Reef Matrix Research Articles

Age and growth of a habitat-forming deep-sea coral Solenosmilia variabilis in the New Zealand region: implications for fisheries management

ABSTRACT One of the most widespread and abundant habitat forming deep-sea corals in the South Pacific region is Solenosmilia variabilis. The age of this species was assessed using radiocarbon content (14C) on long dead, recently dead, and live branch sections of coral reef matrix sampled from the New Zealand region. Conventional 14C colony ages (yrs BP), for the living, recently dead, and long dead samples, ranged from 803 to 1186 years (Graveyard Knolls, Chatham Rise), and 907 to 11, 694 years (Louisville Seamount Chain east of New Zealand). Overall calendar ages, ranged from 84 to 292 years, and similar linear and step-wise growth rate data were obtained. Linear growth ranged from 0.2 to 1.3 mm/yr. From a conservative estimate of matrix height of ∼20 cm, it could take hundreds of years (∼150–660) of growth for a colony of S. variabilis to attain this height, and around ∼2000 years to build a colony diameter of 1 metre. Defining the age, growth and recovery timeframes of deep-sea coral can inform risk assessments of the level of susceptibility to trawling activity and their potential to recover, as well as provide options for the considered management of deep-sea habitats.

Responses of the coral reef cryptobiome to environmental gradients in the Red Sea.

An essential component of the coral reef animal diversity is the species hidden in crevices within the reef matrix, referred to as the cryptobiome. These organisms play an important role in nutrient cycling and provide an abundant food source for higher trophic levels, yet they have been largely overlooked. Here, we analyzed the distribution patterns of the mobile cryptobiome (>2000 μm) along the latitudinal gradient of the Saudi Arabian coast of the Red Sea. Analysis was conducted based on 54 Autonomous Reef Monitoring Structures. We retrieved a total of 5273 organisms, from which 2583 DNA sequences from the mitochondrially encoded cytochrome c oxidase I were generated through sanger sequencing. We found that the cryptobiome community is variable over short geographical distances within the basin. Regression tree models identified sea surface temperature (SST), percentage cover of hard coral and turf algae as determinant for the number of operational taxonomic units present per Autonomous Reef Monitoring Structures (ARMS). Our results also show that the community structure of the cryptobiome is associated with the energy available (measured as photosynthetic active radiation), sea surface temperature, and nearby reef habitat characteristics (namely hard corals, turf and macroalgae). Given that temperature and reef benthic characteristics affect the cryptobiome, current scenarios of intensive climate change are likely to modify this fundamental biological component of coral reef functioning. However, the trajectory of change is unknow and can be site specific, as for example, diversity is expected to increase above SST of 28.5°C, and with decreasing hard coral and turf cover. This study provides a baseline of the cryptobenthic community prior to major coastal developments in the Red Sea to be used for future biodiversity studies and monitoring projects. It can also contribute to better understand patterns of reef biodiversity in a period where Marine Protected Areas are being discussed in the region.

Newly deceased Caribbean reef-building corals experience rapid carbonate loss and colonization by endolithic organisms

Coral mortality triggers the loss of carbonates fixed within coral skeletons, compromising the reef matrix. Here, we estimate rates of carbonate loss in newly deceased colonies of four Caribbean reef-building corals. We use samples from living and recently deceased colonies following a stony coral tissue loss disease (SCTLD) outbreak. Optical densitometry and porosity analyses reveal a loss of up to 40% of the calcium carbonate (CaCO3) content in dead colonies. The metabolic activity of the endolithic organisms colonizing the dead skeletons is likely partially responsible for the observed dissolution. To test for the consequences of mass mortality events over larger spatial scales, we integrate our estimates of carbonate loss with field data of the composition and size structure of coral communities. The dissolution rate depends on the relative abundance of coral species and the structural properties of their skeletons, yet we estimate an average reduction of 1.33 kg CaCO3 m−2, nearly 7% of the total amount of CaCO3 sequestered in the entire system. Our findings highlight the importance of including biological and chemical processes of CaCO3 dissolution in reef carbonate budgets, particularly as the impacts of global warming, ocean acidification, and disease likely enhance dissolution processes.

