Results of wave modelling for Moreton Bay, Southeast Queensland, and a reef lagoon off Lizard Island, Great Barrier Reef, Australia

The distribution, abundance, behaviour, and morphology of marine species is affected by spatial variability in the wave environment. Maps of wave metrics (e.g. significant wave height Hs, peak energy wave period Tp, and benthic wave orbital velocity URMS) are therefore useful for predictive ecological models of marine species and ecosystems. A number of techniques are available to generate maps of wave metrics, with varying levels of complexity in terms of input data requirements, operator knowledge, and computation time. Relatively simple "fetch-based" models are generated using geographic information system (GIS) layers of bathymetry and dominant wind speed and direction. More complex, but computationally expensive, "process-based" models are generated using numerical models such as the Simulating Waves Nearshore (SWAN) model. We generated maps of wave metrics based on both fetch-based and process-based models and asked whether predictive performance in models of benthic marine habitats differed. Predictive models of seagrass distribution for Moreton Bay, Southeast Queensland, and Lizard Island, Great Barrier Reef, Australia, were generated using maps based on each type of wave model. For Lizard Island, performance of the process-based wave maps was significantly better for describing the presence of seagrass, based on Hs, Tp, and URMS. Conversely, for the predictive model of seagrass in Moreton Bay, based on benthic light availability and Hs, there was no difference in performance using the maps of the different wave metrics. For predictive models where wave metrics are the dominant factor determining ecological processes it is recommended that process-based models be used. Our results suggest that for models where wave metrics provide secondarily useful information, either fetch- or process-based models may be equally useful.

Seawater carbonate chemistry and calcification during tropical reef studies at Younge reef (Great Barrier Reef), 1996

Community metabolism was investigated using a Lagrangian flow respirometry technique on 2 reef flats at Moorea (French Polynesia) during austral winter and Yonge Reef (Great Barrier Reef) during austral summer. The data were used to estimate related air-sea CO2 disequilibrium. A sine function did not satisfactorily model the diel light curves and overestimated the metabolic parameters. The ranges of community gross primary production and respiration (Pg and R; 9 to 15 g C m-2 d-1) were within the range previously reported for reef flats, and community net calcification (G; 19 to 25 g CaCO3 m-2 d-1) was higher than the 'standard' range. The molar ratio of organic to inorganic carbon uptake was 6:1 for both sites. The reef flat at Moorea displayed a higher rate of organic production and a lower rate of calcification compared to previous measurements carried out during austral summer. The approximate uncertainty of the daily metabolic parameters was estimated using a procedure based on a Monte Carlo simulation. The standard errors of Pg,R and Pg/R expressed as a percentage of the mean are lower than 3% but are comparatively larger for E, the excess production (6 to 78%). The daily air-sea CO2 flux (FCO2) was positive throughout the field experiments, indicating that the reef flats at Moorea and Yonge Reef released CO2 to the atmosphere at the time of measurement. FCO2 decreased as a function of increasing daily irradiance.

Objectives for management of socio-ecological systems in the Great Barrier Reef region, Australia

A wide range of goals and objectives have to be taken into account in natural resources management. Defining these objectives in operational terms, including dimensions such as sustainability, productivity, and equity, is by no means easy, especially if they must capture the diversity of community and stakeholder values. This is especially true in the coastal zone where land activities affect regional marine ecosystems. In this study, the aim was firstly to identify and hierarchically organise the goals and objectives for coastal systems, as defined by local stakeholders. Two case study areas are used within the Great Barrier Reef region being Mackay and Bowen–Burdekin. Secondly, the aim was to identify similarities between the case study results and thus develop a generic set of goals to be used as a starting point in other coastal communities. Results show that overarching high-level goals have nested sub-goals that contain a set of more detailed regional objectives. The similarities in high-level environmental, governance, and socio-economic goals suggest that regionally specific objectives can be developed based on a generic set of goals. The prominence of governance objectives reflects local stakeholder perceptions that current coastal zone management is not achieving the outcomes they feel important and that there is a need for increased community engagement and co-management. More importantly, it raises the question of how to make issues relevant for the local community and entice participation in the local management of public resources to achieve sustainable environmental, social, and economic management outcomes. © 2015 Springer-Verlag Berlin Heidelberg

