Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis

PeerJ
Xiao-Xiao SunLi-Li Geng

Abstract

The interactions between rhizosphere microorganisms and plants are important for the health and development of crops. Analysis of plant rhizosphere bacterial compositions, particularly of those with resistance to biotic/abiotic stresses, may improve their applications in sustainable agriculture. Large-scale rhizosphere samplings in the field are usually required; however, such samples, cannot be immediately frozen. We found that the storage of samples at room temperature for 2 days leads to a considerable reduction in the operational taxonomic unit (OTU) number and the indices of bacterial alpha-diversity of rhizosphere communities. In this study, in order to overcome these problems, we established a method using guanidine thiocyanate (GTC) solution for the preservation of rhizosphere samples after their collection. This method allowed the maintenance of the samples for at least 1 day at room temperature prior to their cryopreservation and was shown to be compatible with conventional DNA isolation protocols. Illumina sequencing of V3 and V4 hypervariable regions of the 16S rRNA gene was used to assess the feasibility and reliability of this method, and no significant differences were observed in the number of OTUs and in the Ch...Continue Reading

References

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Datasets Mentioned

BETA
SRP134256

Methods Mentioned

BETA
electrophoresis
Illumina sequencing

Software Mentioned

Greengenes
SPSS Statistics
USEARCH
SPSS
UCHIME
R
Trimmomatic

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