Coral Geochemical Records Track Millennial-Scale Ecosystem Change and Resilience in the Tropical Eastern Pacific

Along the coastal Tropical Eastern Pacific (TEP), regions of strong seasonal upwelling bring cold, nutrient-rich waters, controlling ecological conditions and sustaining millions of people through large-scale fisheries. The TEP is also important for the regulation of global climate and is affected by large-scale environmental processes such as ENSO. How the nutrient dynamics of this region will respond to climate change and what the implications will be for coastal ecology remains unknown. Environmental records are needed that capture intra and inter-decadal variation and extend over millennia where these biotic and abiotic processes interact. Here, we develop a new sampling approach and construct two coral skeleton records (n = >600) from reef matrix cores that extend six millennia, from the upwelling Gulf of Panamá and the non-upwelling Gulf of Chiriquí. We ask what effects millennial-scale climate patterns have on upwelling in the region, and how the magnitude of upwelled nutrients influences ecological productivity and even human habitation. We combined multiple proxies using climatic (carbonate δ18O), nutrient (skeletal-organic matrix δ15N), diagenetic (taphonomic scoring), ecological (benthic community composition), and temporal (U-Th dates) data. Using Generalised Additive Models to assess variability, we find strong divergences in the nutrient (δ15N; range >5 ‰) records between Gulfs, while δ18O (range ~2‰) is more stable. The greatest variation in δ15N values occurs during times of high reef accretion whereas δ18O is constant, suggesting that nutrients, not temperature, are driving reef productivity. Taphonomic, taxonomic, and age data reveal periodic shifts and collapses of coral communities that differ between Gulfs. We end by drawing connections between these ecological shifts to the episodic human habitation documented during the late-Holocene and hypothesize what this may mean for ecosystem resilience and environmental management under future climate.

Remote reef cryptobenthic diversity: Integrating autonomous reef monitoring structures and in situ environmental parameters

Coral reef sessile organisms inhabiting cryptic spaces and cavities of the reef matrix perform vital and varied functional roles but are often understudied in comparison to those on exposed surfaces. Here, we assess the composition of cryptobenthic taxa from three remote tropical reef sites (Central Indian Ocean) alongside a suite of in situ environmental parameters to determine if, or how, significant patterns of diversity are shaped by local abiotic factors. To achieve this, we carried out a point-count analysis of autonomous reef monitoring structure (ARMS) plate images and employed in situ instrumentation to recover long-term (12 months) profiles of flow velocity, wave heights, temperature, dissolved oxygen, and salinity, and short-term (3 weeks) profiles of light and pH. We recovered distinct environmental profiles between sampling sites and observed that ocean-facing reefs experienced frequent but short-lived cooling internal wave events and that these were key in shaping in situ temperature variability. By comparing temperature and wave height profiles recovered using in situ loggers with ex situ models, we discovered that global satellite products either failed to recover site-specific profiles or both over- and underestimated actual in situ conditions. We found that site choice and recruitment plate face (top or bottom) significantly impacted the percentage cover of bryozoans, gastropods, soft and calcified tube worms, as well as crustose coralline algae (CCA) and fleshy red, brown, and green encrusting macroalgae on ARMS. We observed significant correlations between the abundance of bryozoans, CCA, and colonial tunicates with lower mean temperature and higher mean dissolved oxygen profiles observed across sites. Red and brown encrusting macroalgae abundance correlated significantly with medium-to-high flow velocities and wave height profiles, as well as higher pH and dissolved oxygen. This study provides the first insight into cryptobenthic communities in the Chagos Archipelago marine-protected area and adds to our limited understanding of tropical reef sessile communities and their associations with environmental parameters in this region. With climate change accelerating the decline of reef ecosystems, integrating analyses of cryptobenthic organisms and in situ physicochemical factors are needed to understand how reef communities, if any, may withstand the impacts of climate change.

Observation of juvenile Eastern Blue Groper (Achoerodus viridis) on remnant oyster reefs in New South Wales, Australia.

Observation of juvenile Eastern Blue Groper (Achoerodus viridis) on remnant oyster reefs in New South Wales, Australia.

