An Investigation of the Impacts of Ponded Pastures on Barramundi and Other Finfish Populations in Tropical Coastal Wetlands

Objectives: 1) To document the extent of ponded pastures and other pondage systems in and adjacent to coastal wetlands on the central coast of Queensland. 2) To assess the movement, growth and survival of barramundi in ponded pastures. 3) To assess the utilisation by barramundi of ponded pastures and wetlands dominated by exotic grass species. 4) To identify appropriate wetland management strategies for facilitating barramundi movement and survival in ponded pastures and other pondage systems. 5) To document the species composition of finfish populations and their relative abundance in ponded pastures.

Eicosapentaenoic acid, arachidonic acid and eicosanoid metabolism in juvenile barramundi Lates calcarifer

A two part experiment was conducted to assess the response of barramundi (Lates calcarifer; initial weight = 10.3 ± 0.03 g; mean ± S.D.) fed one of five diets with varying eicosapentaenoic acid (diets 1, 5, 10, 15 and 20 g/kg) or one of four diets with varying arachidonic acid (1, 6, 12, 18 g/kg) against a fish oil control diet. After 6 weeks of feeding, the addition of EPA or ARA did not impact on growth performance or feed utilisation. Analysis of the whole body fatty acids showed that these reflected those of the diets. The ARA retention demonstrated an inversely related curvilinear response to either EPA or ARA. The calculated marginal utilisation efficiencies of EPA and ARA were high (62.1 and 91.9 % respectively) and a dietary ARA requirement was defined (0.012 g/kg(0.796)/day). The partial cDNA sequences of genes regulating eicosanoid biosynthesis were identified in barramundi tissues, namely cyclooxygenase 1 (Lc COX1a, Lc COX1b), cyclooxygenase 2 (Lc COX2) and lipoxygenase (Lc ALOX-5). Both Lc COX2 and Lc ALOX-5 expression in the liver tissue were elevated in response to increasing dietary ARA, meanwhile expression levels of Lc COX2 and the mitochondrial fatty acid oxidation gene carnitine palmitoyltransferase 1 (Lc CPT1a) were elevated in the kidney. A low level of EPA increased the expression of Lc COX1b in the liver. Consideration should be given to the EPA to ARA balance for juvenile barramundi in light of nutritionally inducible nature of the cyclooxygenase and lipoxygenase enzymes.

Defining the allometric relationship between size and individual fatty acid turnover in barramundi Lates calcarifer

An experiment was conducted with barramundi (Asian seabass; Lates calcarifer) to examine the allometric scaling effect of individual fatty acids. Six treatment size classes of fish were deprived of food for 21days (Treatment A, 10.5±0.13g; Treatment B, 19.2±0.11g; Treatment C, 28.3±0.05g; Treatment D, 122.4±0.10g; Treatment E, 217.6±0.36g; Treatment F, 443.7±1.48g; mean±SD) with each treatment comprising of fifteen fish, in triplicate. The assessment of somatic losses of whole-body energy and lipid were consistent with previous studies, validating the methodology to be extended to individual fatty acids. Live-weight (LW) exponent values were determined to be 0.817±0.010 for energy and 0.895±0.007 for lipid. There were significant differences among the fatty acids ranging from 0.687±0.005 for 20:5n-3 (eicosapentaenoic acid) and 0.954±0.008 for 18:1n-9 (oleic acid). The LW exponent values were applied to existing fatty acid intake and deposition data of barramundi fed with either 100% fish oil or 100% poultry oil. From this the maintenance requirement for each fatty acid was determined. The metabolic demands for maintenance and growth were then iteratively determined for fish over a range of size classes. Application of these exponent values to varying levels of fatty acid intake demonstrated that the biggest driver in the utilisation of fatty acids in this species is deposition demand and despite their reputed importance, the long-chain polyunsaturated fatty acids had nominal to no maintenance requirement.

