Toward routine, DNA-based detection methods for marine pests.

Marine pest incursions can cause significant ongoing damage to aquaculture, biodiversity, fisheries habitat, infrastructure and social amenity. They represent a significant and ongoing economic burden. Marine pests can be introduced by several vectors including aquaculture, aquarium trading, commercial shipping, fishing, floating debris, mining activities and recreational boating. Despite the inherent risks, there is currently relatively little routine surveillance of marine pest species conducted in the majority of countries worldwide. Accurate and rapid identification of marine pest species is central to early detection and management. Traditional techniques (e.g. physical sampling and sorting), have limitations, which has motivated some progress towards the development of molecular diagnostic tools. This review provides a brief account of the techniques traditionally used for detection and describes developments in molecular-based methods for the detection and surveillance of marine pest species. Recent advances provide a platform for the development of practical, specific, sensitive and rapid diagnosis and surveillance tools for marine pests for use in effective prevention and control strategies.

[1]  L. Kohn,et al.  Single Nucleotide Polymorphism-Based Diagnostic System for Crop-Associated Sclerotinia Species , 2009, Applied and Environmental Microbiology.

[2]  P. O’Farrell,et al.  Manipulating the Metazoan Mitochondrial Genome with Targeted Restriction Enzymes , 2008, Science.

[3]  J. Fernández-Tajes,et al.  Identification of the razor clam species Ensis arcuatus, E. siliqua, E. directus, E. macha, and Solen marginatus using PCR-RFLP analysis of the 5S rDNA region. , 2007, Journal of agricultural and food chemistry.

[4]  W. Claxton,et al.  A new molecular technique for identifying field collections of zebra mussel (Dreissena polymorpha) and quagga mussel (Dreissena bugensis) veliger larvae applied to eastern Lake Erie, Lake Ontario, and Lake Simcoe , 1998 .

[5]  R. Nutter,et al.  Applied Biosystems SOLiD™ System: Ligation‐Based Sequencing , 2008 .

[6]  T. F. Smith,et al.  Real-Time PCR in Clinical Microbiology: Applications for Routine Laboratory Testing , 2006, Clinical Microbiology Reviews.

[7]  M T Clegg,et al.  Evolution of a noncoding region of the chloroplast genome. , 1993, Molecular phylogenetics and evolution.

[8]  C. Saint,et al.  Comparison of SYTO9 and SYBR Green I for real-time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis. , 2005, Analytical biochemistry.

[9]  Loren B. Byrne,et al.  Biodiversity loss and the taxonomic bottleneck: emerging biodiversity science , 2006, Ecological Research.

[10]  Mauro Magnani,et al.  Development of a Real-Time PCR Assay for Rapid Detection and Quantification of Alexandrium minutum (a Dinoflagellate) , 2004, Applied and Environmental Microbiology.

[11]  L. Anderson California’s Reaction to Caulerpa taxifolia: A Model for Invasive Species Rapid Response* , 2005, Biological Invasions.

[12]  M. Magnani,et al.  IDENTIFICATION OF ALEXANDRIUM (DINOPHYCEAE) SPECIES USING PCR AND rDNA‐TARGETED PROBES , 1999 .

[13]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[14]  K. Mullis,et al.  Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. , 1986, Cold Spring Harbor symposia on quantitative biology.

[15]  K. Ueda,et al.  Variability in the rbcL Introns of Caulerpalean Algae (Chlorophyta, Ulvophyceae) , 2000, Journal of Plant Research.

[16]  T. Notomi,et al.  Loop-mediated isothermal amplification of DNA. , 2000, Nucleic acids research.

[17]  Inger Wallentinus,et al.  Introduced marine organisms as habitat modifiers. , 2007, Marine pollution bulletin.

[18]  Simon C. Barry,et al.  Ballast water risk assessment: principles, processes, and methods , 2008 .

