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

New Zealand Journal of Marine and Freshwater Research

Volumn 47, Issue 1, 2013, Pages 90-119

  Wood, S A ^a,b   Smith, K F ^a,b   Banks, J C ^a,b   Tremblay, L A ^a,c   Rhodes, L ^a   Mountfort, D ^a   Cary, S C ^b   Pochon, X ^a  

^a CAWTHRON INSTITUTE   (New Zealand)

^b UNIVERSITY OF WAIKATO   (New Zealand)

^c UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

automated ribosomal intergenic spacer analysis; fluorescent in situ hybridisation; next generation sequencing; polymerase chain reaction; quantitative polymerase chain reaction; sandwich hybridisation arrays; Sanger DNA sequencing; terminal restriction fragment length polymorphism

Indexed keywords

AQUATIC COMMUNITY; AQUATIC ENVIRONMENT; ARRAY; ASSESSMENT METHOD; ENVIRONMENTAL MONITORING; FISH; GENETIC ANALYSIS; HABITAT TYPE; HYBRIDIZATION; IDENTIFICATION METHOD; INVASIVE SPECIES; LAKE; LEGISLATIVE IMPLEMENTATION; MACROINVERTEBRATE; MARINE ECOSYSTEM; MOLECULAR ANALYSIS; POLYMERASE CHAIN REACTION; POLYMORPHISM; TAXONOMY;

NEW ZEALAND;

EID: 84874470141     PISSN: 00288330     EISSN: 11758805     Source Type: Journal    
DOI: 10.1080/00288330.2012.745885     Document Type: Article

References (178)

1. Acosta H, White P 2011. Atlas of biosecurity surveillance. Wellington, New Zealand, Ministry of Agriculture and Forestry. 51 p.
2. Adams SM, Tremblay LA 2003. Integration of chemical and biological tools in environmental management and regulation. Australasian Journal of Ecotoxicology 9: 157-164.
3. Adams SM, Giesy JP, Tremblay LA, Eason CT 2001. The use of biomarkers in ecological risk assessment: recommendations from the Christchurch conference on biomarkers in ecotoxicology. Biomarkers 6: 1-6. (Pubitemid 32066499)
4. Afonina IA, Reed MW, Lusby E, Shishkina IG, Belousov YS 2002. Minor groove binder conjugated DNA probes for quantitative DNA detection by hybridization-triggered fluorescence. Biotechniques 32: 940-949. (Pubitemid 34298721)
5. Agrawal N, Hassan YA, Ugaz VMA 2007. Pocketsized convective PCRthermocycler. Angewandte Chemie International Edition 46: 4316-4319.
6. Andersen K, Bird KL, Rasmussen M, Haile J, Breuning-Madsen H, Kjaer KH, Orlando L, Gilbert MT, Willerslev E 2012. Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity. Molecular Ecology 8: 1966-1979.
7. Ansorge WJ 2009. Next-generation DNA sequencing techniques. New Biotechnology 25: 195-203.
8. Ayers K, Rhodes LL, Tyrrell JV, Gladstone M, Scholin CA 2005. International accreditation of sandwich hybridisation assay format DNA probes for micro-algae. New Zealand Journal of Marine and Freshwater Research 39: 1225-1231. (Pubitemid 43096044)
9. Banks JC, Duggan ID, Hogg ID 2010a. Barcoding freshwater zooplankton. In: Lake Ecosystem Restoration New Zealand Annual Science Review Meeting. Hamilton, New Zealand, Waikato University.
10. Banks JC, Hicks BJ, Lobb R, Blair J 2010b. Genetic identification of fish. CBER Report 109. 17 p.
11. Bartlett JMS, Stirling D 2003. A short history of the polymerase chain reaction. PCR Protocols 226: 3-6.
12. Bartlett JM, Bartlett JMS 2004. Fluorescence in situ hybridization: technical overview. Methods in Molecular Medicine 97: 77-87.
13. Bax N, Dunstan P, Gunasekera R, Patil JG, Sutton C 2006. Evaluation of national control plan management options for the North Pacific seastar Asterias amurensis. Final report for the Department of Environment and Heritage. Canberra, Australia, CSIRO Marine Research. 85 p.
14. Becker A, Reith A, Napiwotzki J, Kadenbach B 1996. A quantitative method of determining initial amounts of DNA by polymerase chain reaction cycle titration using digital imaging and a novel DNA stain. Analytical Biochemistry 237: 204-207. (Pubitemid 26177081)
15. Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Sayers E 2009. GenBank. Nucleic Acids Research 37: D26-31.
16. Biosecurity New Zealand 2011. Import health standard for ornamental fish and marine invertebrates from all countries. Wellington, Ministry of Agriculture and Forestry. 72 p.
17. Bott NJ, Ophel-Keller KM, Sierp MT, Herdina, Rowling KP, McKay AC, Loo MGK, Tanner JE, Deveney MR 2010. Toward routine, DNAbased detection methods for marine pests. Biotechnology Advances 28: 706-714.
18. Burns NM, Rutherford JC, Clayton JS 1999. A monitoring and classification system for New Zealand lakes and reservoirs. Journal of Lake and Reservoir Management 15: 255-271.
