Permafrost pore structure and its influence on microbial diversity: Insights from X-ray computed tomography
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 increas...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-02-01
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| Series: | Geoderma |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0016706125000308 |
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| author | Nathan D. Blais Joy M. O’Brien Hannah Holland-Moritz Lauren Farnsworth Robyn A. Barbato Thomas A. Douglas Alexandra Contosta Julie Bobyock Erin C. Rooney Taylor Sullivan Jessica Gilman Ernakovich |
| author_facet | Nathan D. Blais Joy M. O’Brien Hannah Holland-Moritz Lauren Farnsworth Robyn A. Barbato Thomas A. Douglas Alexandra Contosta Julie Bobyock Erin C. Rooney Taylor Sullivan Jessica Gilman Ernakovich |
| author_sort | Nathan D. Blais |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-09169a58bcd840cc8c70e7167b4a5b56 |
| institution | Kabale University |
| issn | 1872-6259 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Geoderma |
| spelling | doaj-art-09169a58bcd840cc8c70e7167b4a5b562025-02-07T04:46:34ZengElsevierGeoderma1872-62592025-02-01454117192Permafrost pore structure and its influence on microbial diversity: Insights from X-ray computed tomographyNathan D. Blais0Joy M. O’Brien1Hannah Holland-Moritz2Lauren Farnsworth3Robyn A. Barbato4Thomas A. Douglas5Alexandra Contosta6Julie Bobyock7Erin C. Rooney8Taylor Sullivan9Jessica Gilman Ernakovich10Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America; Center of Soil Biogeochemistry and Microbial Ecology, University of New Hampshire, Durham, New Hampshire, United States of America; Corresponding author at: Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America.Department of Biology, Indiana University, Bloomington, Indiana, United States of AmericaDepartment of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America; Center of Soil Biogeochemistry and Microbial Ecology, University of New Hampshire, Durham, New Hampshire, United States of AmericaU.S. Army Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of AmericaU.S. Army Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, United States of AmericaU.S. Army Cold Regions Research and Engineering Laboratory, Fort Wainwright, Alaska, United States of AmericaDepartment of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America; Center of Soil Biogeochemistry and Microbial Ecology, University of New Hampshire, Durham, New Hampshire, United States of America; Earth Systems Research Center, University of New Hampshire, Durham, New Hampshire, United States of AmericaLawrence Berkeley National Laboratory, Berkeley, California, United States of AmericaUSDA-NRCS National Soil Survey Center, Lincoln, Nebraska, United States of AmericaU.S. Army Cold Regions Research and Engineering Laboratory, Fort Wainwright, Alaska, United States of AmericaDepartment of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America; Center of Soil Biogeochemistry and Microbial Ecology, University of New Hampshire, Durham, New Hampshire, United States of AmericaSoil 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.http://www.sciencedirect.com/science/article/pii/S0016706125000308 |
| spellingShingle | Nathan D. Blais Joy M. O’Brien Hannah Holland-Moritz Lauren Farnsworth Robyn A. Barbato Thomas A. Douglas Alexandra Contosta Julie Bobyock Erin C. Rooney Taylor Sullivan Jessica Gilman Ernakovich Permafrost pore structure and its influence on microbial diversity: Insights from X-ray computed tomography Geoderma |
| title | Permafrost pore structure and its influence on microbial diversity: Insights from X-ray computed tomography |
| title_full | Permafrost pore structure and its influence on microbial diversity: Insights from X-ray computed tomography |
| title_fullStr | Permafrost pore structure and its influence on microbial diversity: Insights from X-ray computed tomography |
| title_full_unstemmed | Permafrost pore structure and its influence on microbial diversity: Insights from X-ray computed tomography |
| title_short | Permafrost pore structure and its influence on microbial diversity: Insights from X-ray computed tomography |
| title_sort | permafrost pore structure and its influence on microbial diversity insights from x ray computed tomography |
| url | http://www.sciencedirect.com/science/article/pii/S0016706125000308 |
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