[19]  Russell Higuchi,et al.  Kinetic PCR Analysis: Real-time Monitoring of DNA Amplification Reactions , 1993, Bio/Technology.

[20]  I. Cross,et al.  Species identification of Crassostrea and Ostrea oysters by polymerase chain reaction amplification of the 5S rRNA gene. , 2006, Journal of AOAC International.

[21]  Yong Wang,et al.  Genome Sequencing in Open Microfabricated High Density Picoliter Reactors , 2005 .

[22]  P. Kwok,et al.  Homogeneous genotyping assays for single nucleotide polymorphisms with fluorescence resonance energy transfer detection. , 1999, Genetic analysis : biomolecular engineering.

[23]  T. Eickbush,et al.  Finely Orchestrated Movements: Evolution of the Ribosomal RNA Genes , 2007, Genetics.

[24]  D. Rand Thermal habit, metabolic rate and the evolution of mitochondrial DNA. , 1994, Trends in ecology & evolution.

[25]  Keith K. Stanley,et al.  Multiplexed tandem PCR: gene profiling from small amounts of RNA using SYBR Green detection , 2005, Nucleic acids research.

[26]  J. Elder,et al.  Concerted Evolution of Repetitive DNA Sequences in Eukaryotes , 1995, The Quarterly Review of Biology.

[27]  Jaysheel D. Bhavsar,et al.  Metagenomics: Read Length Matters , 2008, Applied and Environmental Microbiology.

[28]  S. Quake,et al.  Single-Molecule DNA Sequencing of a Viral Genome , 2008, Science.

[29]  A. Zhan,et al.  A new strategy for species identification of planktonic larvae : PCR-RFLP analysis of the internal transcribed spacer region of ribosomal DNA detected by agarose gel electrophoresis or DHPLC , 2006 .

[30]  C. Bogi,et al.  Mytilopsis sallei (Mollusca: Bivalvia: Dreissenidae) established on the Mediterranean coast of Israel , 2009 .

[31]  L. Edler,et al.  Intercalibration of classical and molecular techniques for identification of Alexandrium fundyense (Dinophyceae) and estimation of cell densities , 2007 .

[32]  Tadashi Maruyama,et al.  Development of Molecular Probes for Dinophysis (Dinophyceae) Plastid: A Tool to Predict Blooming and Explore Plastid Origin , 2005, Marine Biotechnology.

[33]  T. Comtet,et al.  In situ hybridization on whole larvae: a novel method for monitoring bivalve larvae , 2007 .

[34]  Herdina,et al.  Development of a routine DNA-based testing service for soilborne diseases in Australia , 2008, Australasian Plant Pathology.

[35]  Y. Sako,et al.  Development of a novel molecular marker on the mitochondrial genome of a toxic dinoflagellate, Alexandrium spp., and its application in single-cell PCR , 2008, Journal of Applied Phycology.

[36]  R. Harrison Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. , 1989, Trends in ecology & evolution.

[37]  A. Meyer,et al.  Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Carol A. Stepien,et al.  Diagnostic genetic markers and evolutionary relationships among invasive dreissenoid and corbiculoid bivalves in North America: phylogenetic signal from mitochondrial 16S rDNA. , 1999, Molecular phylogenetics and evolution.

[39]  R. Raine,et al.  Discrimination of Alexandrium andersoni and A. minutum (Dinophyceae) using LSU rRNA-targeted oligonucleotide probes and fluorescent whole-cell hybridization , 2007 .

[40]  E. Lyamuya,et al.  Molecular Characterization of Haemophilus ducreyi Isolates from Different Geographical Locations , 2006, Journal of Clinical Microbiology.

[41]  R. Gasser,et al.  Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation , 2006, Nature Protocols.

[42]  B. Deagle,et al.  Specific Detection of Pacific Oyster (Crassostrea gigas) Larvae in Plankton Samples Using Nested Polymerase Chain Reaction , 2005, Marine Biotechnology.

