Impact of storage and extraction methods on peat soil microbiomes
Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage con...
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PeerJ Inc.
2024-12-01
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| author | Dylan Cronin Yueh-Fen Li Paul Evans Gene W. Tyson Ben J. Woodcroft Virginia I. Rich IsoGenie 2016 and 2019 Field Teams |
| author_facet | Dylan Cronin Yueh-Fen Li Paul Evans Gene W. Tyson Ben J. Woodcroft Virginia I. Rich IsoGenie 2016 and 2019 Field Teams |
| author_sort | Dylan Cronin |
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| description | Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modified PowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations. |
| format | Article |
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| institution | Kabale University |
| issn | 2167-8359 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj-art-78b865b0b3be48a9892cd7ac3537fa012024-12-25T15:05:41ZengPeerJ Inc.PeerJ2167-83592024-12-0112e1874510.7717/peerj.18745Impact of storage and extraction methods on peat soil microbiomesDylan Cronin0Yueh-Fen Li1Paul Evans2Gene W. Tyson3Ben J. Woodcroft4Virginia I. Rich5IsoGenie 2016 and 2019 Field TeamsCenter of Microbiome Science, Ohio State University, Columbus, Ohio, United StatesDepartment of Microbiology, Ohio State University, Columbus, Ohio, United StatesSchool of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, University of Queensland, St Lucia, Queensland, AustraliaCentre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, AustraliaCentre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, AustraliaCenter of Microbiome Science, Ohio State University, Columbus, Ohio, United StatesRecovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modified PowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations.https://peerj.com/articles/18745.pdfMicrobiomeSoilStorageExtractionMethodsPeatland |
| spellingShingle | Dylan Cronin Yueh-Fen Li Paul Evans Gene W. Tyson Ben J. Woodcroft Virginia I. Rich IsoGenie 2016 and 2019 Field Teams Impact of storage and extraction methods on peat soil microbiomes PeerJ Microbiome Soil Storage Extraction Methods Peatland |
| title | Impact of storage and extraction methods on peat soil microbiomes |
| title_full | Impact of storage and extraction methods on peat soil microbiomes |
| title_fullStr | Impact of storage and extraction methods on peat soil microbiomes |
| title_full_unstemmed | Impact of storage and extraction methods on peat soil microbiomes |
| title_short | Impact of storage and extraction methods on peat soil microbiomes |
| title_sort | impact of storage and extraction methods on peat soil microbiomes |
| topic | Microbiome Soil Storage Extraction Methods Peatland |
| url | https://peerj.com/articles/18745.pdf |
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