A unique opportunity to study both benthic microbial mats and modern stromatolites from a common niche is presented by the hypersaline environment of Hamelin Pool, Shark Bay, Australia. However, prior to this study, the microbial mat communities have not been well characterised. To investigate the taxonomic and functional diversity of Hamelin Pool pustular and smooth mats, and their similarity to Hamelin Pool stromatolites, culturing, culture-independent, and lipid analysis methods were employed. The cultured isolates obtained included heterotrophic bacteria similar to those obtained from other hypersaline environments, and 19 strains of cyanobacteria including potentially novel species. For the first time archaeal isolates were obtained from the pustular and smooth mats, and further characterisation of two strains indicated they might represent novel species of the genus Haloferax. Total DNA was extracted from the mats and 16S rRNA gene clone libraries were generated targeting the bacteria, cyanobacteria, archaea and eukarya. Both the pustular and smooth mat bacterial clone libraries were highly diverse, with 11 bacterial divisions represented, and Chao1 estimates of total species richness indicating ~3000 ??? 6000 species. Cyanobacterial and archaeal clone libraries revealed unique phylotypes associated with sediments of differing morphology. Statistically significant differences between the mat populations and Hamelin Pool stromatolite communities were identified using !-LIBSHUFF, a program designed to compare two 16S rRNA gene libraries. Signature lipid biomarkers were assessed for the pustular and smooth mats and an intertidal stromatolite from Hamelin Pool. Fatty acids (as methyl esters), wax esters, hydrocarbons, ether-bound lipids, hopanoids and sterols indicated the presence of oxygenic phototrophs, anoxygenic phototrophs, sulfate-reducing bacteria, sulfur-oxidising bacteria, heterotrophic bacteria and archaea in each of the sediment types. Limited contributions from diatoms, bivalves and their dinoflagellate symbionts, and from higher plant aerosols were also detected. Significantly, 2-methyl hopanoids and eight pseudohomologous series of branched alkanes with quaternary carbon centers were identified in the mats and stromatolites. Although differing in lithification status and precise microbial composition, the pustular and smooth mats are excellent analogues for the extant stromatolites of Hamelin Pool, and by corollary, provide a fascinating link to Precambrian microbial communities.

A unique opportunity to study both benthic microbial mats and modern stromatolites from a common niche is presented by the hypersaline environment of Hamelin Pool, Shark Bay, Australia. However, prior to this study, the microbial mat communities have not been well characterised. To investigate the taxonomic and functional diversity of Hamelin Pool pustular and smooth mats, and their similarity to Hamelin Pool stromatolites, culturing, culture-independent, and lipid analysis methods were employed. The cultured isolates obtained included heterotrophic bacteria similar to those obtained from other hypersaline environments, and 19 strains of cyanobacteria including potentially novel species. For the first time archaeal isolates were obtained from the pustular and smooth mats, and further characterisation of two strains indicated they might represent novel species of the genus Haloferax. Total DNA was extracted from the mats and 16S rRNA gene clone libraries were generated targeting the bacteria, cyanobacteria, archaea and eukarya. Both the pustular and smooth mat bacterial clone libraries were highly diverse, with 11 bacterial divisions represented, and Chao1 estimates of total species richness indicating ~3000 ??? 6000 species. Cyanobacterial and archaeal clone libraries revealed unique phylotypes associated with sediments of differing morphology. Statistically significant differences between the mat populations and Hamelin Pool stromatolite communities were identified using !-LIBSHUFF, a program designed to compare two 16S rRNA gene libraries. Signature lipid biomarkers were assessed for the pustular and smooth mats and an intertidal stromatolite from Hamelin Pool. Fatty acids (as methyl esters), wax esters, hydrocarbons, ether-bound lipids, hopanoids and sterols indicated the presence of oxygenic phototrophs, anoxygenic phototrophs, sulfate-reducing bacteria, sulfur-oxidising bacteria, heterotrophic bacteria and archaea in each of the sediment types. Limited contributions from diatoms, bivalves and their dinoflagellate symbionts, and from higher plant aerosols were also detected. Significantly, 2-methyl hopanoids and eight pseudohomologous series of branched alkanes with quaternary carbon centers were identified in the mats and stromatolites. Although differing in lithification status and precise microbial composition, the pustular and smooth mats are excellent analogues for the extant stromatolites of Hamelin Pool, and by corollary, provide a fascinating link to Precambrian microbial communities.

