ArticlePeerJ2017
Successive DNA extractions improve characterization of soil microbial communities.
Article in PeerJ, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Redundancy maintains microbial ecosystem functional potential despite taxonomic shifts between serpentine and nonserpentine soils.Microbial genomics · 2026Article
- Methylation Mesa define functional regulatory elements for targeted gene activation.Nature communications · 2026Article
- Optimization of the Quantification of Antibiotic Resistance Genes in Media from the Yangtze River Estuary.Toxics · 2026Article
- Article
- Microbiome resilience of Amazonian forests: Agroforest divergence to bacteria and secondary forest succession convergence to fungi.Global change biology · 2023Article
- Current Challenges and Pitfalls in Soil Metagenomics.Microorganisms · 2022Article
- The Requirement of Genetic Diagnostic Technologies for Environmental Surveillance of Antimicrobial Resistance.Sensors (Basel, Switzerland) · 2021Article
- New Estimation of Antibiotic Resistance Genes in Sediment Along the Haihe River and Bohai Bay in China: A Comparison Between Single and Successive DNA Extraction Methods.Frontiers in microbiology · 2021Article
- Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi.Sensors (Basel, Switzerland) · 2020Article
- Article
- Improved Protocol for DNA Extraction from Subsoils Using Phosphate Lysis Buffer.Microorganisms · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1-374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.
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