ArticleApplied and environmental microbiology2009
Assessment of bias associated with incomplete extraction of microbial DNA from soil.
Article in Applied and environmental microbiology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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Who cites it
96 citing papers in PubMed, 309 citations in OpenAlex.
- Choosing Between Short-Read 16S, Full-Length ONT 16S, and Long-Read Shotgun Metagenomics for Soil Microbiome Studies: A Critical Review of the Benchmarking Evidence.Microorganisms · 2026Review
- Enhancing DNA recovery in low-biomass snow algae samples: a comparative study of extraction methods and their effect on community composition.Applied and environmental microbiology · 2026Article
- Quantitative metagenomics using a portable protocol.Applied and environmental microbiology · 2026Article
- Optimization of the Quantification of Antibiotic Resistance Genes in Media from the Yangtze River Estuary.Toxics · 2026Article
- Toward reproducible pig gut microbiome profiling through standardized methodologies.ISME communications · 2026Article
- Nasal microbiota profiles are similar at two swabbing depths in healthy awake dogs.Frontiers in veterinary science · 2026Article
- Beyond dikarya: 28S metabarcoding uncovers cryptic fungal lineages across a tidal estuary.Environmental microbiome · 2025Article
- CABO-16S-a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples.NAR genomics and bioinformatics · 2025Article
- Plant Species Richness and the Root Economics Space Drive Soil Fungal Communities.Ecology letters · 2025Article
- Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics.Scientific reports · 2024Article
- Plant roots affect free-living diazotroph communities in temperate grassland soils despite decades of fertilization.Communications biology · 2024Article
- Survival and rapid resuscitation permit limited productivity in desert microbial communities.Nature communications · 2024Article
- Article
- Benchmarking DNA isolation methods for marine metagenomics.Scientific reports · 2023Article
- Urbanization and edge effects interact to drive mutualism breakdown and the rise of unstable pathogenic communities in forest soil.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Comparison of four DNA extraction kits efficiency for 16SrDNA microbiota profiling of diverse human samples.Future science OA · 2023Article
- Defining Composition and Function of the Rhizosphere Microbiota of Barley Genotypes Exposed to Growth-Limiting Nitrogen Supplies.mSystems · 2022Article
- Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding.Environmental monitoring and assessment · 2021Article
- Review
- Soil ammonia-oxidizing archaea in a paddy field with different irrigation and fertilization managements.Scientific reports · 2021Article
36 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA extraction bias is a frequently cited but poorly understood limitation of molecular characterizations of environmental microbial communities. To assess the bias of a commonly used soil DNA extraction kit, we varied the cell lysis protocol and conducted multiple extractions on subsamples of clay, sand, and organic soils. DNA, as well as bacterial and fungal ribosomal gene copies as measured by quantitative PCR, continued to be isolated in successive extractions. When terminal restriction fragment length polymorphism was used, a significant shift in community composition due to extraction bias was detected for bacteria but not for fungi. Pyrosequencing indicated that the relative abundances of sequences from rarely cultivated groups such as Acidobacteria, Gemmatimonades, and Verrucomicrobia were higher in the first extraction than in the sixth but that the reverse was true for Proteobacteria and Actinobacteria. This suggests that the well-known phylum-level bacterial cultivation bias may be partially exaggerated by DNA extraction bias. We conclude that bias can be adequately reduced in many situations by pooling three successive extractions, and additional measures should be considered when divergent soil types are compared or when comprehensive community analysis is necessary.
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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.