Kate Osborne

Disturbance and the Dynamics of Coral Cover on the Great Barrier Reef (1995–2009)

Coral reef ecosystems worldwide are under pressure from chronic and acute stressors that threaten their continued existence. Most obvious among changes to reefs is loss of hard coral cover, but a precise multi-scale estimate of coral cover dynamics for the Great Barrier Reef (GBR) is currently lacking. Monitoring data collected annually from fixed sites at 47 reefs across 1300 km of the GBR indicate that overall regional coral cover was stable (averaging 29% and ranging from 23% to 33% cover across years) with no net decline between 1995 and 2009. Subregional trends (10–100 km) in hard coral were diverse with some being very dynamic and others changing little. Coral cover increased in six subregions and decreased in seven subregions. Persistent decline of corals occurred in one subregion for hard coral and Acroporidae and in four subregions in non-Acroporidae families. Change in Acroporidae accounted for 68% of change in hard coral. Crown-of-thorns starfish (Acanthaster planci) outbreaks and storm damage were responsible for more coral loss during this period than either bleaching or disease despite two mass bleaching events and an increase in the incidence of coral disease. While the limited data for the GBR prior to the 1980s suggests that coral cover was higher than in our survey, we found no evidence of consistent, system-wide decline in coral cover since 1995. Instead, fluctuations in coral cover at subregional scales (10–100 km), driven mostly by changes in fast-growing Acroporidae, occurred as a result of localized disturbance events and subsequent recovery.

Contribution of climate change to degradation and loss of critical fish habitats in Australian marine and freshwater environments

Australiasaquaticecosystemsareunique,supportingahighdiversityofspeciesandhighlevelsofendemism; however, they are also extremely vulnerable to climate change. The present review assesses climate-induced changes to structuralhabitatsthathaveoccurredindifferentaquaticecosystems.Climaticimpactsareoftendifficulttodiscernagainst the background of habitat degradation caused by more direct anthropogenic impacts. However, climate impacts will become more pronounced with ongoing changes in temperature, water chemistry, sea level, rainfall patterns and ocean currents. Each of these factors is likely to have specific effects on ecosystems, communities or species, and their relative importance varies across different marine and freshwater habitats. In the Murray-Darling Basin, the greatest concern relates to declines in surface water availability and riverine flow, owing to declining rainfall and increased evaporative loss.OntheGreatBarrierReef,increasingtemperaturesandoceanacidificationcontributetosustainedandongoinglossof habitat-forming corals. Despite the marked differences in major drivers and consequences of climate change, the solution is always the same. Greenhouse-gas emissions need to be reduced as a matter of urgency, while also minimising non- climatic disturbances. Together, these actions will maximise opportunities for adaptation by species and increase ecosystem resilience.

Expectations and Outcomes of Reserve Network Performance following Re-zoning of the Great Barrier Reef Marine Park

Networks of no-take marine reserves (NTMRs) are widely advocated for preserving exploited fish stocks and for conserving biodiversity. We used underwater visual surveys of coral reef fish and benthic communities to quantify the short- to medium-term (5 to 30 years) ecological effects of the establishment of NTMRs within the Great Barrier Reef Marine Park (GBRMP). The density, mean length, and biomass of principal fishery species, coral trout (Plectropomus spp., Variola spp.), were consistently greater in NTMRs than on fished reefs over both the short and medium term. However, there were no clear or consistent differences in the structure of fish or benthic assemblages, non-target fish density, fish species richness, or coral cover between NTMR and fished reefs. There was no indication that the displacement and concentration of fishing effort reduced coral trout populations on fished reefs. A severe tropical cyclone impacted many survey reefs during the study, causing similar declines in coral cover and fish density on both NTMR and fished reefs. However, coral trout biomass declined only on fished reefs after the cyclone. The GBRMP is performing as expected in terms of the protection of fished stocks and biodiversity for a developed country in which fishing is not excessive and targets a narrow range of species. NTMRs cannot protect coral reefs directly from acute regional-scale disturbance but, after a strong tropical cyclone, impacted NTMR reefs supported higher biomass of key fishery-targeted species and so should provide valuable sources of larvae to enhance population recovery and long-term persistence.

