Egg microbiome of the yellow-spotted Amazon river turtle (Podocnemis unifilis) modulates fusariosis fungal infection and hatching success

Turtle egg fusariosis, caused by pathogens of the Fusarium solani species complex (FSSC), threatens turtle populations globally, through embryonic mortality and hatching failure. Host-associated microbiomes, including the bacteriome and mycobiome, are hypothesized to mediate disease outcomes in oviparous vertebrates, but this remains largely unexplored. Here, we characterised the inner-egg bacteriome and mycobiome of uninfected and FSSC-infected eggs at three developmental stages in the vulnerable yellow-spotted Amazon river turtle (Podocnemis unifilis). Lower mycobiome evenness was strongly associated with increased FSSC infection propensity and intensity. Regardless of infection status, higher microbial diversity positively correlated with hatching success, and hatched eggs showed more complex interkingdom interactions. We also identified bacterial and fungal genera whose relative abundance was negatively associated with FSSC infection. These findings support the hypothesis that the egg microbiome may influence infection and hatching outcomes, with implications for microbiome-informed conservation strategies for threatened turtle populations.