"Exotic willows (Salix spp.) are widespread riparian tree species of streams in temperate Australian and New Zealand. In Australian willow speicies are declared weeds of national significance, yet little is known about the novel habitats they create not the impact on aquatic biota of vegetation change following willow management programs ..." [leaf i] / Doctor of Philosophy

Nototodarus sloanii is an important component of the Southern Ocean fauna, and the basis of a large commercial fishery. Despite this, much is unknown about the biology of this species. This study examines some aspects of the biology of N. sloanii. Stomach contents analysis identified no significant differences in diet between male and female squid. Sixteen putative species, including 12 identifiable teleosts, 2 crustaceans, and 2 cephalopods were identified in the diet of this species. The euphausid, Nyctiphanes australis was the most important prey item, Lanternfish, Lampanyctodes hectoris, and Pearlside, Maurolicus muelleri, were of secondary importance. Squid were aged using counts of statolith micro-increments and back-calculation from the date of capture showed that hatching occurred between August and February, with a peak in the austral winter/spring and another smaller peak in the austral summer. Growth rate for male squid differed depending on whether squid were hatched in the winter/spring or summer. Growth rates were more variable in the winter/spring-hatched individuals, and they attained larger size than summer-hatched squid. This was not the case for female squid. Mean age for immature winter/spring-hatched squid was significantly higher than for summer-hatched squid, although there was no significant difference in mean mantle length or body mass. No significant differences between mean age, mantle length, or body mass for same-gender mature squid, regardless of hatch season, were apparent. However, mature female squid hatched in the winter/spring season were significantly longer (ML) than mature male squid hatched in winter/spring. No squid was found to be older than 211 days. All squid had started to mature by 91-120 days old and all were fully mature at 180 days. Validation experiments run on juvenile squid using calcein markers were inconclusive, however the increments in the statoliths were very similar to those found in other validated species of ommastrephid squid, thus for the purposes of this study they were assumed to be of daily periodicity. Gladius increments identify a gender difference in growth rate, with female squid having a shorter initial slow growth phase than male squid. Gonadosomatic indices (GSIs) were calculated for male and female squid. These were low (7.12%�0.3% for females and 1.9%�0.2% for males) suggesting that these squid are intermittent spawners. This is further supported by a histological examination, which found germinal cells of different stages present in the same gonad. Lack of mature individuals in this study means that these results are suggestive rather than definitive; more examination of the reproductive process of this squid is required. Histological examination was also used to validate the Lipinski maturity scale for use with this species, while some misidentification occurred the scale is useful to place squid into the broad categories of immature, maturing, or mature. New maturity scales were created for N. sloanii utilising these broad categories. Finer-scale identification is not possible using this scale, as maturation appears to be a continuous process. Morphometric measurements were taken from both hard and soft tissues and were analysed using non-metric multidimensional scaling and analysis of similarity. Divisions were only apparent in the hard structure measurements. They did not appear to be age, dietary or reproductive differences.

"Exotic willows (Salix spp.) are widespread riparian tree species of streams in temperate Australian and New Zealand. In Australian willow speicies are declared weeds of national significance, yet little is known about the novel habitats they create not the impact on aquatic biota of vegetation change following willow management programs ..." [leaf i] / Doctor of Philosophy

Aquatic microalgae produce a variety of toxic secondary metabolites, which are a concern for public health and seafood industries, while also presenting a source of pharmacologically valuable compounds. The present study deals with the physiology and molecular genetics of saxitoxin (STX), a cyanobacterial neurotoxic alkaloid. Ecological and chemical parameters have been investigated for their effects on growth and STX production in the cyanobacterium Cylindrospermopsis raciborskii T3, in order to better understand the physiological responses of this cyanobacterium to the anthropogenic eutrophication of water bodies. The results indicated that phosphate, in particular, had an incremental effect on STX production, as well as promoting the up-regulation of transcription of the STX biosynthetic gene cluster (sxt). High temperature was found to negatively affect growth and STX production in this organism. The effects of the plant hormone, jasmonic acid, were also tested, since it has previously been shown to affect plant alkaloid production. The hypothesised similarity between cyanobacterial and plant secondary metabolism in response to this plant hormone was confirmed in the neurotoxic cyanobacterium, C. raciborskii T3, as well as the non-toxic Anabaena sp. PCC7120. Furthermore, investigation of the sxt gene cluster transcriptional map in C. raciborskii T3 was carried out, with identification of three main polycistronic and one monocistronic transcripts. Promoter regions putatively involved in the regulation of STX production in C. raciborskii T3 were also identified. Transcription factor consensus motifs, the pho boxes, were identified in the main promoter region. These conserved motifs are the binding regions for the transcriptional regulator, PhoB, to the pho regulon genes, involved in phosphate uptake during conditions of its depletion in the environment. Moreover, a genomic region adjacent to the sxt gene cluster in C. raciborskii T3 was identified and characterised, putatively encoding a regulatory two-component system. This system appears to be involved in the sensing of environmental signals, in particular depleted phosphate, while activating the transcription of genes involved in its uptake and transport. The results of this study lead to a greater understanding of the complex factors associated with the regulation of STX biosynthesis and bloom-formation, by the cyanobacterium C. raciborskii T3.