Effects of trawling on sessile megabenthos in the Great Barrier Reef and evaluation of the efficacy of management strategies

A series of related research studies over 15 years assessed the effects of prawn trawling on sessile megabenthos in the Great Barrier Reef, to support management for sustainable use in the World Heritage Area. These large-scale studies estimated impacts on benthos (particularly removal rates per trawl pass), monitored subsequent recovery rates, measured natural dynamics of tagged megabenthos, mapped the regional distribution of seabed habitats and benthic species, and integrated these results in a dynamic modelling framework together with spatio-temporal fishery effort data and simulated management. Typical impact rates were between 5 and 25% per trawl, recovery times ranged from several years to several decades, and most sessile megabenthos were naturally distributed in areas where little or no trawling occurred and so had low exposure to trawling. The model simulated trawl impact and recovery on the mapped species distributions, and estimated the regional scale cumulative changes due to trawling as a time series of status for megabenthos species. The regional status of these taxa at time of greatest depletion ranged from ∼77% relative to pre-trawl abundance for the worst case species, having slow recovery with moderate exposure to trawling, to ∼97% for the least affected taxon. The model also evaluated the expected outcomes for sessile megabenthos in response to major management interventions implemented between 1999 and 2006, including closures, effort reductions, and protected areas. As a result of these interventions, all taxa were predicted to recover (by 2-14% at 2025); the most affected species having relatively greater recovery. Effort reductions made the biggest positive contributions to benthos status for all taxa, with closures making smaller contributions for some taxa. The results demonstrated that management actions have arrested and reversed previous unsustainable trends for all taxa assessed, and have led to a prawn trawl fishery with improved environmental sustainability. © 2015 International Council for the Exploration of the Sea 2015. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Assessment of a data-limited, multi-species shark fishery in the Great Barrier Reef Marine Park and south-east Queensland

The status of five species of commercially exploited sharks within the Great Barrier Reef Marine Park (GBRMP) and south-east Queensland was assessed using a data-limited approach. Annual harvest rate, U, estimated empirically from tagging between 2011 and 2013, was compared with an analytically-derived proxy for optimal equilibrium harvest rate, UMSY Lim. Median estimates of U for three principal retained species, Australian blacktip shark, Carcharhinus tilstoni, spot-tail shark, Carcharhinus sorrah, and spinner shark, Carcharhinus brevipinna, were 0.10, 0.06 and 0.07 year-1, respectively. Median U for two retained, non-target species, pigeye shark, Carcharhinus amboinensis and Australian sharpnose shark, Rhizoprionodon taylori, were 0.27 and 0.01 year-1, respectively. For all species except the Australian blacktip the median ratio of U/UMSY Lim was <1. The high vulnerability of this species to fishing combined with life history characteristics meant UMSY Lim was low (0.04-0.07 year-1) and that U/UMSY Lim was likely to be > 1. Harvest of the Australian blacktip shark above UMSY could place this species at a greater risk of localised depletion in parts of the GBRMP. Results of the study indicated that much higher catches, and presumably higher U, during the early 2000s were likely unsustainable. The unexpectedly high level of U on the pigeye shark indicated that output-based management controls may not have been effective in reducing harvest levels on all species, particularly those caught incidentally by other fishing sectors including the recreational sector. © 2016 Elsevier B.V.

Stable oxygen isotope record of Globigerinoides ruber of ODP Site 133-820 off the Great Barriere Reef

Oxygen-isotope ratio measurements are presented for the planktonic species Globigerinoides ruber collected from shallow-water, upper-slope sediments from Holes 820A and 820B in 280 m of water, on the seaward edge of the Great Barrier Reef. Correlation of the Site 820 isotope curve with deep-sea reference curves of the Pacific Ocean (Core V28-238, Hole 677A, Hole 607A) permits the definition of isotope stages 1 to 19 in the top 145 m of Holes 820A and 820B. However, paleontological data indicate that stages 4 and 7 might be missing and that two hiatuses occur at a depth of 8.05 to 12.1 and 34.55 to 35.8 mbsf. Using deep-sea Hole 677A as a reference for ice-volume variations, we determine the difference in isotopic signature between it and Site 820. We propose that this difference is a regional signal representing a progressive 4°C increase in surface-water temperature at Site 820. The proposed temperature change was initiated at about 400 k.y. and corresponds to a change from high-to-low frequency variations in Pleistocene isotope signals. We postulate that these changes may have catalyzed the growth of the Great Barrier Reef. The shift also coincides with changes in seismic character and some physical and chemical sediment characteristics.

