Regional patterns of fish diversity, abundance, distribution, and assemblage composition are driven by a combination of biotic and abiotic conditions in the marine environment, but these conditions can be altered through anthropogenic activities, such as those associated with oil and gas extraction. The present study utilises data on fish relative abundance and diversity obtained from 1546 baited remote underwater video deployments conducted between 2004 – 2019 in depths of 9 – 170 m across 2000 km of coastline in north-west Australia on natural habitats and subsea pipelines to understand the influence of oil and gas infrastructure on fish assemblages. A total of 450 fish taxa from 56 families was observed, with populations dominated by generalist and invertebrate carnivore taxa. At the regional scale, subsea pipelines had lower diversity (lower taxonomic richness) than natural environments, but possessed a higher abundance of piscivorous and herbivorous fish taxa. Clear patterns in fish assemblage composition were observed in multivariate analyses, reflecting the proximity of oceanic shoals and banks, depth, and to a lesser extent, oil and gas infrastructure. Shallow-water and close to shoals assemblages were characterised by a diversity of site-attached (e.g., wrasses, tuskfish), reef-associated taxa (e.g., emperors). Mesophotic fish assemblages were characterised by commercially important (e.g., goldband snapper), wide-ranging (e.g., sharks) and sand-affiliated (e.g., toadfish, threadfin bream) taxa. Proximity to pipelines and platforms ranked low as predictors in the multivariate analyses suggesting a negligible regional influence of these structures on fish communities in comparison to depth and shoal habitats. Local-scale influences of subsea infrastructure, however, may be important for some fish species (infrastructure vs. immediate surrounds). Our study highlights the influence of abiotic factors on regional-scale patterns in fish assemblage structure across north-west Australia.

Knowledge of marine ecosystems that grow and reside on and around subsea oil and gas infrastructure is required to understand impacts of this offshore industry on the marine environment and inform decommissioning decisions. This study used baited remote underwater stereo-video systems (stereo-BRUVs) to compare species richness, fish abundance and size along 42.3 km of subsea pipeline and in adjacent areas of varying habitats. The pipeline is laid in an onshore-offshore direction enabling surveys to encompass a range of depths from 9 m nearshore out to 140 m depth offshore. Surveys off the pipeline were performed across this depth range and in an array of natural habitats (sand, macroalgae, coral reef) between 1 km and 40 km distance from the pipeline. A total of 14,953 fish were observed comprising 240 species (131 on the pipeline and 225 off-pipeline) and 59 families (39 on the pipeline and 56 off-pipeline) and the length of 8,610 fish were measured. The fish assemblage on and off the pipeline was similar in depths of <80 m. In depths beyond 80 m, the predominant habitat off-pipeline was sand and differences between fish assemblages on and off-pipeline were more pronounced. The pipeline was characterised by higher biomass and abundances of larger-bodied, commercially important species such as: Pristipomoides multidens (goldband snapper), Lutjanus malabaricus (saddletail snapper) and Lutjanus russellii (Moses' snapper) among others, and possessed a catch value 2-3 times higher per stereo-BRUV deployment than that of fish observed off-pipeline. Adjacent natural seabed habitats possessed higher abundances of Atule mate (yellowtail scad), Nemipterus spp. (threadfin bream) and Terapon jarbua (crescent grunter), species of no or low commercial value. This is the first published study to use stereo-BRUVs to report on the importance of subsea infrastructure to commercially important fishes over a depth gradient and increases our knowledge of the fish assemblage associated with subsea infrastructure off north-west Australia. These results provide a greater understanding of ecological and fisheries implications of decommissioning subsea infrastructure on the north-west shelf, and will help better inform decision-making on the fate of infrastructure at different depths.

