COS 145-3 - Looking beyond composition: Structural reorganization of the Plethodon cinereus cutaneous microbiome across an urbanization gradient

Abstract: Amphibians are disproportionately affected by anthropogenic environmental degradation and associated introductions of the fungal pathogen Batrachochytrium dendrobatidis (Bd). The eastern redback salamander, Plethodon cinereus, is endemic to the urbanized northeastern USA and exhibits low susceptibility to Bd throughout its range. This is attributed to the presence of putatively Bd-inhibitory microbes in the P. cinereus cutaneous microbiome. Previous research identified high dissimilarity in skin microbial assemblages of individual P. cinereus hosts sampled along an urbanization gradient despite no significant differences in alpha diversity. This suggests that the protective function of P. cinereus skin microbiota is driven by more than composition. In fact, subtle alterations to microbiome composition can produce substantial changes in microbial associations and overall community function. Considering this, we examined the bacterial diversity, composition, and network structure of the P. cinereus cutaneous microbiome and its soil reservoir, sampled along a 65-km urbanization gradient originating in New York City, USA. We aimed to understand the structural and compositional relationship between the salamander skin microbial community and its soil reservoir under differing levels of stress from urbanization and disease.

To address our goals, we constructed network graphs using 16S rRNA amplicon data from the P. cinereus skin and soil microbiomes with the SPIEC-EASI R Package. Models were generated for both sample types in urban, suburban, and exurban land uses. Network properties were extracted and used to identify putative keystone taxa. We found that the salamander skin and soil bacterial communities in each land use classifier experienced shifts in the taxonomic identity of putative keystones, resulting in the reorganization of first neighbor networks. Further, the average connectivity of taxa in the P. cinereus skin microbiome increased with the intensity of urbanization, suggesting that network reorganization under stress may favor increased cooperation among microbes. When comparing the salamander skin and soil microbiomes across the urbanization gradient, we found that soil bacterial communities had greater complexity (i.e., more nodes and edges) but reduced stability (i.e., fewer modules and more positive associations) relative to salamander cutaneous bacterial communities. Our findings suggest that structural differences in the salamander skin and soil microbiomes have consequences for community complexity and stability. This work illuminates the need to move beyond compositional surveys of amphibian skin microbiota. Exploring the host skin microbiome under different environmental contexts and from a variety of perspectives is essential to the development of targeted probiotic therapies as we look to the future of amphibian conservation.