Unravelling the microbiome of eggs of the endangered sea turtle Eretmochelys imbricata identifies bacteria with activity against the emerging pathogen Fusarium falciforme

Abstract

Habitat bioaugmentation and introduction of protective microbiota have been proposed as potential conservation strategies to rescue endangered mammals and amphibians from emerging diseases. For both strategies, insight into the microbiomes of the endangered species and their habitats is essential. Here, we sampled nests of the endangered sea turtle species Eretmochelys imbricata that were infected with the fungal pathogen Fusarium falciforme. Metagenomic analysis of the bacterial communities associated with the shells of the sea turtle eggs revealed approximately 16,664 operational taxonomic units, with Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes as the most dominant phyla. Subsequent isolation of Actinobacteria from the eggshells led to the identification of several genera (Streptomyces, Amycolaptosis, Micromomospora Plantactinospora and Solwaraspora) that inhibit hyphal growth of the pathogen F. falciforme. These bacterial genera constitute a first set of microbial indicators to evaluate the potential role of microbiota in conservation of endangered sea turtle species.

Figure 1. Sea turtle nesting area sampled for this study.

A) Nests of the sea turtle Eretmochelys imbricata in La Playita beach at Machalilla National Park, Ecuador. B) Nest containing hatched and unhatched Fusarium-infected eggs. C) Fusarium-infected hatched eggs. D) Fusarium-infected unhatched eggs.

Figure 2. Composition of the microbial community of shells of Fusarium-infected eggs detected by the PhyloChip analysis.

A) Number of OTUs per phylum detected on hatched (H) and unhatched (UH) eggshells collected from two nests (numbers 1 and 2). Values with >0.25% of occurrence. B) Average distribution of OTUs for all the samples (n = 4).