Great Barrier Reef butterflyfish community structure: the role of shelf position and benthic community type

The extent to which fish communities are structured by spatial variability in coral reef habitats versus stochastic processes (such as larval supply) is very important in predicting responses to sustained and ongoing habitat degradation. In this study, butterflyfish and benthic communities were surveyed annually over 15 years on 47 reefs (spanning 12° of latitude) of the Great Barrier Reef (GBR). Spatial autocorrelation in the structure of butterflyfish communities versus key differences in reef habitats was investigated to assess the extent to which the structure of these fish communities is influenced by habitat conditions. Benthic communities on each of the 47 reefs were broadly categorised as either: 1. Poritidae/Alcyoniidae, 2. mixed taxa, 3. soft coral or 4. Acropora-dominated habitats. These habitat types most reflected increases in water clarity and wave exposure, moving across the GBR shelf from coastal to outer-shelf environments. In turn, each habitat type also supported very distinct butterflyfish communities. Hard coral feeders were always the dominant butterflyfish species in each community type. However, the numerically dominant species changed according to habitat type, representing spatial replacement of species across the shelf. This study reveals clear and consistent differences in the structure of fish communities among reefs associated with marked differences in habitat structure.

A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity

Summary River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane‐oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4–30°C, pH 6–8, 1–15 g l−1 NaCl), communities were enriched by sequences affiliated with M ethylobacter and M ethylomonas spp. and specifically a M ethylobacter psychrophilus‐related species at 4–21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l−1 selected for putative thermophiles (M ethylocaldum), acidophiles (M ethylosoma) and haloalkaliphiles (M ethylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary.

Origins and Implications of a Primary Crown-of-Thorns Starfish Outbreak in the Southern Great Barrier Reef

The crown-of-thorns starfish (COTS) is a major predator of hard corals. Repeated COTS outbreaks in the Cairns and Central sections of the Great Barrier Reef (GBR) have been responsible for greater declines in coral cover than any other type of disturbance, including cyclones, disease, and coral bleaching. Knowledge of the precise timing and location of primary outbreaks could reveal the initial drivers of outbreaks and so could indicate possible management measures. In the central GBR, COTS outbreaks appear to follow major flooding events, but despite many years of observations, no primary outbreak has ever been unequivocally identified in the central and northern GBR. Here we locate a primary outbreak of COTS on the southern GBR which is not correlated with flooding. Instead it appears to have been the result of a combination of life history traits of COTS and prevailing oceanographic conditions. The hydrodynamic setting implies that the outbreak could disperse larvae to other reefs in the region.

Determining background levels and defining outbreaks of crustose coralline algae disease on the Great Barrier Reef

Crustose coralline algae (CCA) play a vital role in coral-reef ecosystems and, like other marine organisms, they are vulnerable to disease. Between 2006 and 2011, incidence of two types of CCA disease was systematically recorded over a large portion of the Great Barrier Reef (GBR). The two CCA diseases that were recorded, coralline lethal orange disease and coralline white-band syndrome, were ubiquitous on the GBR, but generally at low levels comparable to those found on reefs in other parts of the Indo-Pacific. The present broad-scale study of the distribution and abundance of CCA disease on the GBR provides information on background levels of these diseases and allows regional thresholds for outbreaks to be defined. This will allow managers and researchers to focus attention on areas of high incidence of CCA disease to increase our understanding of causes and the environmental impacts of CCA disease at a time when coral reefs are under growing anthropogenic threats.