Sustained calcification is fundamental for maintaining tropical coral reef ecosystems which are under increasing pressure from global and local changes to the marine environment. Annual density bands in massive corals provide a robust means to retrospectively monitor growth and identify the environmental drivers. We present Porites growth characteristics for 60 coral cores from 18 reef sites and five environmental regions off Western Australia (WA) over the period 1950–2008. This remote region encompasses diverse coral reef ecosystems and is an economically important natural resource hub. Despite high variability, average calcification is highest in the offshore shelf reefs and lowest in the most southerly reefs. The primary environmental drivers of these spatial variations are annual and winter minimum sea surface temperature (SST) and annual winter minimum photosynthetically active radiation. Average growth characteristics for WA reefs are comparable to those of Australia's Great Barrier Reef. Calcification rates at the two most southerly WA reefs are anomalously high, which may be due to the unusual environmental conditions generated by the Leeuwin Current. Variable rates of SST warming across the 18 reefs are, however, changing the strength of the relationship between SST and calcification. We found no evidence to support the contention that annual density banding is driven by environmental seasonality. Retrospective monitoring of growth rates provides a critical tool for both assessing coral growth responses to ongoing rapid climate change and possible responses to increasing anthropogenic pressures related to natural resource development in the region.

Understanding the sedimentation and turbidity thresholds for corals is critical in assessing the potential impacts of dredging projects in tropical marine systems. In this study, we exposed two species of coral sampled from offshore locations to six levels of total suspended solids (TSS) for 16 weeks in the laboratory, including a 4 week recovery period. Dose-response relationships were developed to quantify the lethal and sub-lethal thresholds of sedimentation and turbidity for the corals. The sediment treatments affected the horizontal foliaceous species (Montipora aequituberculata) more than the upright branching species (Acropora millepora). The lowest sediment treatments that caused full colony mortality were 30 mg l(-1) TSS (25 mg cm(-2) day(-1)) for M. aequituberculata and 100 mg l(-1) TSS (83 mg cm(-2) day(-1)) for A. millepora after 12 weeks. Coral mortality generally took longer than 4 weeks and was closely related to sediment accumulation on the surface of the corals. While measurements of damage to photosystem II in the symbionts and reductions in lipid content and growth indicated sub-lethal responses in surviving corals, the most reliable predictor of coral mortality in this experiment was long-term sediment accumulation on coral tissue.

Responses of bioindicator candidates for water quality were quantified in two studies on inshore coral reefs of the Great Barrier Reef (GBR). In Study 1, 33 of the 38 investigated candidate indicators (including coral physiology, benthos composition, coral recruitment, macrobioeroder densities and FORAM index) showed significant relationships with a composite index of 13 water quality variables. These relationships were confirmed in Study 2 along four other water quality gradients (turbidity and chlorophyll). Changes in water quality led to multi-faceted shifts from phototrophic to heterotrophic benthic communities, and from diverse coral dominated communities to low-diversity communities dominated by macroalgae. Turbidity was the best predictor of biota; hence turbidity measurements remain essential to directly monitor water quality on the GBR, potentially complemented by our final calibrated 12 bioindicators. In combination, this bioindicator system may be used to assess changes in water quality, especially where direct water quality data are unavailable.

