Finding the pond through the weeds: <scp>eDNA</scp> reveals underestimated diversity of pondweeds

Kuzmina, Maria L.; Braukmann, Thomas; Zakharov, Evgeny

doi:10.1002/aps3.1155

Cited by 24 publications

(31 citation statements)

References 42 publications

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“…So far, most eDNA studies have focused on monitoring animal species, and only recently has this powerful method been applied to tracking aquatic plants. Typically, the eDNA is further analysed either by using species specific qPCR or traditional barcoding applied to water [31] for tracking invading or threatened species, or using metabarcoding for water [62] or soil samples [63] for global ecosystem biodiversity monitoring. In this study we have developed a specific probe assay for eDNA detection of the aquatic plant E .…”

Section: Discussionmentioning

confidence: 99%

“…Another study successfully tested eDNA detection of H . verticillata in north American rivers and lakes [34] and three studies detected eDNA where the species had not yet been observed [31, 34, 35]. Several laboratory mesocosm experiments have tested the changes in aquatic plant eDNA over time, during and after introduction, and with and without grazers [32–34].…”

Section: Introductionmentioning

confidence: 99%

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Detection of an invasive aquatic plant in natural water bodies using environmental DNA

et al. 2019

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The ability to detect founding populations of invasive species or rare species with low number of individuals is important for aquatic ecosystem management. Traditional approaches use historical data, knowledge of the species’ ecology and time-consuming surveys. Within the past decade, environmental DNA (eDNA) has emerged as a powerful additional tracking tool. While much work has been done with animals, comparatively very little has been done with aquatic plants. Here we investigated the transportation and seasonal changes in eDNA concentrations for an invasive aquatic species, Elodea canadensis , in Norway. A specific probe assay was developed using chloroplast DNA to study the fate of the targeted eDNA through space and time. The spatial study used a known source of Elodea canadensis within Lake Nordbytjern 400 m away from the lake outlet flowing into the stream Tveia. The rate of disappearance of E . canadensis eDNA was an order of magnitude loss over about 230 m in the lake and 1550 m in the stream. The time series study was performed monthly from May to October in lake Steinsfjorden harbouring E . canadensis , showing that eDNA concentrations varied by up to three orders of magnitude, peaking during fall. In both studies, the presence of suspended clay or turbidity for some samples did not hamper eDNA analysis. This study shows how efficient eDNA tools may be for tracking aquatic plants in the environment and provides key spatial and temporal information on the fate of eDNA.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Detection of an invasive aquatic plant in natural water bodies using environmental DNA

et al. 2019

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“…In general, assays can target one or a small number of target species using taxon‐specific primers and PCR, or can simultaneously characterize multiple species by generating metabarcodes. eDNA assays of aquatic vascular plants from water samples have so far been based exclusively on the former approach (Gantz, Renshaw, Erickson, Lodge, & Egan, 2018; Kuzmina, Braukmann, & Zakharov, 2018; Matsuhashi, Doi, Fujiwara, Watanabe, & Minamoto, 2016; Scriver, Marinich, Wilson, & Freeland, 2015). Although metabarcoding has been used to characterize terrestrial plant communities (Bell et al., 2016; Fahner, Shokralla, Baird, & Hajibabaei, 2016; Hawkins et al., 2015), it has not yet been applied to aquatic plant communities despite its potential as an effective approach for describing plant communities that may include alien species and species at risk.…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, no single marker has revealed a barcoding gap, in which interspecific sequence divergence consistently exceeds intraspecific sequence divergence, across all plant taxonomic comparisons. ITS might be more likely to show a gap than the commonly used plastid markers (Gill et al., 2019; Kuzmina et al., 2018), although this can be influenced by factors such as the relatedness of the taxa being compared (Gill et al., 2019) and the biogeographic region under consideration (Mosa et al., 2019). There is a clear lack of consensus on the most useful markers for plant barcoding and metabarcoding.…”

Section: Introductionmentioning

confidence: 99%

Development of an environmental DNA metabarcoding assay for aquatic vascular plant communities

