Behavioral smearing and physiological secretion shape divergent microbiome assembly in breeding Crested ibis

Understanding host–microbiota interactions is crucial for elucidating animal adaptation strategies, especially in species with seasonal shifts in behavior and physiology. In birds, breeding-related behaviors may influence symbiotic microbiomes; however, the mechanisms remain unclear. Crested ibis undergoes a seasonal plumage color change from white to grey during the breeding period due to its smearing behavior and black secretion from the neck. Here, we compared breeding (gray-feather) and non-breeding (white-feather) stages to characterize seasonal dynamics of body surface microbiomes in the endangered Crested ibis (Nipponia nippon) using 16S rRNA sequencing across three body sites. Breeding individuals showed reduced microbial diversity, potentially associated with black neck secretions. Microbial communities clustered more by season than body site, with increased similarity during breeding, possibly related to smearing behavior. Our findings also revealed that microbial assembly could present seasonal and body site-specific dynamics. Neck feathers exhibited a 36.5% better fit to a neutral model, suggesting more stochastic community assembly likely linked to smearing of black secretions, whereas neck skin showed a 36.3% lower neutrality and 11.87% more host-selected variants, indicating stronger deterministic selection associated with breeding-related secretions. These patterns imply that Crested ibises may adopt dual mechanisms to regulate their microbiome during breeding: behavioral smearing for dispersal of microbes and physiological secretion of microbes for selection. This regulation may contribute to seasonal microbiome variation that supports seasonal adaptation. It highlights how birds may integrate behavior and physiology to regulate host–microbiota interactions during critical life stages and provides a new path for ibis conservation.