Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities

Summary Assessing soil microbial community structure by the use of molecular techniques requires a satisfactory sampling strategy that takes into account the high microbial diversity and the heterogeneous distribution of microorganisms in the soil matrix. The influence of the sample size of three di...

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Published in:Environmental microbiology 2003-11, Vol.5 (11), p.1111-1120
Main Authors: Ranjard, Lionel, Lejon, David P. H., Mougel, Christophe, Schehrer, Lucie, Merdinoglu, Didier, Chaussod, Rémi
Format: Article
Language:English
Subjects:
Bacteria - genetics
Biomass
DNA - analysis
DNA - isolation & purification
DNA Fingerprinting - methods
DNA, Ribosomal Spacer - analysis
DNA, Ribosomal Spacer - isolation & purification
Ecology - methods
Electrophoresis, Polyacrylamide Gel
Fungi - genetics
Life Sciences
Microbiology and Parasitology
Polymerase Chain Reaction - methods
Polymorphism, Genetic
Principal Component Analysis
Soil - analysis
Soil Microbiology - standards
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Summary:Summary Assessing soil microbial community structure by the use of molecular techniques requires a satisfactory sampling strategy that takes into account the high microbial diversity and the heterogeneous distribution of microorganisms in the soil matrix. The influence of the sample size of three different soil types (sand, silt and clay soils) on the DNA yield and analysis of bacterial and fungal community structure were investigated. Six sample sizes from 0.125 g to 4 g were evaluated. The genetic community structure was assessed by automated ribosomal intergenic spacer analysis (A‐RISA fingerprint). Variations between bacterial (B‐ARISA) and fungal (F‐ARISA) community structure were quantified by using principal component analysis (PCA). DNA yields were positively correlated with the sample size for the sandy and silty soils, suggesting an influence of the sample size on DNA recovery, whereas no correlation was observed in the clay soil. B‐ARISA was shown to be consistent between the different sample sizes for each soil type indicating that the sampling procedure has no influence on the assessment of bacterial community structure. On the contrary for F‐ARISA profiles, strong variations were observed between replicates of the smaller samples (
ISSN:1462-2912
1462-2920
DOI:10.1046/j.1462-2920.2003.00521.x