The increasing frequency and severity of mass bleaching events in the past few decades has raised considerable concerns. Here we report on the numerical simulations of Low Reynolds turbulence models coral microenvironments to determine surface temperature rise in reef corals and test whether our model is capable to estimate of the extent of warming likely to be encountered in the nature during calm conditions. The Computational Fluid Dynamics (CFD) simulation uses the OPENFOAM CFD libraries to implement a steady-state turbulent flow porous medium model, with heat transfer accounted for using a transport equation for temperature. We validated the model using controlled laboratory experiment observations. Introduction Corals are one of the most ecologically and economically important habitat-forming species. However, they can bleach in response to stressful thermal conditions. The increasing frequency and severity of bleaching over the past few decades has raised considerable concern for the long-term viability of coral reefs. The combination of both elevated sea-surface temperature and solar irradiance is widely acknowledged to be the most important trigger for coral bleaching. Other environmental factors though such as low flow, low salinity and low water turbidity can contribute to the bleaching responses by corals. These parameters vary considerably on coral species and morphologies, which can potentially determine the extent and variation of the fluid flow and mass and heat transfer in corals, and ultimately their susceptibility to bleaching. The study of coral bleaching has been dominated by laboratory and field experiments, in-situ observations, and predictive modelling based on remotely sensed sea conditions. However, the reasons corals bleach are not fully understood. Laboratory studies can be confounded by sensitivity of most coral species to laboratory conditions and the difficulties inherent in accurately simulating the complexity and variability of oceanic conditions, while, field-based approaches are typically costly and are difficult to generalise from because of uncontrolled natural variation that may be relevant only to specific sites. Numerical methods on the other hand provide a powerful, holistic approach to solve physics associated with coral bleaching including a wide range of scales of fluid motion, heat transfer, and the morphology of the corals. Conventionally, bleaching has been assessed on the basis of sea surface temperature (SST) data, however, it is the deviation of surface coral temperature from ambient SST, called thermal stress, that is most likely to trigger and determine the severity of bleaching. Previously, we established the potential of CFD in predicting the thermal stress imposed on corals by their thermal microenvironments under laminar flow conditions [1]. However, in the overwhelming majority of cases, the external flow stream carries with it a certain degree of turbulence. In essence, the laminar boundary layers are relatively easy to measure but in turbulent although there exists a very thin layer next to the wall called laminar or viscous sublayer, its thickness is so small that it is almost impossible or very difficult to observe under experimental conditions. Here we validate our computational predictions for the surface warming of corals that varied in pigmentations and validate our findings with the experimental observations [2]. Thermal regions in coral Heat transfer within and around corals is affected by three main mechanisms: (1) the rate of incident radiation absorbed by the exposed tissue surface, (2) the rate of heat loss due to convection from the tissue and skeleton into the surrounding water, and (3) the rate of heat conduction from the tissue into the skeleton. The model presented here considers all of these mechanisms, with the tissue and skeleton layers each possessing slightly distinctive thermal properties. Although here we assumed that the living tissue is almost impermeable, however, in many cases, the activity of borers and coral grazers will result in openings allowing percolation and increased skeletal porosity. Model validation The experimental study of Fabricius et al. (2006) [2] was used to validate our turbulent CFD model. They conducted an experiment which exposed a range of different coral darkness (hemispherical coral (Favia matthaii), ≃90 mm) to direct sunlight ranging from high irradiance (1,500-1,600 μmol m−2 s−1 or ∼800 W m−2) to low irradiance (120-350 μmol m−2 s−1 or ∼150 W m−2) (Figure 1). Pigmentation was measured as background fluorescence, F0, which here defined as a proxy of a light-absorptivity coefficient where F0=100 as near white and F0=600 as dark brown. Measurements were taken outdoors in flow chambers (consisting of four 15-cm-deep and 45-cm-long working sections) creating an unidirectional flow with a steady inlet flow maintained at 0.01, 0.02, and 0.05 m s−1 (only the latter flow speed was investigated since we are interested in validating the turbulence models, Re≃ 4600), and a temperature of 29.3◦C. Coral surface warming was given as the difference between coral surface temperature and ambient water temperature after a period of exposure to solar irradiance. Figure 1: Model set-up and boundary conditions for the simulation

Anthropogenic increases of atmospheric carbon dioxide lead to warmer sea surface temperatures and altered ocean chemistry. Experimental evidence suggests that coral calcification decreases as aragonite saturation drops but increases as temperatures rise toward thresholds optimal for coral growth. In situ studies have documented alarming recent declines in calcification rates on several tropical coral reef ecosystems. We show there is no widespread pattern of consistent decline in calcification rates of massive Porites during the 20th century on reefs spanning an 11° latitudinal range in the southeast Indian Ocean off Western Australia. Increasing calcification rates on the high-latitude reefs contrast with the downward trajectory reported for corals on Australia's Great Barrier Reef and provide additional evidence that recent changes in coral calcification are responses to temperature rather than ocean acidification.

