DNA Extraction from Soils: Old Bias for New Microbial Diversity Analysis Methods

By F. Martin-Laurent, L. Philippot, S. Hallet, R. Chaussod, J. Germon, G. Soulas, G. Catroux. Applied and Environmental Microbiology, 2001

766 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6a91dc9b082db7bbba9b981ca73a817d20358af3

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Citations in the corpus

Functional and molecular responses of soil microbial communities under differing soil management practices (2004, result): “Our molecular data seem therefore to substantiate the statement that comparison of bacterial communitites are dependent on the DNA recovery method used (Martin-Laurent et al., 2001).”
Microbial diversity and soil functions (2003, methodology): “Bromodeoxyuridinelabelled DNA extracted from soil DNA by immunocapture was subjected to RISA analysis.”
Extraction of DNA from soil (2003, methodology): “Ribosomal intergenic spacer analysis (RISA) of soil microbial diversity also revealed that both abundance and apparent members of the bacterial community are affected by the extraction method [38].”
Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis (2004, methodology): “, 2003), however, the impact on the detected soil microbial diversity is only sparsely investigated (Kozdrój and van Elsas, 2000; Martin-Laurent et al., 2001; Westergaard et al., 2001).”
Quantitative analyses of relationships between ecotoxicological effects and combined pollution (2004, methodology): “Total soil-microbial DNA was extracted based on the method suggested by Martin-Laurent et al.([13]).”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, background): “Many comparisons of DNA extraction methods for soil, sediment and leaf litter samples have been published (Frostegard et al. 1999; Miller et al. 1999; Martin-Laurent et al. 2001; Miller 2001; Dineen et al. 2010; Mahmoudi et al. 2011) including for the recovery of ancient DNA (Haile 2012), each highl”
A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing (2016, background): “…Fierer et al., 2005), this requires an additional step in the analyses, and the quantitative PCR analyses are also subject to biases due to differences in DNA extraction ef ﬁ ciencies and varying DNA ampli ﬁ cation ef ﬁ ciencies across samples (Martin-Laurent et al., 2001; Fierer et al., 2005).”
Vibrio Related Diseases in Aquaculture and Development of Rapid and Accurate Identification Methods (2012, background): “Vibrios colonized the host tissue of shrimps after crossing the epithelial cells [34].”
DNA-based methods for monitoring invasive species: a review and prospectus (2007, background): “For instance, it has been demonstrated for microbial communities that different extraction techniques can result in different estimates of community diversity, indicating bias in extraction procedures (Martin-Laurent et al. 2001).”
Who is eating what: diet assessment using next generation sequencing (2012, background): “Biases may also appear during DNA extraction (e.g. Martin-Laurent et al. 2001), DNA pooling (e.g. Harris et al. 2010), sequencing (e.g. Porazinska et al. 2010) and during bioinformatic sorting (Amend et al. 2010).”
Thematic Issue on Horizontal Gene Transfer Review Release and persistence of extracellular DNA in the environment (2007, neutral): “A loss of signal during sampling, shipping, storage, and processing can occur as well (Martin-Laurent et al., 2001).”
Microbial Community Analysis of Opalinus Clay Drill Core Samples from the Mont Terri Underground Research Laboratory, Switzerland (2007, methodology): “The method developed in Belgium for Boom Clay (Boivin-Jahns et al. 1996), adapted for microtube use according to methods for soils of diverse composition (Miller et al. 1999; Martin-Laurent et al. 2001 ) was also used, with an additional DNA purification step on Sepharose 4B (Sigma-Aldrich) as desc”