Fatty acid metabolism in barramundi (Lates Calcarifer)

This PhD contributes towards an complete understanding of lipid metabolism in the barramundi (Lates calcarifer), a culturally important and profitable aquaculture species. The work extended from a more general applied approach through to a complex understanding of molecular mechanisms and lipid bioenergetics.

The influence of dietary fatty acid and fasting on the hepatic lipid metabolism of barramundi (Lates calcarifer)

For many fish species, dietary fish oil (FO) has been substituted with other oils such as poultry oil (PO) without affecting growth performance. However, in barramundi, the mechanisms by which fatty acid metabolism is regulated are poorly understood, and the effects of FO substitution are unknown. This study defined changes in the expression of genes controlling the metabolism of fatty acids in barramundi over a 24-h time period after a single meal. From one to 12 h after a single feeding event, the expression of fatty acid synthesis genes in the liver was upregulated, while genes involved in the β-oxidation showed minimal alteration. However, the expression of β-oxidation genes was significantly correlated with the expression of genes regulating fatty acid synthesis. In a second experiment, the changes in liver fatty acid composition and gene expression were defined after FO was substituted with PO. Liver fatty acid profile reflected the diet composition, with some subtle exceptions supporting the enrichment of certain long-chain polyunsaturated fatty acids in the liver. The fish from all experimental groups preferentially retained more docosahexaenoic acid than eicosapentaenoic acid in the liver, suggesting a bioconversion of this fatty acid to intermediate fatty acids. Replacement of FO with PO significantly regulated genes controlling both fatty acid synthesis and catabolism pathways, potentially related to a higher percentage of monounsaturated fatty acids, in the livers of fish fed these diets. The results demonstrated that diet composition significantly altered the lipid metabolism in barramundi and that there was a balance between direct dietary effects and endogenous synthetic capacity.

A broad-scale analysis of links between coastal fisheries production and mangrove extent : a case-study for northeastern Australia

The paradigm that mangroves are critical for sustaining production in coastal fisheries is widely accepted, but empirical evidence has been tenuous. This study showed that links between mangrove extent and coastal fisheries production could be detected for some species at a broad regional scale (1000s of kilometres) on the east coast of Queensland, Australia. The relationships between catch-per-unit-effort for different commercially caught species in four fisheries (trawl, line, net and pot fisheries) and mangrove characteristics, estimated from Landsat images were examined using multiple regression analyses. The species were categorised into three groups based on information on their life history characteristics, namely mangrove-related species (banana prawns Penaeus merguiensis, mud crabs Scylla serrata and barramundi Lates calcarifer), estuarine species (tiger prawns Penaeus esculentus and Penaeus semisulcatus, blue swimmer crabs Portunus pelagicus and blue threadfin Eleutheronema tetradactylum) and offshore species (coral trout Plectropomus spp.). For the mangrove-related species, mangrove characteristics such as area and perimeter accounted for most of the variation in the model; for the non-mangrove estuarine species, latitude was the dominant parameter but some mangrove characteristics (e.g. mangrove perimeter) also made significant contributions to the models. In contrast, for the offshore species, latitude was the dominant variable, with no contribution from mangrove characteristics. This study also identified that finer scale spatial data for the fisheries, to enable catch information to be attributed to a particular catchment, would help to improve our understanding of relationships between mangroves and fisheries production.

Rapid assessment of genotype-by-environment interactions and heritability for growth rate in aquaculture species using in vitro fertilisation and DNA tagging

Commercial environments may receive only a fraction of expected genetic gains for growth rate as predicted from the selection environment This fraction is the result of undesirable genotype-by-environment interactions (G x E) and measured by the genetic correlation (r(g)) of growth between environments. Rapid estimates of genetic correlation achieved in one generation are notoriously difficult to estimate with precision. A new design is proposed where genetic correlations can be estimated by utilising artificial mating from cryopreserved semen and unfertilised eggs stripped from a single female. We compare a traditional phenotype analysis of growth to a threshold model where only the largest fish are genotyped for sire identification. The threshold model was robust to differences in family mortality differing up to 30%. The design is unique as it negates potential re-ranking of families caused by an interaction between common maternal environmental effects and growing environment. The design is suitable for rapid assessment of G x E over one generation with a true 0.70 genetic correlation yielding standard errors as low as 0.07. Different design scenarios were tested for bias and accuracy with a range of heritability values, number of half-sib families created, number of progeny within each full-sib family, number of fish genotyped, number of fish stocked, differing family survival rates and at various simulated genetic correlation levels