We present Computational Fluid Dynamics (CFD) models of the coupled dynamics of water flow, heat transfer and irradiance in and around corals to predict temperatures experienced by corals. These models were validated against controlled laboratory experiments, under constant and transient irradiance, for hemispherical and branching corals. Our CFD models agree very well with experimental studies. A linear relationship between irradiance and coral surface warming was evident in both the simulation and experimental result agreeing with heat transfer theory. However, CFD models for the steady state simulation produced a better fit to the linear relationship than the experimental data, likely due to experimental error in the empirical measurements. The consistency of our modelling results with experimental observations demonstrates the applicability of CFD simulations, such as the models developed here, to coral bleaching studies. A study of the influence of coral skeletal porosity and skeletal bulk density on surface warming was also undertaken, demonstrating boundary layer behaviour, and interstitial flow magnitude and temperature profiles in coral cross sections. Our models compliment recent studies showing systematic changes in these parameters in some coral colonies and have utility in the prediction of coral bleaching.

Background Lipids in reef building corals can be divided into two classes; non-polar storage lipids, e.g. wax esters and triglycerides, and polar structural lipids, e.g. phospholipids and cholesterol. Differences among algal endosymbiont types are known to have important influences on processes including growth and the photobiology of scleractinian corals yet very little is known about the role of symbiont types on lipid energy reserves. Methodology/Principal Findings The ratio of storage lipid and structural lipid fractions of Scott Reef corals were determined by thin layer chromatography. The lipid fraction ratio varied with depth and depended on symbiont type harboured by two corals (Seriatopora hystrix and Pachyseris speciosa). S. hystrix colonies associated with Symbiodinium C1 or C1/C# at deep depths (>23 m) had lower lipid fraction ratios (i.e. approximately equal parts of storage and structural lipids) than those with Symbiodinium D1 in shallow depths (<23 m), which had higher lipid fraction ratios (i.e. approximately double amounts of storage relative to structural lipid). Further, there was a non-linear relationship between the lipid fraction ratio and depth for S. hystrix with a modal peak at ∼23 m coinciding with the same depth as the shift from clade D to C types. In contrast, the proportional relationship between the lipid fraction ratio and depth for P. speciosa, which exhibited high specificity for Symbiodinium C3 like across the depth gradient, was indicative of greater amounts of storage lipids contained in the deep colonies. Conclusions/Significance This study has demonstrated that Symbiodinium exert significant controls over the quality of coral energy reserves over a large-scale depth gradient. We conclude that the competitive advantages and metabolic costs that arise from flexible associations with divergent symbiont types are offset by energetic trade-offs for the coral host.

A snapshot of the fish-habitat associations in the vicinity of James Price Point was obtained during a single expedition in October 2009, when Baited Remote Underwater Video Stations (BRUVS) were deployed in coastal waters to survey the demersal and semi-demersal ichthyofauna. A total of 7108 individuals from 116 species of fishes, sharks, rays and sea snakes were recorded from 154 sites. Bony fishes were represented by 8 orders, and cartilaginous fishes were well represented by the Carcharhiniformes, Rajiformes and Orectolobiformes. There were 2 species of hydrophiid sea snakes. Multivariate analysis showed that species responded to the amount of epibenthic cover in the study area and that there was an interaction between depth and sediment composition, as well as depth and epibenthic cover, in defining four fish assemblages to the north and south of James Price Point. Diversity appeared to increase with depth amongst these assemblages. The seabed offshore from James Price Point was inhabited by a deep sandy fish assemblage, which intruded inshore across the study area, and was characterised by the presence of ponyfish (Leiognathus), threadfin bream (Nemipterus) and queenfish (Scomberoides). On either side were shallow, northern and deeper, southern, assemblages inhabiting gardens of macroalgae, filter-feeders and some seagrass beds. These epibenthic habitats at the northern and southern ends of the survey area were clearly important to many species, but in general there appeared to be little association of particular vertebrate species or biotic habitat types with the James Price Point area itself. The study area was notable for the diversity and abundance of the fauna, given the shallow depth, lack of rugose seafloor topography and lack of sub-tidal coral reefs in the area sampled. Coarse comparison with the fauna at similar distance to shore in similar latitudes in the Great Barrier Reef Marine Park, the Burrup Peninsula and the Kimberley indicated that the study area had more small pelagic planktivores and more large semi-demersal predators. There was also an absence of some species normally associated with muddy seafloors and fringing coral reefs that are common on BRUVS set elsewhere in regions with less extreme tidal ranges. © Royal Society of Western Australia 2011.

