The bacterial skin microbiome of the Endangered South African endemic Pickersgill’s Reed Frog (Hyperolius pickersgilli)

Pickersgill’s Reed Frog (Hyperolius pickersgilli) is an Endangered (IUCN, 2016) species, endemic to South Africa and restricted to the KwaZulu-Natal coastal region. The species occurs in fragmented patches of coastal reed-bed wetland and the habitat is threatened by urbanisation, agriculture, mining, and forestry. We used a 16S rRNA Next Generation Sequencing approach to characterize the bacterial skin microbiome of 20 adult Pickersgill’s Reed Frog from three localities, and to determine the prevalence of anti-Batrachochytrium dendrobatidis (Bd) associated bacteria. Results from three different populations were found to harbour similar skin microbial communities, dominated by a common core set of bacterial taxa that included Proteobacteria (39.67% of total amplicon sequence variants (ASVs)), Actinobacteria (14.83%) and Firmicutes (11.21%). Anti-Bd associated bacterial communities were identified at all three localities (4.12-15.47% of total ASVs), that may be contributing to the reported low frequency of occurrence of the fungal pathogen; Batrachochytrium dendrobatidis (Bd) and the resultant lack of known morbidity or mortality from chytridiomycosis. A higher ratio of Firmicutes suggests that sampled frogs were undergoing a dietary shift from metamorphosis to maturity. The identification of a high prevalence of Chlamydiae in the Mount Moreland population warrants further monitoring and investigation.