Nest-associated microbial communities of the Kemp’s Ridley Sea Turtle (Lepidochelys kempii) support conservation management at Rancho Nuevo sanctuary

Abstract

Introduction Microbial communities in nesting habitats of critically endangered species remain understudied despite their potential influence on embryonic development and hatching success.

Methods

Using high-throughput 16S rRNA amplicon sequencing, we characterized bacterial communities in nest sands of the Kemp’s ridley sea turtle ( Lepidochelys kempii ) at Rancho Nuevo Sanctuary, Mexico. Twenty-five samples from natural nests, artificial corrals, and beach controls were analyzed for composition, diversity, networks, and function.

Results

Gammaproteobacteria dominated most samples, but relative abundances varied by site. Alcaligenaceae was most abundant at the family level, with Lysobacteriaceae co-dominant in Central corral and Calabazas beach samples. Alpha diversity did not differ among sites (Kruskal-Wallis, p > 0.05) or between nest types (Mann-Whitney U, p > 0.05). Beta diversity showed significant site-level structuring (PERMANOVA: pseudo-F = 1.338, R² = 0.355, p = 0.002), but significant heterogeneity of dispersions was detected. No difference was found between natural and artificial nests (PERMANOVA: pseudo-F = 1.181, R² = 0.049, p = 0.170). LEfSe, indicator species analysis, and PICRUSt2 functional prediction identified no taxa or metabolic pathways associated with either nest type. Lysobacteriaceae was detected in both nest types, while potential pathogens (e.g., Vibrio spp.) were at low relative abundances. However, functional implications cannot be inferred from 16S data alone.

Discussion Within our dataset's limitations (small sample size, single time point), nest relocation does not result in statistically detectable alterations to microbial diversity, composition, networks, or predicted function. These results are preliminary and do not demonstrate absolute microbiological safety. They support continued use of artificial corrals at Rancho Nuevo without evident microbiological consequences based on current data. We recommend targeted monitoring of site-specific variability and future integration of functional metagenomics.