No description available.

The genus Ceratomyxa Thélohan, 1892 is one of the largest myxozoan genera, the species of which almost always infect the gall bladder of marine teleosts. Although there are over 180 species known globally, prior to this study only three had been described from Australia. This study explores the systematics, host specificity and species richness of Ceratomyxa species from a diverse range of Queensland marine fishes. The first part of this thesis deals with the issues associated with spore based taxonomy and incorporates the first molecular studies to investigate host specificity and radiation in three common families of Great Barrier Reef (GBR) fishes. Twenty-two new species were described in these chapters, and although they were superficially similar in morphology all were genetically distinct. A focus on Ceratomyxa spp. infecting labrid, pomacentrid and serranid fish revealed tight host specificity of parasite species, confirmed the presence of multiple parasite species in a single host and revealed that no parasite radiation had occurred that could be associated with co-evolution with host families. Exploration of intra- and inter-specific variation by sequencing of multiple replicates from host/parasite combinations allowed interpretation of species boundaries within the system. Ten additional species described in Chapter 5 supported the findings from the labrid, pomacentrid and serranid studies but broadened the host range studied. In total 32 Ceratomyxa species were described from Queensland fishes increasing the number of described species in the genus by 15%. This study also reports on undescribed species collected from a further 70 host species and broadens the known host range to seven families of fishes. A checklist of bivalvulidans from marine teleosts in Australia is compiled of described and undescribed species and highlights the abundance of Ceratomyxa relative to other gall bladder dwelling myxosporeans. A phylogeny of the Ceratomyxa based on SSU rDNA analyses explored the taxonomic integrity of the genus. In general, the morphological diagnostic characters that divide the Myxozoa into genera are not well supported by molecular phylogenetic analyses. The relationship between 42 Ceratomyxa spp. and 36 other marine myxosporeans was examined using Bayesian inference, maximum likelihood and maximum parsimony. Results indicate Ceratomyxa is one of the most cohesive lineages within the Myxozoa and that the freshwater fish parasite, C. shasta, does not represent an independent lineage as suggested in previous studies. The strict host specificity of Ceratomyxa species prompted the investigation of species richness on the GBR. Species accumulation curves were used to explore species richness by using Choa2 and Jackknife1 estimators. The estimates suggested Ceratomyxa is almost as rich as their teleost hosts and that 1,600 species could be present on the GBR and as many as 15,000 species may exist globally. As an unexpected result, Ceratomyxa may be the richest metazoan genus in the sea. In light of what the study revealed, a revision of a second genus within the family Ceratomyxidae, Leptotheca, is presented. The boundaries between Ceratomyxa and Leptotheca were unclear. The diagnostic characters that separate these genera (length to thickness ratios) were found to be plastic and the type species of Leptotheca ultimately fitted the diagnosis for Ceratomyxa. To eliminate confusion between these genera and also between Sphaerospora and Leptotheca, the genus Leptotheca was considered invalid, with all species appropriately assigned to other genera based on morphological and biological characters and supported by genetic evidence.

