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Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis

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. Lar...

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Autores principales: Sun, Xiaoxiao, Wang, Meiling, Guo, Lin, Shu, Changlong, Zhang, Jie, Geng, Lili
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385689/
https://www.ncbi.nlm.nih.gov/pubmed/30809445
http://dx.doi.org/10.7717/peerj.6440
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author Sun, Xiaoxiao
Wang, Meiling
Guo, Lin
Shu, Changlong
Zhang, Jie
Geng, Lili
author_facet Sun, Xiaoxiao
Wang, Meiling
Guo, Lin
Shu, Changlong
Zhang, Jie
Geng, Lili
author_sort Sun, Xiaoxiao
collection PubMed
description 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 Chao and Shannon indices between samples stored at −70 °C and those stored in GTC solution. Moreover, the representation of Pseudomonas spp. in samples stored in GTC solution was not significantly different from that in samples stored at −70 °C, as determined by real-time quantitative polymerase chain reaction (p > 0.05). Both types of samples were shown to cluster together according to principal coordinate analysis. Furthermore, GTC solution did not affect the bacterial taxon profiles at different storage periods compared with those observed when storing the samples below −70 °C. Even incubation of thawed samples (frozen at −70 °C) for 15 min at room temperature induced minor changes in the bacterial composition. Taken together, our results demonstrated that GTC solution may provide a reliable alternative for the preservation of rhizosphere samples in the field.
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spelling pubmed-63856892019-02-26 Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis Sun, Xiaoxiao Wang, Meiling Guo, Lin Shu, Changlong Zhang, Jie Geng, Lili PeerJ Agricultural Science 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 Chao and Shannon indices between samples stored at −70 °C and those stored in GTC solution. Moreover, the representation of Pseudomonas spp. in samples stored in GTC solution was not significantly different from that in samples stored at −70 °C, as determined by real-time quantitative polymerase chain reaction (p > 0.05). Both types of samples were shown to cluster together according to principal coordinate analysis. Furthermore, GTC solution did not affect the bacterial taxon profiles at different storage periods compared with those observed when storing the samples below −70 °C. Even incubation of thawed samples (frozen at −70 °C) for 15 min at room temperature induced minor changes in the bacterial composition. Taken together, our results demonstrated that GTC solution may provide a reliable alternative for the preservation of rhizosphere samples in the field. PeerJ Inc. 2019-02-19 /pmc/articles/PMC6385689/ /pubmed/30809445 http://dx.doi.org/10.7717/peerj.6440 Text en © 2019 Sun et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Agricultural Science
Sun, Xiaoxiao
Wang, Meiling
Guo, Lin
Shu, Changlong
Zhang, Jie
Geng, Lili
Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis
title Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis
title_full Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis
title_fullStr Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis
title_full_unstemmed Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis
title_short Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis
title_sort guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis
topic Agricultural Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385689/
https://www.ncbi.nlm.nih.gov/pubmed/30809445
http://dx.doi.org/10.7717/peerj.6440
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