Permafrost pore structure and its influence on microbial diversity: Insights from X-ray computed tomography

• Micro-CT scanning of three distinct permafrost soils. • Pore connectivity and size distribution quantified in permafrost. • Macropore connectivity affects microbial community diversity. 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.