Background The Symbiodinium community associated with scleractinian corals is widely considered to be shaped by seawater temperature, as the coral's upper temperature tolerance is largely contingent on the Symbiodinium types harboured. Few studies have challenged this paradigm as knowledge of other environmental drivers on the distribution of Symbiodinium is limited. Here, we examine the influence of a range of environmental variables on the distribution of Symbiodinium associated with Acropora millepora collected from 47 coral reefs spanning 1,400 km on the Great Barrier Reef (GBR), Australia. Methodology/Principal Findings The environmental data included Moderate Resolution Imaging Spectroradiometer (MODIS) satellite data at 1 km spatial resolution from which a number of sea surface temperature (SST) and water quality metrics were derived. In addition, the carbonate and mud composition of sediments were incorporated into the analysis along with in situ water quality samples for a subset of locations. Analyses were conducted at three spatio-temporal scales [GBR (regional-scale), Whitsunday Islands (local-scale) and Keppel Islands/Trunk Reef (temporal)] to examine the effects of scale on the distribution patterns. While SST metrics were important drivers of the distribution of Symbiodinium types at regional and temporal scales, our results demonstrate that spatial variability in water quality correlates significantly with Symbiodinium distribution at local scales. Background levels of Symbiodinium types were greatest at turbid inshore locations of the Whitsunday Islands where SST predictors were not as important. This was not the case at regional scales where combinations of mud and carbonate sediment content coupled with SST anomalies and mean summer SST explained 51.3% of the variation in dominant Symbiodinium communities. Conclusions/Significance Reef corals may respond to global-scale stressors such as climate change through changes in their resident symbiont communities, however, management of local-scale stressors such as altered water quality is also necessary for maintenance of coral-Symbiodinium associations.

Studies of the regulation and importance of physiological processes such as coral photosynthesis and respiration on coral reefs require knowledge of spatio-temporal patterns of variability at different scales.Oxygen microelectrodes were used to measure photosynthesis and dark respiration of 2 corals, Pocillopora damicornis and Turbinaria reniformis, in the northern (Lizard Island) and central (Davies and Broadhurst Reefs) regions of the Great Barrier Reef (GBR) in winter and summer.Genetic characterisation of Symbiodinium revealed that P. damicornis hosted a single symbiont type (Symbiodinium C1) in both regions, whereas T. reniformis harboured 2 types, dependent on location.Colonies at Lizard Island harboured Symbiodinium D, whereas colonies at Davies Reef harboured Symbiodinium C2.Rates of gross photosynthesis were greater in the central than in the northern GBR in summer.A similar pattern was detected for dark respiration rates in T. reniformis.No seasonal change in either photosynthesis or dark respiration was evident in the northern GBR, possibly due to less annual variability in light conditions, and for T. reniformis, additionally the presence of Symbiodinium D. These results highlight that environmental conditions coupled with regional-scale distribution of Symbiodinium are likely to exert important influences on respiration and photosynthetic performance of reef-building corals.

Photo-acclimatisation by the algal endosymbionts of scleractinian corals to changes in environmental conditions may influence their density and/or the concentration of photosynthetic pigments, and hence coral brightness, on short time-scales. To examine coral pigmentation as a bioindicator of water quality, the brightness of massive corals was quantified using colour charts, concentrations of the pigment chlorophyll a and reflectance spectrometry in the field and with manipulative experiments. Along a water quality gradient, massive Porites became progressively lighter as nutrients decreased and irradiance increased. A laboratory experiment showed that Porites nubbins darkened within 25 days following exposure to reduced water quality. The results of a transplantation experiment of Porites nubbins in a manipulation incorporating multiple depths and zones of water quality confirmed colony brightness as a simple tool to monitor changes in marine water quality, provided effects due to other influences on pigmentation, e.g. seawater temperatures, are taken into consideration.