Patterns of species diversity in the gastrointestinal helminths of a coral reef fish, Epinephelus merra (Serranidae), from French Polynesia and the south Pacific Ocean

Large-scale patterns of species diversity in the gastrointestinal helminth faunas of the coral reef fish Epinephelus merra (Serranidae) were investigated in French Polynesia and the South Pacific Ocean. The richer barrier reef community in French Polynesia supported richer parasite communities in E. merra than that on the fringing reef. While parasite communities among fish from the same archipelago were similar, differences in potential host species and the distance between archipelagos may have contributed to a qualitative difference in parasite communities between archipelagos. Digenean community diversity in coral reef fishes was greater in the western South Pacific, following similar patterns in free-living species. However, overall species diversity of camallanid nematodes of coral reef fishes does not appear to have been similarly affected.

Photoinhibition and photoprotection in symbiotic dinoflagellates from reef-building corals

Pulse-amplitude-modulation fluorometry and oxygen respirometry were used to investigate diel photosynthetic responses by symbiotic dinoflagellates to light levels in summer and winter on a high latitude coral reef. The symbiotic dinoflagellates from 2 species of reef-building coral (Porites cylindrica and Stylophora pistillata) showed photoinhibitory decreases in the ratio of variable (F-v) to maximal (F-m) fluorescence (F-v/F-m) as early as 09:00 h on both summer and winter days on the reefs associated with One Tree Island (23 degrees 30' S, 152 degrees 06' E; Great Barrier Reef, Australia). This was due to decreases in maximum, F-m, and to a smaller extent minimum, F-0, chlorophyll fluorescence. Complete recovery took 4 to 6 h and began to occur as soon as light levels fell each day. Chlorophyll fluorescence quenching analysis of corals measured during the early afternoon revealed classic regulation of photosystem II (PSII) efficiency through non-photochemical quenching (NPQ). These results appear to be similar to data collected for other algae and higher plants, suggesting involvement of the xanthophyll cycle of symbiotic dinoflagellates in regulating the quantum efficiency of PSII. The ability of symbiotic dinoflagellates to develop significant NPQ, however, depended strongly on when the symbiotic dinoflagellates were studied. Whereas symbiotic dinoflagellates from corals in the early afternoon showed a significant capacity to regulate the efficiency of PSII using NPQ, those sampled before sunrise had a slower and much reduced capacity, suggesting that elements of the xanthophyll cycle are suppressed prior to sunrise. A second major finding of this study is that the quantum efficiency of PSII in symbiotic dinoflagellates is strongly diurnal, and is as much as 50% lower just prior to sunrise than later in the day. When combined with oxygen flux data, these results indicate that a greater portion of the electron transport occurring later in the day is likely to be due to the increases in the rate of carbon fixation by Rubisco or to higher flutes through the Mehler-Ascorbate-Peroxidase (MAP) cycle.

Closely related Symbiodinium spp. differ in relative dominance in coral reef host communities across environmental, latitudinal and biogeographic gradients

