History, status and future of Australia's native Sydney rock oyster industry

The Sydney rock oyster (Saccostrea glomerata) (SRO) is an oyster species that only occurs in estuaries along Australia's east coast. The SRO industry evolved from commercial gathering of oyster in the 1790s to a high production volume aquaculture industry in the 1970s. However, since the late 1970s the SRO industry has experienced a significant and continuous decline in production quantities and the industry's future commercial viably appears to be uncertain. The aim of this study was to review the history and the status of the SRO industry and to discuss the potential future prospects of this industry. This study summarised findings of the existing literature about the industry and defined development stages of the industry. Particular focus was put on the more recent development within the industry (1980s-present) which has not been covered adequately in the existing literature. The finding from this study revealed that major issues of the industry are linked to the management of prevailing diseases, the handling of water quality impairments from increasing coastal development, increasing competition from Australia's Pacific oyster (Crassostrea gigas) industry and the current socio-economic profile of the industry. The study also found that policy makers are currently confronted by the dilemma of saving a "dying art". Findings from this industry review may be vital for current and future fisheries managers and stakeholders as a basis for reviewing industry management and development strategies. This review may also be of interest for other aquaculture industries and fisheries who are dealing with similar challenges as the SRO industry.

Identification of bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei reveals distinct temperature-driven patterns

Change in temperature is often a major environmental factor in triggering waterborne disease outbreaks. Previous research has revealed temporal and spatial patterns of bacterial population in several aquatic ecosystems. To date, very little information is available on aquaculture environment. Here, we assessed environmental temperature effects on bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei (FASFL). Water samples were collected over a one-year period, and aquatic bacteria were characterized by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rDNA pyrosequencing. Resulting DGGE fingerprints revealed a specific and dynamic bacterial population structure with considerable variation over the seasonal change, suggesting that environmental temperature was a key driver of bacterial population in the FASFL. Pyrosequencing data further demonstrated substantial difference in bacterial community composition between the water at higher (WHT) and at lower (WLT) temperatures in the FASFL. Actinobacteria, Proteobacteria and Bacteroidetes were the highest abundant phyla in the FASFL, however, a large number of unclassified bacteria contributed the most to the observed variation in phylogenetic diversity. The WHT harbored remarkably higher diversity and richness in bacterial composition at genus and species levels when compared to the WLT. Some potential pathogenenic species were identified in both WHT and WLT, providing data in support of aquatic animal health management in the aquaculture industry.

Factors affecting reproductive performance of the prawn, Penaeus monodon

The growth of the Penaeus monodon prawn aquaculture industry in Australia is hampered by a reliance on wild-caught broodstock. This species has proven difficult to breed from if broodstock are reared in captivity. Studies were therefore carried out to investigate factors controlling reproduction and influencing egg quality. Results of the studies revealed that patterns of nutrient accumulation during early ovary development are altered by captive conditions, possibly contributing to reduce larval quality. The sinus gland hormones were shown, together with the environment, to regulate two stages of ovary development. In a separate study it was further revealed that the hormone methyl farnesoate (MF) could negatively regulate the final stages of ovary development. Lastly it was shown that broodstock reared in captivity are less likely to mate and that this is due to inherent problems in both the male and the female prawns.

Genetic resources in wild and cultured stocks of the Asian mud crab, Scylla paramamosain

