Date of Award

Winter 2022

Project Type


Program or Major

Natural Resources

Degree Name

Master of Science

First Advisor

Jessica Ernakovich

Second Advisor

Robyn Barbato

Third Advisor

Alexandra Contosta


Soil structure plays a critical role in shaping soil microbial communities, who directly influence biogeochemical cycling1–4. Although well-studied in temperate systems, the importance of physical structure on soil microbial community diversity, function, and overall activity in permafrost soils is largely unknown. I hypothesized that (1) decreases in pore connectivity would increase microbial diversity based on an expected inverse relationship between diversity and connectivity; (2) soil with an increased abundance of larger pores (> 75 µm), which are uninhabitable because they are too large to sustain liquid water, will exhibit lower bacterial and archaeal abundance and (3) the surface area of ice inclusions, which represents potentially habitable space in the form of brine channels, will be positively correlated with the abundance of active microbes. To test these hypotheses, I analyzed eight permafrost cores from three distinct sites in Alaska. Fine scale heterogeneity in soil physical and biological characteristics was captured from triplicate subsamples per core. To quantify soil ice inclusions and pore architecture, I scanned permafrost at -10 ºC using X-ray Computed Tomography to maintain its structure. Following scanning, both DNA and RNA were extracted from the permafrost and analyzed via amplicon sequencing and quantitative PCR of the 16S region. I analyzed the total and active microbial community diversity, and abundance. I found that at a scanning resolution of 20 µm only macro-scale features (>75 µm) could be quantified. Despite the limitation to the resolution, permafrost soil appears to share characteristics with temperate soils like the dominant pore size class (75-100 µm) and the positive relationship between total porosity and pore connectivity. I also found a negative relationship between macroporosity and microbial diversity, indicating that dispersal limitation in permafrost and past soil conditions may contribute to the spatial structure of microbial community diversity currently seen in permafrost. Additionally, soil structure did not influence the abundance of the active microbial community, indicating. I require finer scale structural and microbial data to disentangle any existing relationships. Gaining these insights could help us understand how soil physical structure acts to influence community structure in this extreme environment.