Thesis (Ph.D.)--University of Melbourne, Dept. of Zoology, 2009. / Typescript. Includes bibliographical references (p. 108-119)

This study investigated the feasibility of ranching the abalone Haliotis rubra (Leach) and Haliotis laevigata (Donovan) on concrete artificial reefs at a site chosen by industry investors on silty bottom off Altona Beach, Port Phillip Bay, Victoria, Australia. The study started from the premise that artificial reef deployment combined with abalone stock enhancement may achieve the dual purpose of habitat and stock improvement. It evaluated the hydrodynamics of the site in relation to artificial reef structural stability and drift algal transport, the development and ecology of the artificial reef assemblage, and abalone enhancement by seeding the reefs with hatchery juvenile abalone and transplanting adult broodstock abalone. Despite a scarcity of reports on culturing abalone on artificial reef, a literature review examined broadly the functions of artificial reefs, particularly in the context of abalone enhancement, and the relationship between artificial reefs, hydrodynamics and ecology. The major finding was that the success of artificial reef projects is highly dependent on the environment of the chosen site, and that preliminary studies are essential to predict their likely success. This consideration alone provided strong justification to undertake this study. The topography at the Altona site was generally flat, with natural patches of low basalt boulder reef, offering low habitat complexity, yet supporting a diverse range of flora and fauna, including a low-density wild stock of H. rubra. Water depth was a mean of 3.3 m at low tide and 4.4 m at high tide. A single, uncomplicated, concrete artificial reef of H-shape design, was tested as abalone habitat. The hydrodynamic analysis confirmed previous studies of Port Phillip Bay, with mild current speeds of mean 0.045 m.s-1, and maximum-modelled wave height (H1/3) of 1.21 m and period (T1/3) of 4.51 sec. Water temperature ranged from 9.9ºC during July to 23.8ºC during January, with salinity averaging of 35.5 ppt. The site had a low probability of receiving drift algae, necessary as a food source for abalone, because of its geographic location, potentially affecting ranch productivity. Ecological monitoring of the three-year old artificial reef shows complex changes in the flora and fauna over time, particularly in respect of the sessile fauna. Key differences between the artificial reef and a nearby natural reef community were: lower cover of corallines and late colonisers, such as sponges. High levels of sedimentation were recorded at the Altona site. Hatchery juvenile H. laevigata, with mean survival of 15% after two years and a mean annual growth rate of 39 mm, showed the most promise for outplanting. In comparison, for hatchery juvenile H. rubra, mean survival was 9% after three years and mean annual growth rate was 22 mm. No natural recruitment of H. laevigata was recorded on artificial reef despite transplants of adult broodstock on the reefs. Natural recruitment of H. rubra was also low and insufficient to reliably contribute to abalone ranch stock. Having examined the hydrodynamic, ecological and enhancement attributes of the Altona site, the study concluded that the site was marginally viable for abalone ranching, and that an alternative site near Werribee, 20 km further southwest, had superior attributes for growth and survival of abalone.

Boundaries between adjacent habitats can create unique biotic and abiotic conditions, varying species compositions and abundances between the edge and interior of habitats. As habitats become fragmented, the relative amount of edge increases. Understanding the role that habitat edges have in determining species compositions and abundances is fundamental for conservation and management of habitats, particularly those under threat from fragmentation. Seagrass habitats are common nearshore habitats that harbour a rich and diverse faunal assemblage that are under threat worldwide from human disturbance. Human induced fragmentation, and the propensity of seagrass to form naturally patchy landscapes, makes it an ideal system to study the effects of edges on fauna. / Evidence of fish displaying edge effects in seagrass habitats is equivocal. Assessment of fish edge effects was done by sampling seven positions within seagrass habitats at fine spatial scales. Strong, consistent patterns in fish distributions demonstrated clear edge effects both within and alongside seagrass at these sites. The total number of fish sampled was greater at the seaward seagrass edge than the seagrass middle, but there was little difference between the seagrass middle and the shoreward seagrass edge. Four individual fish species showed preferences for the seagrass edges. Further investigation revealed that patch size could influence the magnitude of edge effects in seagrass beds. Fish were sampled in ten variously sized seagrass patches in three positions within each patch. Two species showed variations in edge effects across patches which could be attributed to the area of the patch. Changes in patch size can influence the magnitude of edge effects that species display, suggesting that patch area effects (fish density varying with patch size) could be caused by edge effects. / Food availability and predation are mechanisms commonly used to explain edge effect patterns. Gut analysis was done on Stigmatopora nigra sampled at the edge and middle of patches to determine if prey consumption varied between positions, and explain S. nigra distribution. There was little difference in prey consumed by S. nigra at the edge and middle of patches, suggesting that food was unlikely to be causing S. nigra edge effects, or that the influence of prey distribution was being masked by other factors such as seagrass structure. Predator abundances and foraging efficiency may vary at the edge and middle of patches, and consequently influence the distribution of prey fish within patches. Underwater videos were placed at four positions within seagrass habitats to assess predator distributions. Predatory Australian salmon, Arripis spp., spend more time over adjacent sand than other positions, while small potential prey species (King George whiting, Sillaginodes punctata, recruits) appear to prefer the middle of seagrass patches, possibly to avoid encounters with salmon. To test if the predator-prey distributions reflected actual predation pressure, a tethering experiment was done to determine if predation was causing edge effects in small fishes. / King George whiting recruits and pipefish (Stigmatopora spp.) were tethered at each of the four positions at different depths. Survival time of whiting recruits was greater in the middle of shallow seagrass patches than other positions. Few pipefish were preyed upon, and survival time was lower over sand adjacent to seagrass than at the seagrass edge or middle. Video footage revealed that salmon was the dominant predator of both whiting recruits and pipefish. The distribution of predators and associated predation can explain edge effects for some species (whiting) but other mechanisms, or a combination of mechanisms, are determining edge effects for other species (pipefish). / Edge effects were common amongst fish species in seagrass habitats, and included permanent, temporary and predatory species. Patch size was found to influence the extent of the edge effect. There was little evidence to support prey consumption as an underlying mechanism causing higher fish abundances at the interior or edge of patches, however there was evidence that predation could be causing edge effects. Changes in fish distributions within seagrass patches due to patch size and predation when seagrass undergoes fragmentation need to be considered by not only ecologists, but also by managers in the development of plans for seagrass conservation. Future studies should investigate the relative contribution of different edge characteristics in determining the degree of seagrass edge effects.

