Using environmental DNA to detect an endangered crayfish Cambaroides japonicus in streams

Ikeda, Kazuko; Doi, Hideyuki; Tanaka, Kazunori; Kawai, Tadashi; Negishi, Junjiro N.

doi:10.1007/s12686-016-0541-z

Cited by 63 publications

(60 citation statements)

References 14 publications

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“…Although Tréguier et al (2014) found some disagreements between eDNA detections of the invasive red swamp crayfish Procambarus clarkii (Girard, 1852) in French ponds as related to results of baited trapping for this species, Dougherty et al (2016) instead found generally high concordance between baited trapping estimates of presence or absence and eDNA results for O. rusticus from inland lakes of the northern US. Beyond applications to invasive crayfishes, Ikeda et al (2016) tested an eDNA assay for the endangered crayfish Cambaroides japonicus (De Haan, 1841) in streams of Japan, and detected eDNA for this crayfish from all sites where it was manually collected. Improvements in performance of eDNA for detecting crayfish occupancy, or better reflecting relative abundance for these species, might also be achieved from more mechanistic laboratory studies that can address habitat or environmental factors affecting eDNA persistence times or transport distances (Barnes & Turner, 2016;Goldberg et al, 2016;Shogren et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America

et al. 2017

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We report results of a study that made reciprocal comparisons of environmental DNA (eDNA) assays for two major invasive crayfishes between their disparate invasive ranges in North America. Specifically, we tested for range expansions of the signal crayfish Pacifastacus leniusculus (Dana, 1852) into the Laurentian Great Lakes region known to be invaded by the rusty crayfish Orconectes rusticus (Girard, 1852), as well as for the invasion of O. rusticus into large lakes of California and Nevada, US known to be invaded by P. leniusculus. We compared eDNA detections to historic localities for O. rusticus within the Great Lakes, and to recent sampling for presence/absence and relative abundance of P. leniusculus in California and Nevada via overnight sets of baited traps. We successfully detected O. rusticus eDNA at six sites from the Great Lakes and P. leniusculus from six of seven lakes where it was known to occur in California and Nevada, but did not detect any range expansions by either species across the North American continent. eDNA appears suitable to detect benthic arthropods from exceptionally large lakes, and will likely be useful in applications for monitoring of new biological invasions into these and other freshwater and marine habitats.

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Section: Discussionmentioning

confidence: 99%

Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America

et al. 2017

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“…Most of the studies which targeted specific species employed real-time PCR platforms and emphasized the high detection sensitivity of eDNA assays (Biggs et al, 2015;Dougherty et al, 2016;Ikeda, Doi, Tanaka, Kawai, & Negishi, 2016;Takahara, Minamoto, & Doi, 2013). Most of the studies which targeted specific species employed real-time PCR platforms and emphasized the high detection sensitivity of eDNA assays (Biggs et al, 2015;Dougherty et al, 2016;Ikeda, Doi, Tanaka, Kawai, & Negishi, 2016;Takahara, Minamoto, & Doi, 2013).…”

Section: Introductionmentioning

confidence: 99%

Comparison of inhibition resistance among PCR reagents for detection and quantification of environmental DNA

et al. 2019

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Background: Real-time PCR has been widely employed in environmental DNA (eDNA) surveys to detect and quantify target species. The biggest obstacle in realtime PCR based eDNA assays is the inhibition of PCR amplification that results in false-negative detection and uncertainty of quantification.Aims: Here, we aimed to evaluate inhibition resistance of PCR reagents for detection and quantification of environmental DNA. Materials & Methods:We compared six commercial PCR reagents, including four inhibitor-resistant reagents, for resistance to major PCR inhibitory substances, i.e., humic, fulvic, and tannic acids. Then, we selected three inhibitorresistant reagents to test for their resistance to multiple natural inhibitors using field eDNA samples collected from various habitats. Results:We found that each inhibitor-resistant reagent had its advantage and disadvantage depending on which inhibitory substance was used. Similarly, the inhibitory effects caused by field samples differed among the three inhibitor-resistant reagents, where none of the reagents consistently showed strong resistance to all field samples. Conclusion:Our results indicate that the selection of appropriate PCR reagent would greatly ease PCR inhibition, and consequently improve the estimation of species distribution by real-time PCR-based eDNA assays. K E Y W O R D S fulvic acid, humic acid, PCR inhibition, real-time PCR, tannic acid 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: Uchii K, Doi H, Okahashi T, et al. Comparison of inhibition resistance among PCR reagents for detection and quantification of environmental DNA.

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“…Therefore, eDNA is being used as a tool to determine whether an invasion has taken place [22] or to track an endangered species [23]. The size fraction used to describe eDNA is the size fraction that removes larger eukaryotes (passing through a 0.5 mm mesh) but retains microbes (>0.45 µm filter).…”

Section: Introductionmentioning

confidence: 99%

A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater

Flaviani

Schroeder

Balestreri

et al. 2017

Viruses

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The aquatic microbiome is composed of a multi-phylotype community of microbes, ranging from the numerically dominant viruses to the phylogenetically diverse unicellular phytoplankton. They influence key biogeochemical processes and form the base of marine food webs, becoming food for secondary consumers. Due to recent advances in next-generation sequencing, this previously overlooked component of our hydrosphere is starting to reveal its true diversity and biological complexity. We report here that 250 mL of seawater is sufficient to provide a comprehensive description of the microbial diversity in an oceanic environment. We found that there was a dominance of the order Caudovirales (59%), with the family Myoviridae being the most prevalent. The families Phycodnaviridae and Mimiviridae made up the remainder of pelagic double-stranded DNA (dsDNA) virome. Consistent with this analysis, the Cyanobacteria dominate (52%) the prokaryotic diversity. While the dinoflagellates and their endosymbionts, the superphylum Alveolata dominates (92%) the microbial eukaryotic diversity. A total of 834 prokaryotic, 346 eukaryotic and 254 unique virus phylotypes were recorded in this relatively small sample of water. We also provide evidence, through a metagenomic-barcoding comparative analysis, that viruses are the likely source of microbial environmental DNA (meDNA). This study opens the door to a more integrated approach to oceanographic sampling and data analysis.

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Using environmental DNA to detect an endangered crayfish Cambaroides japonicus in streams

Cited by 63 publications

References 14 publications

Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America

Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America

Comparison of inhibition resistance among PCR reagents for detection and quantification of environmental DNA

A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater

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