Part B | 16.3
442 Part B Tools and Methods in Marine Biotechnology
culture, fisheries, and tourism, and negative impacts
on human health [16.3]. The total economic cost of
a marine pest incursion is difficult to accurately define but in Australia, a major marine pest eradication
has been estimated to cost up to AUD$263M [16.6].
The few examples of successful eradication of marine invasive species worldwide have been when the
invasion has been detected in its very early stages,
and/or it is restricted to an area that can be isolated from the rest of the marine environment (e.g.,
Caulerpa taxifolia eradication in Southern California [16.7]; black-striped mussels, Mytilopsis sallei, in
Darwin, Australia [16.8, 9]).
Marine invasive species include a wide range of
plant and animal taxa. These include macro and microalgae, molluscs, crustaceans, annelids, echinoderms,
cnidarians, ascidians, and teleosts. The development
and implementation of rapid, sensitive, and accurate
diagnostic techniques for the identification and surveillance of marine pests from environmental samples (e.g.,
sea water, sediments, and ships’ ballast), particularly in
areas that are currently pest free, is an essential step in
early detection and control of marine pests [16.10–12].
In this chapter, we:
i) Briefly describe techniques traditionally used for
the identification and/or surveillance of marine
pests.
ii) Review DNA technical approaches for the identification of species and definition of genetic markers.
iii) Describe recent PCR-based and ecogenomic methods for the detection of marine invasive species.
iv) Propose some options for the development of improved molecular diagnostic techniques.
16.2 Traditional Techniques
Baseline surveys and repeated monitoring conducted
by experienced biologists are the prime requirement
for early detection of marine pest species using standard methods. Campbell et al. [16.13] reviewed the five
survey methods commonly employed for the detection
of marine pest species: Hewitt and Martin protocols,
rapid assessment surveys, Bishop Museum protocols,
Chilean aquaculture surveys, and passive sampling protocols. These methods typically involve physical sampling, sorting, and identification to understand the resident biota and identify marine pests.
Traditional survey methods typically require specialized taxonomic experts, trained in identifying organisms across a range of life-cycle stages. The sorting
and identification of plants and animals is time consuming, sometimes taking years before species are
accurately identified, but the sampling data provided by
surveys of this kind provide an important baseline understanding of biodiversity for future pest surveillance
and ecological research. There is a global decline in taxonomic expertise [16.14, 15]. Given the wide range of
taxa required to be identified in marine pest surveys
and the inherent difficulties in identification, there is
a need to develop methods that work in conjunction
with, and are complementary to, available taxonomic
expertise.
16.3 Sample Collection
The development of sensitive and specific molecular
tools is highly important and has been the focus of
most recent published studies on the development of
marine invasive species surveillance. Without effective
environmental sampling strategies and DNA extraction
techniques, these molecular tools will prove largely
ineffective.
16.3.1 Extraction of Genomic DNA
from Environmental Samples
Mackie and Geller [16.16] developed a qPCR (quantitative PCR) for the detection of brine shrimp. The principle behind this was to use brine shrimp (Artemia spp.)
as an additive to plankton samples. Artemia spp. inhabit hypersaline environments, so they are perfectly
suited to being utilized as a quality control spike in
marine plankton samples. Recently, the approach used
by [16.16] was modified and used a sample quality control for the marine invasive species monitoring of Port
plankton samples in Australia (personal observations).
Freeze-dried Artemia sp. are added to each individual plankton sample at the time of collection and the
Artemia qPCR assay is utilized to assess whether samples have been stored and preserved adequately for
further analysis for marine invasive species.
442 Part B Tools and Methods in Marine Biotechnology
culture, fisheries, and tourism, and negative impacts
on human health [16.3]. The total economic cost of
a marine pest incursion is difficult to accurately define but in Australia, a major marine pest eradication
has been estimated to cost up to AUD$263M [16.6].
The few examples of successful eradication of marine invasive species worldwide have been when the
invasion has been detected in its very early stages,
and/or it is restricted to an area that can be isolated from the rest of the marine environment (e.g.,
Caulerpa taxifolia eradication in Southern California [16.7]; black-striped mussels, Mytilopsis sallei, in
Darwin, Australia [16.8, 9]).
Marine invasive species include a wide range of
plant and animal taxa. These include macro and microalgae, molluscs, crustaceans, annelids, echinoderms,
cnidarians, ascidians, and teleosts. The development
and implementation of rapid, sensitive, and accurate
diagnostic techniques for the identification and surveillance of marine pests from environmental samples (e.g.,
sea water, sediments, and ships’ ballast), particularly in
areas that are currently pest free, is an essential step in
early detection and control of marine pests [16.10–12].
In this chapter, we:
i) Briefly describe techniques traditionally used for
the identification and/or surveillance of marine
pests.
ii) Review DNA technical approaches for the identification of species and definition of genetic markers.
iii) Describe recent PCR-based and ecogenomic methods for the detection of marine invasive species.
iv) Propose some options for the development of improved molecular diagnostic techniques.
16.2 Traditional Techniques
Baseline surveys and repeated monitoring conducted
by experienced biologists are the prime requirement
for early detection of marine pest species using standard methods. Campbell et al. [16.13] reviewed the five
survey methods commonly employed for the detection
of marine pest species: Hewitt and Martin protocols,
rapid assessment surveys, Bishop Museum protocols,
Chilean aquaculture surveys, and passive sampling protocols. These methods typically involve physical sampling, sorting, and identification to understand the resident biota and identify marine pests.
Traditional survey methods typically require specialized taxonomic experts, trained in identifying organisms across a range of life-cycle stages. The sorting
and identification of plants and animals is time consuming, sometimes taking years before species are
accurately identified, but the sampling data provided by
surveys of this kind provide an important baseline understanding of biodiversity for future pest surveillance
and ecological research. There is a global decline in taxonomic expertise [16.14, 15]. Given the wide range of
taxa required to be identified in marine pest surveys
and the inherent difficulties in identification, there is
a need to develop methods that work in conjunction
with, and are complementary to, available taxonomic
expertise.
16.3 Sample Collection
The development of sensitive and specific molecular
tools is highly important and has been the focus of
most recent published studies on the development of
marine invasive species surveillance. Without effective
environmental sampling strategies and DNA extraction
techniques, these molecular tools will prove largely
ineffective.
16.3.1 Extraction of Genomic DNA
from Environmental Samples
Mackie and Geller [16.16] developed a qPCR (quantitative PCR) for the detection of brine shrimp. The principle behind this was to use brine shrimp (Artemia spp.)
as an additive to plankton samples. Artemia spp. inhabit hypersaline environments, so they are perfectly
suited to being utilized as a quality control spike in
marine plankton samples. Recently, the approach used
by [16.16] was modified and used a sample quality control for the marine invasive species monitoring of Port
plankton samples in Australia (personal observations).
Freeze-dried Artemia sp. are added to each individual plankton sample at the time of collection and the
Artemia qPCR assay is utilized to assess whether samples have been stored and preserved adequately for
further analysis for marine invasive species.