Growth curves with time-dependent explanatory variables

A class of growth models incorporating time-dependent factors and stochastic perturbations are introduced. The proposed model includes the existing growth models used in fisheries as special cases. Particular attention is given to growth of a population (in average weight or length) from which observations are taken randomly each time and the analysis of tag-recapture data. Two real data sets are used for illustration: (a) to estimate the seasonal effect and population density effect on growth of farmed prawn (Penaeus monodon) from weight data and (b) to assess the effect of tagging on growth of barramundi (Lates calcarifer)

Growth curves with explanatory variables and estimation of the effect of tagging

The von Bertalanffy growth model is extended to incorporate explanatory variables. The generalized model includes the switched growth model and the seasonal growth model as special cases, and can also be used to assess the tagging effect on growth. Distribution-free and consistent estimating functions are constructed for estimation of growth parameters from tag-recapture data in which age at release is unknown. This generalizes the work of James (1991, Biometrics 47 1519-1530) who considered the classical model and allowed for individual variability in growth. A real dataset from barramundi (Lates calcarifer) is analysed to estimate the growth parameters and possible effect of tagging on growth.

Correlation of plasma IGF-I concentrations and growth rate in aquacultured finfish: a tool for assessing the potential of new diets

A recently developed radioimmunoassay (RIA) for measuring insulin-like growth factor (IGF-I) in a variety of fish species was used to investigate the correlation between growth rate and circulating IGF-I concentrations of barramundi (Lates calcarifer), Atlantic salmon (Salmo salar) and Southern Bluefin tuna (Thunnus maccoyii). Plasma IGF-I concentration significantly increased with increasing ration size in barramundi and IGF-I concentration was positively correlated to growth rates obtained in Atlantic salmon (r2=0.67) and barramundi (r2=0.65) when fed a variety of diet formulations. IGF-I was also positively correlated to protein concentration (r2=0.59). This evidence suggested that measuring IGF-I concentration may provide a useful tool for monitoring fish growth rate and also as a method to rapidly assess different aquaculture diets. However, no such correlation was demonstrated in the tuna study probably due to seasonal cooling of sea surface temperature shortly before blood was sampled. Thus, some recommendations for the design and sampling strategy of nutritional trials where IGF-I concentrations are measured are discussed

Improved Approach for Analyzing Bromophenols in Seafood Using Stable Isotope Dilution Analysis in Combination with SPME

An analytical method for the measurement of five naturally occurring bromophenols of sensory relevance in seafood (barramundi and prawns) is presented. The method combines simultaneous distillation−extraction followed by alkaline back extraction of a hexane extract and subsequent acetylation of the bromophenols. Analysis of the bromophenol acetates was accomplished by headspace solid phase microextraction and gas chromatography−mass spectrometry using selected ion monitoring. The addition of 13C6 bromophenol stable isotope internal standards for each of the five congeners studied permitted the accurate quantitation of 2-bromophenol, 4-bromophenol, 2,6-dibromophenol, 2,4-dibromophenol, and 2,4,6-tribromophenol down to a limit of quantification of 0.05 ng/g of fish flesh. The method indicated acceptable precision and repeatability and excellent linearity over the typical concentration range of these compounds in seafood (0.5−50 ng/g). The analytical method was applied to determine the concentration of bromophenols in a range of farmed and wild barramundi and prawns and was also used to monitor bromophenol uptake in a pilot feeding trial.

