Temporal and spatial variation in the growth parameters skeletal density, linear extension and calcification rate in massive Porites from two nearshore regions of the northern Great Barrier Reef (GBR) were examined over a 16-year study period. Calcification rates in massive Porites have declined by approximately 21% in two regions on the GBR $ 450 km apart. This is a function primarily of a decrease in linear extension ($ 16%) with a smaller decline in skeletal density ($ 6%) and contrasts with previous studies on the environmental controls on growth of massive Porites on the GBR. Changes in the growth parameters were linear over time. tures had no effect on skeletal density, but a modal effect on annual extension and calcification with maxima at $26.7 1C. There were minor differences in the growth parameters between regions. A decline in coral calcification of this magnitude with increasing seawater temperatures is unprecedented in recent centuries based on analysis of growth records from long cores of massive Porites. We discuss the decline in calcification within the context of known environmental controls on coral growth. Although our findings are consistent with studies of the synergistic effect of elevated seawater temperatures and pCO 2 on coral calcification, we conclude that further data on seawater chemistry of the GBR are required to better understand the links between environmental change and effects on coral growth.

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.

Tropical storms (cyclones, hurricanes, or typhoons) are the most severe form of mechanical disturbance of coral reefs. In 2005, severe tropical cyclone Ingrid crossed the far northern Great Barrier Reef, a region that had not been affected by a major disturbance for several decades, and where benthic data had been collected before the cyclone crossed. This storm provided a unique opportunity to improve understanding of the extent and type of damage inflicted on inshore and offshore coral reefs along a gradient of wind speeds. Modeled maximum wind speeds ranged from 46 m s 21 (equivalent to category 4) near the path to 22 m s 21 (category 1) ,70 km to either side of the path. Surveys of 82 sites on 32 reefs along the wind gradient showed that the types and intensity of disturbance were well explained by local maximum wind speed, and by spatial and biotic factors. While offshore reefs had the deepest depth of damage, inshore reefs had the greatest rates of coral breakage and dislodgement. On a severely affected inshore reef, hard coral cover decreased about 800%, taxonomic richness decreased 250%, the density of coral recruits decreased by 30%, while massive coral cover remained unaltered. Maximum winds ,28 m s 21 for ,12 h inflicted only minor damage on any reef, but winds .33 m s 21 and .40 m s 21 caused catastrophic damage on inshore and offshore reefs, respectively. Observations from this cyclone were used to predict potential changes in storm-related coral loss under altered cyclone-intensity scenarios.

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.

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.

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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 coralreef 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.