This body of work examines the influence of land use on nearshore water quality, and how this can drive changes to algal and invertebrate communities along Australia's southern coastline. The overall aim of the thesis was to investigate links between increasing coastal water-column nitrogen concentrations (derived from terrestrial inputs) and the expansion of turf-forming habitats that can alter the structure and function of subtidal ecosystems. I initially tested whether human activities in coastal catchments can increase subsidies of nitrogen to open rocky coasts. I identified landscape-scale variation in the supply of Dissolved Inorganic Nitrogen (DIN) to coastal waters adjacent to natural, agricultural and urban catchments. Compared to natural catchments, subsidies of DIN were 8 - 407 times greater in urban catchments, and 1 - 63 times greater in agricultural catchments. Subsidies of nitrogen from urban catchments were attributed to the release of sewage effluent, as delineated by δ¹ ⁵N isotopic values of transplanted algae. Having made this link, I then assessed whether catchment-scale variation in nitrogen subsidies may predict patterns of subtidal habitat structure, particularly as related to theories of regime shifts from forested landscapes to structurally depauperate turf-forming habitats. I validated this hypothesis, demonstrating that both relative covers and patch-sizes of turfed habitat were greater where the ratio of terrestrial nitrogen inputs to ambient coastal resources was large. An important realisation was that loss of forests may be more strongly related to the size of subsidy (i.e. the relative increases in water column nitrogen concentrations along urban coasts) rather than the size of coastal populations. Together, these data link coastal development with modified land-to-sea subsidies, and indirectly support the model that ecological effects may be proportional to the disparity between donor and recipient resources. Having demonstrated a link between nitrogen subsidies and subtidal habitat change, I then investigated factors likely to initiate and maintain such shifts. My results demonstrate that nutrient elevation can alter the natural phenology of turfs, sustaining dense covers throughout periods of natural senescence (winter). Perennial turf covers are able to accumulate large volumes of sediment; a synergy can impede the winter recruitment of canopy-forming species (kelps and fucoid algae). My observations of reduced forest recovery along urban coasts serve to highlight the complex interaction between elevated nutrients, persistent turf covers and increased sediment accumulation, which can reduce the resilience of coastal ecosystems to disturbance. In recognition that regime shifts are likely to have consequences for higher trophic levels, I compared the diet of invertebrate herbivores from healthy and degraded coastlines using stable isotope analysis (δ¹³C and δ¹⁵N). Dietary modelling showed that turfs contributed more to the diet of consumers along degraded coastlines where turfed landscapes have replaced extensive covers of macroalgal forest. Additionally, there were strong correlations between covers of turfed habitat, herbivore diet and relative densities. Changes to ambient food quality associated with regime shift may be an important aspect of nutrient-driven change along human-dominated coastlines. The final component of my thesis redressed some of the uncertainty about restoration initiatives for urban coasts by demonstrating that regime shifts are not necessarily permanent. I showed that turf removal can facilitate the recovery of degraded forests. Future restoration, therefore, is a possible outcome of polices that aim to decouple the link between nutrient inputs and recalcitrant turfed habitats that prevent forest recovery. Initiatives that reduce nutrient discharge to coastal waters (e.g., wastewater recycling) are likely to restore the resilience of nearshore marine ecosystems and promote their rehabilitation. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1473469 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2009

