Microbial Community Succession and Its Environmental Response in Bighead Carp (Hypophthalmichthys nobilis) Muscle During Low-Temperature Modified Atmosphere Transportation

Microbial community succession contributes to quality changes in fresh freshwater fish during cold-chain transportation. In this study, bighead carp (Hypophthalmichthys nobilis) was used as the research material. Using 16S rRNA high-throughput sequencing, we characterized microbial community dynamics in fish muscle after 12 h and 24 h of simulated transportation under combined low-temperature (0 °C, 4 °C, 8 °C) and gradient CO2 modified atmosphere packaging (MAP) treatments. We further identified key environmental factors associated with shifts in bacterial communities during cold-chain logistics. The results showed that transportation temperature was the primary factor structuring microbial communities in bighead carp muscle, with stronger effects than MAP composition and transportation duration. Under 8 °C temperature conditions, low-to-moderate CO2 MAP corresponded with elevated microbial diversity and spoilage-associated succession, alongside enrichment of spoilage taxa including Pseudomonas. High-CO2 (80%) MAP altered community composition and reduced community complexity under low-temperature conditions, and the community changes exhibited a time-dependent pattern during extended transport. The combined treatment of 0 °C and 80% CO2 MAP generated distinct microbial succession profiles within 24 h and lowered the relative abundance of Pseudomonas. This study described the response patterns of bighead carp muscle microbiota to coupled low-temperature and MAP treatments and characterized community succession during cold-chain transport. The findings provide microbiota-based references for understanding microbial variation in freshwater fish cold-chain logistics.