The first aim of this thesis was to test the hypothesis that the spatial and food resources in the nearshore waters of a subtropical embayment in Western Australia (Shark Bay) will be partitioned within and amongst the main elasmobranch species that occur in that large water body. The size and age compositions, growth rates and reproductive biology of females and males of the nervous shark Carcharhinus cautus in Shark Bay were then determined to better understand the mode of life of this abundant species in this embayment. The second aim was to determine the species and size compositions of chondrichthyans landed by fisheries employing different methods in south-eastern Indonesia. The implications of these data for management were next determined and aspects of the reproductive biology of the most abundant of those species were explored, in a very preliminary manner. The nearshore, shallow waters of Shark Bay are used as a nursery area by several shark species and the different habitats in those waters are partitioned, to a certain degree, amongst those species. Ten species of shark (5 families), five species of ray (4 families) and twelve species of teleost (10 families) were caught in those waters. Carcharhinus cautus was the most abundant species, contributing 59.9% to the total number of elasmobranchs and 42.3% to all fish caught. This species and Negaprion acutidens were collected mainly or entirely from unvegetated sites, whereas Rhizoprionodon acutus, Carcharhinus brevipinna and Chiloscyllium punctatum were caught largely or exclusively at the seagrass site. The number of elasmobranch species and number of individuals of elasmobranchs were greatest in the seagrass site and least in the unvegetated site where no vegetation was present nearby, and they were significantly less in the latter site than in the one where dense mangroves were present nearby. These two biotic variables were also significantly greater in summer and autumn than in winter when temperatures were lowest. The species composition of elasmobranchs in each habitat type almost invariably differed significantly from that in each of the other habitat types and there was evidence that the species composition of elasmobranchs varied in a similar seasonal manner at the three unvegetated sites. Carcharhinus cautus, and probably also Hemigaleus microstoma and Chiloscyllium punctatum, were the only species that completed their life cycles in the nearshore, shallow waters of Herald Bight. However, the capture of the juveniles of a further four species with umbilical scars emphasises the importance of these waters as a nursery habitat for shark species. The dietary compositions of one ray species (Rhinobatus typus) and three shark species (Carcharhinus cautus, Negaprion acutidens, Rhizoprionodon acutus) undergo size-related changes and differ among these species, thereby reducing the potential for competition for food within and among these four species. Rhinobatus typus fed almost exclusively on penaeid prawns and portunid crabs, which is reflected in its narrow dietary breadth, whereas different species of teleosts constituted a major component of the diets of each size class of the three shark species. The relative contributions of the different species of teleost to the diets of the three shark species varied. The variations in dietary composition among the four species reflect differences in behaviour, modes of feeding and relative mouth sizes. Carcharhinus cautus copulates in late October–early November, shortly followed by ovulation (and thus conception) and parturition occurs about 11 months later. The reproductive cycle of C. cautus is biennial. Female and male C. cautus reached ca 28 and 32% of their lengths at their maximum observed ages, respectively, at the time of parturition. Females and males of C. cautus attained maximum total lengths of 1330 and 1110 mm, respectively, and maximum ages after parturition of 16 and 12 years, respectively. Maturity was attained at about 1010 mm by females and 910 mm by males and at least 50% of females and males had become mature by the end of their sixth and fourth years of life, respectively. The three-parameter von Bertalanffy growth curves provided reasonably good fits to the lengths at age of females and males of C. cautus during just postnatal life and throughout the whole of pre- and postnatal life. However, the four-parameter Schnute growth curve significantly improved the fit to these data for both females and males from conception and for females from birth. The question of when, from a biological view point, it might be appropriate to switch from using a von Bertalanffy growth curve to the more complex Schnute growth curve are discussed. A total of 139 chondrichthyan species, comprising 77 species of shark representing 17 families, 61 species of ray representing 11 families and a single species of holocephalan, were recorded at the ten landing sites surveyed in south-eastern Indonesia. However, it should be recognised that up to 49 of the 139 chondrichthyan species recorded have apparently not yet been described and thus assigned a species name. The most speciose and commonly recorded families were the Dasyatidae and Carcharhinidae, which collectively contributed 84.8%, respectively, to the total number of individuals of all species. The use of MDS ordination demonstrated that the species compositions at the eight main landing sites reflected to a greater extent the fishing methods used rather than the geographical location of those sites. Data on the reproductive biology of males demonstrated that a number of elasmobranch species were fished prior to the time that they attained maturity. The three most abundant chondrichthyan species that were caught both as juveniles and adults were Dasyatis kuhlii, Dasyatis zugei and Himantura walga. Since the reproductive cycle of each of these species did not follow a seasonal pattern, the timing of conception and parturition and the duration of gestation of these species could not be determined. The fecundity of these three species was very low, i.e. maximum of two but usually only a single embryo. The size at maturity of the three species, using data on the prevalence of mature fish, ranged from minima of 163 mm for females and males of H. walga to maxima of 237 mm for females and 239 mm for males of D. kuhlii. The translucent zones on the vertebral centra of D. kuhlii were apparently deposited annually and were thus used to estimate the ages of the individuals of this species. The maximum estimated ages of female and male D. kuhlii were 15 and 10 years, respectively.