This body of work examines the influence of land use on nearshore water quality, and how this can drive changes to algal and invertebrate communities along Australia's southern coastline. The overall aim of the thesis was to investigate links between increasing coastal water-column nitrogen concentrations (derived from terrestrial inputs) and the expansion of turf-forming habitats that can alter the structure and function of subtidal ecosystems. I initially tested whether human activities in coastal catchments can increase subsidies of nitrogen to open rocky coasts. I identified landscape-scale variation in the supply of Dissolved Inorganic Nitrogen (DIN) to coastal waters adjacent to natural, agricultural and urban catchments. Compared to natural catchments, subsidies of DIN were 8 - 407 times greater in urban catchments, and 1 - 63 times greater in agricultural catchments. Subsidies of nitrogen from urban catchments were attributed to the release of sewage effluent, as delineated by δ¹ ⁵N isotopic values of transplanted algae. Having made this link, I then assessed whether catchment-scale variation in nitrogen subsidies may predict patterns of subtidal habitat structure, particularly as related to theories of regime shifts from forested landscapes to structurally depauperate turf-forming habitats. I validated this hypothesis, demonstrating that both relative covers and patch-sizes of turfed habitat were greater where the ratio of terrestrial nitrogen inputs to ambient coastal resources was large. An important realisation was that loss of forests may be more strongly related to the size of subsidy (i.e. the relative increases in water column nitrogen concentrations along urban coasts) rather than the size of coastal populations. Together, these data link coastal development with modified land-to-sea subsidies, and indirectly support the model that ecological effects may be proportional to the disparity between donor and recipient resources. Having demonstrated a link between nitrogen subsidies and subtidal habitat change, I then investigated factors likely to initiate and maintain such shifts. My results demonstrate that nutrient elevation can alter the natural phenology of turfs, sustaining dense covers throughout periods of natural senescence (winter). Perennial turf covers are able to accumulate large volumes of sediment; a synergy can impede the winter recruitment of canopy-forming species (kelps and fucoid algae). My observations of reduced forest recovery along urban coasts serve to highlight the complex interaction between elevated nutrients, persistent turf covers and increased sediment accumulation, which can reduce the resilience of coastal ecosystems to disturbance. In recognition that regime shifts are likely to have consequences for higher trophic levels, I compared the diet of invertebrate herbivores from healthy and degraded coastlines using stable isotope analysis (δ¹³C and δ¹⁵N). Dietary modelling showed that turfs contributed more to the diet of consumers along degraded coastlines where turfed landscapes have replaced extensive covers of macroalgal forest. Additionally, there were strong correlations between covers of turfed habitat, herbivore diet and relative densities. Changes to ambient food quality associated with regime shift may be an important aspect of nutrient-driven change along human-dominated coastlines. The final component of my thesis redressed some of the uncertainty about restoration initiatives for urban coasts by demonstrating that regime shifts are not necessarily permanent. I showed that turf removal can facilitate the recovery of degraded forests. Future restoration, therefore, is a possible outcome of polices that aim to decouple the link between nutrient inputs and recalcitrant turfed habitats that prevent forest recovery. Initiatives that reduce nutrient discharge to coastal waters (e.g., wastewater recycling) are likely to restore the resilience of nearshore marine ecosystems and promote their rehabilitation. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1473469 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2009

Aquatic microalgae produce a variety of toxic secondary metabolites, which are a concern for public health and seafood industries, while also presenting a source of pharmacologically valuable compounds. The present study deals with the physiology and molecular genetics of saxitoxin (STX), a cyanobacterial neurotoxic alkaloid. Ecological and chemical parameters have been investigated for their effects on growth and STX production in the cyanobacterium Cylindrospermopsis raciborskii T3, in order to better understand the physiological responses of this cyanobacterium to the anthropogenic eutrophication of water bodies. The results indicated that phosphate, in particular, had an incremental effect on STX production, as well as promoting the up-regulation of transcription of the STX biosynthetic gene cluster (sxt). High temperature was found to negatively affect growth and STX production in this organism. The effects of the plant hormone, jasmonic acid, were also tested, since it has previously been shown to affect plant alkaloid production. The hypothesised similarity between cyanobacterial and plant secondary metabolism in response to this plant hormone was confirmed in the neurotoxic cyanobacterium, C. raciborskii T3, as well as the non-toxic Anabaena sp. PCC7120. Furthermore, investigation of the sxt gene cluster transcriptional map in C. raciborskii T3 was carried out, with identification of three main polycistronic and one monocistronic transcripts. Promoter regions putatively involved in the regulation of STX production in C. raciborskii T3 were also identified. Transcription factor consensus motifs, the pho boxes, were identified in the main promoter region. These conserved motifs are the binding regions for the transcriptional regulator, PhoB, to the pho regulon genes, involved in phosphate uptake during conditions of its depletion in the environment. Moreover, a genomic region adjacent to the sxt gene cluster in C. raciborskii T3 was identified and characterised, putatively encoding a regulatory two-component system. This system appears to be involved in the sensing of environmental signals, in particular depleted phosphate, while activating the transcription of genes involved in its uptake and transport. The results of this study lead to a greater understanding of the complex factors associated with the regulation of STX biosynthesis and bloom-formation, by the cyanobacterium C. raciborskii T3.