[43]  J. Graves,et al.  Mitochondrial and nuclear DNA analysis of population subdivision among young-of-the-year Spanish mackerel (Scomberomorus maculatus) from the western Atlantic and Gulf of Mexico , 2001 .

[44]  E. Lusby,et al.  Minor groove binder-conjugated DNA probes for quantitative DNA detection by hybridization-triggered fluorescence. , 2002, BioTechniques.

[45]  L. Rasmussen,et al.  Single-step nested multiplex PCR to differentiate between various bivalve larvae , 2005 .

[46]  L. Rhodes,et al.  International accreditation of sandwich hybridisation assay format DNA probes for micro‐algae , 2005 .

[47]  M. Mansur,et al.  Testing a molecular protocol to monitor the presence of golden mussel larvae (Limnoperna fortunei) in plankton samples , 2007 .

[48]  J. Burkholder,et al.  Development of Real-Time PCR Assays for Rapid Detection of Pfiesteria piscicida and Related Dinoflagellates , 2000, Applied and Environmental Microbiology.

[49]  Keith R Hayes,et al.  Identifying potential marine pests--a deductive approach applied to Australia. , 2003, Marine pollution bulletin.

[50]  L. Rasmussen,et al.  Temporal occurrence of planktotrophic bivalve larvae identified morphologically and by single step nested multiplex PCR , 2007 .

[51]  J. Rothberg,et al.  The development and impact of 454 sequencing , 2008, Nature Biotechnology.

[52]  B. Deagle,et al.  Development and evaluation of a PCR-based test for detection of Asterias (Echinodermata : Asteroidea) larvae in Australian plankton samples from ballast water , 2003 .

[53]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[54]  B. Morton,et al.  Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[55]  L. Rhodes,et al.  Fluorescent in situ hybridisation assay as a species‐specific identifier of the northern Pacific seastar, Asterias amurensis , 2007 .

[56]  E. Madsen,et al.  Evaluation and Optimization of DNA Extraction and Purification Procedures for Soil and Sediment Samples , 1999, Applied and Environmental Microbiology.

[57]  M. Waycott,et al.  Molecular Discrimination of Perna (Mollusca: Bivalvia) Species Using the Polymerase Chain Reaction and Species-Specific Mitochondrial Primers , 2006, Marine Biotechnology.

[58]  Carl T Wittwer,et al.  High-resolution genotyping by amplicon melting analysis using LCGreen. , 2003, Clinical chemistry.

[59]  A. Rogers,et al.  Specificity and sensitivity of microsatellite markers for the identification of larvae , 2001 .

[60]  Daniela Bartels,et al.  Finding novel genes in bacterial communities isolated from the environment , 2006, ISMB.

[61]  K. Chu,et al.  MOLECULAR PHYLOGENETICS OF THE MITTEN CRAB SPECIES IN ERIOCHEIR, SENSU LATO (BRACHYURA: GRAPSIDAE) , 2003 .

[62]  Marcus Droege,et al.  The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. , 2008, Journal of biotechnology.

[63]  R. Rodriguez,et al.  Molecular detection of native and invasive marine invertebrate larvae present in ballast and open water environmental samples collected in Puget Sound , 2009 .

[64]  S. Woodward The Deep Sea , 2003 .

[65]  Jang‐Seu Ki,et al.  A low-density oligonucleotide array study for parallel detection of harmful algal species using hybridization of consensus PCR products of LSU rDNA D2 domain. , 2006, Biosensors & bioelectronics.

[66]  C. Scholin,et al.  Monitoring for Heterosigma akashiwo using a sandwich hybridization assay , 2002 .

[67]  K. Livak,et al.  Real time quantitative PCR. , 1996, Genome research.

[68]  Cohen,et al.  Accelerating invasion rate in a highly invaded estuary , 1998, Science.

[69]  C. Maggs,et al.  Species‐specific oligonucleotide probes for macroalgae: molecular discrimination of two marine fouling species of Enteromorpha (Ulvophyceae) , 2000, Molecular ecology.