Research into seed biology and restoration ecology of areas disturbed by mining is crucial to their revegetation. Shark Bay Salt, a solar salt facility in the Shark Bay World Heritage Area in Western Australia has several areas of disturbance as a result of 'soil borrowing'. Soil from these areas termed 'borrow pits' was used to create infrastructure such as the roads and embankments surrounding the evaporation ponds. Many of the pits contain little to no vegetation after >10 years since disturbance ceased, hence research into their restoration is now essential. A vegetation survey at the site established the key species in the undisturbed vegetation, and investigated the vegetation in borrow pits subject to natural migration and topsoil replacement. The vegetation communities in the borrow pits were vastly different to those in the undisturbed vegetation, highlighting the need for research into revegetation. An investigation into the use of 'borrowed' topsoil on a small scale showed that seedling recruitment from 'borrowed' topsoil was generally similar in the donor site (natural vegetation) and the borrow pits. Due to the absence of topsoil for further revegetation, it was necessary to understand seed germination and dormancy characteristics to establish seed pre-treatments prior to seed broadcasting and seedling (greenstock) planting. An investigation into seed germination and dormancy characteristics of 18 common species revealed that most species germinated equally well at 26/13oC and 33/18oC, however seven species had improved performance at 26/13oC. Untreated seeds of seven species exhibited high germination. Seeds of two species had low imbibition, which increased with hot-water treatment, and hence require scarification for germination. Germination of seeds of three species substantially increased with gibberellic acid (GA3), smoke water (SW) and karrikinolide (KAR1, a butenolide isolated from smoke). Seeds of the remaining six species had low germination regardless of treatment. As a result, species were classified as likely to be non-dormant (44%), physiologically dormant (44%) or physically dormant (11%). Physiological dormancy of three species was at least partly alleviated by dry afterripening, whereby moisture content of seeds was adjusted to 13% or 50% equilibrium relative humidity and seeds were stored at 30oC or 45oC for several months. All iv after-ripening conditions increased germination percentage and rate of two species with one only germinating when treated with GA3 or KAR1. The germination of the third species was dependent on after-ripening temperature and seed moisture content.

Shark Bay is an extensive marine embayment located on the central coast of Western Australia that is recognised as a World Heritage Property on the basis of the Outstanding Universal Value of the natural environment of the region. This thesis examines the history of science at Shark Bay between the arrival of the first European explorers in the seventeenth century through to the official recognition of Shark Bay as a World Heritage Area in 1991. Each of the seven chapters is devoted to a different period in the development of scientific investigations, beginning with Dutch and English mariners and naturalists, passing on to French scientific explorers and British surveyors naturalists, and explorers, continuing through a variety of investigations in marine science and research in biogeography and evolution carried out by foreign expeditions and Australian field-workers, and culminating in the transformation of scientific investigations as a result of the rise and development of modern ecological science in the second half of the twentieth century. This development of science at Shark Bay is considered in light of existing frameworks for the development or spread of science in Australia, and in relation to current literature concerning the development or emergence of ecology in Australia. After evaluating the history of science at Shark Bay relative to existing knowledge of the spread of science and the emergence of ecology, the thesis concludes by proposing a new framework for the development of science and the emergence of ecology based on the experience at Shark Bay and with wider application to the history of science in Western Australia.

