Transcriptomic adaptation of Litopenaeus vannamei to biofloc conditions in an indoor aquaculture system

Abstract

Shrimp aquaculture is a crucial sector in global seafood production, yet environmental stressors adversely affect shrimp metabolism and immunity. Biofloc technology (BFT) addresses these challenges through the formation of microbial aggregates in floc, but the underlying molecular mechanisms remain poorly understood. This exploratory study evaluated transcriptomic alterations in the midgut of Litopenaeus vannamei cultured in an Indoor Multi-Trophic Aquaculture System (IMTAS). Two BFT treatments (GRG1 and GRG2) were compared against a non-BFT control. Differential expression analysis, hierarchical clustering, and KEGG pathway enrichment analysis were performed on the sequenced midgut RNA. A total of 1245 differentially expressed genes (DEGs) were identified in GRG1 vs. Control, 1145 in GRG2 vs. Control, and 681 in GRG1 vs. GRG2. Treatment-specific expression profiles were observed, with GRG1 and GRG2 clustering separately from the control. Enriched pathways included Proteasome, Autophagy, and Phagosome for GRG1 vs. Control, indicating enhanced protein turnover and immune function. GRG2 vs. Control enriched Aminoacyl-tRNA biosynthesis and Endoplasmic reticulum processing, reflecting adaptive metabolic responses. Oxidative phosphorylation was differentially enriched between the two biofloc treatments, suggesting treatment-specific energy metabolic differences. The greater enrichment of pathways associated with protein turnover, immune regulation, and energy metabolism in GRG1 may be associated with its higher production performance. These exploratory findings provide a foundation for future hypothesis-driven investigations into the molecular mechanisms of biofloc-mediated effects in L. vannamei, though qPCR validation is needed to confirm the observed transcriptomic patterns.