Evaluating the effects of the changing permafrost ecosystem through the lens of genomics

Devin Drown, (University of Alaska Fairbanks, US) starts the talk by discussing the effect of climate fluctuations on Alaskan communities who are at the centre of the resultant rapid environmental change. Devin explains that Artic temperatures are rising two times faster than the global average and the thawing permafrost is particularly vulnerable to temperature increases, which leads to disturbances in the active layer of soil and, in turn, changes the microbial communities within it.

In the first step of the research, the effect of thawing permafrost-induced disturbance to the active layer of soil was measured. Then plant health and ARG (Antibiotic Resistance Gene) presence was tracked and mapped relative to disturbance.

Devin explains that using a MinION to sequence samples from the active layer soil with varying degrees of disturbance and then processing the long-reads with Cracken and Bracken revealed microbial community abundance. Visualisation of these data showed how a shift in microbial community population size corresponded with the level of disturbance.

Next, the effect of active layer soil disturbance on microbe plant interactions was established before the change in plant output was measured. Devin explained that microbe-plant interactions are critical for the acquisition and cycling of nutrients in the soil, with small changes in these microbial communities affecting plant output. Five plant species that local communities depend on were used to test this hypothesis. Data revealed that the majority of plant species showed decreased productivity in disturbed vs non-disturbed soil.

To quantify the impact of the melting permafrost on plant health, biomarkers that are known to be associated with plant health were screened for. Biomarkers associated with healthy plant growth and high output were found in the plant samples from undisturbed active layer soil samples. In contrast, biomarkers pertaining to unhealthy plants were found in the disturbed active layer soil samples.

Devin went on to explain that functional gene analysis was then conducted using long-read sequence data. Devin discussed how the subsequent analysis of these data with Megan revealed a shift in the genes present in disturbed soil samples and may explain the changes observed in plant productivity.

Next Devin discussed how both abiotic and biotic factors act as a driving force for ARG selection and horizontal gene transfer. Cultured isolates and culture-independent isolates were screened to identify genes present which are resistant to antibiotics and are clinically relevant. While the data revealed that ARG abundance was driven to a greater extent by phylogeny, an increased quantity of ARGs present in disturbed soil vs non-disturbed active layer soil samples was noted. Devin then relayed that that this data may explain the changes in microbial communities observed in disturbed active layer soil. Before concluding, Devin shared how phylogenetic analyses revealed the host taxa of microbes, demonstrating a nonlinear/complex relationship between community shifts and ARG abundance.

Summary:

In the concluding slides, Devin explained that subarctic soils are a reservoir for ARGs, some of which are clinically relevant. He summarised the finding of both ARGs with 100% homology with clinically derived isolates and novel ARGs in this research. Devin explained that these results highlight the need for novel therapeutics to combat antibiotic-resistant bacteria and how this work formalises the link between climate change, the melting permafrost, changing microbial communities, plant health, ARGs, and broader community health.

Devin called attention to the importance of other research projects that form part of ‘Our One Health Perspective’, including research evaluating the effect of climate on boreal forests, which are central to the subsistence-based diets of native Alaskan communities.