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.

森林砍伐对生物多样性具有不利影响，可在多个尺度上干扰物种种间相互作用。脊椎动物、病原体及其偏利共生/互利共生微生物群落（即微生物组）之间的关联，对生物多样性保护具有重要的下游效应，但目前学界对森林砍伐如何影响宿主微生物多样性及病原体丰度仍知之甚少。
本研究以巴西境内景观的森林砍伐梯度为研究对象，检验了土地覆盖、森林连通性以及蛙壶菌（Batrachochytrium dendrobatidis，Bd）感染对两栖动物皮肤细菌多样性的影响。若自然栖息地的干扰会如脊椎动物宿主群落那般改变皮肤微生物组，则我们预期天然林生境中的宿主细菌多样性会更高。此外，这类密闭冠层森林中的Bd感染负荷通常更高，这可能反过来影响皮肤相关细菌群落。
研究结果显示，森林廊道可塑造宿主皮肤微生物组的组成；高森林连通性可预示宿主种群间的皮肤细菌群落相似性更高。此外，我们发现宿主皮肤细菌多样性与Bd负荷随天然植被占比提升呈上升趋势。
鉴于共生细菌可潜在为宿主抵御Bd感染提供保护，我们同时评估了微生物组与Bd之间的双向关联，但未发现皮肤细菌多样性可显著降低Bd感染的统计学证据。尽管相关性较弱，但我们的结果支持两个推论：一是Bd可提高皮肤细菌多样性，二是核心细菌的优势度可降低Bd负荷。
本研究通过将景观环境异质性与宿主-病原体-微生物组三角关联相结合，为宿主微生物组研究纳入了一项关键要素。