic bacteria. A total of 241 phyla, 5494 genera and 24846 species from WH and JD were detected, with Proteobacteria and Bacteroidota dominant. The diversity results suggested that the JD samples exhibited higher abundance of these microbiota compared to the WH samples. Full-length 16S rRNA gene sequencing assigned the red plaque bacterial community to 84 species, belonging to 96 OTUs, most of which were attributed to Proteobacteria and Firmicutes. Several species belonging to Vibrio were found in both the red plaque and JD water samples, such as Vibrio alginolyticus and Vibrio fluvialis , implying that genus Vibrio might be one of the potential predisposing bacteria leading to the death of the S. paramamosain broodstock. The number of common bacterial species among the red plaque, JD and WH samples was 43, mainly belonging to the genus Vibrio , Serratia , Sphingomonas , Pseudomonas , Pseudochrobactrum , Klebsiella , Comamonas , Exiguobacterium , and Bacillus , implying that these bacteria could be potentially conditioned pathogenic bacteria. Most species of bacteria in the red plaque samples could be found in JD, indicating that the bacterial species in mariculture environment may affect the composition of pathogenic bacteria. Our findings provide a theoretical basis for the notion of some bacteria acting as a potential pathogen source in the mariculture environment during S. paramamosain broodstock cultivation. • A total of 241 phyla and 5494 genera were detected in the mariculture environment. • Vibrio, and Serratia, etc. could be pathogenic bacteria during the crab cultivation. • Abundance and diversity of the microbiota were higher when disease outbreak. • Bacterial species in water environment affect the composition of pathogenic bacteria.