19. Byappanahalli M, Fowler M, Shively D, Whitman R 2003. Ubiquity and persistence of Escherichia coli in a midwestern coastal stream. Applied and Environmental Microbiology 69: 4549-4555. (Pubitemid 36992911)
20. Byappanahalli MN, Whitman RL, Shively DA, Ting WTE, Tseng CC, Nevers MB 2006. Seasonal persistence and population characteristics of Escherichia coli and enterococci in deep backshore sand of two freshwater beaches. Journal of Water and Health 4: 313-320. (Pubitemid 44480018)
21. Cadel-Six S, Iteman I, Peyraud-Thomas C, Mann S, Ploux O, Méjean A 2009. Identification of a polyketide synthase coding sequence specific for anatoxin-a-producing Oscillatoria cyanobacteria. Applied Environmental Microbiology 75: 4909-4912.
22. Cary SC, Hicks BJ, Coyne KJ, Rueckert A, Gemmill CEC, Barnett CME 2007. A sensitive geneticbased detection capability for Didymosphenia geminata (Lyngbye) M. Schmidt: Phases Two and Three. CBER Contract Report 62. Client report prepared for MAF Biosecurity New Zealand. Hamilton, New Zealand, Centre for Biodiversity and Ecology Research, University of Waikato. 87 p.
23. Castiglioni B, Rizzi E, Frosini A, Sivonen K, Rajaniemi P, Rantala A, Mugnai MA, Ventura S, Wilmotte A, Boutte C, Grubisic S, Balthasart P, Consolandi C, Bordoni R, Mezzelani A, Battaglia C, De Bellis G 2004. Development of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria. Applied Environmental Microbiology 70: 7161-7172. (Pubitemid 39643779)
24. Chang FH, Anderson C, Boustead NC 1990. First record of a Heterosigma (Raphidophyceae) bloom with associated mortality of cage-reared salmon in Big Glory Bay, New Zealand. New Zealand Journal of Marine and Freshwater Research 24: 461-469.
25. Chen X, Kwok PY 1999. Homogeneous genotyping assays for single nucleotide polymorphisms with fluorescence resonance energy transfer detection. Genetic Analysis: Biomolecular Engineering 14: 157-163. (Pubitemid 29095373)
26. Collins RA, Armstrong KF, Meier R, Yi Y, Brown SDJ, Cruickshank RH, Keeling S, Johnston C 2012. Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. PLoS ONE 7: e28381.
27. Cornelisen CD, Kirs M, Gilpin B, Scholes P 2012. Microbial source tracking (MST) tools for water quality monitoring. Prepared for Regional Councils and the Coastal Special Interest Group, Cawthron Report 2047. Nelson, New Zealand, Cawthron Institute. 28 p.
28. D'Archino R, Nelson WA, Zuccarello GC 2007. Invasive marine red alga introduced to New Zealand waters: first record of Grateloupia turuturu (Halymeniaceae, Rhodophyta). New Zealand Journal of Marine and Freshwater Research 41: 35-42. (Pubitemid 46658552)
29. Darling JA, Blum MJ 2007. DNA-based methods for monitoring invasive species: a review and prospectus. Biological Invasions 9: 751-765. (Pubitemid 47414776)
30. Darling JA, Mahon AR 2011. From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environmental Research 111: 978-988.
31. Deagle BE, Bax N, Patil JG 2003. Development and evaluation of a PCR-based test for detection of Asterias (Echinodermata: Asteroidea) larvae in Australian plankton samples from ballast water. Marine and Freshwater Research 54: 709-719. (Pubitemid 37506914)
32. Duggan IC, Green JD, Shiel RJ 2001a. Distribution of rotifers in North Island, New Zealand, and their potential use as bioindicators of lake trophic state. Hydrobiologia 446/447: 155-164. (Pubitemid 32731418)
33. Duggan IC, Green JD, Thomasson K 2001b. Do rotifers have potential as bioindicators of lake trophic state? Verhandlungen*Internationale Vereinigung fü r Theoretische und Angewandte Limnologie 27: 3497-3502.
34. Dyhrman ST, Erdner DL, La DuJ, Galac M, Anderson DM 2006. Molecular quantification of toxic Alexandrium fundyense in the Gulf of Maine using real-time PCR. Harmful Algae 5: 242-250. (Pubitemid 43374643)
35. Ehrenfeld JG 2010. Ecosystem consequences of biological invasions. Annual Review of Ecology, Evolution, and Systematics 41: 59-80.
36. Espy MJ, Uhl JR, Sloan LM, Buckwalter SP, Jones MF, Vetter EA, Yao JD, Wengenack NL, Rosenblatt JE, Cockerill FR III, Smith TF 2006. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clinical Microbiology Reviews 19: 165-256. (Pubitemid 43158452)
37. Evans CW, Wilson DA, Mills GN 2001. Quantitative competitive (qc) RT-PCR as a tool in biomarker analysis. Biomarkers. 6: 7-14. (Pubitemid 32066500)
38. Ficetola GF, Miaud C, Pompanon F, Taberlet P 2008. Species detection using environmental DNA from water samples. Biology Letters 4: 423-425. (Pubitemid 351961462)
39. Field KG, Samadpour M 2007. Fecal source tracking, the indicator paradigm, and managing water quality. Water Research 41: 3517-3538. (Pubitemid 47179855)
40. Galil BS 2007. Loss or gain? Invasive aliens and biodiversity in the Mediterranean Sea. Marine Pollution Bulletin 55: 314-322. (Pubitemid 46551183)
41. Gescher C, Metfies K, Medlin LK 2008. The ALEX CHIP: development of a DNA chip for identification and monitoring of Alexandrium. Harmful Algae 7: 485-494.
