Understanding the host-microbe-environment interactions: Intestinal microbiota and transcriptomes of black tiger shrimp Penaeus monodon at different salinity levels

Disease outbreak has continued to be a major challenge for shrimp aquaculture industry. In recent years, manipulation of gut microbiota has been shown to improve the health of host shrimp and disease resistance. Therefore, understanding how various factors can shape the gut microbiota of shrimp is crucial for future utilization of gut microbiota as tools for disease controls. The salinity of the rearing environment can potentially affect shrimp gut microbiota as well as the host-microbe interactions. The effects of salinity adaptation on intestinal microbiota and transcriptomes of juvenile black tiger shrimp Penaeus monodon were examined in this experiment. Intestinal microbiota and transcriptomic profiles from juvenile black tiger shrimp of the same cohort adapted to three different salinity levels were examined using 16S rDNA amplicon sequencing and RNA sequencing, respectively. Shrimp were acclimatized from the original 20 ppt salinity to either 10 ppt or 30 ppt over a period of 10 days, and intestinal samples were collected on Day 0, Day 10, and Day 20 after reaching the target salinity. Across all salinity levels, the dominant phyla composition in the intestine of shrimp was relatively similar with Proteobacteria (83.4%), Bacteroidetes (8.1%), Planctomycetes (3.2%), Verrucomicrobia (2.5%), and Firmicutes (1.5%). The most abundant genus was Vibrio. While it can be found at all salinity levels, a relative abundance of Vibrio was lower at 10 ppt than at higher salinity. A shift toward the higher relative abundance of Vibrio ASVs belonging to the Harveyi Glade was observed at higher salinity. On the other hand, the relative abundance of Shewanella was higher at 10 ppt than at higher salinity. Other dominant genera in the intestines not affected by the change in salinity were Pseudoaltermonas and Tenacibaculum. The shift in the rearing water microbiota with different salinity levels was also observed. The most abundant intestinal transcripts responding to different salinity levels based on GO classification were intracellular anatomical structure (cellular component), protein binding (molecular function), and organic substance metabolic process (biological function). Genes involved with stress and immune responses were differentially expressed, and correlations between potentially pathogenic Vibrio and genes relating to innate immunity and peritrophic matrix were observed. The results confirmed the influence of rearing water salinity on both the intestinal microbiota and transcriptomes of shrimp. Efforts to shape the microbiota of aquatic animals should take into consideration the rearing salinity to ensure its efficacy. Using multi-omic platform allowed for better understanding of the microbiota and the host-microbe interaction, which will help support the sustainability of aquaculture production.