Metagenomic insights into the geographic divergence and functional adaptation of gut microbiota in the endangered Scaly-sided Merganser (Mergus squamatus)

Investigating geographical variation and functional adaptation of gut microbiomes in endangered species is an emerging field in conservation biology. Here, we investigated the endangered waterbird, Scaly-sided Merganser (Mergus squamatus), that is endemic to East Asia. Using metagenomic sequencing, we characterized variations in gut microbiota composition and functional adaptation across Scaly-sided Merganser populations inhabiting the Fuer River, Manjiang River, and Lushui River basins in Northeast China. Furthermore, we investigated these variations at different developmental stages (adults and juveniles). Significant differences were observed in gut microbiota composition among the river populations, with the Fuer and Lushui groups exhibiting similar compositions that differed from the Manjiang group. However, no significant differences were found in the functional characteristics of gut microbiota among the three groups; these functions were primarily enriched in core pathways related to carbohydrate metabolism, amino acid metabolism, and translation. This finding suggests functional redundancy, where key metabolic functions remain stable despite differentiation in microbial community composition. The adult Scaly-sided Merganser gut microbiota exhibited higher alpha diversity and showed significant enrichment in pathways related to detoxification metabolism, environmental adaptation, and energy conversion efficiency, suggesting the capacity to adapt to complex habitats. In contrast, the gut microbiota of juveniles was enriched in metabolic pathways related to the essential and conditionally essential amino acids methionine and cysteine, supporting the high protein synthesis demand during the rapid growth and developmental stage. This study highlights the structural plasticity and functional adaptability of the gut microbiota in the Scaly-sided Merganser, providing an empirical basis for the species’ conservation and habitat management from a gut microbiome perspective.