Individual-based modelling of the development and transport of a Karenia mikimotoi bloom on the North-West European continental shelf

In 2006, a large and prolonged bloom of the dinoflagellate Karenia mikimotoi occurred in Scottish coastal waters, causing extensive mortalities of benthic organisms including annelids and molluscs and some species of fish ( Davidson et al., 2009). A coupled hydrodynamic-algal transport model was developed to track the progression of the bloom around the Scottish coast during June–September 2006 and hence investigate the processes controlling the bloom dynamics. Within this individual-based model, cells were capable of growth, mortality and phototaxis and were transported by physical processes of advection and turbulent diffusion, using current velocities extracted from operational simulations of the MRCS ocean circulation model of the North-west European continental shelf. Vertical and horizontal turbulent diffusion of cells are treated using a random walk approach. Comparison of model output with remotely sensed chlorophyll concentrations and cell counts from coastal monitoring stations indicated that it was necessary to include multiple spatially distinct seed populations of K. mikimotoi at separate locations on the shelf edge to capture the qualitative pattern of bloom transport and development. We interpret this as indicating that the source population was being transported northwards by the Hebridean slope current from where colonies of K. mikimotoi were injected onto the continental shelf by eddies or other transient exchange processes. The model was used to investigate the effects on simulated K. mikimotoi transport and dispersal of: (1) the distribution of the initial seed population; (2) algal growth and mortality; (3) water temperature; (4) the vertical movement of particles by diurnal migration and eddy diffusion; (5) the relative role of the shelf edge and coastal currents; (6) the role of wind forcing. The numerical experiments emphasized the requirement for a physiologically based biological model and indicated that improved modelling of future blooms will potentially benefit from better parameterisation of temperature dependence of both growth and mortality and finer spatial and temporal hydrodynamic resolution.

Individual-based modelling of the development and transport of a Karenia mikimotoi bloom on the North-West European continental shelf

In 2006, a large and prolonged bloom of the dinoflagellate Karenia mikimotoi occurred in Scottish coastal waters, causing extensive mortalities of benthic organisms including annelids and molluscs and some species of fish ( Davidson et al., 2009). A coupled hydrodynamic-algal transport model was developed to track the progression of the bloom around the Scottish coast during June–September 2006 and hence investigate the processes controlling the bloom dynamics. Within this individual-based model, cells were capable of growth, mortality and phototaxis and were transported by physical processes of advection and turbulent diffusion, using current velocities extracted from operational simulations of the MRCS ocean circulation model of the North-west European continental shelf. Vertical and horizontal turbulent diffusion of cells are treated using a random walk approach. Comparison of model output with remotely sensed chlorophyll concentrations and cell counts from coastal monitoring stations indicated that it was necessary to include multiple spatially distinct seed populations of K. mikimotoi at separate locations on the shelf edge to capture the qualitative pattern of bloom transport and development. We interpret this as indicating that the source population was being transported northwards by the Hebridean slope current from where colonies of K. mikimotoi were injected onto the continental shelf by eddies or other transient exchange processes. The model was used to investigate the effects on simulated K. mikimotoi transport and dispersal of: (1) the distribution of the initial seed population; (2) algal growth and mortality; (3) water temperature; (4) the vertical movement of particles by diurnal migration and eddy diffusion; (5) the relative role of the shelf edge and coastal currents; (6) the role of wind forcing. The numerical experiments emphasized the requirement for a physiologically based biological model and indicated that improved modelling of future blooms will potentially benefit from better parameterisation of temperature dependence of both growth and mortality and finer spatial and temporal hydrodynamic resolution.