Cover Image

COVER PHOTO: Lighthouse Reef, Palau, Micronesia, in a healthy state in 2012 prior to a super typhoon which reduced coral cover to zero percent. In their study published in The Scientific Naturalist section of this issue, Doropoulos et al. (Article e3621; doi:10.1002/ecy.3621) document the recovery of corals at Lighthouse Reef over a seven-year period through the growth of cryptic recruits that were dormant in the reef matrix. Photo credit: George Roff.

Millennial‐scale change on a Caribbean reef system that experiences hypoxia

Coastal hypoxia has become an increasingly acknowledged threat to coral reefs that is potentially intensifying because of increased input of anthropogenic nutrients. Almirante Bay (Caribbean Panama) is a semi‐enclosed system that experiences hypoxia in deeper waters which occasionally shoals onto shallow coral reefs, suffocating most aerobic benthic life. To explore the long‐term history of reefs in the bay we extracted reef matrix cores from two reefs that today experience contrasting patterns of oxygenation. We constructed a 1800‐year‐long record of gastropod assemblages and isotope compositions from six U‐Th chronologically‐constrained reef matrix cores. We extracted two cores from each reef at 3 m water depth and two additional cores from a deeper part (4.8 m) of the hypoxia‐exposed reef. Results show that the deeper part of the hypoxic reef slowed in growth and stopped accreting approximately 1500 years BP while the shallow part of the reef continued to accrete to the present day, in agreement with a model of expanding hypoxia at this time. Our proxy‐based approach suggests that the patterns of increasing herbivores and decreasing carbon isotope values in the deeper part of the hypoxic reef may have been driven by an increase in hypoxia via eutrophication caused by either natural changes or human impacts. Similar patterns in these paleoindicators occurred in the shallow part of the hypoxic reef during the last few decades. This suggests that the deep water hypoxia may be expanding to depths as shallow as 3 m and that shallow reefs are at greater risk due to increased human activity.

Re-evaluating mid-Holocene reef “turn-off” on the inshore Southern Great Barrier Reef

In the face of changing global climate the future of corals reefs is uncertain. High latitude reefs may offer potential refugia for corals under projected increasing sea surface temperatures (SSTs). To understand the reef growth potential of modern high latitude reefs it is first necessary to understand past reef growth and response to climatic and environmental changes. The history of the Great Barrier Reef (GBR) has been shown to be punctuated by a multi-millennial Mid-Holocene reef “turn-off” or initiation hiatus in the Northern and Southern GBR (∼5500–2500 years before present [yr. BP]). Here we present the results of chronologically constrained reef matrix cores from five continental island fringing reefs and coral communities in the Keppel Islands to revaluate the timing, extent and possible drivers of the Mid-Holocene hiatus in the Southern GBR. Earliest initiation occurred at Wedge and Halfway Islands at 7773 ± 19 yr. BP and 7455 ± 20 yr. BP, respectively. Following initiation, vertical reef accretion at Halfway was comparable to previously reported rates for the GBR of ∼3.4 mm yr−1, increasing to ∼8.0 mm yr−1 between 6100 and 5500 yr. BP. Conversely, the coral community at Wedge Island, located closer to mainland terrestrial influence, accreted <1.0 mm yr−1 to 5500 yr. BP after which a 3000-year stratigraphic hiatus is observed. A negative relative sea level oscillation at 5500 yr. BP coincides with the transition of Halfway reef from vertical accretion to lateral progradation and the “turn-off” of the Wedge Island coral community. The reef at Middle Island appears to have initiated in the midst of the Mid-Holocene hiatus period at ∼3500 yr. BP, with vertical accretion at both Middle and Halfway Islands being the highest for the region’s history at 12.5 ± 3.3 mm yr−1 and 15.0 ± 6.0 mm yr−1, respectively, between 3500 and 3000 yr. BP. A proposed late-Holocene relative sea level highstand of ∼1 m at ∼2000 yr. BP coincides with the first dates identified at near-shore Divided Island, and the re-initiation of coral growth at Wedge Island, although both showed limited net vertical accretion. These near-shore sites “turned-off” again between 1300 and 900 yr. BP, likely associated with a rapid relative sea level fall. Reef progradation also slowed at Halfway Island and Middle Island after 1200 yr. BP until a recent increase in reef growth at Middle Island since the late 1970’s associated with modern increases in average SSTs. Our data suggests that although reef-scale “turn-off” events occurred, there is no evidence for a regional scale hiatus in coral growth or initiation comparable to that found further north on the GBR. A comparison with other Southern and south-Central GBR reef cores suggests that relative sea level oscillations in conjunction with changes to climate, appear to have driven varying, but synchronous, modifications to reefs at 5500, 4600, 2800 and 1200 yr. BP.

