Turtle egg microbiome modulates fusariosis fungal infection and hatching success

Background Emerging fungal diseases pose a significant threat to global wildlife, driving mass mortality events, population declines, and ecosystem disruption. Turtle egg fusariosis, caused by members of the Fusarium solani species complex (FSSC), is an emerging global disease associated with high rates of embryonic mortality and hatching failure in turtles. Although vertebrate eggs harbor distinct microbial communities, the role of these microbiomes in mediating disease susceptibility and immune defense remains poorly understood. Here, we characterised the inner-egg bacteriome and mycobiome of both uninfected and FSSC-infected eggs of the critically endangered yellow-spotted Amazon river turtle ( Podocnemis unifilis ) across three developmental stages. Results Among 121 eggs from 31 artificial nests, 63 were infected with F. solani or F. keratoplasticum . Eggs with higher fungal (mycobiome) evenness showed significantly reduced susceptibility and lower infection intensity, whereas bacterial (bacteriome) diversity was not significantly associated with infection status. Independent of infection, higher bacterial and fungal diversity was positively associated with hatching success. Several bacterial (e.g., Pseudomonas , Sphingobacterium ) and fungal genera (e.g., Penicillium , Bionectriaceae ) were linked to infection resistance and hatching success. Functional predictions identified 33 bacterial metabolic pathways enriched in successfully hatched eggs. Notably, the reductive acetyl-CoA pathway was also enriched in uninfected eggs, suggesting a potential protective role against FSSC infection. Microbial co-occurrence network analyses revealed more complex interkingdom interactions in hatched eggs, even among infected eggs, suggesting that microbial resilience may support hatching despite FSSC infection. Conclusions Our findings support a critical role for the inner-egg microbiome in influencing disease susceptibility and hatching success. Specifically, greater fungal diversity is associated with reduced fusariosis susceptibility, and complex, diverse microbial communities enriched in taxa known or predicted to possess antifungal properties against Fusarium pathogens correlate with increased hatching success. These results underscore the importance of microbiome-mediated disease resistance during early developmental stages and provide a foundation for microbiome-informed conservation strategies to enhance the reproductive success of endangered turtle species.