The Assembly of Fish Gut Microbiomes Through Habitat Variation Provides Insight Into Redbelly Tilapia Invading a Large Subtropical River

The environment in which fish reside markedly shapes the composition of their gut microbiome. However, the precise mechanisms by which the assembly process of fish gut microbiota adapts to diverse habitat conditions remain largely uncharted, especially in the case of invasive tilapia, renowned for its remarkable adaptability to environmental changes. In this study, we employed high-throughput 16S rRNA gene sequencing to explore the gut microbiome of redbelly tilapia from three distinct habitats. Our results showed substantial disparities in both the composition and diversity (alpha and beta) of the gut microbiome between wild and pond-cultured redbelly tilapia. Notably, stochastic processes emerged as the dominant forces governing the assembly of the gut microbial community in redbelly tilapia. As the habitat shifted from pond-cultured to wild, the influence of undominated processes in gut microbial community assembly waned, while the effect of dispersal limitation intensified. Co-occurrence network analysis suggested that habitat variation contributed to the enhanced complexity of the gut microbial network in invasive tilapia during their transition from pond to wild environments. Across the three distinct habitats, variations were observed in the influence of environmental factors on the gut microbiota of tilapia. Moreover, our findings demonstrated that the gut microbiome of wild tilapia possessed unique characteristics, such as higher alpha diversity and a relatively greater abundance of genes encoding putative cellulolytic enzymes crucial for digesting the preferred food source of tilapia (hydrophytes), particularly in fragmented habitats with well-developed cascade dams. Additionally, we identified that OTU8895 (<i>Clostridum_sensu_stricto_1</i>) and OTU11387 (<i>unclassified Bacilli</i>) were core biomarkers of the gut bacterial community in wild redbelly tilapia, offering valuable insights for the monitoring and management of invasive tilapia populations.