Superconducting Transition-Edge Sensor Physics

Despite record-setting performance demonstrated by superconducting Transition Edge Sensors (TESs) and growing utilization of the technology, a theoretical model of the physics governing TES devices superconducting phase transition has proven elusive. Earlier attempts to describe TESs assumed them to be uniform superconductors. Sadleir et al. 2010 shows that TESs are weak links and that the superconducting order parameter strength has significant spatial variation. Measurements are presented of the temperature T and magnetic field B dependence of the critical current Ic measured over 7 orders of magnitude on square Mo/Au bilayers ranging in length from 8 to 290 microns. We find our measurements have a natural explanation in terms of a spatially varying order parameter that is enhanced in proximity to the higher transition temperature superconducting leads (the longitudinal proximity effect) and suppressed in proximity to the added normal metal structures (the lateral inverse proximity effect). These in-plane proximity effects and scaling relations are observed over unprecedentedly long lengths (in excess of 1000 times the mean free path) and explained in terms of a Ginzburg-Landau model. Our low temperature Ic(B) measurements are found to agree with a general derivation of a superconducting strip with an edge or geometric barrier to vortex entry and we also derive two conditions that lead to Ic rectification. At high temperatures the Ic(B) exhibits distinct Josephson effect behavior over long length scales and following functional dependences not previously reported. We also investigate how film stress changes the transition, explain some transition features in terms of a nonequilibrium superconductivity effect, and show that our measurements of the resistive transition are not consistent with a percolating resistor network model.

Tide-topography interaction along the eastern Brazilian shelf

In the Tropics, continental shelves governed by western boundary currents are considered to be among the least productive ocean margins in the world, unless eddy-induced shelf-edge upwelling becomes significant. The eastern Brazilian shelf in the Southwest Atlantic is one of these, and since the slight nutrient input from continental sources is extremely oligotrophic. It is characterized by complex bathymetry with the presence of shallow banks and seamounts. In this work, a full three-dimensional nonlinear primitive equation ocean model is used to demonstrate that the interaction of tidal currents and the bottom topography of the east Brazil continental shelf is capable of producing local upwelling of South Atlantic Central Water, bringing nutrients up from deep waters to the surface layer. Such upper layer enrichment is found to be of significance in increasing local primary productivity. (c) 2005 Elsevier Ltd. All rights reserved.

Brucite Microbialites in Living Coral Skeletons: Indicators of Extreme Microenvironments in Shallow-Marine Settings

Brucite [Mg(OH)2] microbialites occur in vacated interseptal spaces of living scleractinian coral colonies (Acropora, Pocillopora, Porites) from subtidal and intertidal settings in the Great Barrier Reef, Australia, and subtidal Montastraea from the Florida Keys, United States. Brucite encrusts microbial filaments of endobionts (i.e., fungi, green algae, cyanobacteria) growing under organic biofilms; the brucite distribution is patchy both within interseptal spaces and within coralla. Although brucite is undersaturated in seawater, its precipitation was apparently induced in the corals by lowered pCO2 and increased pH within microenvironments protected by microbial biofilms. The occurrence of brucite in shallow-marine settings highlights the importance of microenvironments in the formation and early diagenesis of marine carbonates. Significantly, the brucite precipitates discovered in microenvironments in these corals show that early diagenetic products do not necessarily reflect ambient seawater chemistry. Errors in environmental interpretation may arise where unidentified precipitates occur in microenvironments in skeletal carbonates that are subsequently utilized as geochemical seawater proxies.