The diversity and community structures of symbiotic dinoflagellates are described from reef invertebrates in southern and central provinces of the Great Barrier Reef (GBR), Australia, and Zamami Island, Okinawa, Japan. The symbiont assemblages from region to region were dominated by Clade C Symbiodinium spp. and consisted of numerous host-specific and/or rare types (specialists), and several types common to many hosts (generalists). Prevalence in the host community among certain host-generalist symbionts differed between inshore and offshore environments, across latitudinal (central versus southern GBR) gradients, and over wide geographic ranges (GBR versus Okinawa). One particular symbiont (C3h) from the GBR had a dramatic shift in dominance. Its prevalence ranged from being extremely rare, or absent on high-latitude reefs to dominating the scleractinian diversity on a mid-latitude inshore reef. These changes occurred among coral fauna whose larvae must acquire symbionts from environmental sources (horizontal symbiont acquisition). Such differences did not occur among 'vertical transmitters' such as Porites spp., Montipora spp. and pocilloporids (corals that directly transmit symbionts to their offspring) or among those hosts displaying 'horizontal acquisition', but that associate with specific symbionts. Most host-specialized types were found to be characteristic of a particular geographic region (i.e. Okinawa versus Central GBR versus Southern GBR). The mode of symbiont acquisition may play an important role in how symbiont composition may shift in west Pacific host communities in response to climate change. There is no indication that recent episodes of mass bleaching have provoked changes in host-symbiont combinations from the central GBR.

Holocene sediments of Wistari Reef: towards a global quantification of coral reef related neritic sedimentation in the Holocene

Wistari Reef. within the southern Great Barrier Reef. is a shallow coral reef platform featuring a very clearly defined leeward accretionary wedge of carbonate sediments. The total global area of shallowly submerged coral reef has been quantified as 255 000 km(2). The question then becomes: What additional area of sediment of significant thickness is associated with the measured shallow reef areas T At Wistari Reef, the leeward sedimentary wedge has an area and a thickness that are roughly equal to the Holocene sediments that have accumulated on the platform. Several important observations can be made from these data. Firstly. the area of significant neritic carbonate sedimentation ( > 1 m/ka) associated with coral reefs is near 500000 km(2). Secondly, the production rate of neritic carbonates at Wistari Reef is almost 50%, less than the accumulation rate needed to obtain the volume of Holocene reef sediments observed. This implies that both production and accumulation neritic carbonate must have been more than a factor of two higher in the early to mid Holocene. (C) 2001 Elsevier Science B.V. All rights reserved.

Lecithophyllum kitrii n. sp (Digenea : Lecithasteridae) from Australian coral reef fishes of the genus Siganus

Lecithophyllum kitrii n. sp. is described from Siganus punctatus and S. lineatus off Heron Island on the southern Great Barrier Reef, Australia. It differs from most other species in the genus in its elongate pars prostatica and globular sinus-sac, and from all other species in having the seminal vesicle almost always entirely in the hindbody.

Cleaner fish Labroides dimidiatus reduce 'temporary" parasitic corallanid isopods on the coral reef fish Hemigymnus melapterus

To determine if cleaners affect 'temporary' parasitic corallanid isopods (Argathona macronema) on fish, we used caged fish Hemigymnus meldpterus (Labridae) on 5 patch reefs on Lizard Island, Great Barrier Reef, and removed all cleaner fish Labroides dimidiatus (Labridae) from 3 of the reefs, In a short-term experiment, fish were sampled after 12 or 24 h, at dawn and sunset respectively, and in a long-term experiment they were sampled after 12 d at sunset. Isopod prevalence, abundance and size were measured. In the short-term experiment, on reefs without cleaners the prevalence of A. macronema was higher after 24 h than after 12 h while on reefs with cleaners, prevalence was low at all times, Although the abundance of A, macronema did not vary after 12 and 24 h, when combined over the 24 h, the effect of cleaners was significant with only 2 % of all the A. macronema found on reefs with cleaners. Cleaners had no effect on the size frequency distribution of A. macronema in the short-term experiment, most likely because fish had so few isopods on reef with cleaners. In the longer-term experiment, the effects of cleaners on isopod prevalence and abundance were less clear. Their effect on isopod size was, however, significant with smaller parasites on reefs without cleaners. The reduction of isopod prevalence and abundance by cleaner fish over a period of hours may explain why these A, macronema are rare on wild fish. Our findings support the idea that cleaning is beneficial to clients and has important implications for the control of parasites of fish farmed in cages,

Carbonate chemistry, temperature and salinity of Lady Elliot Island Reef 2009-2010