42. Girones R, Ferrú s MA, Alonso JL, Rodriguez-Manzano J, Calgua B, de Abreu Corrêa A, Hundesa A, Carratala A, Bofill-Mas S 2010. Molecular detection of pathogens in water: the pros and cons of molecular techniques. Water Research 44: 4325-4339.
43. Glenn TC 2011. Field guide to next-generation DNA sequencers. Molecular Ecology Resources 11: 759-769.
44. Godhe A, Cusack C, Pedersen J, Anderson P, Anderson DM, Breasnan E, Cembella A, Dahl E, Diercks S, Elbrachter M, Edler L, Galluzzi L, Gescher C, Gladstone M, Karlson B, Kulis D, LeGresley M, Lindahl O, Marin R, McDermott G, Medlin LK, Naustvoll L-J, Penna A, Tobe K 2007. Intercalibration of classical and molecular techniques for identification of Alexandrium fundyense (Dinophyceae) and estimation of cell densities. Harmful Algae 6: 56-72. (Pubitemid 46043456)
45. Goldberg CS, Pilliod DS, Arkle RS, Waits LP 2011. Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders. PLoS ONE 6: e22746.
46. Gordon DP 2012. The New Zealand inventory of biodiversity. Volume 1: Kingdom Animalia: Radiata, Lophotrochozoa, and Deuterostomia. Christchurch, New Zealand, Canterbury University Press. 566 p.
47. Greenfield DI, Marin R, Doucette GJ, Mikulski C, Jones K, Jensen S, Roman B, Alvarado N, Feldman J, Scholin C 2008. Field applications of the second-generation environmental sample processor (ESP) for remote detection of harmful algae: 2006-2007. Limnology and Oceanography-Methods 6: 667-679.
48. Griffin DW, Lipp EK, McLaughlin MR, Rose JB 2001. Marine recreation and public health microbiology: quest for the ideal indicator. Bioscience 51: 817-826.
49. Hajibabaei M, Shokralla S, ZhouX, Singer GAC, Baird DJ 2011. Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6 (4): 17497.
50. Harvey JBJ, Hoy MS, Rodriguez RJ 2009. Molecular detection of native and invasive marine invertebrate larvae present in ballast and open water environmental samples collected in Puget Sound. Journal of Experimental Marine Biology and Ecology 369: 93-99.
51. Harvey JBJ, Ryan JP, Marin R, Preston CM, Alvarado N, Scholin CA, Vrijenhoek RC 2012. Robotic sampling, in situmonitoring and molecular detection of marine zooplankton. Journal of Experimental Marine Biology and Ecology 413: 60-70.
52. Havens KE 2008. Cyanobacteria blooms: effects on aquatic ecosystems. Advances in Experimental Medicine and Biology 619: 733-747.
53. Hayes KR, Cannon R, Neil K, Inglis G 2005. Sensitivity and cost considerations for the detection and eradication of marine pests in ports. Marine Pollution Bulletin 50: 823-834. (Pubitemid 41184630)
54. Heath M, Wood SA, Ryan K 2010. Polyphasic assessment of freshwater benthic mat forming cyanobacteria isolated from New Zealand. FEMS Microbiology Ecology 73: 95-109.
55. Hebert PDN, Cywinska A, Ball SL, deWaard JR 2003. Biological identification through DNA barcodes. Proceedings of the Royal Society of London B 270: 313-321. (Pubitemid 36228536)
56. Heid CA, Stevens J, Livak KJ, Williams PM 1996. Real-time quantitative PCR. Genome Research 6: 986-994.
57. Hewitt CL, Willing J, Bauckham A, Cassidy AM, Cox CMS, Jones L, Wotton DM 2004. New Zealand marine biosecurity: delivering outcomes in a fluid environment. New Zealand Journal of Marine and Freshwater Research 38: 429-438. (Pubitemid 39474412)
58. Hewitt J, Bell D, Simmons GC, Rivera-Aban M, Wolf S, Greening GE 2007. Gastroenteritis outbreak caused by waterborne norovirus at a New Zealand ski resort. Applied and Environmental Microbiology 73: 7853-7857. (Pubitemid 350308801)
59. Hickey CW 1995. Ecotoxicity in New Zealand. Australasian Journal of Ecotoxicology 1: 43-50.
60. Hogg ID, Smith BJ, Banks JC, Dewaard JR, Hebert PDN 2009. Testing use of mitochondrial COI sequences for the identification and phylogenetic analysis of New Zealand caddis flies (Trichoptera). New Zealand Journal of Freshwater and Marine Research 43: 1137-1146.
61. Hopkins GA, Forrest BM 2010. Challenges associated with pre-border management of biofouling on oil rigs. Marine Pollution Bulletin 60: 1924-1929.
62. Humbert JF, Quiblier C, Gugger M 2010. Molecular approaches for monitoring potential toxic marine and freshwater phytoplankton species. Analytical and Bioanalytical Chemistry 397: 1723-1732.
63. Jasperse JA 1993. Marine toxins and New Zealand shellfish. Proceedings of a workshop on research issues, 10-11 June 1993. Royal Society of New Zealand Miscellaneous Series 24. 68 p.
64. Jerde CL, Mahon AR, Chadderton WL, Lodge DM 2011. Sight-unseen' detection of rare aquatic species using environmental DNA. Conservation Letters 4: 150-157.