The rapid formation of calcium carbonate coral skeletons (calcification) fuelled by the coral-algal symbiosis is the backbone of tropical coral reef ecosystems. However, the efficacy of calcification is measurably influenced by the sea's physico-chemical environment, which is changing rapidly. Warming oceans have already led to increased frequency and severity of coral bleaching, and ocean acidification has a demonstrable potential to cause reduced rates of calcification. There is now general agreement that ocean warming and acidification are attributable to human activities increasing greenhouse gas concentrations in the atmosphere, and the large part of the extra carbon dioxide (the main greenhouse gas) that is absorbed by oceans. Certain massive corals provide historical perspectives on calcification through the presence of dateable annual density banding patterns. Each band is a page in an environmental archive that reveals past responses of growth (linear extension, skeletal density and calcification rate) and provides a basis for prediction of future of coral growth. A second major line of research focuses on the measurement of various geochemical tracers incorporated into the growth bands, allowing the reconstruction of past marine climate conditions (i.e. palaeoclimatology). Here, we focus on the structural properties of the annual density bands themselves (viz. density; linear extension), exploring their utility in providing both perspectives on the past and pointers to the future of calcification on coral reefs. We conclude that these types of coral growth records, though relatively neglected in recent years compared to the geochemical studies, remain immensely valuable aids to unravelling the consequences of anthropogenic climate change on coral reefs. Moreover, an understanding of coral growth processes is an essential pre-requisite for proper interpretation of studies of geochemical tracers in corals.

Approximately one quarter of zooxanthellate coral species have a depth distribution from shallow waters (< 30 m) down to mesophotic depths of 30-60 m. The deeper populations of such species are less likely to be affected by certain environmental perturbations, including high temperature/high irradiance causing coral bleaching. This has led to the hypothesis that deep populations may serve as refuges and a source of recruits for shallow reef habitats. The extent of vertical connectivity of reef coral species, however, is largely unquantified. Using 10 coral host microsatellite loci and sequences of the host mtDNA putative control region, as well as ribosomal DNA (rDNA) ITS2 sequences of the coral's algal endosymbionts (Symbiodinium), we examine population structure, connectivity and symbiont specificity in the brooding coral Seriatopora hystrix across a depth profile in both northwest (Scott Reef) and northeast Australia (Yonge Reef). Strong genetic structuring over depth was observed in both regions based on the microsatellite loci; however, Yonge Reef exhibited an additional partitioning of mtDNA lineages (associated with specific symbiont ITS2 types), whereas Scott Reef was dominated by a single mtDNA lineage (with no apparent host-symbiont specificity). Evidence for recruitment of larvae of deep water origin into shallow habitats was found at Scott Reef, suggesting that recovery of shallow water habitats may be aided by migration from deep water refuges. Conversely, no migration from the genetically divergent deep slope populations into the shallow habitats was evident at Yonge Reef, making recovery of shallow habitats from deeper waters at this location highly unlikely.

The photobiology of two reef corals and the distribution of associated symbiont types were investigated over a depth gradient of 0–60 m at Scott Reef, Western Australia. Pachyseris speciosa hosted mainly the same Symbiodinium C type similar to C3 irrespective of sampling depth. By contrast, Seriatopora hystrix hosted predominantly Symbiodinium type D1a or D1a-like at shallow depths while those in deeper water were dominated by a Symbiodinium C type closely related to C1. The photosynthesis/respiration (P/R) ratio increased consistently with depth at the two sampling times (November 2008 and April 2009) for P. speciosa and in November 2008 only for S. hystrix , suggesting a reduction in metabolic energy expended for every unit of energy obtained from photosynthesis. However, in April 2009, shallow colonies of S. hystrix exhibited decreased P/R ratios down to depths of approximately 23 m, below which the ratio increased towards the maximum depth sampled. This pattern was mirrored by changes in tissue biomass determined as total protein content. The depth of change in the direction of the P/R ratio correlated with a shift from Symbiodinium D to C-dominated colonies. We conclude that while photobiological flexibility is vital for persistence in contrasting light regimes, a shift in Symbiodinium type may also confer a functional advantage albeit at a metabolic cost with increased depth.