[70]  B. Galil Loss or gain? Invasive aliens and biodiversity in the Mediterranean Sea. , 2007, Marine pollution bulletin.

[71]  D. Hillis,et al.  Ribosomal DNA: Molecular Evolution and Phylogenetic Inference , 1991, The Quarterly Review of Biology.

[72]  Nicholas J. Bax,et al.  Marine invasive alien species: a threat to global biodiversity , 2003 .

[73]  G. Hallegraeff,et al.  Development of a Real-Time PCR Probe for Quantification of the Heterotrophic Dinoflagellate Cryptoperidiniopsis brodyi (Dinophyceae) in Environmental Samples , 2007, Applied and Environmental Microbiology.

[74]  Paula E. Whitfield,et al.  Distribution and Identification of an Invasive Gracilaria Species that is Hampering Commercial Fishing Operations in Southeastern North Carolina, USA , 2006, Biological Invasions.

[75]  Kun-song Chen,et al.  DNA quantification using EvaGreen and a real-time PCR instrument. , 2006, Analytical biochemistry.

[76]  J. Palmer,et al.  Contrasting modes and tempos of genome evolution in land plant organelles. , 1990, Trends in genetics : TIG.

[77]  G. Yoshizaki,et al.  Mitochondrial DNA variation and population structure of the Japanese mitten crab Eriocheir japonica , 2006, Fisheries Science.

[78]  M. Adams,et al.  Differential gene flow of mitochondrial and nuclear DNA markers among chromosomal races of Australian morabine grasshoppers (Vandiemenella, viatica species group) , 2007, Molecular ecology.

[79]  D. Anderson,et al.  Identification and enumeration of Alexandrium spp. from the Gulf of Maine using molecular probes , 2005 .

[80]  M. Pie,et al.  A fast and accurate molecular method for the detection of larvae of the golden mussel Limnoperna fortunei (Mollusca: Mytilidae) in plankton samples , 2006 .

[81]  I. Karunasagar,et al.  Polymerase Chain Reaction in Detection of Gymnodinium mikimotoi and Alexandrium minutum in Field Samples from Southwest India , 2001, Marine Biotechnology.

[82]  J. Compton,et al.  Nucleic acid sequence-based amplification , 1991, Nature.

[83]  R. Vrijenhoek,et al.  A diagnostic molecular marker for zebra mussels (Dreissena polymorpha) and potentially co-occurring bivalves: mitochondrial COI. , 1996, Molecular marine biology and biotechnology.

[84]  D. Crosetti,et al.  Identification of bivalve species at an early developmental stage through PCR-SSCP and sequence analysis of partial 18S rDNA , 2006 .

[85]  Marine Pest Incursions – A Tool to Predict the Cost of Eradication Based on Expert Assessments , 2007 .

[86]  Amalio Telenti,et al.  Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis , 1998, Nature Biotechnology.

[87]  K. Mullis,et al.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. , 1988, Science.

[88]  A. Jex,et al.  High resolution melting-curve (HRM) analysis for the diagnosis of cryptosporidiosis in humans. , 2009, Molecular and cellular probes.

[89]  M. Frischer,et al.  Specific amplification of the 18S rRNA gene as a method to detect zebra mussel (Dreissena polymorpha) larvae in plankton samples , 2002, Hydrobiologia.

[90]  D. Anderson,et al.  IDENTIFICATION OF GROUP‐ AND STRAIN‐SPECIFIC GENETIC MARKERS FOR GLOBALLY DISTRIBUTED ALEXANDRIUM (DINOPHYCEAE). I. RFLP ANALYSIS OF SSU rRNA GENES 1 , 1994 .

[91]  Roman Marin,et al.  Molecular Detection of Marine Invertebrate Larvae , 2005, Marine Biotechnology.

[92]  Brendan Gould,et al.  Survey evaluations to assess marine bioinvasions. , 2007, Marine pollution bulletin.

