Temperature drives transcriptomic shifts in amphibian skin bacterial communities with consequences for fungal pathogen control

Emma Thompson, Elle Barnes 

The chytrid fungi Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are two of the largest threats to amphibian populations worldwide. While the amphibian skin microbiome can inhibit these fungal pathogens, microbial composition varies substantially across host and environmental contexts. In addition, habitat-wide mitigation methods that capitalize on the thermal mismatch between Bd/Bsal and their hosts (e.g., warming the host or environment) have been proposed to combat infection. Preliminary experimental application of these methods shows promising results for host infection load, but has yet to consider the indirect effects that warming has on the microbiome. Here, we exposed synthetic microbial communities–comprising ten core members of the blue-spotted salamander (Ambystoma laterale) skin microbiome–and Bd/Bsal to five different temperatures reflecting proposed mitigation methods and a climate change scenario. Microbial community composition and gene expression were assessed via metabarcoding and metatranscriptomics. We found that both temperature and time play a significant role in shaping community composition. Temperature exerted a small but significant effect on Bd/Bsal inhibition, indicating that microbe-mediated mechanisms likely act alongside host physiological responses during thermal shifts. Metatranscriptomic profiling revealed distinct differential expression of bacterial genes involved in secretion systems, antimicrobial compound resistance, and heat-shock across temperature treatments. These findings demonstrate that thermal mitigation strategies can alter both microbiome composition and function, highlighting the need to account for off-target microbial responses when designing environmental disease interventions.