New particle formation and growth at a remote, sub-tropical coastal location

A month-long intensive measurement campaign was conducted in March/April 2007 at Agnes Water, a remote coastal site just south of the Great Barrier Reef on the east coast of Australia. Particle and ion size distributions were continuously measured during the campaign. Coastal nucleation events were observed in clean, marine air masses coming from the south-east on 65% of the days. The events usually began at ~10:00 local time and lasted for 1-4 hrs. They were characterised by the appearance of a nucleation mode with a peak diameter of ~10 nm. The freshly nucleated particles grew within 1-4 hrs up to sizes of 20-50 nm. The events occurred when solar intensity was high (~1000 W m-2) and RH was low (~60%). Interestingly, the events were not related to tide height. The volatile and hygroscopic properties of freshly nucleated particles (17-22.5 nm), simultaneously measured with a volatility-hygroscopicity-tandem differential mobility analyser (VH-TDMA), were used to infer chemical composition. The majority of the volume of these particles was attributed to internally mixed sulphate and organic components. After ruling out coagulation as a source of significant particle growth, we conclude that the condensation of sulphate and/or organic vapours was most likely responsible for driving particle growth during the nucleation events. We cannot make any direct conclusions regarding the chemical species that participated in the initial particle nucleation. However, we suggest that nucleation may have resulted from the photo-oxidation products of unknown sulphur or organic vapours emitted from the waters of Hervey Bay, or from the formation of DMS-derived sulphate clusters over the open ocean that were activated to observable particles by condensable vapours emitted from the nutrient rich waters around Fraser Island or Hervey Bay. Furthermore, a unique and particularly strong nucleation event was observed during northerly wind. The event began early one morning (08:00) and lasted almost the entire day resulting in the production of a large number of ~80 nm particles (average modal concentration during the event was 3200 cm-3). The Great Barrier Reef was the most likely source of precursor vapours responsible for this event.

Clypeotheca, a new skeletal structure in scleractinian corals : a potential stress indicator

Physiological responses to environmental stress are increasingly well studied in scleractinian corals. This work reports a new stress-related skeletal structure we term clypeotheca. Clypeotheca was observed in several livecollected common reef-building coral genera and a two to three kya subfossil specimen from Heron Reef, Great Barrier Reef and consists of an epitheca-like skeletal wall that seals over the surface of parts of the corallum in areas of stress or damage. It appears to form from a coordinated process wherein neighboring polyps and adjoining coenosarc seal themselves off from the surrounding environment as they contract and die. Clypeotheca forms from inward skeletal centripetal growth at the edges of corallites and by the merging of flange-like outgrowths that surround individual spines over the surface of the coenosteum. Microstructurally, the merged flanges are similar to upsidedown dissepiments and true epitheca. Clypeotheca is interpreted primarily as a response to stress that may help protect the colony from invasion of unhealthy tissues by parasites or disease by retracting tissues in areas that have become unhealthy for the polyps. Identification of skeletal responses of corals to environmental stress may enable the frequency of certain types of environmental stress to be documented in past environments. Such data may be important for understanding the nature of reef dynamics through intervals of climate change and for monitoring the effects of possible anthropogenic stress in modern coral reef habitats.

Earliest diagenesis in scleractinian coral skeletons : implications for palaeoclimate-sensitive geochemical archives

Live-collected samples of four common reef building coral genera (Acropora, Pocillopora, Goniastrea, Porites) from subtidal and intertidal settings of Heron Reef, Great Barrier Reef, show extensive early marine diagenesis where parts of the coralla less than 3 years old contain abundant macro- and microborings and aragonite, high-Mg calcite, low-Mg calcite, and brucite cements. Many types of cement are associated directly with microendoliths and endobionts that inhabit parts of the corallum recently abandoned by coral polyps. The occurrence of cements that generally do not precipitate in normal shallow seawater (e.g., brucite, low-Mg calcite) highlights the importance of microenvironments in coral diagenesis. Cements precipitated in microenvironments may not reXect ambient seawater chemistry. Hence, geochemical sampling of these cements will contaminate trace-element and stable-isotope inventories used for palaeoclimate and dating analysis. Thus, great care must be taken in vetting samples for both bulk and microanalysis of geochemistry. Visual inspection using scanning electron microscopy may be required for vetting in many cases.

Toward robust image detection of crown-of-thorns starfish for autonomous population monitoring

Robust texture recognition in underwater image sequences for marine pest population control such as Crown-Of-Thorns Starfish (COTS) is a relatively unexplored area of research. Typically, humans count COTS by laboriously processing individual images taken during surveys. Being able to autonomously collect and process images of reef habitat and segment out the various marine biota holds the promise of allowing researchers to gain a greater understanding of the marine ecosystem and evaluate the impact of different environmental variables. This research applies and extends the use of Local Binary Patterns (LBP) as a method for texture-based identification of COTS from survey images. The performance and accuracy of the algorithms are evaluated on a image data set taken on the Great Barrier Reef.

