Low-Temperature Modulation of Microbial Communities in the Intestine of Octoploid Allogynogenetic Gibel Carp (Carassius gibelio) and Aquaculture Pond Water

Water temperature is a key driver of microbial succession in aquaculture ponds and may indirectly influence fish intestinal homeostasis, nutrient metabolism, and pathogen risk. This study investigated temperature effects (16 °C vs. 30 °C) on microbial communities in both the intestines of octoploid allogynogenetic gibel carp (Carassius gibelio) (Experiment I, with fish) and the rearing water-column (Experiment II, without fish) over a 20-day experimental period under controlled conditions. The results showed that temperature affected water-column microbiota more strongly than fish intestinal microbiota. In the water-column, diversity indices (Shannon, Simpson, Chao1, and Sobs) decreased over time at both 16 °C and 30 °C, while fish intestinal microbiota showed no significant overall change in alpha diversity. Functional prediction suggested that low-temperature (16 °C) was associated with higher relative abundance of pathways related to amino acid metabolism, carbohydrate metabolism, and genetic information processing in the fish intestine. In contrast, the enrichment of predicted potentially pathogenic phenotypes in the water-column occurred earlier at 30 °C than at 16 °C. These findings indicate that, compared with 30 °C, 16 °C was associated with potentially transient changes in microbial community diversity, slower enrichment of predicted potentially pathogenic phenotypes, and higher predicted nutrient-metabolism potential in intestinal microbiota of allogynogenetic gibel carp during the 20-day experimental period.