20 Apr 2026

Permafrost Pore Structure and its Influence on Microbial Diversity: Insights from X-Ray Computed Tomography

Abstract: Soil pore structure plays a critical role in shaping soil microbial communities, which directly influence biogeochemical cycling. A notable impact of soil pore structure on microbial communities is the inverse relationship between microbial diversity and hydrological pore connectivity, where increased hydrological pore connectivity reduces microbial diversity. Although well-studied in temperate systems, the importance of hydrological pore connectivity on soil microbial community diversity in permafrost soils is largely unknown. Although once thought to be devoid of microbial activity, more recent advances demonstrate permafrost is an active ecosystem albeit less than most unfrozen soil. Thus, these principles that govern unfrozen soils could remain impactful in permafrost. In this study, our objective was to quantify permafrost pore structure and determine if the inverse relationship between soil hydrological pore connectivity and microbial diversity persists in permafrost. To address these objectives, we analyzed eight permafrost cores from three distinct sites in Alaska. To quantify soil pore characteristics, we scanned intact permafrost using X-ray computed tomography. The Euler characteristic number was used to measure pore connectivity and serve as a proxy for potential hydrological connectivity, as direct measurement of hydrological connectivity was not possible. DNA and RNA were extracted from the scanned permafrost and analyzed via amplicon sequencing of the 16S region to quantify the total and active microbial community diversity. We found that permafrost soil shares characteristics with temperate soils despite limits in our analytical resolution (i.e., at an instrument scanning resolution of 20 µm, only macro-scale features (>75 µm) could be quantified). For example, we found that pores in the range of 75–1000 µm are the dominant pore size class and a positive relationship between total porosity and pore connectivity. Additionally, we identified pore connectivity as a potential driver of microbial diversity and provided evidence that conditions before the formation of permafrost exert a strong legacy effect on currently observed permafrost microbial diversity. These insights help to explain how soil physical structure acts to influence microbial communities in this extreme environment.

7 Sep 2022

Extracting Sintered Snow Properties from MicroCT Imagery to Initialize a Discrete Element Method Model

Abstract: Modeling snow’s mechanical behavior is important for many cold regions engineering problems. Because snow’s microstructure plays a significant role in its mechanical response, it is imperative to initialize models with accurate bond characteristics and realistic snow-grain geometries to precisely capture the microstructure interactions. Previous studies have processed microcomputed tomography scans of snow samples with a watershed method to extract grain geometries. This approach relies on identification of seed points to segment each grain. Our new methodology, called the “moving window method,” does not require prior knowledge of the snow-grain-size distribution to identify seed points. We use the interconnectivity of the segmented grains to identify bond characteristics. We compare the resultant grain-size and bond-size distributions to the known grain sizes of the laboratory-made snow samples. The grain-size distributions from the moving window method closely match the known grain sizes, while both results from the traditional method produce grains that are too large. We propose that the bond net-work identified using the traditional method underestimates the number of bonds and overestimates bond radii. Our method allows us to segment realistic snow grains and their associated bonds, without prior knowledge of the samples, from which we can initialize numerical models of the snow.