Van Koppen, Linsey; Aiyer, Harini S; Davis, Jesse; Tremblay, Julien; Bainard, Harini S et Bainard, Luke D. (2025). The amount of soil used for DNA extractions has a minimal effect on characterization of microbial communities in a temperate agricultural region Pedobiologia , vol. 110 , nº 151051. pp. 1-8. DOI: 10.1016/j.pedobi.2025.151051.
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The ability to analyze soil microbial communities continues to improve with methodological advancements. The amount of soil used for DNA extractions to characterize the microbial community has been suggested to alter results. However previous efforts to quantify this variation have not always utilized consistent methodology, making it difficult to assess when and how the amount of soil impacts the results. In this study, we pooled technical replicates of DNA extractions using a standardized protocol with the most commonly used kit (i.e., 0.25 g starting soil weight with the Qiagen PowerSoil Pro kit) into five treatments: 0.25 g, 0.5 g, 1.0 g, 2.0 g, and 4.0 g to characterize the soil microbial communities from four distinct land use systems (grazed pasture, conventional forage, woodlot, and blueberry). Following DNA extraction, we assessed total DNA yield, fungal and bacterial abundance (qPCR), and alpha and beta diversity (amplicon sequencing) of the soil microbial community to determine the effect of soil weight on these metrics. Soil weight did not have a significant effect on any of these metrics. Land use system had a significant effect on all metrics except for prokaryotic Shannon diversity. The land use systems and the spatial organization within each system (i.e., field replicates) were easily distinguishable regardless of the amount of soil used to assess the samples. These results confirm the suitability of 0.25 g soil to accurately (and affordably) assess soil microbial communities in temperate agricultural soils, and accentuate the importance of methodological consistency within a study.
Type de document: | Article |
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Mots-clés libres: | DNA extraction; Soil microbial community; Fungi; Prokaryotes; Methodology |
Centre: | Centre INRS-Institut Armand Frappier |
Date de dépôt: | 07 juill. 2025 18:56 |
Dernière modification: | 07 juill. 2025 18:56 |
URI: | https://espace.inrs.ca/id/eprint/16508 |
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