65. Jofre J, Blasi M, Bosch A, Lucena F 1989. Occurrence of bacteriophages infecting Bacteroides fragilis and other viruses in polluted marine sediments. Water Science and Technology 21: 15-19. (Pubitemid 19178422)
66. John U, Medlin LK, Groben R 2005. Development of specific rRNA probes to distinguish between geographic clades of the Alexandrium tamarense species complex. Journal of Plankton Research 27: 199-204. (Pubitemid 40307291)
67. Jones WJ, Preston CM, Marin R, Scholin CA, Vrijenhoek RC 2008. A robotic molecular method for in situdetection of marine invertebrate larvae. Molecular Ecology Resources 8: 540-550. (Pubitemid 351703591)
68. Kellmann R, Mihali TK, Jeon YJ, Pickford R, Pomati F, Neilan BA 2008. Biosynthetic intermediate analysis and functional homology reveal a saxitoxin gene cluster in cyanobacteria. Applied and Environmental Microbiology 7: 4044-4053. (Pubitemid 351962430)
69. Ki JS, Han MS 2006. A low-density oligonucleotide array study for parallel detection of harmful algal species using hybridization of consensus PCR products of LSU rDNA D2 domain. Biosensors and Bioelectronics 21: 1812-1821.
70. Kilroy C 2004. A new alien diatom, Didymosphenia geminata (Lyngbye) Schmidt: its biology, distribution, effects and potential risks for New Zealand fresh waters. Client Report CHC2004-128. Christchurch, New Zealand, National Institute of Water and Atmospheric Research. 34 p.
71. Kilroy C, Larned ST, Biggs BJF 2009. The nonindigenous diatom Didymosphenia geminata alters benthic communities in New Zealand rivers. Freshwater Biology 54: 1990-2002.
72. Kim KC, Byrne LB 2006. Biodiversity loss and the taxonomic bottleneck: emerging biodiversity science. Ecological Research 21: 794-810. (Pubitemid 44760451)
73. Kirs M, Cornelisen C 2011. MST technology for shellfish. Final report. Cawthron Report 2002. Nelson, New Zealand, Cawthron Institute. 36 p.
74. Kirs M, Harwood VJ, Gillespie PA, Fidler AE, Cornelisen CD, Fyfe WR 2008. Application of microbial source tracking (MST) technologies for identifying the source of microbial contamination in the lower Maitai River and Little Sydney Stream. Prepared for the Nelson City Council. Cawthron Report 1447. Nelson, New Zealand, Cawthron Institute. 42 p.
75. Kirs M, Harwood VJ, Fidler AE, Gillespie PA, Fyfe WR, Blackwood AD, Cornelisen CD 2011. Source tracking faecal contamination in an urbanised and a rural waterway in the Nelson-Tasman region, New Zealand. New Zealand Journal of Marine and Freshwater Research 45: 43-58.
76. Knox MA, Hicks BJ, Banks JC, Hogg ID 2009. Fish biosurveillance by genetic methods: a feasibility study. CBER Contract Report 90. Hamilton, New Zealand, Waikato University. 26 p.
77. Kuhajek J, Smith KF, Adamson JE, Wood SA 2011. PCR assay for the Mediterranean fan worm (Sabella spallanzanii). Prepared for MAF. Cawthron Report 1940. Nelson, New Zealand, Cawthron Institute. 42 p.
78. Laurie AD 2004. Quantitation of metallothionein mRNA from the New Zealand common bully (Gobiomorphus cotidianus) and its implications for biomonitoring. New Zealand Journal of Marine and Freshwater Research 38: 869-877. (Pubitemid 40199529)
79. Lear G, Boothroyd IKG, Turner SJ, Roberts K, Lewis GD 2009. A comparison of bacterial and benthic invertebrate community assemblages as indicators of ecological health within freshwater streams. Freshwater Biology 54: 1532-1543.
80. Lear G, Lewis GD 2009. Impact of catchment land use on bacterial communities within stream biofilms. Ecological Indicators 9: 848-855.
81. Lecroq B, Lejzerowicz F, Christen R, Esling P, Baerlocher L, Osteras M, Farinelli L, Pawlowski J 2011. Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments. Proceedings of the National Academy of Sciences USA 108: 13177-13182.
82. Leusch FDL, van den Heuvel MR, Laurie AD, Chapman HF, Gooneratne SR, Tremblay LA 2005. Quantification of vitellogenin mRNA induction in mosquitofish (Gambusia affinis) by reverse transcription real-time polymerase chain reaction (RT-PCR). Biomarkers 10: 429-438.
83. Lewis GD, Washington V, Lear G, Roberts K, Curran J, Fan V, Neale M 2011. A bacterial community index (BCI) for New Zealand streams. Auckland Regional Council Technical Report TR 2010/068. Auckland, New Zealand, Auckland City Council. 200 p.