Developments in controlled green-water larval culture technologies for estuarine fishes in Queensland, Australia and elsewhere

Since 1989, researchers with the Department of Primary Industries and Fisheries (DPI&F) in Queensland, Australia, have successfully used controlled low-water exchange green-water cultures to rear the larvae of estuarine fishes and crustaceans through to metamorphosis. High survivals and excellent fry condition have been achieved for several commercially important endemic species produced for various projects. They include barramundi or sea bass, Lates calcarifer, Australian bass, Macquaria novemaculeata, dusky flathead, Platycephalus fuscus, sand whiting, Sillago ciliata, red sea bream or snapper, Pagrus auratus, banana prawn, Fenneropenaeus merguiensis, and others. The consistent success of our standardised and relatively simple approach at different localities has led to it being incorporated into general fingerling production practices at several establishments in Australia. Although post-metamorphosis rearing methods have differed for each species investigated, due to various biological and behavioural traits and project requirements, these larval rearing methods have been successful with few species-specific modifications. Initially modelled on the Taiwanese approach to rearing Penaeids in aerated low-water exchange cultures, the approach similarly appears to rely on a beneficial assemblage of micro-organisms. Conceptually, these micro-organisms may include a mixture of the air-borne primary invaders of pure phytoplankton cultures when exposed to outdoor conditions. Whilst this would vary with different sites, our experiences with these methods have consistently been favourable. Mass microalgal cultures with eco-physiological youth are used to regularly augment larval fish cultures so that rearing conditions simulate an exponential growth-phase microalgal bloom. Moderate to heavy aeration prevents settlement of particulate matter and encourages aerobic bacterial decomposition of wastes. The green-water larval rearing approach described herein has demonstrated high practical utility in research and commercial applications, and has greatly simplified marine finfish hatchery operations whilst generally lifting production capacities for metamorphosed fry in Australia. Its potential uses in areas of aquaculture other than larviculture are also discussed.

Phylogenetic analysis of betanodavirus isolates from Australian finfish

In Australia, disease caused by betanodavirus has been reported in an increasing number of cultured finfish since the first report of mortalities in 1990. Partial coat protein gene sequences from the T2 or T4 regions of 8 betanodaviruses from barramundi Lates calcarifer, sleepy cod Oxyeleotris lineolata, striped trumpeter Latris lineata, barramundi cod Cromileptes altivelis, Australian bass Macquaria novemaculata and gold-spotted rockcod Epinephelus coioides from several Australian states were determined. Analysis of the 606 bp nucleotide sequences of the T2 region of 4 isolates demonstrated the close relationship with isolates from the red-spotted grouper nervous necrosis virus (RGNNV) genotype and the Cluster Ia subtype. Comparison of a smaller 289 bp sequence from the T4 region identified 2 distinct groupings of the Australian isolates within the RGNNV genotype. Isolates from barramundi from the Northern Territory, barramundi, sleepy cod, barramundi cod and gold-spotted rockcod from Queensland, and striped trumpeter from Tasmania shared a 96.2 to 99.7%, nucleotide identity with each other. These isolates were most similar to the RGNNV genotype Cluster Ia. Isolates from Australian bass from New South Wales and from barramundi from South Australia shared a 98.6% sequence identity with each other. However, these isolates only shared an 85.8 to 87.9%, identity with the other Australian isolates and representative RGNNV isolates. The closest nucleotide identity to sequences reported in the literature for the New South Wales and South Australian isolates was to an Australian barramundi isolate (Ba94Aus) from 1994. These 2 Australian isolates formed a new subtype within the RGNNV genotype, which is designated as Cluster Ic.

Flow impacts on estuarine finfish fisheries of the Gulf of Carpentaria

The estuaries of Australia s tropical rivers support commercial fisheries for finfish and shellfish valued at over $220 million per annum. There are also significant tourism-related and local recreational and indigenous fisheries for icon species such as barramundi. Development of water resources in Australia's Tropical Rivers region is being considered for the Flinders, Mitchell, McArthur, Roper, Daly and Victoria catchments. Greater knowledge of the freshwater requirements of tropical aquatic ecosystems, including estuaries is crucial, so that the communities of catchments where water resource development occurs can be assured that the downstream effects of such development are considered and managed based on the best available knowledge.