Environmental DNA (eDNA): A tool for quantifying the abundant but elusive round goby (Neogobius melanostomus)

Nevers, Meredith B.; Byappanahalli, Muruleedhara N.; Morris, Charles; Shively, Dawn A.; Przybyla‐Kelly, Katarzyna; Spoljaric, Ashley M.; Dickey, Joshua; Roseman, Edward F.

doi:10.1371/journal.pone.0191720

Cited by 80 publications

(78 citation statements)

References 56 publications

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“…At one end of the analytical spectrum is quantitative PCR (qPCR), a highly precise and sensitive way to monitor template eDNA abundance in real‐time PCR reactions (Murray, Coghlan, & Bunce, ; Taberlet et al, ). qPCR has become the standard for detection of rare species (Lacoursière‐Roussel et al, ; Nevers et al, ; Wilcox et al, ), and can provide information about species abundances based on eDNA biomass (Tillotson et al, ; Yamamoto et al, ). However, qPCR is limited in that fewer species can be studied at a time with species‐specific primers, making community‐wide abundance data more technically challenging, costly, and time consuming to ascertain (Harper et al, ).…”

Section: Introductionmentioning

confidence: 99%

Rapid assessment of coral cover from environmental DNA in Hawai'i

Nichols

Marko²

2019

Environmental DNA

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Coral reefs support the most diverse assemblages of marine life on Earth, yet are declining due to local and global stressors. Rapid and widespread monitoring is essential for tracking ecosystem responses, but assessment of coral communities traditionally relies on time‐consuming visual estimates of coral cover, the percentage of substrate occupied by living corals. The analysis of environmental DNA (eDNA) offers fast and efficient insights into the abundance and distribution of species, yet it remains untested to monitor coral biomass. Here, we demonstrate that visual estimates are highly correlated with the abundance of coral eDNA on reefs in Hawai'i measured with a relatively simple, rapid, but replicated PCR‐based metabarcoding approach. Target sequence length was also tested by amplifying short (~120 base‐pairs) and long (~400 base‐pairs) fragments from the same region of two mitochondrial DNA genes, 16S ribosomal DNA, and cytochrome oxidase‐1 using primers designed to preferentially amplify Hawaiian coral genera. Careful primer selection and target sequence lengths play an important role in determination of coral abundance from eDNA biomass. Given its broad applicability and ease of use, eDNA metabarcoding can provide complementary analytical support for biomonitoring programs and management initiatives tracking changes in coral cover caused by climate change and other disturbances on coral reefs.

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Section: Introductionmentioning

confidence: 99%

Rapid assessment of coral cover from environmental DNA in Hawai'i

Nichols

Marko²

2019

Environmental DNA

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“…Initial aquatic eDNA research was limited to determining the presence or absence of a species in freshwater ecosystems (Dejean et al, 2012;Ficetola et al, 2008;Jerde et al, 2011). Subsequently, many applications have started to emerge, including the use of eDNA to determine species abundance (Pilliod et al, 2013;Thomsen et al, 2016), biomass (Jane et al, 2015;Nevers et al, 2018;Takahara, Minamoto, Yamanaka, Doi, & Kawabata, 2012), and population structure Parsons, Everett, Dahlheim, & Park, 2018). Additionally, eDNA research has developed into sampling in the more challenging marine environment (Baker et al, 2018;Bakker et al, 2017;Foote et al, 2012;Minamoto et al, 2017;Parsons et al, 2018;Sigsgaard et al, 2016;Thomsen, Kielgast, Iversen, Møller et al, 2012;Thomsen et al, 2016;Thomsen & Willerslev, 2015).…”

Section: Introductionmentioning

confidence: 99%

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

et al. 2019

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While environmental DNA (eDNA) is becoming increasingly established in biodiversity monitoring of freshwater ecosystems, the use of eDNA surveys in the marine environment is still in its infancy. Here, we use two approaches: targeted quantitative PCR (qPCR) and whole-genome enrichment capture followed by shotgun sequencing in an effort to amplify killer whale DNA from seawater samples. Samples were collected in close proximity to killer whales in inshore and offshore waters, in varying sea conditions and from the surface and subsurface but none returned strongly positive detections of killer whale eDNA. We validated our laboratory methodologies by successfully amplifying a dilution series of a positive control of killer whale DNA. Furthermore, DNA of Atlantic mackerel, which was present at all sites during sampling, was successfully amplified from the same seawater samples, with positive detections found in ten of the eighteen eDNA extracts. We discuss the various eDNA collection and amplification methodologies used and the abiotic and biotic factors that influence eDNA detection. We discuss possible explanations for the lack of positive killer whale detections, potential pitfalls, and the apparent limitations of eDNA for genetic research on cetaceans, particularly in offshore regions. K E Y W O R D S eDNA, environmental DNA, metagenomics, Orcinus orca, PCR, Scomber scombrus, wholegenome enrichment | 317 PINFIELD Et aL. S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section at the end of the article. How to cite this article: Pinfield R, Dillane E, Runge AKW, et al. False-negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca).

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“…Despite this, degree of correlation between eDNA concentration and abundance demonstrated in the field is variable between studies. A recent study of a stream‐dwelling char demonstrated a high correlation (Wilcox et al, ), but other studies reported marginally significant correlations or secondary contribution of abundance to eDNA amount (Doi et al, ; Erickson et al, ; Lacoursière‐Roussel, Côté, Leclerc, & Bernatchez, ; Klobucar, Rodgers, & Budy, ; Nevers et al, ; Pilliod, Goldberg, Arkle, Waits, & Richardson, ; Thomsen et al, ; Yamamoto et al, ). In some studies, eDNA concentration did not correlate with the biomass of the target animals (Biggs et al, ; Spear, Groves, Williams, & Waits, ).…”

Section: Introductionmentioning

confidence: 99%

Environmental DNA analysis as a non‐invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers

Maruyama

Sugatani

Watanabe

et al. 2018

Ecology and Evolution

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Quantitative information regarding reproduction is essential for conserving endangered animals; however, some conventional quantitative methods can be damaging to the target population and their habitats. In the present study, the reproductive migration of a threatened endemic fish, three‐lips (Opsariichthys uncirostris uncirostris), was non‐invasively monitored by quantitative PCR of species‐specific environmental DNA (eDNA), the usefulness of which has been not sufficiently explored. Water sampling and from‐shore visual inspection were performed weekly along a tributary of Lake Biwa (Japan), where adult fish seasonally migrate upstream to reproduce as well as at lake sites near the river mouth. Species‐specific eDNA was collected at all locations at times when the fish were visually observed and at certain sites where the fish were not observed. Log‐transformed individual counts from visual inspection were positively correlated with log‐transformed eDNA concentration in the river sites, indicating that eDNA analysis can be a reliable quantitative tool for fish abundance in rivers. Furthermore, distance from the lake did not influence eDNA concentration, suggesting that eDNA transport by river flow had a negligible effect on eDNA quantification. Both eDNA concentration and individual counts gradually increased from May–July, and decreased in August. Importantly, eDNA analysis showed that the fish occupied more habitats in the peak reproductive season and stayed for longer time at any given site. An additional underwater survey confirmed unexpected eDNA detections as true positives. eDNA analysis has great potential to quantitatively monitor reproductive fish migrations under certain conditions.

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Environmental DNA (eDNA): A tool for quantifying the abundant but elusive round goby (Neogobius melanostomus)

Cited by 80 publications

References 56 publications

Rapid assessment of coral cover from environmental DNA in Hawai'i

Rapid assessment of coral cover from environmental DNA in Hawai'i

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

Environmental DNA analysis as a non‐invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers

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