84. Lipp EK, Farrah SA, Rose JB 2001. Assessment and impact of microbial fecal pollution and human enteric pathogens in a coastal community. Marine Pollution Bulletin 42: 286-293. (Pubitemid 32293540)
85. Liu W, Marsh T, Cheng H, Forney L 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Applied and Environmental Microbiology 63: 4516-4522. (Pubitemid 27485783)
86. Lougheed VL, Crosbie B, Chow-Fraser P 1998. Predictions on the effect of common carp (Cyprinus carpio) exclusion on water quality, zooplankton, and submergent macrophytes in a Great Lakes wetland. Canadian Journal of Fisheries and Aquatic Sciences 55: 1189-1197. (Pubitemid 28490062)
87. MacKenzie L, de Salas M, Adamson J, Beuzenberg V 2004. The dinoflagellate genus Alexandrium (Halim) in New Zealand coastal waters: comparative morphology, toxicity and molecular genetics. Harmful Algae 3: 71-92. (Pubitemid 38105885)
88. Mackenzie L 1991. Toxic and noxious phytoplankton in Big Glory Bay, Stewart Island, New Zealand. Journal of Applied Phycology 3: 19-34.
89. MacKenzie LA, Smith KF, Rhodes LL, Brown A, Langi V, Edgar M, Lovell G, Preece M 2011a. Mortalities of sea-cage salmon (Oncorhynchus tshawytscha) due to a bloom of Pseudochattonella verruculosa (Dictyochophyceae) in Queen Charlotte Sound, New Zealand. Harmful Algae 11: 45-53.
90. MacKenzie L, Harwood T, Boundy M, Smith K, Knight B, Jiang W, McNabb P, Selwood A, van Ginkel R, Langi V, Edgar M, Moisan C 2011b. An Alexandrium catenella bloom and associated saxitoxin contamination of shellfish, Queen Charlotte Sound, March-April 2011. Prepared for MAF Food Safety, Cawthron Report 1945. 31 p.
91. McCulloch GA 2011. Evolutionary genetics of southern stoneflies. PhD thesis. Department of Zoology. University of Otago, Dunedin, New Zealand.
92. McDowall RM 1990. New Zealand freshwater fishes: a natural history and guide. Auckland, New Zealand, Heinemann Reed. 553 p.
93. McDowall RM 2000. The Reed guide to New Zealand freshwater fishes. Auckland, New Zealand, Reed Books. 224 p.
94. McDowall RM 2004. Shoot first, and then ask questions: a look at aquarium fish imports and invasiveness in New Zealand. New Zealand Journal of Marine and Freshwater Research 38: 503-510. (Pubitemid 39464590)
95. Metzker ML 2010. Sequencing technologies: the next generation. Nature Reviews Genetics 11: 31-46.
96. Meyerson LA, Reaser JK 2002. Biosecurity: moving toward a comprehensive approach. Bioscience 52: 593-600. (Pubitemid 34780421)
97. Mihali TK, Kellmann R, Muenchoff J, Barrow KD, Neilan BA 2008. Characterization of the gene cluster responsible for cylindrospermopsin biosynthesis. Applied and Environmental Microbiology 74: 716-722. (Pubitemid 351225723)
98. Minamoto T, Yamanaka H, Takahara T, Honjo M, Kawabata Z 2011. Surveillance of fish species composition using environmental DNA. Limnology. doi: 10.1007/s10201-011-0362-4: 1-5
99. Ministry for the Environment 2007. Environment New Zealand 2007. Wellington, New Zealand, Ministry for the Environment. 455 p.
100. Ministry for the Environment and Ministry of Health 2009. New Zealand guidelines for managing cyanobacteria in recreational fresh waters: interim guidelines. Prepared for the Ministry for the Environment and the Ministry of Health by SA Wood, DP Hamilton, WJ Paul, KA Safi, WM Williamson. Wellington, New Zealand, Ministry for the Environment. 89 p.
101. Monis PT, Giglio S, Saint CP 2005. 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. Analytical and Bioanalytical Chemistry 340: 24-34. (Pubitemid 40404098)
102. Moriarty E, Gilpin B 2009. Faecal source tracking in the Avon River, Christchurch March-May 2009. Report R09/67 prepared for Environment Canterbury. Christchurch, New Zealand, Institute of Environmental Science and Research Ltd. 36 p.
103. Mountfort D, Rhodes L, Broom J, Gladstone M, Tyrell J 2007. Fluorescent in situ hybridization assay as a species-specific identifier of the Northern Pacific seastar, Asterias amurensis. New Zealand Journal of Marine and Freshwater Research 41: 283-290. (Pubitemid 350057729)
104. Mountfort D, Smith KF, Kirs M, Kuhajek J, Adamson JE, Wood SA 2012. Development of single and multispecies detection methods for the surveillance and monitoring of marine pests in New Zealand. Aquatic Invasions 7: 125-128.
105. Murray SA, Wiese M, Stuken A, Brett S, Kellmann R, Hallegraeff G, Neilan BA 2011. sxtA-based quantitative molecular assay to identify saxitoxin-producing harmful algal blooms in marine waters. Applied and Environmental Microbiology 77: 7050-7057.
106. Myers JH, Simberloff D, Kuris AM, Carey JR 2000. Eradication revisited: dealing with exotic species. Trends in Ecology & Evolution 15: 316-320. (Pubitemid 30484255)
107. Novis P, Halle C, Wilson B, Tremblay LA 2009. Identification and characterisation of freshwater algae isolated from a pollution gradient using rbcL sequences and toxicity testing. Archives of Environmental Contamination and Toxicology 57: 504-514.
108. Olsen D, Wood SA, Fidler A, Hitchings T, Waters J 2007. Phylogeny of New Zealand leptophlebiid mayflies: molecular evidence. In: Joint meeting of the New Zealand Freshwater Sciences Society and the Australian Society for Limnology, 3-7 December. Queenstown, New Zealand.
