Multi-Omics Investigation of Stress Response Mechanisms in Nile Tilapia (Oreochromis "niloticus") Reared in Plastic Tank, Concrete Pond, and Earthen Pond Culture Systems

Abstract 
Aquaculture intensification exposes fish to 
environmental stressors that can compromise 
growth, immunity, and welfare. We applied a 
multi-omics approach integrating physiology, 
targeted transcriptomics (qPCR), and 
proteomic profiling to investigate stress 
responses of Oreochromis niloticus reared for 
8(weeks in plastic tanks, concrete ponds, and 
earthen ponds under standardized feeding. 
Water quality, growth, survival, cortisol and 
antioxidant biomarkers (SOD, CAT), relative 
expression of stress/immune genes (HSP70, 
CAT, IL-1β, TNF-α), and differentially 
expressed protein categories were evaluated. 
Earthen ponds yielded superior water quality, 
growth, FCR, and survival, along with lower 
cortisol and pro-inflammatory gene expression, 
and higher antioxidant capacity. Plastic tanks 
showed the inverse pattern; concrete ponds 
were intermediate. The multi-omics integration 
indicates that oxidative stress, heat-shock 
response, and pro-inflammatory signaling 
dominate in tanks, whereas immune 
homeostasis and efficient redox metabolism 
characterize ponds. Findings highlight 
system-dependent stress biology and practical

 levers for welfare-oriented, productive tilapia 
culture.