Microhabitat partitioning correlates with opsin gene expression in coral reef cardinalfishes (Apogonidae)

Abstract Fish are the most diverse vertebrate group, and they have evolved equally diverse visual systems, varying in terms of eye morphology, number and distribution of spectrally distinct photoreceptor types, visual opsin genes and opsin gene expression levels. This variation is mainly due to adaptations driven by two factors: differences in the light environments and behavioural tasks. However, while the effects of large‐scale habitat differences are well described, it is less clear whether visual systems also adapt to differences in environmental light at the microhabitat level. To address this, we assessed the relationship between microhabitat use and visual system features in fishes inhabiting coral reefs, where habitat partitioning is particularly common. We suggest that differences in microhabitat use by cardinalfishes (Apogonidae) drive morphological and molecular adaptations in their visual systems. To test this, we investigated diurnal microhabitat use in 17 cardinalfish species and assessed whether this correlated with differences in visual opsin gene expression and eye morphology. We found that cardinalfishes display six types of microhabitat partitioning behaviours during the day, ranging from specialists found exclusively in the water column to species that are always hidden inside the reef matrix. Species predominantly found in exposed microhabitats had higher expression of the short‐wavelength‐sensitive violet opsin (SWS2B) and lower expression of the dim‐light active rod opsin (RH1). Species of intermediate exposure, on the other hand, expressed opsins that are mostly sensitive to the blue‐green central part of the light spectrum (SWS2As and RH2s), while fishes entirely hidden in the reef substrate had a higher expression of the long‐wavelength‐sensitive red opsin. We also found that eye size relative to body size differed between cardinalfish species, and relative eye size decreased with an increase in habitat exposure. Retinal topography did not show co‐adaptation with microhabitat use, but data suggested co‐adaptation with feeding mode. We suggest that, although most cardinalfishes are nocturnal foragers, their visual systems—and possibly those of other (reef) fishes—have also adapted to the light intensity and the light spectrum of their preferred diurnal microhabitats. A free Plain Language Summary can be found within the Supporting Information of this article.

Millennial‐scale change in the structure of a Caribbean reef ecosystem and the role of human and natural disturbance

Caribbean coral reefs have transformed into algal‐dominated habitats over the past half‐century, but the role of specific anthropogenic drivers is unresolved due to the lack of ecosystem‐level data predating human disturbance. To better understand the extent and causes of long‐term Caribbean reef declines, we produced a continuous 3000‐yr record of the ecosystem state of three reefs in Bocas del Toro, Caribbean Panama. From fossils and sediments obtained from reef matrix cores, we tracked changes in reef accretion rates and the taxonomic and functional group composition of fish, coral, urchin, bivalve and benthic foraminifera. This dataset provided a comprehensive picture of reef community and environmental change. At all sites, reefs shifted from systems with greater relative abundance of herbivorous fish, epifaunal suspension feeding bivalves and Diadema urchins to systems with greater relative abundance of micropredator fish, infaunal bivalves and Echinometra urchins. These transitions were initiated a millennium ago at two less‐degraded reefs fringing offshore islands and ~250 yr ago at a degraded patch reef near the continental coast. Ecosystem shifts were accompanied by a decline in reef accretion rates, and at the patch reef, a decline in water quality since the 18th century. Within all cores, synchronous increases in infaunal bivalves and declines in herbivorous fish regardless of water quality suggest a loss of hard substrate and increasingly hypoxic sediment conditions related to herbivore loss. While the early timing of ecosystem transitions at the fringing reefs implicates large‐scale hydrological change, the more recent timing of change and loss of water quality at the patch reef implicates terrigenous runoff from land‐clearing. Our whole‐ecosystem reconstruction reveals that reef ecosystem deterioration appears to follow a predictable trajectory whether driven by natural or anthropogenic disturbances and that historical local human activities have quickly unraveled reefs at a scale similar to longer‐term natural environmental change.

