Effect of preservation method on the assessment of bacterial community structure in soil and water samples.
The methods used in sample preservation may affect the description of the microbial community structure by DNA-based techniques. This study aims at evaluating the effect of different storage conditions, including freezing, adding two liquid-based preservatives or simply storing samples with no preservative, on the structure of the microbial communities in aliquots of organic-rich soil and water samples as revealed by a terminal restriction fragment length polymorphisms. The results showed that the number of terminal restriction fragments (TRFs) detected in soil aliquots stored with LifeGuard(™) solution was significantly lower than that of samples analyzed immediately after sampling. Moreover, cluster and PCA analyses showed that soil aliquots stored using LifeGuard(™) clustered separately from those stored with the other methods. Conversely, soil and water aliquots stored with DMSO-EDTA-salt solution did not show either significant reduction in the number of TRFs or any change in the structure of the microbial community. Finally, the number of TRFs and the structure of microbial communities from soil aliquots stored with no preservative did not differ from those of aliquots analyzed immediately after sampling. Preservation methods should therefore be accurately evaluated before collecting samples that have to be stored for long time before DNA extraction.
Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy.
Valeria
V
Tatangelo
Andrea
A
Franzetti
Isabella
I
Gandolfi
Giuseppina
G
Bestetti
Roberto
R
Ambrosini
D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D064307:Microbiota; D015999:Multivariate Analysis; D012150:Polymorphism, Restriction Fragment Length; D011309:Preservation, Biological / Q000379:methods; D025341:Principal Component Analysis; D012988:Soil Microbiology; D014871:Water Microbiology
D004269:DNA, Bacterial
DNA extraction; microbial community storage conditions; terminal restriction fragment length polymorphisms