Measurement of belowground diversity of fine roots in subtropical forests based on a quantitative real-time PCR (qPCR) method

Zeng, Weixian; Xiang, Wenhua; Zhou, Bo; Zeng, Yelin

doi:10.1007/s11104-017-3402-y

Cited by 8 publications

(6 citation statements)

References 52 publications

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“…In several instances, a greater number of species were detected belowground than aboveground, consistent with previous reports (Pärtel et al 2012). This is likely due to the wide lateral spread of roots, with belowground species occasionally corresponding to trees from outside the plots (Kesanakurti et al 2011, Zeng et al 2017). Furthermore, we likely underestimated aboveground species richness by only including trees with a DBH ≥ 4 cm.…”

Section: Discussionmentioning

confidence: 99%

“…Until recently, the identification of fine roots was a limiting factor in ecological studies since the roots of distinct species closely intermingle and can be difficult to distinguish morphologically (Mommer et al 2010). Molecular methods provide an effective approach to identify roots in diverse plant communities (Jones et al 2011, Hiiesalu et al 2012, Frank et al 2015, Zeng et al 2015, 2017), making it possible to estimate standing root biomass at the species level (Valverde‐Barrantes et al 2015, Oram et al 2018).…”

Section: Introductionmentioning

confidence: 99%

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Positive tree diversity effect on fine root biomass: via density dependence rather than spatial root partitioning

Zeng

Xiang

Zhou

et al. 2020

Oikos

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The importance of species richness to ecosystem functioning and services is a central tenet of biological conservation. However, most of our theory and mechanistic understanding is based on diversity found aboveground. Our study sought to better understand the relationship between diversity and belowground function by studying root biomass across a plant diversity gradient. We collected soil cores from 91 plots with between 1 and 12 aboveground tree species in three natural secondary forests to measure fine root (≤ 2 mm in diameter) biomass. Molecular methods were used to identify the tree species of fine roots and to estimate fine root biomass for each species. This study tested whether the spatial root partitioning (species differ by belowground territory) and symmetric growth (the capacity to colonize nutrient-rich hotspots) underpin the relationship between aboveground species richness and fine root biomass. All species preferred to grow in nutrient-rich areas and symmetric growth could explain the positive relationship between aboveground species richness and fine root biomass. However, symmetric growth only appeared in the nutrient-rich upper soil layer (0-10 cm). Structural equation modelling indicated that aboveground species richness and stand density significantly affected fine root biomass. Specifically, fine root biomass depended on the interaction between aboveground species richness and stand density, with fine root biomass increasing with species richness at lower stand density, but not at higher stand density. Overall, evidence for spatial (i.e. vertical) root partitioning was inconsistent; assumingly any roots growing into deeper unexplored soil layers were not sufficient contributors to the positive diversity-function relationship. Alternatively, density-dependent biotic interactions affecting tree recruitment are an important driver affecting productivity in diverse subtropical forests but the usual root distribution patterns in line with the spatial root partitioning hypothesis are unrealistic in contexts where soil nutrients are heterogeneously distributed.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Positive tree diversity effect on fine root biomass: via density dependence rather than spatial root partitioning

Zeng

Xiang

Zhou

et al. 2020

Oikos

Self Cite

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“…Moreover, these authors found that the DNA detected by the qPCR assays primarily originated from living cells, which overcomes the major difficulty of determining living versus dead root mass by morphological characteristics. Other studies have demonstrated that qPCR can be used to estimate the relative proportion of a given species in mixed fine-root samples from (sub) tropical forest (Zeng et al 2017) and greenhouse experiments (Mommer et al 2008). Our study is the first to utilize qPCR to quantify fine root mass in soils from natural environments, such as forest soils.…”

Section: Discussionmentioning

confidence: 99%

Quantification of tree fine roots by real-time PCR

et al. 2019

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Aims Tree roots contribute large quantities of biomass in forests and are important drivers of different ecosystem processes. However, estimation of root biomass remains a challenge. We have developed a method to quantify fine root biomass of trees, tested on Pinus sylvestris L. and Betula sp. in soils in natural environment, by applying specific qPCR primers to soil DNA extracts. Methods We first validated the molecular probes in the laboratory by constructing regression equations among known root biomass in soil and the number of gene copies obtained by qPCR. Then, to test the applicability of the method in an ecosystem setting and because Pinus and Betula are important components of boreal forests after wildfire, we quantified fine root biomass from these trees in soils from forests with different degrees of tree mortality after wildfire. Results The new primers specifically amplified ITS (Internal Transcribed Spacer) markers from DNA extracted from fine roots of Pinus and Betula, and regression equations allowed us to calculate root biomass in soil from the number of gene copies obtained by qPCR. Root biomass of Pinus correlated positively with fireinduced canopy mortality, confirming the adequacy of the method. The biomass of Betula roots in soil did not differ across the fire severity gradient due to an overall low and stochastic presence of birch, and did not relate to the establishment of new birch seedlings. Conclusions This study shows that DNA-based qPCR methods can be used for rapid, quantitative and speciesspecific analysis of tree root biomass in natural forest ecosystems.

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“…Of the current tools, molecular approaches have been identified as effective and reliable methods to identify roots to species (Rewald et al., ) (Table ). For instance, species‐specific primers that amplify DNA of target species have been used to amplify fragments of distinct sizes characteristic of grassland (McNickle et al., ) and forest plant species (Zeng et al., ). However, creating species‐specific primers may be impractical because sequence information is not readily available for many plant species, primers take time to test and optimize, and there is a limit to how many unique species‐specific size profiles can be created for a DNA region that is only a few hundred base pairs long.…”

Section: Comparison Of Current Molecular Methods Available To Identifmentioning

confidence: 99%

Expanding and testing fluorescent amplified fragment length polymorphisms for identifying roots of boreal forest plant species

2019

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Premise of the Study Identifying roots to species is challenging, but is a common problem in ecology. Fluorescent amplified fragment length polymorphisms ( FAFLP s) can distinguish species within a mixed sample, are high throughput, and are inexpensive. To broaden the use of this tool across ecosystems, unique size profiles must be established for species, and its limits identified. Methods Fragments of three noncoding cp DNA regions were used to create size profiles for 193 species common to the western Canadian boreal forest. We compared detection success among congeners using FAFLP s and Sanger sequencing of the trnL intron. We also simulated and experimentally created communities to test the influence of species richness, cp DNA regions used, and extraction/amplification biases on detection success. Results Of the 193 species, 54% had unique size profiles. This value decreased when fewer cp DNA regions were used. In simulated communities, ambiguous species identifications were positively related to the species richness of the community. In mock communities, some species evaded detection owing to poor extraction or amplification. Sequencing did not increase detection success compared to FAFLP s for a subset of 24 species across nine genera. Discussion We recommend FAFLPs are best suited to confirm rather than discover species occurring belowground.

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Measurement of belowground diversity of fine roots in subtropical forests based on a quantitative real-time PCR (qPCR) method

Cited by 8 publications

References 52 publications

Positive tree diversity effect on fine root biomass: via density dependence rather than spatial root partitioning

Positive tree diversity effect on fine root biomass: via density dependence rather than spatial root partitioning

Quantification of tree fine roots by real-time PCR

Expanding and testing fluorescent amplified fragment length polymorphisms for identifying roots of boreal forest plant species

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