ArticlePloS one2021
The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 19 citations in OpenAlex.
- Sampling Design and Sample Processing Affect Soil Biodiversity Assessments.Molecular ecology resources · 2026Article
- Optimized Method for Efficient DNA Extraction from Agricultural Soils.Methods and protocols · 2026Article
- Cost-effective DNA extraction method optimized for high yield and long fragments from coastal sediments.PloS one · 2026Article
- The soil microbiome as an indicator of ecosystem multifunctionality in European soils.Nature communications · 2025Article
- Tracing non-fungal eukaryotic diversity via shotgun metagenomes in the complex mudflat intertidal zones.mSystems · 2025Article
- Whole-genome sequencing and metagenomics reveal diversity and prevalence ofMicrobiology spectrum · 2025Article
- Article
- Variations in different preceding crops on the soil environment, bacterial community richness and diversity of tobacco-planting soil.Frontiers in microbiology · 2024Article
- Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome.Microorganisms · 2023Review
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2 authors at 1 institution in 1 country.
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Abstract
To determine the optimal soil sample size for microbial community structure analysis, DNA extraction, microbial composition analysis, and diversity assessments were performed using soil sample sizes of 0.2, 1, and 5 g. This study focused on the relationship between soil amount and DNA extraction container volume and the alteration in microbial composition at different taxonomic ranks (order, class, and phylum). Horizontal (0.2 and 1 g) and vertical (5 g) shaking were applied during DNA extraction for practical use in a small laboratory. In the case of the 5 g soil sample, DNA extraction efficiency and the value of α-diversity index fluctuated severely, possibly because of vertical shaking. Regarding the 0.2 and 1 g soil samples, the number of taxa, Shannon-Wiener index, and Bray-Curtis dissimilarity were stable and had approximately the same values at each taxonomic rank. However, non-metric multidimensional scaling showed that the microbial compositions of these two sample sizes were different. The higher relative abundance of taxa in the case of the 0.2 g soil sample might indicate that cell wall compositions differentiated the microbial community structures in these two sample sizes due to high shear stress tolerance. The soil sample size and tube volume affected the estimated microbial community structure. A soil sample size of 0.2 g would be preferable to the other sample sizes because of the possible higher shearing force for DNA extraction and lower experimental costs due to smaller amounts of consumables. When the taxonomic rank was changed from order to phylum, some minor taxa identified at the order rank were integrated into major taxa at the phylum rank. The integration affected the value of the β-diversity index; therefore, the microbial community structure analysis, reproducibility of structures, diversity assessment, and detection of minor taxa would be influenced by the taxonomic rank applied.
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