Part B | 16.7
448 Part B Tools and Methods in Marine Biotechnology
have been effectively used for a wide range of taxa, localities, and environs (i. e., sediments and water) such as
Sydney Harbour sediments [16.91], marine anoxic water [16.92], ecological characteristics of viruses [16.93],
and biotic assemblages of soil DNA [16.94]. The development of molecular tools for ecological monitoring
potentially allows for more complete, rapid, and cost effective assessment of biodiversity and ecological shifts
to be conducted [16.73]. These methods, once developed and validated, will be applicable to a range of
marine habitats that are currently poorly understood.
These methods show great potential for the ongoing monitoring and early detection of marine invasive
species. Ecogenomic methods can be used to develop
baseline information of species assemblages, making
subsequent monitoring exercises of ports and harbors
more informative, allowing for the loss of endemic biodiversity to be monitored alongside invasive species
monitoring.
Recent studies [16.74, 95] have shown the effectiveness of 454 pyrosequencing for marine invasive species
detection. Pochon et al. [16.74] were able to demonstrate that the detection limit for the Northern Pacific
seastar, Asterias amurensis is equivalent to qPCR-based
detection methods.
Ecogenomic techniques offer the ability to screen
environmental samples for a broad range of organisms
at once, process large numbers of samples quickly, and
offer the ability to screen not only for invasive species
(or pathogens) but also for endemic species to provide
a broader indication of environmental health [16.91].
Next generation sequencing technology may also facilitate baseline screening of ports and harbors to obtain
a rapid understanding of the presence and population
densities of all species. This may aid in tailoring more
focussed screening for marine invasive species specific
to a geographical area and provide valuable data for
modeling invasion biology.
16.7 Future Approaches
Commercial shipping can act as a major vector in marine pest translocation [16.95, 96]. Ballast water commonly used to control the trim and draft of a vessel
can contain larval and adult stages of marine pest
species [16.97]. The potential for these pests to be discharged into a new environment and flourish is high for
some species [16.4]. Hull-fouling is also a significant
translocation vector, while solid ballast was a dominant
vector in previous centuries. As a consequence, ports
are the major entry points for the majority of new marine pest incursions. Thus port and ballast water surveys
are targeted to areas where effective and efficient detection and management strategies can be implemented to
aid in successful prevention and mitigation of marine
invasive species invasions.
16.7.1 Routine Monitoring
and Surveillance
of Marine Invasive Species
in Port Waters
Routine monitoring using molecular technologies can
alleviate the demand for time-consuming and costly traditional port surveys. Understanding marine invasive
species assemblages in ports is a vital tool for managing ballast water in a cost-effective manner as the
management requirements are reduced or eliminated
for transfers between ports with similar suites of pest
species. Robust qPCR, particularly in laboratories with
high-throughput capability, can be used to rapidly assess samples for a wide range of marine invasive species
at a fraction of the cost of traditional surveys. The vast
majority of existing molecular-based assays for marine
pests (Table 16.1) are not suited to high-throughput applications, so conversion of tests to formats such as
qPCR is important. Continued dedicated research is required to provide reliable, uniform testing procedures
(e.g., qPCR) for pest species that display genetic differences across their range. Routine monitoring programs
utilizing robust, sensitive, and specific assays for a wide
range of marine pest species provide the ability for authorities to monitor and manage marine pest incursions
in a cost-effective way.
16.7.2 Testing Ballast Water
Molecular methods could minimize delays and provide
data on ballast water safety. There are technical and
logistical hurdles to provide suitable testing including
timeliness to avoid unnecessary delays. This would be
best achieved by streamlining sample collection and
DNA extraction.
An effective way to collect ballast water samples is
to filter a known amount of water (and ballast sediment)
448 Part B Tools and Methods in Marine Biotechnology
have been effectively used for a wide range of taxa, localities, and environs (i. e., sediments and water) such as
Sydney Harbour sediments [16.91], marine anoxic water [16.92], ecological characteristics of viruses [16.93],
and biotic assemblages of soil DNA [16.94]. The development of molecular tools for ecological monitoring
potentially allows for more complete, rapid, and cost effective assessment of biodiversity and ecological shifts
to be conducted [16.73]. These methods, once developed and validated, will be applicable to a range of
marine habitats that are currently poorly understood.
These methods show great potential for the ongoing monitoring and early detection of marine invasive
species. Ecogenomic methods can be used to develop
baseline information of species assemblages, making
subsequent monitoring exercises of ports and harbors
more informative, allowing for the loss of endemic biodiversity to be monitored alongside invasive species
monitoring.
Recent studies [16.74, 95] have shown the effectiveness of 454 pyrosequencing for marine invasive species
detection. Pochon et al. [16.74] were able to demonstrate that the detection limit for the Northern Pacific
seastar, Asterias amurensis is equivalent to qPCR-based
detection methods.
Ecogenomic techniques offer the ability to screen
environmental samples for a broad range of organisms
at once, process large numbers of samples quickly, and
offer the ability to screen not only for invasive species
(or pathogens) but also for endemic species to provide
a broader indication of environmental health [16.91].
Next generation sequencing technology may also facilitate baseline screening of ports and harbors to obtain
a rapid understanding of the presence and population
densities of all species. This may aid in tailoring more
focussed screening for marine invasive species specific
to a geographical area and provide valuable data for
modeling invasion biology.
16.7 Future Approaches
Commercial shipping can act as a major vector in marine pest translocation [16.95, 96]. Ballast water commonly used to control the trim and draft of a vessel
can contain larval and adult stages of marine pest
species [16.97]. The potential for these pests to be discharged into a new environment and flourish is high for
some species [16.4]. Hull-fouling is also a significant
translocation vector, while solid ballast was a dominant
vector in previous centuries. As a consequence, ports
are the major entry points for the majority of new marine pest incursions. Thus port and ballast water surveys
are targeted to areas where effective and efficient detection and management strategies can be implemented to
aid in successful prevention and mitigation of marine
invasive species invasions.
16.7.1 Routine Monitoring
and Surveillance
of Marine Invasive Species
in Port Waters
Routine monitoring using molecular technologies can
alleviate the demand for time-consuming and costly traditional port surveys. Understanding marine invasive
species assemblages in ports is a vital tool for managing ballast water in a cost-effective manner as the
management requirements are reduced or eliminated
for transfers between ports with similar suites of pest
species. Robust qPCR, particularly in laboratories with
high-throughput capability, can be used to rapidly assess samples for a wide range of marine invasive species
at a fraction of the cost of traditional surveys. The vast
majority of existing molecular-based assays for marine
pests (Table 16.1) are not suited to high-throughput applications, so conversion of tests to formats such as
qPCR is important. Continued dedicated research is required to provide reliable, uniform testing procedures
(e.g., qPCR) for pest species that display genetic differences across their range. Routine monitoring programs
utilizing robust, sensitive, and specific assays for a wide
range of marine pest species provide the ability for authorities to monitor and manage marine pest incursions
in a cost-effective way.
16.7.2 Testing Ballast Water
Molecular methods could minimize delays and provide
data on ballast water safety. There are technical and
logistical hurdles to provide suitable testing including
timeliness to avoid unnecessary delays. This would be
best achieved by streamlining sample collection and
DNA extraction.
An effective way to collect ballast water samples is
to filter a known amount of water (and ballast sediment)