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A molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests
Understanding of belowground interactions among tree species and the fine root (≤2 mm in diameter) contribution of a species to forest ecosystem production are mostly restricted by experimental difficulties in the quantification of the species composition. The available approaches have various defec...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422015/ https://www.ncbi.nlm.nih.gov/pubmed/25999977 http://dx.doi.org/10.3389/fpls.2015.00313 |
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author | Zeng, Weixian Zhou, Bo Lei, Pifeng Zeng, Yeling Liu, Yan Liu, Cong Xiang, Wenhua |
author_facet | Zeng, Weixian Zhou, Bo Lei, Pifeng Zeng, Yeling Liu, Yan Liu, Cong Xiang, Wenhua |
author_sort | Zeng, Weixian |
collection | PubMed |
description | Understanding of belowground interactions among tree species and the fine root (≤2 mm in diameter) contribution of a species to forest ecosystem production are mostly restricted by experimental difficulties in the quantification of the species composition. The available approaches have various defects. By contrast, DNA-based methods can avoid these drawbacks. Quantitative real-time polymerase chain reaction (PCR) is an advanced molecular technology, but it is difficult to develop specific primer sets. The method of next-generation sequencing has several limitations, such as inaccurate sequencing of homopolymer regions, as well as being time-consuming, and requiring special knowledge for data analysis. This study evaluated the potential of the DNA-sequence-based method to identify tree species and to quantify the relative proportion of each species in mixed fine root samples. We discriminated the species by isolating DNA from individual fine roots and amplifying the plastid trnL(UAA; i.e., tRNA-Leu-UAA) intron using the PCR. To estimate relative proportions, we extracted DNA from fine root mixtures. After the plastid trnL(UAA) intron amplification and TA-cloning, we sequenced the positive clones from each mixture. Our results indicated that the plastid trnL(UAA) intron spacer successfully distinguished tree species of fine roots in subtropical forests. In addition, the DNA-sequence-based approach could reliably estimate the relative proportion of each species in mixed fine root samples. To our knowledge, this is the first time that the DNA-sequence-based method has been used to quantify tree species proportions in mixed fine root samples in Chinese subtropical forests. As the cost of DNA-sequencing declines and DNA-sequence-based methods improve, the molecular method will be more widely used to determine fine root species and abundance. |
format | Online Article Text |
id | pubmed-4422015 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-44220152015-05-21 A molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests Zeng, Weixian Zhou, Bo Lei, Pifeng Zeng, Yeling Liu, Yan Liu, Cong Xiang, Wenhua Front Plant Sci Plant Science Understanding of belowground interactions among tree species and the fine root (≤2 mm in diameter) contribution of a species to forest ecosystem production are mostly restricted by experimental difficulties in the quantification of the species composition. The available approaches have various defects. By contrast, DNA-based methods can avoid these drawbacks. Quantitative real-time polymerase chain reaction (PCR) is an advanced molecular technology, but it is difficult to develop specific primer sets. The method of next-generation sequencing has several limitations, such as inaccurate sequencing of homopolymer regions, as well as being time-consuming, and requiring special knowledge for data analysis. This study evaluated the potential of the DNA-sequence-based method to identify tree species and to quantify the relative proportion of each species in mixed fine root samples. We discriminated the species by isolating DNA from individual fine roots and amplifying the plastid trnL(UAA; i.e., tRNA-Leu-UAA) intron using the PCR. To estimate relative proportions, we extracted DNA from fine root mixtures. After the plastid trnL(UAA) intron amplification and TA-cloning, we sequenced the positive clones from each mixture. Our results indicated that the plastid trnL(UAA) intron spacer successfully distinguished tree species of fine roots in subtropical forests. In addition, the DNA-sequence-based approach could reliably estimate the relative proportion of each species in mixed fine root samples. To our knowledge, this is the first time that the DNA-sequence-based method has been used to quantify tree species proportions in mixed fine root samples in Chinese subtropical forests. As the cost of DNA-sequencing declines and DNA-sequence-based methods improve, the molecular method will be more widely used to determine fine root species and abundance. Frontiers Media S.A. 2015-05-06 /pmc/articles/PMC4422015/ /pubmed/25999977 http://dx.doi.org/10.3389/fpls.2015.00313 Text en Copyright © 2015 Zeng, Zhou, Lei, Zeng, Liu, Liu and Xiang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Zeng, Weixian Zhou, Bo Lei, Pifeng Zeng, Yeling Liu, Yan Liu, Cong Xiang, Wenhua A molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests |
title | A molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests |
title_full | A molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests |
title_fullStr | A molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests |
title_full_unstemmed | A molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests |
title_short | A molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests |
title_sort | molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422015/ https://www.ncbi.nlm.nih.gov/pubmed/25999977 http://dx.doi.org/10.3389/fpls.2015.00313 |
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