109. Penna A, Bertozzini E, Battocchi C, Galluzzi L, Giacobbe MG, Vila M, Garces E, Luglie A, Magnani M 2007. Monitoring of HAB species in the Mediterranean Sea through molecular methods. Journal of Plankton Research 29: 19-38. (Pubitemid 46536690)
110. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J 2009. Metagenomic pyrosequencing and microbial identification. Clinical Chemistry 55: 856-866.
111. Pina B, Casado M, Quiro L 2007. Analysis of gene expression as a new tool in ecotoxicology and environmental monitoring. Trends in Analytical Chemistry 26: 1145-1154. (Pubitemid 350181152)
112. Preston CM, Harris A, Ryan JP, Roman B, Marin R III, Jensen S, Everlove C, Birch J, Dzenitis JM, Pargett D, Adachi M, Turk K, Zehr JP, Scholin CA 2011. Underwater application of quantitative PCR on an ocean mooring. PLoS ONE 6: e22522.
113. Ranjard L, Poly F, Lata JC, Mougel C, Thioulouse J, Nazaret S 2001. Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Applied and Environmental Microbiology 67: 4479-4487. (Pubitemid 33646075)
114. Ratnasingham NS, Hebert PDN 2007. The barcode of life data system (www.barcodinglife.co.org). Molecular Ecology Notes 7: 355-364.
115. Read GB, Inglis G, Stratford P, Ahyong ST 2011. Arrival of the alien fanworm Sabella spallanzanii (Gmelin, 1791) (Polychaeta: Sabellidae) in two New Zealand harbours. Aquatic Invasions 6: 273-279.
116. Rhodes L, Scholin C, Garthwaite I 1998. Pseudonitzschia in New Zealand and the role of DNA probes and immunoassays in refining marine biotoxin monitoring programmes. Natural Toxins 6: 105-111. (Pubitemid 29121547)
117. Rhodes LL, Mackenzie AL, Kaspar HF, Todd KE 2001a. Harmful algae and mariculture in New Zealand. ICES Journal of Marine Science 58: 398-403. (Pubitemid 32533237)
118. Rhodes L, Scholin CA, Tyrrell JV, Adamson J, Todd K 2001b. The integration of DNA probes into New Zealand's routine phytoplankton monitoring programs. In:Hallegraeff GM, Blackburn SI, Bolch CJ, Lewis RJ eds Harmful algal blooms 2000. Proceedings of the 9th International Conference on Harmful Algal Blooms. Paris, Intergovernmental Oceanographic Commission of UNESCO. Pp. 429-432.
119. Rhodes LL, Adamson JE, Rublee PA, Schaefer E 2006. Geographic distribution of Pfiesteria spp. (Pfiesteriaceae) in Tasman Bay and Canterbury, New Zealand (2002-03). New Zealand Journal of Marine and Freshwater Research 40: 211-220. (Pubitemid 43774440)
120. Rhodes L, Smith K, de Salas M 2007. DNA probes, targeting large sub-unit rRNA, for the rapid identification of the paralytic shellfish poison producing dinoflagellate, Gymnodinium catenatum. New Zealand Journal of Marine and Freshwater Research 41: 385-390. (Pubitemid 351236643)
121. Rhodes LL, Smith KF, Moisan C 2012. Shifts and stasis in marine HAB monitoring in New Zealand. Environmental Science and Pollution Research. In press.
122. Richardson P 2010. Special issue: next generation DNA sequencing. Genes 1: 385-387.
123. Robarts RD, Waiser MJ, Arts MT, Evans MS 2005. Seasonal and diel changes of dissolved oxygen in a hypertrophic prairie lake. Lakes & Reservoirs: Research and Management 10: 167-177. (Pubitemid 43922845)
124. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M et al. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-352.
125. Rueckert A, Cary SC 2009. Use of an armored RNA standard to measure microcystin synthetase E gene expression in toxic Microcystis sp. by reverse-transcription QPCR. Limnology and Oceanography: Methods 7: 509-520.
126. Rueckert A, Wood SA, Cary SC 2007. Development and field assessment of a quantitative PCR for the detection and enumeration of the noxious bloom-former Anabaena planktonica. Limnology and Oceanography: Methods 5: 474-483. (Pubitemid 351773955)
127. Ryan J, Greenfield D, Marin R, Preston C, Roman B, Jensen S, Pargett D, Birch J, Mikulski C, Doucette G, Scholin C 2011. Harmful phytoplankton ecology studies using an autonomous molecular analytical and ocean observing network. Limnology and Oceanography 56: 1255-1272.
128. Sanger F, Coulson AR 1975. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Biology 94: 441-448.
129. Scholin CA, Buck KR, Britschgi T, Cangelosi G, Chavez FP 1996. Identification of Pseudonitzschia australis (Bacillariophyceae) using rRNA-targeted probes in whole cell and sandwich hybridization formats. Phycologia 35: 190-197. (Pubitemid 126586706)
130. Scholin CA, Miller PE, Buck K, Chavez F, Harris P, Haydock P, Howard J, Cangelosi G 1997. Detection and quantification of Pseudonitzschia australis in cultured and natural populations using LSU rRNA-targeted probes. Limnology and Oceanography 42: 1265-1272. (Pubitemid 128731833)
131. Scholin CA, Vreiling E, Peperzak L, Rhodes L, Rublee P 2003. Detection of HAB species using lectin, antibody and DNA probes. In: Hallegraeff GM, Anderson DM, Cembella AD eds. Manual on harmful marine micro-algae. Paris, UNESCO Publishing. Pp. 131-164.