The mud crab (Scylla spp.) aquaculture industry has expanded rapidly in recent years in many countries in the Indo - West Pacific (IWP) region as an alternative to marine shrimp culture because of significant disease outbreaks and associated failures of many shrimp culture industries in the region. Currently, practices used to produce and manage breeding crabs in hatcheries may compromise levels of genetic diversity, ultimately compromising growth rates, disease resistance and stock productivity. Therefore, to avoid “genetic pollution” and its harmful effects and to promote further development of mud crab aquaculture and fisheries in a sustainable way, a greater understanding of the genetic attributes of wild and cultured mud crab stocks is required. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations for multiple purposes including for commercial production, recreation and conservation and to increase profitability and sustainability of newly emerging crab culture industries. Phylogeographic patterns and the genetic structure of Asian mud crab populations across the IWP were assessed to determine if they were concordant with those of other widespread taxa possessing pelagic larvae of relatively long duration. A 597 bp fragment of the mitochondrial DNA COI gene was amplified and screened for variation in a total of 297 individuals of S. paramamosain from six sampling sites across the species’ natural geographical distribution in the IWP and 36 unique haplotypes were identified. Haplotype diversities per site ranged from 0.516 to 0.879. Nucleotide diversity estimates among haplotypes were 0.11% – 0.48%. Maximum divergence observed among S. paramamosain samples was 1.533% and samples formed essentially a single monophyletic group as no obvious clades were related to geographical location of sites. A weak positive relationship was observed however, between genetic distance and geographical distance among sites. Microsatellite markers were then used to assess contemporary gene flow and population structure in Asian mud crab populations sampled across their natural distribution in the IWP. Eight microsatellite loci were screened in sampled S. paramamosain populations and all showed high allelic diversity at all loci in sampled populations. In total, 344 individuals were analysed, and 304 microsatellite alleles were found across the 8 loci. The mean number of alleles per locus at each site ranged from 20.75 to 28.25. Mean allelic richness per site varied from 17.2 to 18.9. All sites showed high levels of heterozygosity as average expected heterozygosities for all loci ranged from 0.917 – 0.953 while mean observed heterozygosity ranged from 0.916 – 0.959. Allele diversities were similar at all sites and across all loci. The results did not show any evidence for major differences in allele frequencies among sites and patterns of allele frequencies were very similar in all populations across all loci. Estimates of population differentiation (FST) were relatively low and most probably largely reflect intra – individual variation for very highly variable loci. Results from nDNA analysis showed evidence for only very limited population genetic structure among sampled S. paramamosain, and a positive and significant association for genetic and geographical distance among sample sites. Microsatellite markers were then employed to determine if adequate levels of genetic diversity has been captured in crab hatcheries for the breeding cycle. The results showed that all microsatellite loci were polymorphic in hatchery samples. Culture populations were in general, highly genetically depauperate, compared with comparable wild populations, with only 3 to 8 alleles recorded for the same loci set per population. In contrast, very high numbers of alleles per locus were found in reference wild S. paramamosain populations, which ranged from 18 to 46 alleles per locus per population. In general, this translates into a 3 to 10 fold decline in mean allelic richness per locus in all culture stocks compared with wild reference counterparts. Furthermore, most loci in all cultured S. paramamosain samples showed departures from HWE equilibrium. Allele frequencies were very different in culture samples from that present in comparable wild reference samples and this in particular, was reflected in a large decline in allele diversity per locus. The pattern observed was best explained by significant impacts of breeding practices employed in hatcheries rather than natural differentiation among wild populations used as the source of brood stock. Recognition of current problems and management strategies for the species both for the medium and long-term development of the new culture industry are discussed. The priority research to be undertaken over the medium term for S. paramamosain should be to close the life cycle fully to allow individuals to be bred on demand and their offspring equalised to control broodstock reproductive contributions. Establishing a broodstock register and pedigree mating system will be required before any selection program is implemented. This will ensure that sufficient genetic variation will be available to allow genetic gains to be sustainably achieved in a future stock improvement program. A fundamental starting point to improve hatchery practices will be to encourage farmers and hatchery managers to spawn more females in their hatcheries as it will increase background genetic diversity in culture stocks. Combining crablet cohorts from multiple hatcheries into a single cohort for supply to farmers or rotation of breeding females regularly in hatcheries will help to address immediate genetic diversity problems in culture stocks. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations more efficiently. Over the long-term, application of data on genetic diversity in wild and cultured stocks of Asian mud crab will contribute to development of sustainable and productive culture industries in Vietnam and other countries in the IWP and can contribute towards conservation of wild genetic resources.

