Development of species-specific environmental DNA (eDNA) markers for invasive aquatic plants

Scriver, Michelle; Marinich, Allison; Wilson, Chris C.; Freeland, Joanna R.

doi:10.1016/j.aquabot.2015.01.003

Cited by 71 publications

(55 citation statements)

References 24 publications

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“…We had to design primer sets that could discriminate E. densa from E. nuttallii because these species co-occur in Japan. Primer sets for E. densa were reported by Scriver et al (2015), but the reported primer set targeted the matK region, which is a conserved gene among plant species and has few variations among related species (Tanaka et al 1997). DNA sequences of matK for E. densa and E. nuttallii showed 99% identity.…”

Section: Discussionmentioning

confidence: 99%

“…eDNA detection has been reported for a number of aquatic species, including fish (Jerde et al 2011, 2016, Maruyama et al 2014, Doi et al 2015a, b, Miya et al 2015, Sigsgaard et al 2015, amphibians (Ficetola et al 2008, Goldberg et al 2011, Olson et al 2012, Pilliod et al 2013, Biggs et al 2015, Fukumoto et al 2015, mammals (Foote et al 2012, and invertebrates (Thomsen et al 2012, Deiner and Altermatt 2014, Treguier et al 2014, Deiner et al 2015. However, the detection of eDNA from aquatic plants has been attempted only in aquarium experiments (Scriver et al 2015) and has not been reported from field studies. A field eDNA survey would be a particularly useful technique for invasive submerged plants because such species are difficult to distinguish by visual observation from the shore (Haga and Ishikawa 2014).…”

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confidence: 99%

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Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds

et al. 2016

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The first step toward solving the problems caused by an invasive alien species is to know the distribution of the species. However, species in underwater environments are difficult to investigate. The recent development of environmental DNA (eDNA) analysis has made it possible to investigate the distribution of a target species simply by analyzing the DNA in the water. To date, few investigators have used eDNA detection of aquatic plants. We established an eDNA detection method for Egeria densa, an invasive aquatic plant species in Japan; used eDNA detection to survey the species in aquaria; and applied this method to water samples from 23 outdoor ponds. We also used visual observations of the ponds. The aquarium experiments revealed that the eDNA concentration in the water increased rapidly and peaked 1 or 2 d after starting the experiment, after which it decreased rapidly, reaching its lowest point on the 5 th day. In the field surveys, we visually observed E. densa at 5 ponds, and the eDNA of E. densa was detected from the same 5 ponds. Thus, the eDNA results perfectly matched the observational results. Our work confirms that detection of aquatic plants by eDNA analysis is feasible.

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Section: Discussionmentioning

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Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds

et al. 2016

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“…eDNA has proved useful for the detection of aquatic invertebrates (Deiner, Fronhofer, Mächler, Walser, & Altermatt, 2016;Mächler, Deiner, Steinmann, & Altermatt, 2014) and vertebrates (Piaggio et al, 2014;Sigsgaard et al, 2016;Takahara et al, 2013), but the information on the aquatic plants and algae is still limited. Only a few studies have addressed the detectability of aquatic plants or algae with eDNA (Fujiwara, Matsuhashi, Doi, Yamamoto, & Minamoto, 2016;Keller, Hilderbrand, Shank, & Potapova, 2017;Scriver, Marinich, Wilson, & Freeland, 2015;Zimmermann, Glöckner, Jahn, Enke, & Gemeinholzer, 2015), due to the limited availability of reference databases (Cristescu, 2014) and the lineage-specific barcodes (Zanolla & Andreakis, 2016). To be useful for detecting seaweed, eDNA barcodes need to be specific (Verbruggen et al, 2010) and have a suitable resolution across multiple regions (Zanolla & Andreakis, 2016) within the suspected introduced range of targeted taxa (Geller, Darling, & Carlton, 2010).…”

Section: Introductionmentioning

confidence: 99%

Contrasting seasonal and spatial distribution of native and invasive Codium seaweed revealed by targeting species‐specific eDNA

Muha

Skukan

Borrell

et al. 2019

Ecology and Evolution

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Aim Codium fragile , an invasive seaweed, has spread widely during the last century, impacting on local seaweed communities through competition and disturbance. Early detection of C. fragile can help on its control and management. Environmental DNA (eDNA) has proved successful for early detection of aquatic invasive species but its potential use for seaweed remains understudied. We used a species‐specific eDNA qPCR approach to investigate the spatial distribution, abundance, and coexistence of the invasive C. fragile and three native Codium species ( Codium vermilara , Codium tomentosum , and Codium decorticatum ) in the Cantabrian Sea. Location Bay of Biscay, Northern Atlantic Coast of the Iberian Peninsula; two ports, a beach and a rocky cliff. Methods We designed species‐specific primers in barcoding regions targeting short fragments of the rbcL gene for the invasive Codium species, and the elongation factor Tu (tufA) gene for the native species, to assess their spatial and seasonal distributions using quantitative real‐time PCR in samples collected during summer, autumn, and winter. Results We found seasonal differences in the presence of the invasive Codium fragile and two of the native Codium species, but did not detect C. decorticatum at any point. Species distribution patterns produced with qPCR targeting species‐specific eDNA coincided with the known distribution based on previous conventional sampling, with a seasonal alternance of C. fragile and C. vermilara , and a marked dominance of invasive C. fragile in ports, which are known hotspots for invasive species. Main conclusions Our results demonstrate the utility of using eDNA for early detection and monitoring of invasive seaweed. Native and invasive Codium spp. displayed significant seasonal and spatial differentiation that needs to be taken into account in risk management. Regular monitoring of ports and adjacent areas using eDNA should help to assess the potential expansion of invasive Codium and the need for management interventions to avoid the displacement of native seaweed.

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“…To date, it has primarily focused on the surveillance of animal species, such as freshwater fish and amphibians that are invasive, rare, or difficult to monitor (Dejean et al, 2012;Sigsgaard et al, 2015;Biggs et al, 2015). The detection of plant eDNA in aquatic and soil habitats is understudied (Scriver et al, 2015;Fahner et al, 2016).…”

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confidence: 99%

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

2018

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Premise of the StudyThe detection of environmental DNA (eDNA) using high‐throughput sequencing has rapidly emerged as a method to detect organisms from environmental samples. However, eDNA studies of aquatic biomes have focused on surveillance of animal species with less emphasis on plants. Pondweeds are important bioindicators of freshwater ecosystems, although their diversity is underestimated due to difficulties in morphological identification and monitoring.MethodsA protocol was developed to detect pondweeds in water samples using atpB‐rbcL and ITS2 markers. The water samples were collected from the Grand River within the rare Charitable Research Reserve, Ontario (RARE). Short fragments were amplified using primers targeting pondweeds, sequenced on an Ion Torrent Personal Genome Machine, and assigned to the taxonomy using a local DNA reference library and GenBank.ResultsWe detected two species earlier documented at the experimental site during ecological surveys (Potamogeton crispus and Stuckenia pectinata) and three species new to the RARE checklist (P. foliosus, S. filiformis, and Zannichellia palustris).DiscussionOur targeted approach to track the species composition of pondweeds in freshwater ecosystems revealed underestimation of their diversity. This result suggests that eDNA is an effective tool for monitoring plant diversity in aquatic habitats.

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Development of species-specific environmental DNA (eDNA) markers for invasive aquatic plants

Cited by 71 publications

References 24 publications

Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds

Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds

Contrasting seasonal and spatial distribution of native and invasive Codium seaweed revealed by targeting species‐specific eDNA

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

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