Coral reefs are experiencing increasing levels of stress due to climate change, overfishing, coastal development and nutrient runoff from agriculture to name a few. They are however, economically vital ecosystems in terms of both their income generating capacity and as a source of food for millions of people around the world. This predicament emphasises the need for effective ecosystem management to be able to balance the benefits of coral reefs with the inherent stressors associated with people utilising their resources. It is particularly important given the potential large scale impacts associated with climate change such as mass coral bleaching events. Similarly, much of the need for direct management of coral reefs exists in developing countries where the resources, information, and technology are limited or unavailable for such a task. This places them, in particular, at the high end of management uncertainty and impact vulnerability. Accordingly, there is a pronounced need to improve this capacity to understand coral reef ecosystem function and to use this to better predict the overall systems level outcome of management options. This thesis has sought to improve our understanding of key ecological elements of coral reef ecosystems and to build on this new knowledge to produce a widely applicable ecosystem model that will allow managers to better understand and predict the outcomes of their actions. Coral reef ecosystem behaviour is far from understood in its entirety and there are many facets that require detailed further investigations to be able to more confidently predict ecosystem response to any given disturbance. To enhance the current understanding of coral reef ecosystems prior to the model development, investigations were undertaken into the dynamics of nitrogen on a coral reef following bleaching induced coral mortality. The results showed that the rates of nitrogen fixation on surfaces made available due to a coral mortality event increased dramatically in the three months following coral mortality, potentially acting as a driving force for the ecosystem to pass through a phase shift to algal dominance. Application of these nitrogen dynamics to entire coral reef ecosystems required a methodology for scaling these sub coral colony processes to entire reefs. This scaling issue is particularly pertinent given the improved understanding of the overwhelming significance of micro-scale processes to community dynamics. The surface index (SI) concept, relating the two-dimensional projected area to the three-dimensional area of corals was refined and developed for variations of gross coral morphologies. This allowed for the scaling of nitrogen flux estimates to be made over entire reef systems, enabling the incorporation of these fluxes into an ecosystem scale model. One of the key factors associated with the potential for a coral reef to recover from a mass coral mortality event is the potential for new corals to successfully recruit. The process of coral recovery could potentially be enhanced if recruitment is viable in the immediate aftermath of a mortality event. Although investigations in this area were inconclusive, extensive herbivore action on turf assemblages up to eight months old indicated that recruitment may be inhibited through the high palatability of turf assemblages in this age bracket. Integrating these processes with the many other published dynamics of coral reefs allowed for the development of the dynamic systems model. By constraining the model structure to known relationships between the modelling parameters, the model can be calibrated to replicate the dynamics of any coral reef ecosystem. This allows the model to be applied to systems where limited data and/or resources are available, making it widely implementable in developing countries such as the small island states scattered around the tropics. The model is ideally suited to the adaptive management framework whereby managers can continually assess the potential future outcomes of management interventions. In addition, due to the spatially inexplicit and generic nature of the model, it can be easily adapted and integrated into large scale regional modelling frameworks or combined with other modelling packages such as socio-economic or fisheries models to provide enhanced management packages. The culmination of the targeted research and integration of existing knowledge has allowed for the development of an ecosystem model for coral reefs that can be easily adopted by coral reef managers throughout the world. It is however, by no means a definitive coral reef ecosystem model and there are many facets that can and should continue to be refined to enhance the reliability of the model.

The genus Ceratomyxa Thélohan, 1892 is one of the largest myxozoan genera, the species of which almost always infect the gall bladder of marine teleosts. Although there are over 180 species known globally, prior to this study only three had been described from Australia. This study explores the systematics, host specificity and species richness of Ceratomyxa species from a diverse range of Queensland marine fishes. The first part of this thesis deals with the issues associated with spore based taxonomy and incorporates the first molecular studies to investigate host specificity and radiation in three common families of Great Barrier Reef (GBR) fishes. Twenty-two new species were described in these chapters, and although they were superficially similar in morphology all were genetically distinct. A focus on Ceratomyxa spp. infecting labrid, pomacentrid and serranid fish revealed tight host specificity of parasite species, confirmed the presence of multiple parasite species in a single host and revealed that no parasite radiation had occurred that could be associated with co-evolution with host families. Exploration of intra- and inter-specific variation by sequencing of multiple replicates from host/parasite combinations allowed interpretation of species boundaries within the system. Ten additional species described in Chapter 5 supported the findings from the labrid, pomacentrid and serranid studies but broadened the host range studied. In total 32 Ceratomyxa species were described from Queensland fishes increasing the number of described species in the genus by 15%. This study also reports on undescribed species collected from a further 70 host species and broadens the known host range to seven families of fishes. A checklist of bivalvulidans from marine teleosts in Australia is compiled of described and undescribed species and highlights the abundance of Ceratomyxa relative to other gall bladder dwelling myxosporeans. A phylogeny of the Ceratomyxa based on SSU rDNA analyses explored the taxonomic integrity of the genus. In general, the morphological diagnostic characters that divide the Myxozoa into genera are not well supported by molecular phylogenetic analyses. The relationship between 42 Ceratomyxa spp. and 36 other marine myxosporeans was examined using Bayesian inference, maximum likelihood and maximum parsimony. Results indicate Ceratomyxa is one of the most cohesive lineages within the Myxozoa and that the freshwater fish parasite, C. shasta, does not represent an independent lineage as suggested in previous studies. The strict host specificity of Ceratomyxa species prompted the investigation of species richness on the GBR. Species accumulation curves were used to explore species richness by using Choa2 and Jackknife1 estimators. The estimates suggested Ceratomyxa is almost as rich as their teleost hosts and that 1,600 species could be present on the GBR and as many as 15,000 species may exist globally. As an unexpected result, Ceratomyxa may be the richest metazoan genus in the sea. In light of what the study revealed, a revision of a second genus within the family Ceratomyxidae, Leptotheca, is presented. The boundaries between Ceratomyxa and Leptotheca were unclear. The diagnostic characters that separate these genera (length to thickness ratios) were found to be plastic and the type species of Leptotheca ultimately fitted the diagnosis for Ceratomyxa. To eliminate confusion between these genera and also between Sphaerospora and Leptotheca, the genus Leptotheca was considered invalid, with all species appropriately assigned to other genera based on morphological and biological characters and supported by genetic evidence.

