Toward routine, DNA-based detection methods for marine pests

Bott, Nathan J.; Ophel-Keller, K.; Sierp, Michael T.; Herdina,; Rowling, Keith P; McKay, Alan; Loo, Maylene; Tanner, Jason E.; Deveney, Marty R.

doi:10.1016/j.biotechadv.2010.05.018

Cited by 52 publications

(51 citation statements)

References 105 publications

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“…Many of these methods have been recently summarised by Darling & Blum (2007) and by Bott et al (2010). A key advantage of the SHA is that it targets rRNA, of which there is usually a considerable amount present throughout all cells and therefore an abundant target.…”

Section: Resultsmentioning

confidence: 99%

Application of a sandwich hybridisation assay for rapid detection of the Northern Pacific seastar, Asterias amurensis

Smith

Rhodes

Adamson

et al. 2011

New Zealand Journal of Marine and Freshwater Research

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A sandwich hybridisation assay (SHA) has been developed to detect Asterias amurensis (Lu¨tken 1871), commonly known as the northern Pacific seastar, which is an unwanted, and as yet undetected, pest in New Zealand waters. Probes in SHA format have been developed that target the ribosomal RNA internal transcribed spacer region of A. amurensis. The successful assay utilises the capture probe ITS-C2-110 and the combined signal probes ITS-S1-93 and ITS-S3-240. It has been successfully tested for specificity, including cross-reactivity testing against the common and related seastars, Patiriella regularis (Verrill 1867), P. mortenseni (O'Loughlin et al. 2002), Coscinasterias muricata (Verrill 1867) and Stichaster australis (Verrill 1871). The SHA is a rapid and potentially portable RNA-based test, and opens up the opportunity for direct analysis of water samples, for example, portside during surveillance of marine pests.

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Section: Resultsmentioning

confidence: 99%

Application of a sandwich hybridisation assay for rapid detection of the Northern Pacific seastar, Asterias amurensis

Smith

Rhodes

Adamson

et al. 2011

New Zealand Journal of Marine and Freshwater Research

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“…soil, water, sediment, faeces, air) to be characterised rapidly (Hajibabaei et al 2011;Lecroq et al 2011;Anderson et al 2012;Taberlet et al 2012). Environmental sequences generated by NGS can be compared to a reference library in order to screen, not only for pest/introduced species or pathogens, but also for endemic species to provide a broader indication of environmental health and biodiversity (Bott et al 2010). Several NGS platforms have been commercialised, and the technology is improving at a rapid pace (Glenn 2011).…”

Section: Next-generation Sequencingmentioning

confidence: 99%

“…the identification of the source of bacteria by MST). Identification of individuals by DNA sequencing or barcoding is relatively straightforward, but the technical challenges associated with detecting target species in environmental samples are significantly greater (Darling & Blum 2007;Bott et al 2010). Even if technically feasible, the logistical, economic and political barriers to implementation are great (Darling & Mahon 2011).…”

Section: Microbial Source Trackingmentioning

confidence: 99%

“…A wide array of molecular-based techniques have been employed worldwide for the identification and monitoring of aquatic organisms (Bott et al 2010;Humbert et al 2010;Darling & Mahon 2011). These include a variety of hybridisation techniques, polymerase chain reaction (PCR)-based techniques and recent advances in sequencing technologies.…”

Section: Molecular Techniques Discussed In This Reviewmentioning

confidence: 99%

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Molecular genetic tools for environmental monitoring of New Zealand's aquatic habitats, past, present and the future

Wood

Smith

Banks

et al. 2013

New Zealand Journal of Marine and Freshwater Research

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“…The development of reliable internal controls ("positive controls") may also assist significantly in recognizing experimental detection limits in surveys for species of interest (Bott et al 2010).…”

mentioning

confidence: 99%

Experimental parameters affecting quantitative PCR of Artemia franciscana: a model for a marine zooplanktonic target in natural plankton samples

Mackie

Geller

2010

Limnology & Ocean Methods

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The brine shrimp Artemia franciscana was used as a model zooplankter to explore the range and accuracy of quantitative PCR (QPCR) in detecting a target species in plankton community DNA. Specific primers were designed in the 18S ribosomal RNA and mitochondrial cytochrome c oxidase subunit I genes and analyzed by TaqMan and SYBR Green I reporting systems. Assays were sensitive in detecting A. franciscana nauplii in DNA extractions from bulk plankton: a single nauplius was detected when added to 20 mg wet, packed plankton and distinguished from two added nauplii. Indeed, Artemia DNA diluted to 0.1 picograms per reaction (equivalent to 10−5 nauplii) was detectable. Artemia franciscana was detected without coamplification of other plankton, alleviating concern for errors caused by the presence of similar organisms in the plankton community. A natural plankton DNA sample and purified herring sperm DNA inhibited PCR above 100 ng reaction−1, but these samples could be diluted to eliminate inhibition. Because QPCR could detect 10−5 nauplii, dilution solves inhibition without sacrificing sensitivity. This sensitivity allows for analysis of a mass of plankton made large enough sufficient to include a target organism at low density. The newly hatched nauplius (DNA mass = 6. 1 ng) is a useful internal control in experiments examining plankton samples, providing a means of controlling for variations in DNA extraction and amplification efficiency in surveys for species of interest.

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Toward routine, DNA-based detection methods for marine pests

Cited by 52 publications

References 105 publications

Application of a sandwich hybridisation assay for rapid detection of the Northern Pacific seastar, Asterias amurensis

Application of a sandwich hybridisation assay for rapid detection of the Northern Pacific seastar, Asterias amurensis

Molecular genetic tools for environmental monitoring of New Zealand's aquatic habitats, past, present and the future

Experimental parameters affecting quantitative PCR of Artemia franciscana: a model for a marine zooplanktonic target in natural plankton samples

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