The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil
Open accessAbstract
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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Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
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Phylogenetic identification and in situ detection of individual microbial cells without cultivation
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Ecologically meaningful transformations for ordination of species data
Legendre, P., & Gallagher, E. D. (2001) · Oecologia · doi:10.1007/s004420100716 · Cited by 5,556
Microbial diversity and function in soil: from genes to ecosystems
Torsvik, V., & Øvreås, L. (2002) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(02)00324-7 · Cited by 1,922
Pyrosequencing enumerates and contrasts soil microbial diversity
Roesch, L. F. W., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H., Camargo, F. A. O., Farmerie, W. G., & Triplett, E. W. (2007) · The ISME Journal · doi:10.1038/ismej.2007.53 · Cited by 1,852
Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes
Janssen, P. H. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.3.1719-1728.2006 · Cited by 1,821
Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays
Fierer, N., Jackson, J. A., Vilgalys, R., & Jackson, R. B. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.7.4117-4120.2005 · Cited by 1,581
Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples
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Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts
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Comparison and Validation of Some ITS Primer Pairs Useful for Fungal Metabarcoding Studies
Op De Beeck, M., Lievens, B., Busschaert, P., Declerck, S., Vangronsveld, J., & Colpaert, J. V. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097629 · Cited by 538
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
Vaginal Microbiome Consortium (additional members), Brooks, J. P., Edwards, D. J., Harwich, M. D., Rivera, M. C., Fettweis, J. M., Serrano, M. G., Reris, R. A., Sheth, N. U., Huang, B., et al. (2015) · BMC Microbiology · doi:10.1186/s12866-015-0351-6 · Cited by 528
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Metadata
- Authors
- Feinstein, L. M., Sul, W. J., & Blackwood, C. B.
- Venue
- Applied and Environmental Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2009-08-15
- Volume
- 75
- Issue
- 16
- Pages
- 5428-5433
- ISSN
- 0099-2240 (ISSN-L)
- 1098-5336
- OpenAlex
- W2140319224
- Cited by
- 313
- References
- 28
- FWCI
- 20.54
- Type
- journal article
- Language
- en
- Open access
- green
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