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

The assessment of biological samples is critical for measuring the 'health' of New Zealand aquatic environments. Analysis of these samples commonly requires species identification and enumeration, which usually involves microscopy or microbiological methods. These techniques can be time-co...

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Bibliographic Details
Published in:New Zealand journal of marine and freshwater research 2013-03, Vol.47 (1), p.90-119
Main Authors: Wood, SA, Smith, KF, Banks, JC, Tremblay, LA, Rhodes, L, Mountfort, D, Cary, SC, Pochon, X
Format: Article
Language:English
Subjects:
Algae
automated ribosomal intergenic spacer analysis
Automation
fluorescent in situ hybridisation
Freshwater
Marine
Microbiology
next-generation sequencing
Polymerase chain reaction
quantitative polymerase chain reaction
Rotifera
sandwich hybridisation arrays
Sanger DNA sequencing
terminal restriction fragment length polymorphism
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Summary:The assessment of biological samples is critical for measuring the 'health' of New Zealand aquatic environments. Analysis of these samples commonly requires species identification and enumeration, which usually involves microscopy or microbiological methods. These techniques can be time-consuming, laborious, and are dependent on taxonomic expertise. Recent advances in molecular methods provide promising tools for assessing environmental samples. A range of molecular techniques are now used in New Zealand including: fluorescent in situ hybridisation; automated ribosomal intergenic spacer analysis; quantitative polymerase chain reaction; and, most recently, next-generation sequencing. The organisms (or targets) and environments monitored are equally diverse, ranging from cyanobacteria, rotifers and invasive fish in lakes, to macroinvertebrates, and biofilm communities in rivers, to bacteria, micro- and macro-algae and invertebrates in marine ecosystems. Despite research and validation demonstrating their potential, the application of these tools by monitoring agencies has been limited. Legislative requirements, costs, and a reluctance to change methodologies, are the most likely reasons for this. This review examines molecular tools that have been previously or are currently used for monitoring aquatic environments in New Zealand, and explores how these, and new techniques, may be applied in the future.
ISSN:0028-8330
1175-8805
DOI:10.1080/00288330.2012.745885