Spatial variation in the photophysiology of symbiotic dinoflagellates (zooxanthellae) of the scleractinian coral Pocillopora damicornis was examined along an environmental gradient in the Whitsunday Islands (Great Barrier Reef) at two depths (3m and 6m). Chlorophyll a fluorescence of photosystem II (PSII) and PAR-absorptivity measurements were conducted using an Imaging-PAM (pulse-amplitude-modulation) fluorometer. Most photophysiological parameters correlated with changes in environmental conditions quantified by differences in water quality along the gradient. For example, maximum quantum yield (Fv/Fm) increased and PAR-absorptivity decreased as water quality improved along the gradient from nearshore reefs (low irradiance, elevated nutrients and sediments) to outer islands (high irradiance, low nutrients and sediments). For apparent photosynthetic rate (PSmax) and minimum saturating irradiance (Ek), the direction of change differed depending on sampling depth, suggesting that different mechanisms of photo-acclimatisation operated between shallow and deep corals. Deep corals conformed to typical patterns of light/shade acclimatisation whereas shallow corals exhibited reduced PSmax and Ek with improving water quality coinciding with greater heat dissipation (NPQ241). Furthermore, deep corals on nearshore reefs exhibited elevated Q241 in comparison to outer islands possibly due to effects of sedimentation and/or pollutants rather than irradiance. These results highlight the importance of mesoscale sampling to obtain useful estimates of the variability of photophysiological parameters, particularly if such measures are to be used as bioindicators of the condition of coral reefs.

Effective environmental management requires monitoring programmes that provide specific links between changes in environmental conditions and ecosystem health. This article reviews the suitability of a range of bioindicators for use in monitoring programmes that link changes in water quality to changes in the condition of coral-reef ecosystems. From the literature, 21 candidate bioindicators were identified, whose responses to changes in water quality varied spatially and temporally; responses ranged from rapid (hours) changes within individual corals to long-term (years) changes in community composition. From this list, the most suitable bioindicators were identified by determining whether responses were (i) specific, (ii) monotonic, (iii) variable, (iv) practical and (v) ecologically relevant to management goals. For long-term monitoring programmes that aim to quantify the effects of chronic changes in water quality, 11 bioindicators were selected: symbiont photophysiology, colony brightness, tissue thickness and surface rugosity of massive corals, skeletal elemental and isotopic composition, abundance of macro-bioeroders, micro- and meiobenthic organisms such as foraminifera, coral recruitment, macroalgal cover, taxonomic richness of corals and the maximal depth of coral-reef development. For short-term monitoring programmes, or environmental impact assessments that aim to quantify the effects of acute changes in water quality, a subset of seven of these bioindicators were selected, including partial mortality. Their choice will depend on the specific objectives and the timeframe available for each monitoring programme. An assessment framework is presented to assist in the selection of bioindicators to quantify the effects of changing water quality on coral-reef ecosystems.

There is a need to identify effective coral bioindicators that provide quantifiable links between changes in water quality and the condition of coastal coral reefs. Temporal variation in a range of coral bioindicators including symbiont density, concentration of chlorophyll a, skeletal density and colony brightness of Pocillopora damicornis, as well as colony brightness and density of macro-bioeroders of massive Porites spp. was examined for 2 years on a coastal coral reef of the Great Barrier Reef. The specificity to changes in water quality varied among bioindicators. For example, a 2.5-fold variation in symbiont density of P. damicornis was related strongly to mean 14-day sea surface temperature and seasonal changes in water quality, suggesting medium specificity to changes in water quality. In contrast, the density of macro-bioeroders in Porites did not vary seasonally but there were consistently more macro-bioeroders at the coastal than mid-shelf reference locations, suggesting high specificity of spatial differences in water quality. In situ measurements of benthic irradiance and turbidity allowed the quantification of potential stress thresholds for coastal corals. Our data suggest long-term turbidity > 3 NTU leads to sublethal stress, whereas long-term turbidity > 5 NTU corresponds to severe stress effects on corals at shallow depths.