132. Scholin C, Doucette G, Jensen S, Roman B, Pargett D, Marin R, Preston C, Jones W, Feldman J, Everlove C, Harris A, Alvarado N, Massion E, Birch J, Greenfield D, Vrijenhoek R, Mikulski C, Jones K 2009. Remote detection of marine microbes, small invertebrates, harmful algae, and biotoxins using the environmental sample processor (ESP). Oceanography 22: 158-167.
133. Scott TM, Rose JB, Jenkins TM, Farrah SR, Lukasik J 2002. Microbial source tracking: current methodology and future directions. Applied and Environmental Microbiology 68: 5796-5803. (Pubitemid 36342410)
134. Seafood Industry Council 2012. Economic review of the seafood industry, Edition 1, June 2012. Wellington, New Zealand Seafood Industry Council Ltd. 6 pp.
135. Shokralla S, Spall JL, Gibson JF, Hajibabaei M 2012. Next-generation sequencing technologies for environmental DNA research. Molecular Ecology 21: 1794-1805.
136. Simberloff D 2001. Eradication of island invasives: practical actions and results achieved. Trends in Ecology and Evolution 16: 273-274. (Pubitemid 32706632)
137. Simmons G, Garbutt C, Hewitt J, Greening G 2007. A New Zealand outbreak of norovirus gastroenteritis linked to the consumption of imported raw Korean oysters. The New Zealand Medical Journal 120 (1264): U2773.
138. Smith F, Wood SA, Ginkel Rv, Broady P, Gaw S 2011. First report of saxitoxin production by a species of the freshwater benthic cyanobacterium, Scytonema Agardh. Toxicon 57: 566-573.
139. Smith KF, Rhodes LL, Selwood AI, Marfell MJ, Zeewoldt CM, de Salas MF, Haywood AJ, Scholin CA 2007. Massive Karenia mikimotoi bloom in Northland, New Zealand: use of traditional and molecular techniques for rapid identification of HAB species. Harmful Algae News 34: 1-3.
140. Smith KF, Cahill PL, Fidler AE 2010. First record of the solitary ascidian Ciona savignyi Herdman, 1882 in the southern hemisphere. Aquatic Invasions 5: 363-368.
141. Smith KF, Rhodes LL, Adamson JE, Tyrrell JV, Mountfort DO, Jones WJ 2011. Application of a sandwich hybridisation assay for rapid detection of the Northern Pacific seastar, Asterias amurensis. New Zealand Journal of Marine and Freshwater Research 45: 145-152.
142. Smith KF, Thia J, Gemmill CEC, Cary SC, Fidler AE 2012a. Barcoding of the cytochrome oxidase I (COI) indicates a recent introduction of Ciona savignyi into New Zealand and a rapid method for Ciona species discrimination. Aquatic Invasions 7: 305-313.
143. Smith KF, Wood SA, Mountfort DO, Cary SC 2012b. Development of a real-time PCR assay for the detection of the invasive clam, Corbula amurensis, in environmental samples. Journal of Experimental Marine Biology and Ecology 412: 52-57.
144. Smith PJ, Webber WR, McVeagh SM, Inglis GJ, Gust N 2003. DNA and morphological identification of an invasive swimming crab, Charybdis japonica, in New Zealand waters. New Zealand Journal of Marine and Freshwater Research 37: 753-762. (Pubitemid 38065627)
145. Smith PJ, Page M, Handley SJ, McVeagh SM, Ekins M 2007. First record of the Australian ascidian Eudistoma elongatum in northern New Zealand. New Zealand Journal of Marine and Freshwater Research 41: 347-355. (Pubitemid 351236639)
146. Sogin ML, Morrison HG, Huber JA et al. 2006. Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proceedings of the National Academy of Sciences USA 103: 12115-12120. (Pubitemid 44215820)
147. Sousa R, Gutiérrez J, Aldridge D 2009. Nonindigenous invasive bivalves as ecosystem engineers. Biological Invasions 11: 2367-2385.
148. Souza V, Rocha M, Valera A, Eguiarte LE 1999. Genetic structure of natural populations of Escherichia coli in wild hosts on different continents. Applied and Environmental Microbiology 65: 3373-3385. (Pubitemid 29398959)
149. Stark JD 1985. A macroinvertebrate community index of water quality for stony streams. Water and Soil Miscellaneous Publication 87. Wellington, New Zealand, National Water and Soil Conservation Authority. 53 p.
150. Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner HW, Richards TA 2010. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology 19: 21-31.
151. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH 2012. Environmental DNA: a special issue on DNA metabarcoding. Molecular Ecology 21: 1789-1793.
152. Tillett D, Dittmann E, Erhard M, Dohren H, Borner T. Neilan BA 2000. Structural organization of microcystin biosynthesis in Microcystis aeruginosa PCC7806: an integrated peptidepolyketide synthetase system. Chemistry and Biology 7: 753-764.
153. Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, Willerslev E 2012. Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE 7(8): e41732. doi: 10.1371/journal.pone. 0041732
154. Townsend CR, Winterbourn MJ 1992. Assessment of the environmental risk posed by an exotic fish: the proposed introduction of channel catfish (Ictalurus punctatus) to New Zealand. Conservation Biology 6: 273-282. (Pubitemid 23397095)
155. Townsend CR 2003. Individual, population, community, and ecosystem consequences of a fish invader in New Zealand streams. Conservation Biology 17: 38-47. (Pubitemid 36234398)
156. Tyrrell J, Bergquist PR, Saul D, Mackenzie L, Bergquist PL 1997. Oligonucleotide probe technology as applied to the study of harmful algal blooms. New Zealand Journal of Marine and Freshwater Research 31: 551-560. (Pubitemid 28147014)
157. Tyrrell JV, Connell LB, Scholin CA 2002. Monitoring for Heterosigma akashiwo using a sandwich hybridization assay. Harmful Algae 1: 205-214. (Pubitemid 37379145)
158. Utermö hl H 1958. Zur vervollkommung der quantitativen phytoplankton methodik (Towards a perfection of quantitative phytoplankton methodology). Mitteilungen der Internationale Vereinigung fü r Theoretische und Angewandte Limnologie 9: 1-38.
159. Vaitomaa J, Rantala A, Halinen K, Rouhiainen L, Tallberg P, Mokelke L, Sivonen K 2003. Quantitative real-time PCR for determination of microcystin synthetase E copy numbers for Microcystis and Anabaena in lakes. Applied and Environmental Microbiology 69: 7289-7297. (Pubitemid 38585381)
160. van den Heuvel MR, Michel C, Stevens MI, Clarke AC, Stö lting KN, Hicks BJ, Tremblay LA 2007. Monitoring the effects of pulp and paper effluent is restricted in genetically distinct populations of common bully (Gobiomorphus cotidianus). Environmental Science and Technology 41: 2602-2608. (Pubitemid 46595234)
161. Vitousek PM, D'Antonio CM, Loope LL, Rejmanek M, Westbrooks R 1997. Introduced species: a significant component of human-caused global change. New Zealand Journal of Ecology 21: 1-16.
162. Wallentinus I, Nyberg CD 2007. Introduced marine organisms as habitat modifiers. Marine Pollution Bulletin 55: 323-332. (Pubitemid 46551185)
163. Wang W, Chen K, XuC 2006. DNA quantification using EvaGreen and a real-time PCR instrument. Analytical Biochemistry 356: 303-305. (Pubitemid 44291653)
164. Wang Z, Gerstein M, Snyder M 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10: 57-63.
165. Wear RG, Gardner JPA 2001. Biological effects of the toxic algal bloom of February and March 1998 on the benthos of Wellington Harbour, New Zealand. Marine Ecology Progress Series 218: 63-76. (Pubitemid 32913883)
166. Wittenberg R, Cock MJW eds. 2001. Invasive alien species: a toolkit of best prevention and management practices. Wallingford, UK, CAB International. 228 p.
167. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ 2003. High-resolution genotyping by amplicon melting analysis using LCGreen. Clinical Chemistry 49: 853-860. (Pubitemid 36623462)
168. Wold B, Myers RM 2008. Sequence census methods for functional genomics. Nature Methods 5: 19-21.
169. Wood SA, Stirling DJ, Briggs LR, Sprosen J, Holland PT, Ruck JG, Wear RG 2006. Survey of cyanotoxins in New Zealand waterbodies between 2001 and 2004. New Zealand Journal of Marine and Freshwater Research 40: 585-595.
170. Wood SA, Selwood AI, Rueckert A, Holland PT, Milne JR, Smith KF, Smits B, Watts LF, Cary CS 2007. First report of homoanatoxin-a and associated dog neurotoxicosis in New Zealand. Toxicon 50: 292-301. (Pubitemid 47042145)
171. Wood SA, Jentzsch K, Rueckert A, Hamilton D, Cary SC 2008a. Hindcasting cyanobacterial communities in Lake Okaro with germination experiments and genetic analyses. FEMS Microbiology Ecology 67: 252-260.
172. Wood SA, Rueckert A, Cowan DA, Cary SC 2008b. Sources of edaphic cyanobacterial diversity in the Dry Valleys of Eastern Antarctica. ISME Journal 2: 308-320. (Pubitemid 351334279)
173. Wood SA, Heath M, McGregor G, Holland PT, Munday R, Ryan K 2010a. Identification of a benthic microcystin producing filamentous cyanobacterium (Oscillatoriales) associated with a dog poisoning in New Zealand. Toxicon 55: 987-903.
174. Wood SA, Heath M, Kuhajek J, Ryan K 2010b. Fine scale spatial variability of anatoxin-a and homoanatoxin-a production in benthic cyanobacteria; implication for monitoring and management. Journal of Applied Microbial Ecology 109: 2011-2018.
175. Wood SA, Rueckert A, Cary SC, Hamilton DP, Dietrich DR 2010c. Switching toxin production on and off: intermittent microcystin synthesis in a Microcystis bloom. Environmental Microbiology Reports 3: 118-124.
176. Wood SA, Dietrich DR, Cary SC, Hamilton DP 2012. Increasing Microcystis cell abundance enhances microcystin synthesis: a mesocosm study. Inland Waters 2: 17-22.
177. Zamor RM, Glenn KL, Hambright KD 2012. Incorporating molecular tools into routine HAB monitoring programs: using qPCR to track invasive Prymnesium. Harmful Algae 15: 1-7.
178. Zhang J, Chiodini R, Badr A, Zhang G 2011. The impact of next-generation sequencing on genomics. Journal of Genetic Genomics 38: 95-109.