Ocean acidification leads to changes in marine carbonate chemistry that are predicted to cause a decline in future coral reef calcification. Several laboratory and mesocosm experiments have described calcification responses of species and communities to increasing CO2. The few in situ studies on natural coral reefs that have been carried out to date have shown a direct relationship between aragonite saturation state (Omega arag) and net community calcification (Gnet). However, these studies have been performed over a limited range of Omega arag values, where extrapolation outside the observational range is required to predict future changes in coral reef calcification. We measured extreme diurnal variability in carbonate chemistry within a reef flat in the southern Great Barrier Reef, Australia. Omega arag varied between 1.1 and 6.5, thus exceeding the magnitude of change expected this century in open ocean subtropical/tropical waters. The observed variability comes about through biological activity on the reef, where changes to the carbonate chemistry are enhanced at low tide when reef flat waters are isolated from open ocean water. We define a relationship between net community calcification and Omega arag, using our in situ measurements. We find net community calcification to be linearly related to Omega arag, while temperature and nutrients had no significant effect on Gnet. Using our relationship between Gnet and Omega arag, we predict that net community calcification will decline by 55% of its preindustrial value by the end of the century. It is not known at this stage whether exposure to large variability in carbonate chemistry will make reef flat organisms more or less vulnerable to the non-calcifying physiological effects of increasing ocean CO2 and future laboratory studies will need to incorporate this natural variability to address this question.

Classification of coral reef types in Torres Strait (GIS files in zip-archive 319 kB)

Coral reefs represent major accumulations of calcium carbonate (CaCO3). The particularly labyrinthine network of reefs in Torres Strait, north of the Great Barrier Reef (GBR), has been examined in order to estimate their gross CaCO3 productivity. The approach involved a two-step procedure, first characterising and classifying the morphology of reefs based on a classification scheme widely employed on the GBR and then estimating gross CaCO3 productivity rates across the region using a regional census-based approach. This was undertaken by independently verifying published rates of coral reef community gross production for use in Torres Strait, based on site-specific ecological and morphological data. A total of 606 reef platforms were mapped and classified using classification trees. Despite the complexity of the maze of reefs in Torres Strait, there are broad morphological similarities with reefs in the GBR. The spatial distribution and dimensions of reef types across both regions are underpinned by similar geological processes, sea-level history in the Holocene and exposure to the same wind/wave energetic regime, resulting in comparable geomorphic zonation. However, the presence of strong tidal currents flowing through Torres Strait and the relatively shallow and narrow dimensions of the shelf exert a control on local morphology and spatial distribution of the reef platforms. A total amount of 8.7 million tonnes of CaCO3 per year, at an average rate of 3.7 kg CaCO3 m-2 yr-1 (G), were estimated for the studied area. Extrapolated production rates based on detailed and regional census-based approaches for geomorphic zones across Torres Strait were comparable to those reported elsewhere, particularly values for the GBR based on alkalinity-reduction methods. However, differences in mapping methodologies and the impact of reduced calcification due to global trends in coral reef ecological decline and changing oceanic physical conditions warrant further research. The novel method proposed in this study to characterise the geomorphology of reef types based on classification trees provides an objective and repeatable data-driven approach that combined with regional census-based approaches has the potential to be adapted and transferred to different coral reef regions, depicting a more accurate picture of interactions between reef ecology and geomorphology.

Benthic and substrate cover data derived from photo-transect surveys in Heron Reef

Underwater georeferenced photo-transect survey was conducted on September 23 - 27, 2007 at different sections of the reef flat, reef crest and reef slope in Heron Reef. For this survey a snorkeler or diver swam over the bottom while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. A standard digital compact camera was placed in an underwater housing and fitted with a 16 mm lens which provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by three fin kicks of the survey diver/snorkeler, which corresponded to a surface distance of approximately 2.0 - 4.0 m. The GPS was placed in a dry-bag and logged its position as it floated at the surface while being towed by the photographer. A total of 3,586 benthic photos were taken. A floating GPS setup connected to the swimmer/diver by a line enabled recording of coordinates of each benthic. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Benthic or substrate cover data was derived from each photo by randomly placing 24 points over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned to 1 out of 80 cover types, which represented the benthic feature beneath it. Benthic cover composition summary of each photo scores was generated automatically using CPCE program. The resulting benthic cover data of each photo was linked to gps coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South.