Comparative analysis of the microbiota in wild mud crab (Scylla serrata) intestine, sediment, and water in Koggala Lagoon, Sri Lanka

Mud crabs (Scylla serrata) play crucial roles in coastal ecosystems, and their intestinal microbiota might be greatly affected by the habitats. Illumina NovaSeq sequencing was used to identify the intestinal microbiota of wild S. serrata and the microbiomes in ambient water and sediment in the Koggala lagoon of Sri Lanka. The study found significant differences in the microbiota of mud crab intestines, lagoon water, and sediment. The microbial communities in lagoon sediment and water were richer and more diverse than those in the crab intestine, exclusively detecting 90.66% of microbes in the intestinal microbiota. The lagoon water and sediment showed distinct planktonic and sediment microbiota, with 96.08% and 90.13% differences, respectively, while only 2.8% of classified intestinal microbes, including Photobacterium, Carboxylicivirga, Acinetobacter, Clostridium sensu stricto 1, Desulfovibrio, Bacillus, and Bacteroides could be detected in the water and sediment. Even if its proportion is small, Photobacterium damselae subsp. damselae is a known pathogen, particularly in marine environments and aquaculture. However, the genomic analysis in this study revealed factors that do not contribute to pathogenicity, suggesting that P. damselae subsp. damselae is not pathogenic to S. serrata in Koggala Lagoon. Notably, Vibrio, Shewanella, Stenotrophomonas and Desulfovibrio exhibit a greater propensity to colonize the intestine of S. serrata. The planktonic and sediment microbiota might play an essential role in biogeochemical cycling, especially in nitrification, carbon, and sulfur cycling. Furthermore, harmful Cyanobium, has been detected in the intestine of S. serrata and lagoon water and sediment habitats, might have adverse effects on the ecosystem and human health. Based on the chloroplast 16S rRNA gene sequences, the terrestrial plant materials found in the intestine of S. serrata suggest less herbivorous feeding habits. Our results could provide implications for the effective management of the mud crab, S. serrata in its natural habitat.