[93]  D. Booth,et al.  Molecular approaches to the study of invasive seaweeds , 2007 .

[94]  G. Pierce,et al.  Real-time PCR assay for detection and relative quantification of Liocarcinus depurator larvae from plankton samples , 2008 .

[95]  David R. Walt,et al.  Fiber-Optic Microarray for Simultaneous Detection of Multiple Harmful Algal Bloom Species , 2006, Applied and Environmental Microbiology.

[96]  Dan Minchin,et al.  Aquaculture and transport in a changing environment: overlap and links in the spread of alien biota. , 2007, Marine pollution bulletin.

[97]  N. Bax,et al.  Specific amplification of mt-COI gene of the invasive gastropod Maoricolpus roseus in planktonic samples reveals a free-living larval life-history stage , 2005 .

[98]  D. Anderson,et al.  IDENTIFICATION OF GROUP‐ AND STRAIN‐SPECIFIC GENETIC MARKERS FOR GLOBALLY DISTRIBUTED ALEXANDRIUM (DINOPHYCEAE). II. SEQUENCE ANALYSIS OF A FRAGMENT OF THE LSU rRNA GENE 1 , 1994 .

[99]  J. Braverman,et al.  Parallel rate heterogeneity in chloroplast and mitochondrial genomes of Brazil nut trees (Lecythidaceae) is consistent with lineage effects. , 2008, Molecular biology and evolution.

[100]  K. Zhou,et al.  Molecular systematics of the Asian mitten crabs, genus Eriocheir (Crustacea: Brachyura). , 2003, Molecular phylogenetics and evolution.

[101]  A. Becker,et al.  A quantitative method of determining initial amounts of DNA by polymerase chain reaction cycle titration using digital imaging and a novel DNA stain. , 1996, Analytical biochemistry.

[102]  R. Vrijenhoek,et al.  A robotic molecular method for in situ detection of marine invertebrate larvae , 2008, Molecular ecology resources.

[103]  S. Palumbi,et al.  Single-step species identification of bivalve larvae using multiplex polymerase chain reaction , 2000 .

[104]  R. Freckleton,et al.  Declines in the numbers of amateur and professional taxonomists: implications for conservation , 2002 .

[105]  Robert Pelton,et al.  Detection of DNA using bioactive paper strips. , 2009, Chemical communications.

[106]  M T Clegg,et al.  Rates and patterns of chloroplast DNA evolution. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[107]  Katja Metfies,et al.  Development and adaptation of a multiprobe biosensor for the use in a semi-automated device for the detection of toxic algae. , 2008, Biosensors & bioelectronics.

[108]  O. Jousson,et al.  Genetic polymorphism in Caulerpa taxifolia (Ulvophyceae) chloroplast DNA revealed by a PCR‐based assay of the invasive Mediterranean strain , 2002 .

[109]  B. Deagle,et al.  Development and Evaluation of a PCR Based Assay for Detection of the Toxic Dinoflagellate, Gymnodinium catenatum(Graham) in Ballast Water and Environmental Samples , 2005, Biological Invasions.

[110]  I G Wilson,et al.  Inhibition and facilitation of nucleic acid amplification , 1997, Applied and environmental microbiology.

[111]  N. Dubilier,et al.  Species identification of marine invertebrate early stages by whole-larvae in situ hybridisation of 18S ribosomal RNA , 2007 .

[112]  Adam Osborne,et al.  Monoplex/multiplex linear-after-the-exponential-PCR assays combined with PrimeSafe and Dilute-'N'-Go sequencing , 2007, Nature Protocols.

[113]  P. Hunt,et al.  A combined microscopic-molecular method for the diagnosis of strongylid infections in sheep. , 2009, International journal for parasitology.

[114]  E. Antoine,et al.  Oligonucleotide quartz crystal microbalance sensor for the microalgae Alexandrium minutum (Dinophyceae). , 2006, Biosensors & bioelectronics.