Intestinal microbiota responses to environmental microbiomes and factors across populations of the Manila clam Ruditapes philippinarum.

Intestinal microbiota is essential for the health, immune defense, and environmental adaptability of aquatic animals. Still, the interactions involving the intestinal microbiota of the Manila clam Ruditapes philippinarum, the microbiomes of their habitat, and environmental factors remain unclear. This study analyzed the microbial community structure and functional characteristics in clam intestine, water, and sediment across three distribution areas in Laizhou Bay (LZ), Jiaozhou Bay (JZ), and Sanggou Bay (SG) on the Shandong Peninsula, China. Correlations between microbial communities and water parameters were also examined. The results revealed distinct microbial communities in the intestine and habitats across the three areas, with water parameters serving as key drivers of geographic microbial variation. Intestinal selective pressures overwhelmed environmental factors in shaping intestinal microbiota. Intestinal microbiota closely resembled water microbiomes in richness, diversity, and dominant species abundance, indicating that water microbiomes likely served as the primary source of the clam intestinal microbiota. Microbial networks facilitated environmental adaptation by constructing large networks or boosting network density and modularity. Functional differentiation in the intestinal microbiota, driven by environmental influences, facilitated diverse ecological adaptation strategies. Moreover, low salinity, high dissolved oxygen, and high nutrient contents in the water favored specialized intestinal microbiota with narrower niche breadth, while high salinity, low chlorophyll a, and broader nutrient contents promoted stochastic microbiota with broader niche breadth. These findings provide valuable knowledge on the interactions between clam intestinal microbiota and environmental factors, providing a scientific basis for microbiome management strategies in clam seedling production and aquaculture practices.