2020

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Environmental DNA (eDNA) metabarcodes allow for the simultaneous detection of multiple taxa if the barcode regions meet several key requirements including conserved primer‐binding sites, interspecific variability that exceeds intraspecific variability, and relatively short amplicons. Currently, there are no established metabarcoding assays for aquatic vascular plants, which could limit biodiversity assessments and the early detection of alien species. We used a combination of novel and pre‐existing primers to generate eDNA metabarcodes from three gene regions that are commonly used for plant barcoding: two regions of chloroplast DNA (rbcL and matK) plus a segment of an internal transcribed spacer (ITS2). We optimized the assay on a mock community of 25 known species and then applied it to wild samples collected from two waterbodies in southern Ontario, Canada (Black River and Seymour Lake). Our novel rbcL primers, which amplify a fragment of ~220 bp, provided the most comprehensive description of the mock community, identifying all but one of the taxa to species or genus. In addition, after pooling data from five sites within each sampled waterbody, metabarcodes generated by this same primer pair identified more taxa than all other primer pairs; more specifically, 20 and 26 taxa were identified from Black River and Seymour Lake, respectively, to species or genus. Across the two sites, nine of the identified taxa are alien invasive aquatic plants. Five of these invasive species have no previous reports from our sites, and in some cases have no known established Ontario populations; our data therefore suggest an urgent need to increase surveillance for these aliens. Overall, our study showed that eDNA metabarcoding with a novel rbcL primer pair provides a cost‐effective method for simultaneously detecting multiple aquatic vascular plant taxa and is a valuable tool for the early detection of invasive species.

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“…Similar problems were found by Andújar et al (2018) and for macroinvertebrates. Incomplete reference databases have also been reported by several authors for different biotic groups, such as littoral hard bottom communities (Wangensteen et al 2018), macrophytes (Kuzmina et al 2018) and ichthyoplankton (Hubert et al 2015). In our work, we likely deflated the rate of families detected by metabarcoding because we did not trust hits below 90% similarity, a very conservative approach in terms of assignment.…”

Section: Comparison Between Morphology and Metabarcodingmentioning

confidence: 96%

Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams

Laini¹,

Beermann²,

Bolpagni³

et al. 2020

MBMG

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Taxonomic sufficiency represents the level of taxonomic detail needed to detect ecological patterns to a level that match the requirement of a study. Most bioassessments apply the taxonomic sufficiency concept and assign specimens to the family or genus level given time constraints and the difficulty to correctly identify species. This holds particularly true for stream invertebrates because small and morphologically similar larvae are hard to distinguish. Low taxonomic resolution may hinder detecting true community dynamics, which thus leads to incorrect inferences about community assembly processes. DNA metabarcoding is a new, affordable and cost-effective tool for the identification of multiple species from bulk samples of organisms. As it provides high taxonomic resolution, it can be used to compare results obtained from different identification levels. Measuring the effect of taxonomic resolution on the detection of community dynamics is especially interesting in extreme ecosystems like intermittent streams to test if species at intermittent sites are subsets of those from perennial sources or if independently recruiting taxa exist. Here we aimed to compare the performance of morphological identification and metabarcoding to detect macroinvertebrate community dynamics in the Trebbia River (Italy). Macroinvertebrates were collected from four perennial and two intermittent sites two months after flow resumption and before the next dry phase. The identification level ranged from family to haplotype. Metabarcoding and morphological identifications found similar alpha diversity patterns when looking at family and mixed taxonomic levels. Increasing taxonomic resolution with metabarcoding revealed a strong partitioning of beta diversity in nestedness and turnover components. At flow resumption, beta diversity at intermittent sites was dominated by nestedness when family-level information was employed, while turnover was evidenced as the most important component when using Operational Taxonomic Units (OTUs) or haplotypes. The increased taxonomic resolution with metabarcoding allowed us to detect species adapted to deal with intermittency, like the chironomid Cricotopus bicinctus and the ephemeropteran Cloeon dipterum. Our study thus shows that family and mixed taxonomic level are not sufficient to detect all aspects of macroinvertebrate community dynamics. High taxonomic resolution is especially important for intermittent streams where accurate information about species-specific habitat preference is needed to interpret diversity patterns induced by drying and the nestedness/turnover components of beta diversity are of interest to understand community assembly processes.

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Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds

Cited by 24 publications

References 42 publications

Detection of an invasive aquatic plant in natural water bodies using environmental DNA

Detection of an invasive aquatic plant in natural water bodies using environmental DNA

Development of an environmental DNA metabarcoding assay for aquatic vascular plant communities

Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams

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