Managing the winds of change

Environmental impacts caused during Australia's comparatively recent settlement by Europeans are evident. Governments (both Commonwealth and States) have been largely responsible for requiring landholders – through leasehold development conditions and taxation concessions – to conduct clearing that is now perceived as damage. Most governments are now demanding resource protection. There is a measure of bewilderment (if not resentment) among landholders because of this change. The more populous States, where most overall damage has been done (i.e. Victoria and New South Wales), provide most support for attempts to stop development in other regions where there has been less damage. Queensland, i.e. the north-eastern quarter of the continent, has been relatively slow to develop. It also holds the largest and most diverse natural environments. Tree clearing is an unavoidable element of land development, whether to access and enhance native grasses for livestock or to allow for urban developments (with exotic tree plantings). The consequences in terms of regulations are particularly complex because of the dynamic nature of vegetation. The regulatory terms used in current legislation – such as 'Endangered' and 'Of concern' – depend on legally-defined, static baselines. Regrowth and fire damage are two obvious causes of change. A less obvious aspect is succession, where ecosystems change naturally over long timeframes. In the recent past, the Queensland Government encouraged extensive tree-clearing e.g. through the State Brigalow Development Scheme (mostly 1962 to 1975) which resulted in the removal of some 97% of the wide-ranging mature forests of Acacia harpophylla. At the same time, this government controls National Parks and other reservations (occupying some 4% of the State's 1.7 million km2 area) and also holds major World Heritage Areas (such as the Great Barrier Reef and the Wet Tropics Rainforest) promulgated under Commonwealth legislation. This is a highly prescriptive approach, where the community is directed on the one hand to develop (largely through lease conditions) and on the other to avoid development (largely by unusable reserves). Another approach to development and conservation is still possible in Queensland. For this to occur, however, a more workable and equitable solution than has been employed to date is needed, especially for the remote lands of this State. This must involve resident landholders, who have the capacity (through local knowledge, infrastructure and daily presence) to undertake most costeffectively sustainable land-use management (with suitable attention to ecosystems requiring special conservation effort), that is, provided they have the necessary direction, encouragement and incentive to do so.

Flower animals

The coral reefs around the world may be likened to canaries down the mineshaft of global warming. These sensitive plant-like animals have evolved for life in tropical seas. Their needs are quite specific – not too cold, not too hot. A rise of as little as one degree Celsius is enough to cause some bleaching of these colourful jewels of the sea. Many climate models indicate we can expect sea temperature increases of between two and six degrees Celsius. Research - such as that detailed in a 2004 report by the University of Queensland’s Centre for Marine Studies – indicates that by the year 2050 most of the worlds major reef systems will be dead. Many of us have heard this kind of information, but it remains difficult to comprehend. It’s almost impossible to imagine the death of the Great Barrier Reef. Some six to nine thousand years old and visible from space, it is the world’s largest structure created by living organisms. Yet whilst it is hard to believe, this gentle, sensitive giant is at grave risk because it cannot adapt quickly enough to the changes in the environment. This cluster of fluffy felt brain coral sculptures are connected in real time to temperature data collected by monitoring stations within the Great Barrier Reef, that form part of the Australian Institute of Marine Science’s Great Barrier Reed Ocean Observing System. These corals display illumination patterns showing changes in sea temperature at Heron Reef, one of the 2,900 reefs that comprise the Great Barrier Reef. Their spectrum of colour ranges from cool hues, through warm tones to bright white when temperatures exceed those that tropical corals are able to tolerate over sustained periods. The Flower Animals also blush in colour and make sound when people come within close proximity. In a reef, fishes and other creatures generate significant amounts of sound. These cacophonies are considered an indicator of reef health, and are used by reef fish to determine where they can best live and forage.

