Life stage and proximity to roads shape the skin microbiota of eastern newts (Notophthalmus viridescens)

Abstract

Host-associated microbiomes play an essential role in the health of organisms, including immune system activation, metabolism and energy uptake. It is well established that microbial communities differ depending on the life stage and natural history of the organism. However, the effects of life stage and natural history on microbial communities may also be influenced by human activities. We investigated the effects of amphibian life stage (terrestrial eft vs. aquatic adult) and proximity to roadways on newt skin bacterial communities. We found that the eft and adult life stages differed in bacterial community composition; however, the effects of roads on community composition were more evident in the terrestrial eft stage compared to the aquatic adult stage. Terrestrial efts sampled close to roads possessed richer communities than those living further away from the influence of roads. When accounting for amplicon sequence variants with predicted antifungal capabilities, in the adult life stage, we observed a decrease in anti-fungal bacteria with distance to roads. In contrast, in the eft stage, we found an increase in anti-fungal bacteria with distance to roads. Our results highlight the need to consider the effects of human activities when evaluating how host-associated microbiomes differ across life stages of wildlife.

Fig. 1

Alpha diversity dot plots with mean (long horizontal line) and standard errors (short horizontal line). Alpha diversity measures presented for adult and eft eastern newts include community richness (A), Shannon Diversity index (B) and Phylogenetic Diversity (C). Each point represents the bacterial skin community of an individual sample; point colour indicates proximity to roads (grey is close to roads and white is far from roads) and shape identity indicates newt stage (circles are adult newts and squares are efts).

Fig. 2

Compositional diversity of adult and terrestrial efts living in habitats close and far from roads. NMDS plots of unweighted UniFrac (A) and weighted UniFrac (B) distance matrices from adult and eft eastern newts. Each point represents the bacterial skin community of an individual sample; point colour indicates proximity to roads (grey is close to roads and white is far from roads) and shape identity indicates newt stage (circles are adult newts and squares are efts). Unweighted UniFrac NMDS stress: 12.77%; weighted UniFrac NMDS stress: 12.79%. Phylum composition of the core microbiomes (i.e. ASVs present in at least 50% of individuals) for adult newts living far from roads (C), adult newts living close to roads (D), efts living far from roads (E) and efts living close to roads (F).

Fig. 3

Community richness dot plot for Bd‐inhibitory data with mean (long horizontal line) and standard errors (short horizontal line). Each point represents the Bd‐inhibitory bacterial skin community of an individual sample; point colour indicates proximity to roads (grey is close to roads and white is far from roads) and shape identity indicates newt stage (circles are adult newts and squares are efts).

Fig. 4

Community richness dot plot for the abundance of Bd‐inhibitory ASVs data with mean (long horizontal line) and standard errors (short horizontal line). Each point represents the Bd‐inhibitory bacterial skin community of an individual sample; point colour indicates proximity to roads (grey is close to roads and white is far from roads) and shape identity indicates newt stage (circles are adult newts and squares are efts).