A 3000 year record of Caribbean reef urchin communities reveals causes and consequences of long‐term decline in Diadema antillarum

Urchins are the last abundant grazers of macroalgae on most Caribbean reefs following the historical overexploitation of herbivorous fishes. The long‐spined urchin Diadema antillarum was particularly effective at controlling macroalgae and facilitating coral dominance on Caribbean reefs until its ecological extinction from a catastrophic disease epidemic in the early 1980s. Despite their important role in the structure and functioning of Caribbean reef ecosystems, the natural dynamics of Caribbean reef urchin communities are poorly known due to the paucity of ecological survey data prior to large‐scale human disturbances and the Diadema dieoff. To help resolve the baseline abundances and ecological roles of common urchin taxa, we track changes in urchin abundance and composition over the past 3000 yr from analysis of subfossil urchin spines preserved in reef matrix cores collected in Caribbean Panama. Echinometra consistently dominated the subfossil spine assemblage, while Diadema was consistently rare in the subfossil record in this region. Rather than increasing during a period of heightened human exploitation of their fish competitors and predators, Diadema began declining over a millennium ago. Convergent cross mapping (CCM) causality analyses reveal that Diadema abundance is causally related to coral community composition. Diadema is negatively affected by Acropora cervicornis dominance, likely due to the tight association between this coral and the threespot damselfish, an effective Diadema competitor. Conversely, Diadema positively affects the abundance of the coral Madracis mirabilis, possibly via its control of macroalgae. Causal relationships were not detected among abundances of individual urchin taxa, indicating that inter‐specific echinoid competition is not a factor limiting Diadema recovery. Our detailed record of prehistorical and historical urchin community dynamics suggests that the failure of Diadema to recover over 30 yr after its mass mortality event may be due in part to the prey release of damselfish following the long‐term overfishing of piscivorous fishes.

Intrusive upwelling in the Central Great Barrier Reef

In the Central Great Barrier Reef, the outer continental shelf has an open reef matrix that facilitates the exchange of waters with the Coral Sea. During austral summer, cool water intrudes onto the shelf along the seafloor. Temperature observations reveal cool, bottom intrusions during a 6 year period from the Queensland Integrated Marine Observing System's Palm Passage mooring. A metric is used to identify 64 intrusion events. These intrusions predominantly occur from October to March including the wet season. During an event, the outer-shelf's near-bottom temperature decreases by 1–3°C typically over 1 week. The near-bottom salinity tends to increase, while near-surface changes do not reflect these tendencies. Intrusion events occur predominantly with either weakening equatorward winds or poleward wind bursts. A regional hydrodynamic model for the Great Barrier Reef captures the timing and amplitude of these intrusions. During intrusion events, isotherms tend to uplift over the continental slope and onto the shelf and the East Australian Current intensifies poleward. Over the shelf, a bottom-intensified onshore current coincides with bottom cooling. For numerous events, the model diagnostics reveal that the cross-shelf flow is dominated by the geostrophic contribution. A vertical circulation tilts the isopycnals upward on the southern side of the passage, causing an along-shelf density gradient and geostrophic onshore flow with depth. While wind fluctuations play a major role in controlling the along-shelf currents, model results indicate that a concurrent topographically induced circulation can assist the onshore spread of cool water.

Deeply hidden inside introduced biogenic structures – Pacific oyster reefs reduce detrimental barnacle overgrowth on native blue mussels