Identification of a putative cellulase gene in the giant freshwater prawn, Macrobrachium rosenbergii (De Man, 1879)

Nutrition plays an important role in the development of all organisms and in particular that of farmed aquatic species where costs associated with feed can often exceed 60% of total production costs. Crustacean species in addition, have the added metabolic requirement for regular moulting to allow normal growth and this requires large amounts of energy in the form of sugars (glucose). The current study explored the capacity of the giant freshwater prawn to produce endogenous cellulose-degrading enzymes capable of extracting nutrients (simple sugars) from plant sources in formulated feeds used in the prawn aquaculture industry. We identified a putative cellulase cDNA fragment in the target organism of 1576 base pairs in length of non-microbial origin that after protein modelling exhibited a TM-score of 0.916 with a described cellulase reported from another crustacean species. The functional role of cellulase enzymes is to hydrolyse cellulose to glucose and the fragment identified in GFP was highly expressed in the hepatopancreas, the site of primary food digestion and absorption in crustaceans. Hepatopancreatic tissue from Macrobrachium rosenbergii also showed active digestion of cellulose to glucose following an endoglucanase assay. Cellulase gene(s) are present in the genomes of many invertebrate taxa and play an active role in the conversion of cellulose to available energy. Identification and characterization of endogenous cellulase gene(s) in giant freshwater prawn can assist development of the culture industry because the findings confirm that potentially greater levels of low-cost plant-material could be included in artificial formulated diets in the future without necessarily compromising individual growth performance. Ultimately, this development may contribute to more efficient, cost-effective production systems for freshwater prawn culture stocks that meet the animal's basic nutritional requirements and that also support good individual growth rates.

A quantitative metric to identify critical elements within seafood supply networks

A theoretical basis is required for comparing key features and critical elements in wild fisheries and aquaculture supply chains under a changing climate. Here we develop a new quantitative metric that is analogous to indices used to analyse food-webs and identify key species. The Supply Chain Index (SCI) identifies critical elements as those elements with large throughput rates, as well as greater connectivity. The sum of the scores for a supply chain provides a single metric that roughly captures both the resilience and connectedness of a supply chain. Standardised scores can facilitate cross-comparisons both under current conditions as well as under a changing climate. Identification of key elements along the supply chain may assist in informing adaptation strategies to reduce anticipated future risks posed by climate change. The SCI also provides information on the relative stability of different supply chains based on whether there is a fairly even spread in the individual scores of the top few key elements, compared with a more critical dependence on a few key individual supply chain elements. We use as a case study the Australian southern rock lobster Jasus edwardsii fishery, which is challenged by a number of climate change drivers such as impacts on recruitment and growth due to changes in large-scale and local oceanographic features. The SCI identifies airports, processors and Chinese consumers as the key elements in the lobster supply chain that merit attention to enhance stability and potentially enable growth. We also apply the index to an additional four real-world Australian commercial fishery and two aquaculture industry supply chains to highlight the utility of a systematic method for describing supply chains. Overall, our simple methodological approach to empirically-based supply chain research provides an objective method for comparing the resilience of supply chains and highlighting components that may be critical.

Prediction of the fate of oxytetracycline and oxolinic acid in a fish pond using simulation model: A preliminary study

The fate of two popular antibiotics, oxytetracycline and oxolinic acid, in a fish pond were simulated using a computational model. The VDC model, which is designed based on a model for predicting pesticide fate and transport in paddy fields, was modified to take into account the differences between the pond and the paddies as well as those between the fish and the rice plant behaviors. The pond conditions were set following the typical practice in South East Asia aquaculture. The two antibiotics were administered to the animal in the pond through medicated feed during a period of 5 days as in actual practice. Concentrations of oxytetracycline in pond water were higher than those of oxolinic acid at the beginning of the simulation. Dissipation rate of oxytetracycline is also higher as it is more readily available for degradation in the water. For the long term, oxolinic acid was present at higher concentration than oxytetracycline in pond water as well as pond sediment. The simulated results were expected to be conservative and can be useful for the lower tier assessment of exposure risk of veterinary medicine in aquaculture industry but more data are needed for the complete validation of the model.

