Plant species richness belowground: higher richness and new patterns revealed by next‐generation sequencing

Hiiesalu, Inga; Öpik, Maarja; Metsis, Madis; Lilje, Liisa; Davison, John; Vasar, Martti; Moora, Mari; Zobel, Martin; Wilson, Scott D.; Pärtel, Meelis

doi:10.1111/j.1365-294x.2011.05390.x

Cited by 111 publications

(166 citation statements)

References 72 publications

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“…Hausmann and Hawkes 2010; Jordan et al 2012). Natural grassland soils are, however, a diverse mixture of the roots of many species (Hiiesalu et al 2012). Therefore, the findings from simple pot or field experiments may not be neatly extended to natural grasslands.…”

Section: Discussionmentioning

confidence: 99%

More closely related plants have more distinct mycorrhizal communities

Reinhart¹,

Anacker²

2014

AoB PLANTS

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We observed that mycorrhizal communities were more divergent among closely related plant species than among distantly related plant species. This was counter to the observation that plant mutualists (e.g. pollinators, seed dispersers) are often shared among closely related host plant species. Since mycorrhizae may affect nutrient competition among neighboring plants, closely related plant neighbors that associate with unique mycorrhizae may have greater functional complementarity and a greater capacity to coexist.

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Section: Discussionmentioning

confidence: 99%

More closely related plants have more distinct mycorrhizal communities

Reinhart¹,

Anacker²

2014

AoB PLANTS

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“…We acknowledge that eDNA-based diversity is expected to slightly diverge from observed diversity (see discussion) but they should follow similar trends(Hiiesalu et al, 2012;Träger, Öpik, Vasar, & Wilson, 2019;Yoccoz et al, 2012). We acknowledge that eDNA-based diversity is expected to slightly diverge from observed diversity (see discussion) but they should follow similar trends(Hiiesalu et al, 2012;Träger, Öpik, Vasar, & Wilson, 2019;Yoccoz et al, 2012).…”

mentioning

confidence: 80%

“…The intrinsic properties of eDNA can inflate the diversity compared to traditional surveys because eDNA can persist in the environment or be transported through space depending on the abiotic conditions (e.g. This means that the diversity eDNA estimates not only encompass local and current species, but also species that are dormant (Hiiesalu et al, 2012), that were present in the recent past (Yoccoz et al, 2012) or that are present in the vicinity of the studied area (Taberlet et al, 2018). This means that the diversity eDNA estimates not only encompass local and current species, but also species that are dormant (Hiiesalu et al, 2012), that were present in the recent past (Yoccoz et al, 2012) or that are present in the vicinity of the studied area (Taberlet et al, 2018).…”

Section: Linking Methodsological Choices With Ecological Questionsmentioning

confidence: 99%

From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices?

Calderón‐Sanou

Münkemüller

Boyer

et al. 2019

Journal of Biogeography

114

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Aim Environmental DNA (eDNA) is increasingly used for analysing and modelling all‐inclusive biodiversity patterns. However, the reliability of eDNA‐based diversity estimates is commonly compromised by arbitrary decisions for curating the data from molecular artefacts. Here, we test the sensitivity of common ecological analyses to these curation steps, and identify the crucial ones to draw sound ecological conclusions. Location Valloire, French Alps. Taxon Vascular plants and fungi. Methods Using soil eDNA metabarcoding data for plants and fungi from 20 plots sampled along a 1000‐m elevational gradient, we tested how the conclusions from three types of ecological analyses: (a) the spatial partitioning of diversity, (b) the diversity–environment relationship, and (c) the distance–decay relationship, are robust to data curation steps. Since eDNA metabarcoding data also comprise erroneous sequences with low frequencies, diversity estimates were further calculated using abundance‐based Hill numbers, which penalize rare sequences through a scaling parameter, namely the order of diversity q (Richness with q = 0, Shannon diversity with q ~ 1, Simpson diversity with q = 2). Results We showed that results from different ecological analyses had varying degrees of sensitivity to data curation strategies and that the use of Shannon and Simpson diversities led to more reliable results. We demonstrated that molecular operational taxonomic unit clustering, removal of polymerase chain reaction errors and of cross‐sample contaminations had major impacts on ecological analyses. Main conclusions In the Era of Big Data, eDNA metabarcoding is going to be one of the major tools to describe, model and predict biodiversity in space and time. However, ignoring crucial data curation steps will impede the robustness of several ecological conclusions. Here, we propose a roadmap of crucial curation steps for different types of ecological analyses.

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“…The diversity, interactions and distribution of roots (Hiiesalu et al. ) and dormant, perennating organs (Wilson & Tilman ) regulate species co‐existence, diversity and structure in above‐ground communities (Wilson ). Our ecological understanding of how plant communities respond to environmental variation, however, is restricted to interpretations of above‐ground community patterns.…”

Section: Introductionmentioning

confidence: 99%

Where does the community start, and where does it end? Including the seed bank to reassess forest herb layer responses to the environment

Plue

Frenne

Acharya

et al. 2017

J Vegetation Science

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Question Below‐ground processes are key determinants of above‐ground plant population and community dynamics. Still, our understanding of how environmental drivers shape plant communities is mostly based on above‐ground diversity patterns, bypassing below‐ground plant diversity stored in seed banks. As seed banks may shape above‐ground plant communities, we question whether concurrently analysing the above‐ and below‐ground species assemblages may potentially enhance our understanding of community responses to environmental variation. Location Temperate deciduous forests along a 2000 km latitudinal gradient in NW Europe. Methods Herb layer, seed bank and local environmental data including soil pH, canopy cover, forest cover continuity and time since last canopy disturbance were collected in 129 temperate deciduous forest plots. We quantified herb layer and seed bank diversity per plot and evaluated how environmental variation structured community diversity in the herb layer, seed bank and the combined herb layer–seed bank community. Results Seed banks consistently held more plant species than the herb layer. How local plot diversity was partitioned across the herb layer and seed bank was mediated by environmental variation in drivers serving as proxies of light availability. The herb layer and seed bank contained an ever smaller and ever larger share of local diversity, respectively, as both canopy cover and time since last canopy disturbance decreased. Species richness and β‐diversity of the combined herb layer–seed bank community responded distinctly differently compared to the separate assemblages in response to environmental variation in, e.g. forest cover continuity and canopy cover. Conclusions The seed bank is a below‐ground diversity reservoir of the herbaceous forest community, which interacts with the herb layer, although constrained by environmental variation in e.g. light availability. The herb layer and seed bank co‐exist as a single community by means of the so‐called storage effect, resulting in distinct responses to environmental variation not necessarily recorded in the individual herb layer or seed bank assemblages. Thus, concurrently analysing above‐ and below‐ground diversity will improve our ecological understanding of how understorey plant communities respond to environmental variation.

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Plant species richness belowground: higher richness and new patterns revealed by next‐generation sequencing

Cited by 111 publications

References 72 publications

More closely related plants have more distinct mycorrhizal communities

More closely related plants have more distinct mycorrhizal communities

From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices?

Where does the community start, and where does it end? Including the seed bank to reassess forest herb layer responses to the environment

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