In sedimentary coastal ecosystems shells of epibenthic organisms such as blue mussels (Mytilus edulis) provide the only major attachment surface for barnacle epibionts, which may cause detrimental effects on their mussel basibionts by e.g. reducing growth rate. In the European Wadden Sea, beds of native blue mussels have been invaded by Pacific oysters Crassostrea gigas, which transformed these beds into mixed reefs of oysters with mussels. In this study, we determined the spatial distribution of M. edulis and their barnacle epibionts (Semibalanus balanoides) within the reef matrix. Mean mussel density near the bottom was about twice as high compared to the mussel density near the top of an oyster reef, whereas barnacles on mussels showed a reversed pattern. Barnacle dry weight per mussel was on average 14 times higher near the top than at the bottom. This pattern was confirmed by experimentally placing clean M. edulis at the top and on the bottom of oyster reefs at two sites in the Wadden Sea (island of Texel, The Netherlands; island of Sylt, Germany). After an experimental period of five weeks (April and May 2015, the main settlement period of S. balanoides), the number of barnacles per mussel was at both sites significantly higher on mussels near the top compared to near the bottom. We conclude that the oyster reef matrix offers a refuge for M. edulis: inside reefs they are not only better protected against predators but also against detrimental barnacle overgrowth. This study shows that alien species can cause beneficial effects for native organisms and should not be generally considered as a risk for the recipient marine ecosystems.

Movements of the reef manta ray (Manta alfredi) in the Red Sea using satellite and acoustic telemetry

Populations of mobulid rays are declining globally through a combination of directed fisheries and indirect anthropogenic threats. Understanding the movement ecology of these rays remains an important priority for devising appropriate conservation measures throughout the world’s oceans. We sought to determine manta movements across several temporal and spatial scales with a focus on quantifying site fidelity and seasonality in the northern Farasan Banks, Red Sea. We fitted manta rays with acoustic transmitters (n = 9) and pop-up satellite archival transmitting (PSAT) tags (n = 9), including four with GPS capability (Fastloc), during spring 2011 and 2012. We deployed an extensive array of acoustic receivers (n = 67) to record movements of tagged mantas in the study area. All acoustically tagged individuals traveled frequently among high-use receiver locations and reefs and demonstrated fidelity to specific sites within the array. Estimated and realized satellite tag data indicated regional movements <200 km from the tagging location, largely coastal residency, and high surface occupation. GPS-tagged individuals regularly moved within the coastal reef matrix up to ~70 km to the south but continued to return to the tagging area near the high-occupancy sites identified in the acoustic array. We also tested the accuracy of several geolocation models to determine the best approach to analyze our light-based satellite tag data. We documented significant errors in light-based movement estimates that should be considered when interpreting tracks derived from light-level geolocation, especially for animals with restricted movements through a homogenous temperature field. Despite some error in satellite tag positions, combining results from PSAT and acoustic tags in this study yielded a comprehensive representation of manta spatial ecology across several scales, and such approaches will, in the future, inform the design of appropriate management strategies for manta rays in the Red Sea and tropical regions worldwide.

Chronostratigraphy of Bramston Reef reveals a long-term record of fringing reef growth under muddy conditions in the central Great Barrier Reef

Inshore reefs on Australia's Great Barrier Reef (GBR) are widely argued to be in decline, although recent reports suggest that some may be more resilient than traditionally assumed. Resolution of this debate requires long-term insights into past reef development and variability to provide context for the assessment of present reef condition. Long-term reef growth histories can preserve extended records of reef growth and condition, however they are rare, especially for mainland-attached fringing reefs, which are themselves uncommon on the GBR. We examined the internal structure and ecology at Bramston Reef, a mainland-attached fringing reef located in a protected bay on the central GBR. Eight reef matrix cores were collected across the reef flat. Sedimentological and palaeo-ecological analyses coupled with U–Th dating were used to develop the first reef growth history for a shore-attached fringing reef in this region. Twenty-five hard coral genera were identified in the palaeo-ecological analyses. The key reef-building genera (including Acropora, Montipora, Euphyllia, Porites and Goniopora) have contributed to reef growth since initiation and are represented in the extant coral community, despite a change in accretion ‘mode’ during the late Holocene. Sedimentological and stratigraphic investigations demonstrate Bramston Reef has always grown in a mud-rich setting. U–Th ages indicate that reef initiation occurred at or before 5400yBP in a palaeo-water depth of 2–3m. Bramston Reef reached sea level by 4256yBP when sea level was approximately 1m higher than present, after which rapid seaward progradation occurred until around 3000yBP (~19cm/yr on average). Between approximately 3000 and 1000yBP seaward progradation of the reef flat slowed (to ~9.8cm/yr on average). This deceleration of reef growth occurred long before European settlement of the Queensland coast and was driven by natural constraints, probably associated with limited accommodation space due to late-Holocene sea-level fall. Our results demonstrate that mainland-attached reef initiation and accretion can occur in muddy inshore environments over long timeframes (centuries to millennia).