Automated annotation of corals in natural scene images using multiple texture representations

Current coral reef health monitoring programs rely on biodiversity data obtained through the acquisition and annotation of underwater photographs. Manual annotation of these photographs is a necessary step, but has become problematic due to the high volume of images and the high cost of human resources. While automated and reliable multi-spectral annotation methods exist, coral reef images are often limited to visible light, which makes automation difficult. Much of the previous work has focused on popular texture recognition methods, but the results remain unsatisfactory when compared to human performance for the same task. In this work, we present an improved automatic method for coral image annotation that yields consistent accuracy improvements over existing methods. Our method builds on previous work by combining multiple feature representations. We demonstrate that the aggregation of multiple methods outperforms any single method. Furthermore, our proposed system requires virtually no parameter tuning, and supports rejection for improved results. Firstly, the complex texture diversity of corals is handled by combining multiple feature representations: local binary patterns, hue and opponent angle histograms, textons, and deep convolutional activation feature. Secondly, these multiple representations are aggregated using a score-level fusion of multiple support vector machines. Thirdly, rejection can optionally be applied to enhance classification results, and allows efficient semi-supervised image annotation in collaboration with human experts.

The Bacteriohopanepolyol Inventory of Novel Aerobic Methane Oxidising Bacteria Reveals New Biomarker Signatures of Aerobic Methanotrophy in Marine Systems

Aerobic methane oxidation (AMO) is one of the primary biologic pathways regulating the amount of methane (CH4) released into the environment. AMO acts as a sink of CH4, converting it into carbon dioxide before it reaches the atmosphere. It is of interest for (paleo)climate and carbon cycling studies to identify lipid biomarkers that can be used to trace AMO events, especially at times when the role of methane in the carbon cycle was more pronounced than today. AMO bacteria are known to synthesise bacteriohopanepolyol (BHP) lipids. Preliminary evidence pointed towards 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol) being a characteristic biomarker for Type I methanotrophs. Here, the BHP compositions were examined for species of the recently described novel Type I methanotroph bacterial genera Methylomarinum and Methylomarinovum, as well as for a novel species of a Type I Methylomicrobium. Aminopentol was the most abundant BHP only in Methylomarinovum caldicuralii, while Methylomicrobium did not produce aminopentol at all. In addition to the expected regular aminotriol and aminotetrol BHPs, novel structures tentatively identified as methylcarbamate lipids related to C-35 amino-BHPs (MC-BHPs) were found to be synthesised in significant amounts by some AMO cultures. Subsequently, sediments and authigenic carbonates from methane-influenced marine environments were analysed. Most samples also did not contain significant amounts of aminopentol, indicating that aminopentol is not a useful biomarker for marine aerobic methanotophic bacteria. However, the BHP composition of the marine samples do point toward the novel MC-BHPs components being potential new biomarkers for AMO.

Methanotroph-derived bacteriohopanepolyol (BHP) signatures as a function of temperature related growth, survival, cell death and preservation in the geological record

Interpretation of bacteriohopanepolyol (BHP) biomarkers tracing microbiological processes in modern and ancient sediments relies on understanding environmental controls of production and preservation. BHPs from methanotrophs (35-aminoBHPs) were studied in methane-amended aerobic river-sediment incubations at different temperatures. It was found that: (i) With increasing temperature (4°C-40°C) a 10-fold increase in aminopentol (associated with Crenothrix and Methylobacter spp. growth) occurred with only marginal increases in aminotriol and aminotetrol; (ii) A further increase in temperature (50°C) saw selection for the thermophile Methylocaldum and mixtures of aminopentol and C-3 methylated aminopentol, again, with no increase in aminotriol and aminotetrol. (iii) At 30°C, more aminopentol and an aminopentol isomer and unsaturated aminopentol were produced after methanotroph growth and the onset of substrate starvation/oxygen depletion. (iv) At 50°C, aminopentol and C-3 methylated aminopentol, only accumulated during growth but were clearly resistant to remineralization despite cell death. These results have profound implications for the interpretation of aminoBHP distributions and abundances in modern and past environments. For instance, a temperature regulation of aminopentol production but not aminotetrol or aminotriol is consistent with and, corroborative of, observed aminopentol sensitivity to climate warming recorded in a stratigraphic sequence deposited during the Paleocene-Eocene thermal maximum (PETM).