This body of work examines the influence of land use on nearshore water quality, and how this can drive changes to algal and invertebrate communities along Australia's southern coastline. The overall aim of the thesis was to investigate links between increasing coastal water-column nitrogen concentrations (derived from terrestrial inputs) and the expansion of turf-forming habitats that can alter the structure and function of subtidal ecosystems. I initially tested whether human activities in coastal catchments can increase subsidies of nitrogen to open rocky coasts. I identified landscape-scale variation in the supply of Dissolved Inorganic Nitrogen (DIN) to coastal waters adjacent to natural, agricultural and urban catchments. Compared to natural catchments, subsidies of DIN were 8 - 407 times greater in urban catchments, and 1 - 63 times greater in agricultural catchments. Subsidies of nitrogen from urban catchments were attributed to the release of sewage effluent, as delineated by δ¹ ⁵N isotopic values of transplanted algae. Having made this link, I then assessed whether catchment-scale variation in nitrogen subsidies may predict patterns of subtidal habitat structure, particularly as related to theories of regime shifts from forested landscapes to structurally depauperate turf-forming habitats. I validated this hypothesis, demonstrating that both relative covers and patch-sizes of turfed habitat were greater where the ratio of terrestrial nitrogen inputs to ambient coastal resources was large. An important realisation was that loss of forests may be more strongly related to the size of subsidy (i.e. the relative increases in water column nitrogen concentrations along urban coasts) rather than the size of coastal populations. Together, these data link coastal development with modified land-to-sea subsidies, and indirectly support the model that ecological effects may be proportional to the disparity between donor and recipient resources. Having demonstrated a link between nitrogen subsidies and subtidal habitat change, I then investigated factors likely to initiate and maintain such shifts. My results demonstrate that nutrient elevation can alter the natural phenology of turfs, sustaining dense covers throughout periods of natural senescence (winter). Perennial turf covers are able to accumulate large volumes of sediment; a synergy can impede the winter recruitment of canopy-forming species (kelps and fucoid algae). My observations of reduced forest recovery along urban coasts serve to highlight the complex interaction between elevated nutrients, persistent turf covers and increased sediment accumulation, which can reduce the resilience of coastal ecosystems to disturbance. In recognition that regime shifts are likely to have consequences for higher trophic levels, I compared the diet of invertebrate herbivores from healthy and degraded coastlines using stable isotope analysis (δ¹³C and δ¹⁵N). Dietary modelling showed that turfs contributed more to the diet of consumers along degraded coastlines where turfed landscapes have replaced extensive covers of macroalgal forest. Additionally, there were strong correlations between covers of turfed habitat, herbivore diet and relative densities. Changes to ambient food quality associated with regime shift may be an important aspect of nutrient-driven change along human-dominated coastlines. The final component of my thesis redressed some of the uncertainty about restoration initiatives for urban coasts by demonstrating that regime shifts are not necessarily permanent. I showed that turf removal can facilitate the recovery of degraded forests. Future restoration, therefore, is a possible outcome of polices that aim to decouple the link between nutrient inputs and recalcitrant turfed habitats that prevent forest recovery. Initiatives that reduce nutrient discharge to coastal waters (e.g., wastewater recycling) are likely to restore the resilience of nearshore marine ecosystems and promote their rehabilitation. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1473469 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2009

Due to the complex nature of aquatic food webs, the interaction between abiotic and biotic factors that govern ecosystem dynamics is often elusive. Recent advancements in both the collection of reliable field data and the development of ecological models have enabled researchers to gain insights into these more complex interactions. In this study the relationship between physical and ecological processes has been explored by applying a process based coupled physical and ecological model (DYRESM-CAEDYM) to the data sets of three aquatic ecosystems. In the first, the role of zooplankton in the nutrient cycles of Lake Kinneret, Israel was quantified. The model was parameterized and calibrated using an extensive field data set. It was found that the excretion of dissolved nutrients by zooplankton accounted for up to 58% of phytoplankton demand and that this value varied seasonally in response to patterns of stratification and mixing. In the second ecosystem, Mono Lake, USA, results from model simulations were studied to determine the significance of the transport of nutrient rich hypolimnetic water via the benthic boundary layer (BBL) on lake productivity. Model results indicated that although on average the impact of BBL transport on Mono Lake ecology was not large, significant nutrient fluxes were simulated during periods when BBL transport was most active. The timing of these fluxes in the context of seasonal changes were found to be critical to specific aspects of food web dynamics. In the final application, the ecological gradients of the primary salt ponds of Shark Bay, Australia were studied with specific focus on the role of zooplankton as a determinant of ecosystem dynamics. Model results indicated that zooplankton grazing was responsible for reduced water column particulate organic matter and increased light available for the development of microbial mats. However, no direct 8 link between zooplankton grazing and observed changes in planktonic algal species composition or nutrient limitation across the salinity gradient of the ponds was found. Results from this study demonstrate the potential of a lake ecosystem model to extract useful process information to complement field data collection and address questions related to the relationship between physical and ecological processes in aquatic ecosystems.

Thesis (Ph.D.), University of Adelaide, Dept. of Botany, 1999. / Bibliography: p. 171-181.