Coral reefs are experiencing increasing levels of stress due to climate change, overfishing, coastal development and nutrient runoff from agriculture to name a few. They are however, economically vital ecosystems in terms of both their income generating capacity and as a source of food for millions of people around the world. This predicament emphasises the need for effective ecosystem management to be able to balance the benefits of coral reefs with the inherent stressors associated with people utilising their resources. It is particularly important given the potential large scale impacts associated with climate change such as mass coral bleaching events. Similarly, much of the need for direct management of coral reefs exists in developing countries where the resources, information, and technology are limited or unavailable for such a task. This places them, in particular, at the high end of management uncertainty and impact vulnerability. Accordingly, there is a pronounced need to improve this capacity to understand coral reef ecosystem function and to use this to better predict the overall systems level outcome of management options. This thesis has sought to improve our understanding of key ecological elements of coral reef ecosystems and to build on this new knowledge to produce a widely applicable ecosystem model that will allow managers to better understand and predict the outcomes of their actions. Coral reef ecosystem behaviour is far from understood in its entirety and there are many facets that require detailed further investigations to be able to more confidently predict ecosystem response to any given disturbance. To enhance the current understanding of coral reef ecosystems prior to the model development, investigations were undertaken into the dynamics of nitrogen on a coral reef following bleaching induced coral mortality. The results showed that the rates of nitrogen fixation on surfaces made available due to a coral mortality event increased dramatically in the three months following coral mortality, potentially acting as a driving force for the ecosystem to pass through a phase shift to algal dominance. Application of these nitrogen dynamics to entire coral reef ecosystems required a methodology for scaling these sub coral colony processes to entire reefs. This scaling issue is particularly pertinent given the improved understanding of the overwhelming significance of micro-scale processes to community dynamics. The surface index (SI) concept, relating the two-dimensional projected area to the three-dimensional area of corals was refined and developed for variations of gross coral morphologies. This allowed for the scaling of nitrogen flux estimates to be made over entire reef systems, enabling the incorporation of these fluxes into an ecosystem scale model. One of the key factors associated with the potential for a coral reef to recover from a mass coral mortality event is the potential for new corals to successfully recruit. The process of coral recovery could potentially be enhanced if recruitment is viable in the immediate aftermath of a mortality event. Although investigations in this area were inconclusive, extensive herbivore action on turf assemblages up to eight months old indicated that recruitment may be inhibited through the high palatability of turf assemblages in this age bracket. Integrating these processes with the many other published dynamics of coral reefs allowed for the development of the dynamic systems model. By constraining the model structure to known relationships between the modelling parameters, the model can be calibrated to replicate the dynamics of any coral reef ecosystem. This allows the model to be applied to systems where limited data and/or resources are available, making it widely implementable in developing countries such as the small island states scattered around the tropics. The model is ideally suited to the adaptive management framework whereby managers can continually assess the potential future outcomes of management interventions. In addition, due to the spatially inexplicit and generic nature of the model, it can be easily adapted and integrated into large scale regional modelling frameworks or combined with other modelling packages such as socio-economic or fisheries models to provide enhanced management packages. The culmination of the targeted research and integration of existing knowledge has allowed for the development of an ecosystem model for coral reefs that can be easily adopted by coral reef managers throughout the world. It is however, by no means a definitive coral reef ecosystem model and there are many facets that can and should continue to be refined to enhance the reliability of the model.

No description available.

No description available.