Aquatic sediments are the recipients of a continual rain of organic debris from the water column. The decomposition reactions within the sediment and the rates of material exchange between the sediment and water column are critically moderated by the transport processes within the sediment. The sediment and solute movement induced by burrowing animals – bioturbation and bioirrigation – far exceed abiotic transport processes such as sedimentation burial and molecular diffusion. Thalassinidean shrimp are particularly abundant burrowing animals. Living in high density populations along coastlines around the world, these shrimp build complex burrow networks which they actively maintain and irrigate.¶ I used a laser scanner to map thalassinidean shrimp (Trypaea australiensis) mound formation. These experiments measured rapid two-way exchange between the sediment and depth. Subduction from the sediment surface proved to be just as important as sediment expulsion from depth, yet this is not detected by conventional direct entrapment techniques. The experiments demonstrated that a daily sampling frequency was needed to capture the extent of the two-way exchange.¶ I derived a one-dimensional non-local model accounting for the excavation, infill and collapse (EIC) of burrows. Maximum likelihood analyses were used to test the model against 210Pb and 228Th profiles taken from sediment cores in Port Phillip Bay, Melbourne. The maximum likelihood approach proved to be a useful technique for quantifying parameter confidence bounds and allowing formal comparison with a comparable biodiffusion model. The EIC model generally outperformed the biodiffusion model, and in all cases best EIC model parameter estimates required some level of burrow infill with surface material. The EIC model was expanded to two and three dimensions, which allowed the representation of lateral heterogeneity resulting from the excavation, infill and collapse of burrow structures. A synthetic dataset generated by the two-dimensional model was used to demonstrate the effects of heterogeneity and core sampling on the mixing information that can be extracted from one-dimensional sediment core data.¶ Burrow irrigation brings oxygenated water into burrow depths, and can affect the nitrogen cycle by increasing the rates of coupled nitrification and denitrification reactions. I modelled the nitrogen chemistry in the annulus of sediment surrounding an irrigated burrow using a radially-symmetrical diffusion model. The model was applied to three published case studies involving thalassinidean shrimp experiments and to field data from Port Phillip Bay. The results highlighted divergences between current theoretical understanding and laboratory and field measurements. The model further demonstrated potential limitations of measurements of burrow characteristics and animal behaviour in narrow laboratory tanks. Activities of burrowing animals had been hypothesised to contribute to high denitrification rates within Port Phillip Bay. Modelling work in this thesis suggests that the model burrow density required to explain these high denitrification rates is not consistent with the sampled density of thalassinidean shrimp in the Bay, although dense burrows of other animals are likely to be important. Limitations of one-dimensional representations of nitrogen diagenesis were explored via comparisons between one-dimensional models and the full cylinder model.

Increasing exploitation of pelagic fish populations worldwide has often resulted in overfishing and the collapse of commercial fisheries and associated serious declines in many marine predator populations, including seabirds. These events highlight the competing demands for limited marine resources. Recent emphasis for the ecologically sustainable management of commercial fisheries has stimulated attempts to manage fisheries by incorporating knowledge of trophic interactions and ecosystem functioning, known as ecosystem-based fisheries management. Seabirds are often highly visible, wide-ranging upper trophic level consumers that aggregate in areas of increased ocean productivity and therefore be used as natural monitors of marine environmental conditions. Further, many seabirds commonly fed on commercially-exploited fish stocks (often targeting prey of similar size). In this study, the population dynamics of Australasian gannets (Morus serrator) breeding in Port Phillip Bay, Victoria, is investigated and competition between gannets and commercial fisheries is determined. In addition, the potential use of seabird reproductive and population parameters as indicators of the abundance of commercially exploited fish stocks, and pelagic conditions generally, is assessed.