[Truncated abstract. Formulae and special characters in this field can only be approximated. See PDF version for accurate reproduction.] Solar salt producers use solar energy to evaporate seawater as it flows through a series of ponds. The Shark Bay Salt solar ponds, at Useless Inlet in Western Australia, vary in salinity from that of seawater to four times seawater, over the pond sequence. Water column photosynthesis and biomass decreased markedly with increasing salinity along the pond sequence, while benthic productivity increased as cyanobacterial mats developed. Correspondingly, net productivity shifted from autotrophy to heterotrophy in the water column and from heterotrophy to autotrophy in the benthos. Both shifts occurred at intermediate salinity in the pond sequence, where there was low production in both the water column and benthos. Within individual ponds, productivity, algal biomass and physico-chemical conditions were relatively constant over the year of study. Transitions between benthic and planktonic production along the pond sequence were driven mostly by direct responses to salinity stress, as well as the formation of a gypsum crust on the pond floors at higher salinity (>120 g kg-1). This transition is similar to that which occurs in saline lakes undergoing anthropogenic salinisation and identifies critical salinities for the restoration of these lakes.

Shark Bay is a large inverse estuary, located in Western Australia. It has a number of unique habitats that support important species. The dynamics of circulation in Shark Bay have an influence on the species that inhabit the region, on small, local scales as well as on large Bay-wide scales. Numerical modeling and field data were used to examine small-scale dynamics in relation to an important recreational fish, pink snapper (Pagrus auratus). Icthyoplankton surveys collected and recorded egg density in regions where snapper are found. A barotropic three-dimensional hydrodynamic model was coupled with a two-dimensional Lagrangian particle-tracking program to simulate the passive transport of eggs through regions where spawning is known to occur. Circulation modeling results indicated residual flows on small scales that served to retain the eggs in the region where they were originally spawned. Results corroborate genetic work on adult snapper, which found no evidence intermixing of populations in Shark Bay. The numerical model was then further refined to run in a baroclinic mode. Simulations of salinity and temperature gradients were used to recreate frontal systems in Shark Bay. Frontal regions divide the Bay into a northern and a southern section as well as separate it from the ocean. Application of an analytical method for calculating front locations was consistent with the observed results and indicated that the primary forces determining frontal locations in the Bay are tides and gravitational circulation. Winds are a secondary influence, and solar heating is minimal in influence

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.

As climate change continues, climactic extremes are predicted to become more frequent and intense, in some cases resulting in dramatic changes to ecosystems. The effects of climate change on ecosystems will be mediated, in part, by biotic interactions in those ecosystems. However, there is still considerable uncertainty about where and how such biotic interactions will be important in the context of ecosystem disturbance and climactic extremes. Here, I review the role of consumers in seagrass ecosystems and investigate the ecological impacts of an extreme climactic event (marine heat wave) and subsequent widespread seagrass die-off in Shark Bay, Western Australia. Specifically, I compare seagrass cover, shark catch rates, and encounter rates of air breathing fauna in multiple habitat types before and after the seagrass die-off to describe post-disturbance dynamics of the seagrass community, shifts in consumer abundances, and changes in risk-sensitive habitat use patterns by a variety of mesoconsumers at risk of predation from tiger sharks (Galeocerdo cuvier). Finally, I conducted a 16 month field experiment to assess whether xi loss of top predators, and predicted shifts in dugong foraging, could destabilize remaining seagrass. I found that the previously dominant temperate seagrass Amphibolis antarctica is stable, but not increasing. Conversely, an early-successional tropical seagrass, Halodule uninervis, is expanding. Following the die-off, the densities of several consumer species (cormorants, green turtles, sea snakes, and dugongs) declined, while others (Indo-Pacific bottlenose dolphins, loggerhead sea turtles, tiger sharks) remained stable. Stable tiger shark abundances following the seagrass die-off suggest that the seascape of fear remains intact in this system. However, several consumers (dolphins, cormorants) began to use dangerous but profitable seagrass banks more often following seagrass decline, suggesting a relaxation of anti-predator behavior. Experimental results suggest that a loss of tiger sharks would result in a behaviorally mediated trophic cascade (BMTC) in degraded seagrass beds, further destabilizing them and potentially resulting in a phase shift. My work shows that climactic extremes can have strong but variable impacts on ecosystems mediated in part by species identity, and that maintenance of top predator populations may by important to ecological resilience in the face of climate change.