Animals, environment and microbiota: how microorganisms are changing the way we think about biodiversity conservation

Diverse bacterial, fungal and viral communities characterize the intestinal flora and animal epidermis of all animal species and are known to provide essential services to host health. However, the role of this ‘microbiota’ in animal conservation has only recently been considered. Here we show how amplicon sequencing of the 16S rRNA gene and ITS2 locus from faecal samples and skin swabs collected non- invasively, allow us to study the diversity, composition and function of bacterial and fungal communities living in association with fauna, as well as to define the biological processes that characterize the network of interactions between species’ communities and the surrounding environment ('ecosystem microbiota'). For example, alpine relictual populations of mountain hare (L. timidus) are threatened by climate and anthropic changes that result in snow cover reduction and habitat loss, as well as resource competition and potential hybridization with the European brown hare (L. europaeus). Using faecal pellets from an area of sympatry, we showed that the two species maintain distinct prokaryotic and fungal communities reflecting differences in host microbiota co-evolution. Furthermore, in both Lepus species, elevation influenced intraspecific gut fungal composition, but not prokaryotic diversity, highlighting differences in the resilience of these communities to environmental change. Interconnection between host-associated and environmental microbiota is further exemplified by the study of Bombina variegata. Here, the profiling the skin microbiota from individuals collected across different habitats highlighted a marked association between skin and water microbiota suggesting skin microbial diversity is affected by water quality parameters such as pH, dissolved oxygen, and temperature. The study of microbiodiversity is proposed as an effective tool to estimate the effects of biotic and abiotic factors on the health of charismatic and/or endangered species, as well as changes in biodiversity through time.