From nest to hatchling: nidobiome assembly and host selection in oviparous vertebrates without parental care

Abstract

Early microbial assembly is fundamental for host development and fitness, yet in oviparous vertebrates lacking parental care, the mechanisms by which eggs and neonates acquire their microbiome remain poorly understood. The nidobiome concept predicts that maternal and environmental sources, and host selection, collectively shape early microbial communities. To test this, we conducted a longitudinal study on microbial assembly in the yellow-spotted Amazon river turtle (Podocnemis unifilis). We sampled maternal mucosa, freshly laid outer eggshells, and nest sand before incubation, along with hatchery sand, outer and inner eggshells, and hatchling cloaca after incubation. Using 16S and ITS amplicon sequencing to quantify microbial diversity, we observed that freshly laid outer eggshells shared bacterial diversity with maternal mucosa, whereas nest sand harboured a distinct community, providing evidence of early vertical transmission. After incubation, eggshell microbial communities became more even without a change in richness, while nest sand communities exhibited the opposite pattern, reflecting divergent host-environment assembly dynamics. SourceTracker analyses confirmed contributions from both maternal and environmental sources, yet inner eggshells and hatchling cloaca assembled distinct communities compared with outer eggshells, indicating that host selection is largely deterministic. Interkingdom interactions favoured beneficial microorganisms, suggesting active host filtering throughout development. Even in the presence of fusariosis, a widespread threat in turtle nests, host selection enriched protective taxa, linking microbiome composition to hatching success. These findings demonstrate that maternal seeding, priority effects, and deterministic host selection govern early-life microbiome assembly in oviparous reptiles without parental care, with direct implications for microbe-informed conservation strategies. ImportanceUnderstanding early-life microbial assembly is critical for uncovering the ecological and evolutionary drivers of host-microbiome interactions. This study reveals how microbial communities develop in oviparous vertebrates lacking parental care, highlighting key mechanisms such as vertical transmission, host selection, and environmental modulation that shape early-life microbiomes. Our results demonstrate that maternal microbiota seeding and priority effects play fundamental roles in structuring egg-associated microbial communities, directly influencing host fitness and survival. By identifying deterministic processes that enrich beneficial microorganisms during early development, this research underscores the pivotal role of microbiomes in host resilience and adaptation. These insights carry urgent conservation implications, offering microbe-informed strategies to mitigate emerging threats, such as diseases in vulnerable species like the yellow-spotted Amazon river turtle, and emphasising the broader importance of microbiome stewardship for ecosystem health.