Pesticide runoff from agricultural applications poses a potential threat to water quality in the world heritage listed Great Barrier Reef (GBR) and sensitive monitoring tools are needed to facilitate effective monitoring of these pollutants. This thesis has worked to advance passive sampling tools for monitoring trace organic pollutants and their potential impacts on the GBR. The suitability of several available passive sampling tools for detecting trace concentrations of target pesticide analytes was investigated in a laboratory calibration chamber before experiments were conducted to further understanding of the response of Chemcatcher passive samplers in environmental conditions likely to be experienced in the GBR. Passive samplers were deployed in a survey of pesticides in the GBR environment and extracts were applied in bioassays to investigate their application for predicting mixture toxicity to GBR biota. When employed and interpreted appropriately, passive sampling tools have been shown to provide for sensitive and reproducible detection of organic pollutants in relatively pristine environments. While considerable research has been conducted into the performance and theory of analyte uptake by a range of passive sampling devices, several key knowledge gaps existed and were addressed in this study. The applicability of the performance reference compound (PRC) concept as an in situ calibration method for passive samplers using Empore Disk sampling phases (Chemcatchers) to monitor polar compounds was investigated. This experiment showed that while uptake of pesticides was linear and reproducible, PRC loss was not linear, meaning that the dissipation rates of these PRCs cannot be used to estimate the effect of field exposure conditions on uptake rates. An alternative in situ calibration technique using PRC loaded polydimethylsiloxane (PDMS) disks deployed alongside the Chemcatchers as a surrogate calibration phase has been tested and shows promise for future applications. Pesticide concentrations in waters flowing to the GBR have been shown to undergo dramatic fluctuations over short time periods and the potential for these conditions to limit the integrative period of sampling was investigated by simulating a changing concentration event in a calibration chamber. The ability for samplers to predict average concentrations was dependant on the deployment configuration (with or without membrane) used and the period of deployment relative to the changing concentration event. Passive samplers were employed in a survey of pesticides in GBR waters during a wet and dry season at river mouths, two nearshore regions and an offshore region. The nearshore marine environment was shown to be contaminated with pesticides in both the dry and wet seasons (average water concentrations of 1.3-3.8 ng L-1 and 2.2-6.4 ng L-1, respectively), while no pesticides were detected further offshore. Continuous monitoring of two rivers over 13 months showed waters flowing to the GBR were contaminated with herbicides (diuron, atrazine, hexazinone) year round, with highest average concentrations present during summer months (350 ng L-1). The use of passive samplers has enabled identification of insecticides in GBR waters which have not been reported in the literature previously. Extracts from passive samplers deployed at three sites in the GBR were applied to bioassays targeting integral life stages or functions of coral reef biota: scleractinian coral larvae, sea urchin larvae, a marine diatom and marine bacteria. The results demonstrate the utility of pairing passive sampling with bioassays and reveal that mixtures of organic pollutants in the GBR have the potential to cause detrimental effects to coral reef biota. This research outlines an approach that reduces one of the levels of simplification of risk assessment of pollutants to ecosystems by incorporating mixtures of chemicals present in the environment. The use of passive sampler extracts in toxicity testing allows pollutant mixtures to be assessed at a range of enrichment factors and, with the inclusion of biota from the ecosystem of concern, improves the relevance of results for predicting real world effects. The findings of this thesis are intended to be used to improve the application of passive sampling tools for routine monitoring to provide managers with understanding of the pesticides present, the potential effects of those pollutant mixtures and feedback on the efficacy of implemented land management practices in halting and reversing the impacts of pesticides on the GBR.

