ArticleMethodsX2018
Indirect DNA extraction method suitable for acidic soil with high clay content.
Article in MethodsX, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 31 citations in OpenAlex.
- Optimized Method for Efficient DNA Extraction from Agricultural Soils.Methods and protocols · 2026Article
- Comparing the effectiveness of different DNA extraction methods in MX-80 bentonite.Environmental microbiology reports · 2024Article
- Gene-centered metagenome analysis of Vulcano Island soil (Aeolian archipelago, Italy) reveals diverse microbial key players in methane, hydrogen and sulfur cycles.Antonie van Leeuwenhoek · 2024Article
- Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation.Applied microbiology and biotechnology · 2023Article
- Why eDNA fractions need consideration in biomonitoring.Molecular ecology resources · 2022Review
- Impacts of soybean agriculture on the resistome of the Amazonian soil.Frontiers in microbiology · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA extraction is an essential procedure when investigating microbial communities in environmental samples by sequencing technologies. High clay soils can be problematic as DNA adsorbs to the clay particles and can thereby be preserved from lysed, non-viable cells for a substantial period of time. In order to accurately estimate the intact and living microbial community in the soil, extracellular DNA from dead, remnant bacterial cells needs to be removed prior to DNA extraction. One possibility is to use a sodium phosphate buffer to release both extracellular DNA and bacterial cells from the clay particles. After removing the extracellular DNA by centrifugation, the remaining viable cells can be harvested and DNA extracted. The described method is a modification of a procedure for separating extracellular DNA and bacterial cells from acidic clay soils. •The modified method increases bacterial cell yields from acidic clay soils, such as acid sulfate soil.•The modified method eliminates some steps from the original method, as only DNA from intact bacterial cells is required.•The indirect DNA extraction method increases the workload compared to standard direct extraction methods, but subsequent downstream analyses will give a more representative picture of the viable microbial community composition in the soil.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.