Detecting the pest fish,<i>Gambusia affinis</i>from environmental DNA in New Zealand: a comparison of methods

Banks, Jonathan C.; Kelly, Laura T.; Falleiros, Renan M.; Rojahn, Jack; Gabrielsson, Rasmus; Clapcott, Joanne E.

doi:10.1080/03014223.2020.1858880

Cited by 6 publications

(7 citation statements)

References 27 publications

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“…While both qPCR and ddPCR have been found to produce either similar estimates of DNA concentrations (Nathan et al, 2014) or strong relationships between marker copy numbers and abundances (Wood et al, 2019b), most studies found ddPCR more sensitive than qPCR. This may be because in ddPCR each sample is partitioned into 15,000-20,000 microfluidic droplets (see above), where the amplification reaction occurs independently and concentrations of PCR inhibitors can be strongly reduced (Banks et al, 2021;Brys et al, 2021;Doi et al, 2015; (which was not certified by peer review) is the author/funder. All rights reserved.…”

Section: 4mentioning

confidence: 99%

“…In this approach, sequences belonging to multiple species are obtained from complex environmental samples via HTS, using short regions of one or a few marker genes, which are targeted with broad-spectrum or group-specific primers (Deiner et al, 2017;Taberlet et al, 2012a). Comparisons between metabarcoding and targeted approaches indicated that qPCR or cPCR or ddPCR are more sensitive in the detection of single species or a small set of species, in particular when the target DNA occurs at low densities (Banks et al, 2021;Blackman et al, 2020Blackman et al, , 2018Harper et al, 2018a;Moss et al, 2022;Roy et al, 2018). For instance, qPCR was highly effective in detecting the invasive tunicate Didemnum vexillum Kott, 2002 from seawater eDNA, whereas metabarcoding was unable to recover it, even at locations where it is known to be present, but detected several other established invasive species (Gargan et al, 2022).…”

Section: 4mentioning

confidence: 99%

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Catch me if you can: current status and topical issues on the use of eDNA-based targeted detection of rare and endangered animal species

Duarte

Simões

Costa

2023

Preprint

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Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, which are key to devising tools to efficiently single out a targeted species from an environmental sample, using carefully chosen marker regions and customized primers. Here, we present a comprehensive review of the use of eDNA-based methods for the detection of targeted animal species, such as rare, endangered, or invasive species, through the analysis of 460 publications (2008-2022). Aquatic ecosystems have been the most surveyed, in particular, freshwaters (75%), and to a less extent marine (14%) and terrestrial systems (10%). Vertebrates, in particular, fish (38%), and endangered species, have been the most focused in these studies, and Cytb and COI are the most employed markers. Among invertebrates, assays have been mainly designed for Mollusca and Crustacea species (22%), in particular, to target invasive species, and COI has been the most employed marker. Targeted molecular approaches, in particular qPCR, have been the most adopted (73%), while eDNA metabarcoding has been rarely used to target single or few species (approx. 5%). However, less attention has been given in these studies to the effects of environmental factors on the amount of shed DNA, the differential amount of shed DNA among species, or the sensitivity of the markers developed, which may impact the design of the assays, particularly to warrant the required detection level and avoid false negatives and positives. The accuracy of the assays will also depend on the availability of genetic data from closely related species to assess both marker and primers specificity. In addition, eDNA-based assays developed for a particular species may have to be refined taking into account site-specific populations, as well as any intraspecific variation.

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Section: 4mentioning

confidence: 99%

Section: 4mentioning

confidence: 99%

Catch me if you can: current status and topical issues on the use of eDNA-based targeted detection of rare and endangered animal species

Duarte

Simões

Costa

2023

Preprint

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“…These filters were kept at room temperature until time of extraction. Smith-Root conducted a study showing that DNA did not degrade within 6 months at room temperature (Thomas et al, 2019) and these filters have also been used in other studies (Loeza-Quintana et al, 2020;Skinner et al, 2020;Banks et al, 2021;Nolan et al, 2022). These self-preserving eDNA filters are made of hydrophilic plastic which absorbs any remaining moisture into the package and preserves the DNA and prokaryotes via desiccation which has been shown as an effective preservation technique in other studies (Garcıá, 2011;Manzanera, 2021).…”

Section: Microbiome Analysesmentioning

confidence: 99%

Commercial production of Florida pompano (Trachinotus carolinus) larvae at low salinity induces variable changes in whole-larvae microbial diversity, gene expression, and gill histopathology

et al. 2023

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IntroductionSalinity presents economic and technical challenges in land-based recirculating aquaculture systems (RAS) in the U.S. warm water marine finfish aquaculture industry. Many studies have shown euryhaline fish reared at salinities closer to their iso-osmotic salinity can yield enhanced production performance as well as potential reduced costs to farms. However, there is potential for osmotic stress in fish larvae to negatively impact larvae microbiome and innate immune system. Florida pompano (Trachinotus carolinus) is a popular sportfish has been targeted for land-based RAS due to its impressive market value and euryhaline capacity. This study investigated the impacts of rearing Florida pompano larvae at salinities closer to their iso-osmotic salinity.Materials and methodsLarvae were cultured at 10, 20, and 30 ppt in triplicates, and larvae samples were collected for histopathology, microbiome, and whole transcriptomics analysis every three days from hatching until the time of weaning (24 days post hatch [DPH]). Water samples were also taken for microbiome analysis on every other larval sampling day. DiscussionThese changes were driven more by metamorphosis, causing an increase in expression of antioxidant genes (cat, gss, gsto1, and scara3) than by the presence of potentially pathogenic genera, which failed to induce an immune response (low or unchanged expression of downstream elements of the NOD1 or TLR5 pathways). These findings provide baseline information on Florida pompano low salinity tolerance in larviculture during early developmental stages. In addition, we have shown minimal effects on the immune system at salinities as low as 10 ppt. This work has important implications for larval health management and can be used to refine and direct future research regarding improving commercial production of warm water marine species

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“…Single-species detection using eDNA was one of the earlier established applications of this technology for vertebrate species. In particular, the use of eDNA in detecting invasive species has been particularly popular and Banks et al (2021) has demonstrated this applicability for the detection of Gambusia affinis. This study compared various workflows from collection of the sample through to the laboratory processes and how these impacted on the sensitivity of eDNA for detecting this invasive.…”

Section: Editorialmentioning

confidence: 99%

Zoological applications for environmental DNA: detection, diversity, and health

Gleeson

2021

New Zealand Journal of Zoology

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Detecting the pest fish,Gambusia affinisfrom environmental DNA in New Zealand: a comparison of methods

Cited by 6 publications

References 27 publications

Catch me if you can: current status and topical issues on the use of eDNA-based targeted detection of rare and endangered animal species

Catch me if you can: current status and topical issues on the use of eDNA-based targeted detection of rare and endangered animal species

Commercial production of Florida pompano (Trachinotus carolinus) larvae at low salinity induces variable changes in whole-larvae microbial diversity, gene expression, and gill histopathology

Zoological applications for environmental DNA: detection, diversity, and health

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