Coral reefs are experiencing increasing levels of stress due to climate change, overfishing, coastal development and nutrient runoff from agriculture to name a few. They are however, economically vital ecosystems in terms of both their income generating capacity and as a source of food for millions of people around the world. This predicament emphasises the need for effective ecosystem management to be able to balance the benefits of coral reefs with the inherent stressors associated with people utilising their resources. It is particularly important given the potential large scale impacts associated with climate change such as mass coral bleaching events. Similarly, much of the need for direct management of coral reefs exists in developing countries where the resources, information, and technology are limited or unavailable for such a task. This places them, in particular, at the high end of management uncertainty and impact vulnerability. Accordingly, there is a pronounced need to improve this capacity to understand coral reef ecosystem function and to use this to better predict the overall systems level outcome of management options. This thesis has sought to improve our understanding of key ecological elements of coral reef ecosystems and to build on this new knowledge to produce a widely applicable ecosystem model that will allow managers to better understand and predict the outcomes of their actions. Coral reef ecosystem behaviour is far from understood in its entirety and there are many facets that require detailed further investigations to be able to more confidently predict ecosystem response to any given disturbance. To enhance the current understanding of coral reef ecosystems prior to the model development, investigations were undertaken into the dynamics of nitrogen on a coral reef following bleaching induced coral mortality. The results showed that the rates of nitrogen fixation on surfaces made available due to a coral mortality event increased dramatically in the three months following coral mortality, potentially acting as a driving force for the ecosystem to pass through a phase shift to algal dominance. Application of these nitrogen dynamics to entire coral reef ecosystems required a methodology for scaling these sub coral colony processes to entire reefs. This scaling issue is particularly pertinent given the improved understanding of the overwhelming significance of micro-scale processes to community dynamics. The surface index (SI) concept, relating the two-dimensional projected area to the three-dimensional area of corals was refined and developed for variations of gross coral morphologies. This allowed for the scaling of nitrogen flux estimates to be made over entire reef systems, enabling the incorporation of these fluxes into an ecosystem scale model. One of the key factors associated with the potential for a coral reef to recover from a mass coral mortality event is the potential for new corals to successfully recruit. The process of coral recovery could potentially be enhanced if recruitment is viable in the immediate aftermath of a mortality event. Although investigations in this area were inconclusive, extensive herbivore action on turf assemblages up to eight months old indicated that recruitment may be inhibited through the high palatability of turf assemblages in this age bracket. Integrating these processes with the many other published dynamics of coral reefs allowed for the development of the dynamic systems model. By constraining the model structure to known relationships between the modelling parameters, the model can be calibrated to replicate the dynamics of any coral reef ecosystem. This allows the model to be applied to systems where limited data and/or resources are available, making it widely implementable in developing countries such as the small island states scattered around the tropics. The model is ideally suited to the adaptive management framework whereby managers can continually assess the potential future outcomes of management interventions. In addition, due to the spatially inexplicit and generic nature of the model, it can be easily adapted and integrated into large scale regional modelling frameworks or combined with other modelling packages such as socio-economic or fisheries models to provide enhanced management packages. The culmination of the targeted research and integration of existing knowledge has allowed for the development of an ecosystem model for coral reefs that can be easily adopted by coral reef managers throughout the world. It is however, by no means a definitive coral reef ecosystem model and there are many facets that can and should continue to be refined to enhance the reliability of the model.

The objective of the research reported in this thesis was to develop a technique to monitor the dynamics of sediments and nutrients entering the coastal ocean with river plumes associated with high intensity low frequency events (e.g. floods), using ocean colour remote sensing. To achieve this objective, an inverse bio-optical model was developed, based on analytical and empirical relationships between concentrations of optically significant substances and remote sensing of water-leaving radiance. The model determines concentrations of water-colouring substances such as chlorophyll, suspended sediments, and coloured dissolved organic matter, as well as the values of optical parameters using water-leaving radiances derived from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS). To solve atmospheric correction in coastal waters, the aerosol type over clear waters is transferred to adjacent turbid water pixels. The vicinity of the Herbert River, central Great Barrier Reef zone, Australia, was used as a case study for the application of the algorithm developed. The satellite ocean colour technique was successfully validated using sea-truth measurements of water-colouring constituents acquired in the area during various seasons throughout 2002-2004. A high correlation between chlorophyll and dissolved organic matter was found in the coastal waters of the region, and when the bio-optical model was constrained to make chlorophyll a function of dissolved organic matter, the relationship between in situ and satellite-derived data was substantially improved. With reliable retrieval of the major water-colouring constituents, the technique was subsequently applied to study fluxes of particulate and dissolved organic and inorganic matter following a flood event in the Herbert River during the austral summer of 1999. Extensive field observations covering a seasonal flood in the Herbert River in February 2004 revealed high sediment and nutrient exports from the river to the adjacent coastal waters during the flood event. Due to rapid settling, the bulk of the sediment-rich influx was deposited close inshore, while the majority of nutrients exported from the river were consumed by phytoplankton in a relatively small area of the coastal ocean. With the help of ocean colour remote sensing, it was demonstrated that river-borne sediments and nutrients discharged by a typical flood in the Herbert River are mostly precipitated or consumed within the first 20 km from the coast and therefore are unlikely to reach and possibly affect the midshelf coral reefs of this section of the Great Barrier Reef lagoon.