Effect of habitat split on Atlantic Forest soil microbiome and consequences for amphibian immunity

Abstract

One of the consequences of environmental degradation is the discontinuity between terrestrial and aquatic habitats; hereafter habitat split. In Brazil's Atlantic Forest, this phenomenon results in a high proportion of forest fragments without perennial water bodies. This scenario leads to negative impacts on amphibian populations, due to a greater susceptibility to infectious diseases, among other factors. The amphibian skin microbiome is a mechanism of defence against dermal pathogens, including the pathogenic fungus Batrachochytrium dendrobatidis, the causative agent of the chytridiomycosis pandemic. The structure and the function of the microbiome, however, depend partially on the dynamics of environmental microorganisms. Environmental microbes, in turn, depend on the integrity of terrestrial and aquatic environments. The central hypothesis of this research is that the structure and connectivity of habitats in the landscape determines the diversity and function of the environmental microbial pool recruited by amphibians. The effect of habitat connectivity - aquatic and terrestrial - on the soil microbiome and will be tested, including the Bd-inhibitory and Bd-facilitative capacity of environmental microbiome samples. Furthermore, it will be tested whether the environmental microbiome explains differences in the diversity and the response of the amphibian microbiome to the fungus B. dendrobatidis. Microbial sampling from terrestrial and aquatic environments will be taken in eight forest landscapes composed by continuous and fragmented forests, under two levels of connectivity: presence and absence of water bodies. Metagenomic analyses of the RNAr 16S gene will provide characterization of microbial communities. The profiling of the antifungal activity of isolated bacteria will be done by bioassays and by crossing information with a comprehensive anti-Bd bacteria database. Understanding the mechanisms involved in modulating the animal microbiome in the face of habitat fragmentation has potential for informing biodiversity conservation strategies. These results could inform landscape restoration plans that could aid in microbiome health both for environment and vertebrate hosts. (AU)