Impacts of introduced aquaculture species on markets for native marine aquaculture products : the case of edible oysters in Australia

Economic competition between introduced and native aquaculture species is of interest for industry stakeholders since increased production can affect price formation if both aquaculture species are part of the same market or even substitutes. In this study, we focus on the Australian edible oyster industry, which is dominated by two major species—the native Sydney rock oyster (grown mainly in Queensland and New South Wales) and the non-native Pacific oyster (grown mainly in South Australia and Tasmania). We examine the integration of the Australian oyster market to determine if there exists a single or several markets. Short- and long-run own, cross-price and income flexibilities of demand are estimated for both species using an inverse demand system of equations. The results suggest that the markets for the two species are integrated. We found evidence that the development of the Pacific oyster industry has had an adverse impact on Sydney rock oyster prices. However, our results show that both species are not perfect substitutes. Demand for Sydney rock oysters is relatively inelastic in the long run, yet no long-run relationships can be identified for Pacific oysters, reflecting the developing nature of this sector.

Socio-economic determinants for industry development : the case of Australia’s Sydney rock oyster industry

Socio-economic characteristics such as age, gender, educational attainment, employment status, and income contain vital information about how an industry may respond to changing circumstances, and hence are of importance to decision makers. While some socio-economic studies exist, relatively little attention has been given to fishery and aquaculture industries in regards to their socio-economic profiles and their role in the development prospects of these industries. In this study, by way of example, we focus on Australia’s Sydney rock oyster (Saccostrea glomerata) (SRO) industry. The aim of this study was identify the socio-economic profile of the SRO industry and to illustrate the value of such information for an industry management assessment. The SRO industry has experienced a major decrease in production volume since the late 1970 and continues to be affected by prevailing diseases and increasing market competition from Australia’s Pacific oyster (Crassostrea gigas) industry. It is likely that socio-economic aspects have influenced this development within the SRO industry. The socio-economic profile was developed using data from a SRO industry farm survey which was undertaken in 2012. Findings suggested that this industry is characterised by a mature aged oyster farmer population and a part-time oyster farming approach. These characteristics may affect the farmers’ ability to drive innovation and growth. The results also suggested that there may be potential industry entry barriers present in the SRO industry which may prevent younger people taking up oyster farming. Given the results, the study concluded that the current socio-economic profile of the industry has likely contributed to the present economic status quo of the industry.

Shape up or ship out : can we enhance productivity in coastal aquaculture to compete with other uses?

Coastal resources are coming under increasing pressure from competition between recreational, commercial and conservation uses. This is particularly so in coastal areas adjacent to major population centres. Given high recreational and conservation values in such areas, economic activities need to be highly efficient in order to persist. Management of these industries must therefore also encourage efficient production and full utilisation of the areas available. In order to achieve this, managers must first understand the level and drivers of productivity, and how these can be influenced. In this study, by way of illustration, the focus was on the Sydney rock oyster industry within Queensland's Moreton Bay, a multiple use marine park with high recreational and conservation value adjacent to Australia's third largest city. Productivity of the oyster industry in Moreton Bay is currently low compared to historic levels, and management has an objective of reversing this trend. It is unclear whether this difference is due to oyster farmers' business choices and personal characteristics or whether varying environmental conditions in the Moreton Bay limit the capacity of the oyster industry. These require different management responses in order to enhance productivity. The study examined different productivity measures of the oyster industry using data envelopment analysis (DEA) to determine where productivity gains can be made and by how much. The findings suggest that the industry is operating at a high level of capacity utilisation, but a low level of efficiency. The results also suggest that both demographic and environmental conditions affect technical efficiency in the Bay, with water characteristics improvements and appropriate training potentially providing the greatest benefits to the industry. Methods used in this study are transferable to other industries and provide a means by which coastal aquaculture may be managed to ensure it remains competitive with other uses of coastal resources.

Economic analyses of Australia's Sydney rock oyster industry

This thesis provides the first comprehensive assessment of the economic viability of Australia's Sydney rock oyster industry and forms the bases for future policy and industry management recommendations. In the four separate studies of the thesis, the socio-economic profile of the industry, the market price formation dynamics within Australia's oyster market, efficiency and productivity levels and the potential impact of climate change and market dynamics on the industry's future revenue were investigated. Findings of this project suggest, for example, that market dynamics may pose a greater thread to the future development of this industry than direct effect from climate change.