Data from: Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome

Deforestation has detrimental consequences on biodiversity, affecting
species interactions at multiple scales. The associations among
vertebrates, pathogens and their commensal/symbiotic microbial communities
(i.e. microbiomes) have important downstream effects for biodiversity
conservation, yet we know little about how deforestation contributes to
changes in host microbial diversity and pathogen abundance. Here, we
tested the effects of landcover, forest connectivity and infection by the
chytrid fungus Batrachochytrium dendrobatidis (Bd) on amphibian skin
bacterial diversity along deforestation gradients in Brazilian landscapes.
If disturbance to natural habitat alters skin microbiomes as it does in
vertebrate host communities, then we would expect higher host bacterial
diversity in natural forest habitats. Bd infection loads are also often
higher in these closed-canopy forests, which may in turn impact
skin-associated bacterial communities. We found that forest corridors
shaped composition of host skin microbiomes; high forest connectivity
predicted greater similarity of skin bacterial communities among host
populations. In addition, we found that host skin bacterial diversity and
Bd loads increased towards natural vegetation. Because symbiotic bacteria
can potentially buffer hosts from Bd infection, we also evaluated the
bi-directional microbiome-Bd link but failed to find a significant effect
of skin bacterial diversity reducing Bd infections. Although weak, we
found support for Bd increasing bacterial diversity and/or for core
bacteria dominance reducing Bd loads. Our research incorporates a critical
element in the study of host microbiomes by linking environmental
heterogeneity of landscapes to the host–pathogen–microbiome triangle.