Terrestrial case study
Evaluation of the eDNA method for the detection and
control of invasive exotic plant species
When introduced outside their native range, Invasive Exotic Species (IES) profoundly disrupt ecological balances by spreading persistently and competing with native biodiversity. The management of IES, particularly invasive plant species, has become essential in the context of biodiversity conservation. In a forward-looking and innovative approach, Grenoble Alpes Métropole sought to evaluate a methodology for the early molecular detection of Asteraceae — a family of herbaceous plants, some species of which, such as the lance-leaved aster, are considered invasive — in order to improve the planning of landscape management strategies for biological invasions at the territorial level.
ARGALY's mission:
To test an experimental design based on the eDNA metabarcoding method with the aim of detecting invasive perennial herbaceous species within a natural area of the Grenoble metropolitan region.
Methodology
Hubert Dubedout Park, managed by Grenoble Alpes Métropole, was selected as the study site. Five plots exhibiting varying degrees of infestation and subject to different management treatments were defined as follows:
Soil samples were collected from each plot in biological triplicates across three successive sampling periods: spring 2023 / autumn 2023 / spring 2024. Management interventions on the infested plots were carried out several weeks prior to the second sampling campaign, in order to assess the effect of treatments on the quantity of DNA present in the soil.
The aim of this experimental design was to address the following questions:
Non-infested plot — An area free of any IES, used as a negative control.
Emerging plot — An area with sparse early-stage observations of IES individuals.
Low-infestation plot — An area with a limited number of visible invasive plants.
Infested plot (A) — An area with recurring observations of invasive Asteraceae, subjected to mowing in October 2023.
Infested plot (B) — An area with recurring observations of invasive Asteraceae, subjected to uprooting in October 2023.
Can terrestrial eDNA be used as an early and sensitive biodiagnostic tool for perennial invasive plant species, whose above-ground biomass disappears annually during winter?
Does terrestrial eDNA reveal the effects of different IES management treatments (mowing vs. uprooting), and if so, can it serve as a decision-support tool for landscape management?
Locations of the sampled plots within Hubert Dubedout Park (Grenoble Metropolitan Area) as part of the eDNA analyses for the detection of invasive Asteraceae (left), and photograph of a lance-leaved aster collected following mowing on an infested plot (right).
Following DNA extraction from soil samples, an Asteraceae genetic marker was amplified by PCR (Aste01, Taberlet & al. 2018). Subsequent NGS sequencing and bioinformatic data analysis enabled the identification of a target sequence belonging to the lance-leaved aster (Symphyotrichum lanceolatum).
Molecular detectability of the lance-leaved aster
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The invasive species was detected using the molecular approach in both spring and autumn, across 20 out of 48 collected samples. Visual surveys, by comparison, enabled detection only in autumn, for 8 samples.
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No lance-leaved aster DNA sequences were detected in the non-infested control area, whereas all plots exhibiting varying degrees of infestation tested positive for its molecular presence. Furthermore, eDNA confirmed the presence of the species in 7 out of the 8 samples that were positive upon visual observation in autumn 2023.
These results demonstrate that the eDNA method is reliable, and that the two approaches are complementary. Indeed, since the flowering period of the lance-leaved aster generally extends from late summer through autumn, it is unsurprising that the species was not observed outside of this period. The absence of flowers makes species identification challenging from a taxonomic standpoint, as other morphological characteristics are often insufficient for accurate identification. The species may therefore be present in a vegetative form that precludes visual detection, yet remains detectable through molecular analysis. This finding is particularly promising, as it enables the anticipation of invasive species presence prior to any visible development. It thus becomes possible to make proactive management and treatment decisions for the affected plots, thereby reducing the risk of species expansion and limiting its ecological impact.
Number of sequences (log10)
Seasonal variation in lance-leaved aster sequence counts across sampling plots.
Effect of seasons and treatments on lance-leaved aster detection
The detectability of the aster appears to fluctuate between seasons depending on the plot:
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The effect of management interventions carried out in infested plots on aster eDNA detectability appears to be delayed, as the abundance of plant DNA sequences remains stable throughout 2023, while showing a slight and equivalent decrease for both mowing (A) and uprooting (B) treatments in spring 2024.
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The slight increase in soil DNA sequence counts between spring and autumn 2023 in the emerging and infested (B) plots may be explained by the plant's autumn flowering period. Indeed, when above-ground biomass is fully developed, eDNA is more readily detectable, whereas the biological presence of the species in spring may be more limited, restricting detection to roots and seeds within the soil.
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The eDNA signal indicates the disappearance of the aster in the emerging plot and its growth in the low-infestation plot in spring 2024. Although these two plots are geographically close, potential management interventions or differences in plant development dynamics could account for these observations.
Study Conclusion
The eDNA tool confirms and complements existing distribution data on invasive plant species: perennial invasive species can be detected at an early stage, even in the absence of visible above-ground growth. While molecular sensitivity does not reveal any difference in effectiveness between mowing and uprooting treatments, this preventive approach nonetheless offers a strategic advantage for IES control, by enabling intervention before the species reaches a stage at which eradication becomes more complex and costly.