Lumia : Art | light | motion. The Art of Kuuki.

The State Library of Queensland is delighted to present Lumia: art/light/motion, a culmination of many years of collaboration by the Kuuki collective led by Priscilla Bracks and Gavin Sade. This extraordinary exhibition not only showcases the unique talent of these Queenslanders, it also opens up a world of future possibilities while re-presenting the past and present. These contemporary new media installations sit comfortably within the walls of the library as they are the distinctive products of inquisitive and philosophical minds. In a sense the exhibition highlights the longevity and purposefulness of a cultural learning institution, through the non-traditional use of data, information, research and collection interpretation. The exhibition simultaneously articulates one of our key objectives – to progress the state’s digital agenda. Two academic essays have been commissioned for this joint Kuuki and State Library of Queensland publication. The first is by artist and writer Paul Brown, who has specialised in art, science and technology since the late 1960s and in computational and generative art since the mid 1970s. Brown investigates the history of new media, which is celebrating its 60th anniversary, and clearly places Sade and Bracks at the forefront of this genre nationally. The second essay is by arts writer Linda Carroli, who has delved deeply into the thoughts and processes of the artists to bring to light the complex workings of the artists’ minds. The publication also features an interview Carroli conducted with the artists. This exhibition is playful, informative and contemplative. The audience is invited to play, and consequently to ponder the way we live and the environmental and social implications of our choices. The exhibition tempts us to travel deep into the Antarctic, plunge into the Great Barrier Reef, be swamped by an orchestra of crickets, enter the Charmed world and travel back in time to a Victorian parlour where you can interact with a ‘new-world’ lyrebird and consider a brave new world where our only link to the animal world is with robotic representations. In essence this exhibition is about ideas and knowledge and what better institution than the State Library of Queensland to partner such a project?. State Library is committed to preserving culture, exploring new media and creating new content as a lasting legacy of Queensland for all Queenslanders.

Significant Dot: The 1769 transit of Venus - a tale of astronomy, medicine and empire

This article places the 6 June 2012 transit of Venus in the context of James Cook’s voyage from England to the South Pacific to observe the 1769 transit of Venus. A description is given on how to use a computer program called Stellarium to ‘observe’ the 1769 transit of Venus exactly as Cook saw it from the island of Tahiti in the South Pacific.

Fusion or non fusion of coral fragments in Acropora

Corals inhabit high energy environments where frequent disturbances result in physical damage to coralla, including fragmentation, as well as generating and mobilizing large sediment clasts. The branching growth form common in the Acropora genus makes it particularly susceptible to such disturbances and therefore useful for study of the fate of large sediment clasts. Living Acropora samples with natural, extraneous, broken coral branches incorporated on their living surface and dead Acropora skeletons containing embedded clasts of isolated branch sections of Acropora were observed and/or collected from the reef flat of Heron Reef, southern Great Barrier Reef and Bargara, Australia respectively. Here we report three different outcomes when pebble-sized coral branches became lodged on living coral colonies during sedimentation events in natural settings in Acropora: 1) Where live coral branches produced during a disturbance event come to rest on probable genetic clone-mate colonies they become rapidly stabilised leading to complete soft tissue and skeletal fusion; 2) Where the branch and underlying colony are not clone-mates, but may still be the same or similar species, the branches still may be stabilised rapidly by soft tissue, but then one species will overgrow the other; and 3) Where branches represent dead skeletal debris, they are treated like any foreign clast and are surrounded by clypeotheca and incorporated into the corallum by overgrowth. The retention of branch fragments on colonies in high energy reef flat settings may suggest an active role of coral polyps to recognise and fuse with each other. Also, in all cases the healing of disturbed tissue and subsequent skeletal growth is an adaptation important for protecting colonies from invasion by parasites and other benthos following disturbance events and may also serve to increase corallum strength. Knowledge of such adaptations is important in studies of coral behaviour during periods of environmental stress.