Cross-shelf exchanges between the Coral Sea and the Great Barrier Reef lagoon determined from a regional-scale numerical model

Analyses of the variability in a 3.5-year run of a hydrodynamic model developed for simulating the circulation of the Great Barrier Reef (GBR) are presented. Sea-surface temperature, salinity, currents and cross-shelf transports between the GBR lagoon and the deep ocean offshore are investigated and compare well to available observations. Water mass intrusions and flushing events are critical factors in determining the health of coral reef and continental shelf ecosystems. Results from tracer release experiments provide a synoptic view of the variability of residence times within the GBR and identify critical regions of shelf-ocean exchange. One such region of significant tracer contribution to the shelf is identified in the vicinity of the Pompey Reefs in an area characterised by increased frequency of upslope transported water. Another location of enhanced flux on to the shelf exists in the region bracketing Palm Passage, where the reef matrix is very open, and provides little obstacle to cross-shelf exchange. The Palm Passage location is the origin of a northwards plume of elevated concentration. The model circulation provides a robust and useful picture of the Great Barrier Reef, rendering the model suitable for providing input to biogeochemical and sediment models to simulate, at a broad scale, the ecosystem health, water quality, transport and fate of water and waterborne material, moving through catchments and into the GBR lagoon.

The large-scale influence of the Great Barrier Reef matrix on wave attenuation

Abstract Offshore reef systems consist of individual reefs, with spaces in between, which together constitute the reef matrix. This is the first comprehensive, large-scale study, of the influence of an offshore reef system on wave climate and wave transmission. The focus was on the Great Barrier Reef (GBR), Australia, utilizing a 16-yr record of wave height from seven satellite altimeters. Within the GBR matrix, the wave climate is not strongly dependent on reef matrix submergence. This suggests that after initial wave breaking at the seaward edge of the reef matrix, wave energy that penetrates the matrix has little depth modulation. There is no clear evidence to suggest that as reef matrix porosity (ratio of spaces between individual reefs to reef area) decreases, wave attenuation increases. This is because individual reefs cast a wave shadow much larger than the reef itself; thus, a matrix of isolated reefs is remarkably effective at attenuating wave energy. This weak dependence of transmitted wave energy on depth of reef submergence, and reef matrix porosity, is also evident in the lee of the GBR matrix. Here, wave conditions appear to be dependent largely on local wind speed, rather than wave conditions either seaward, or within the reef matrix. This is because the GBR matrix is a very effective wave absorber, irrespective of water depth and reef matrix porosity.

Using molecular prey detection to quantify rock lobster predation on barrens-forming sea urchins.

We apply qPCR molecular techniques to detect in situ rates of consumption of sea urchins (Centrostephanus rodgersii and Heliocidaris erythrogramma) by rock lobsters (Jasus edwardsii). A non-lethal method was used to source faecal samples from trap-caught lobsters over 2years within two no-take research reserves. There was high variability in the proportion of lobsters with faeces positive for sea urchin DNA across years and seasons dependent on lobster size. Independent estimates of lobster predation rate on sea urchins (determined from observed declines in urchin abundances in the reserves relative to control sites) suggest that rates of molecular prey detection generally overestimated predation rates. Also, small lobsters known to be incapable of directly predating emergent sea urchins showed relatively high rates of positive tests. These results indicate that some lobsters ingest non-predatory sources of sea urchin DNA, which may include (i) ingestion of C.rodgersii DNA from the benthos (urchin DNA is detectable in sediments and some lobsters yield urchin DNA in faeces when fed urchin faeces or sediment); (ii) scavenging; and/or predation by rock lobsters on small pre-emergent urchins that live cryptically within the reef matrix (although this possibility could not be assessed). While the DNA-based approach and direct monitoring of urchin populations both indicate high predation rates of large lobsters on emergent urchins, the study shows that in some cases absolute predation rates and inferences of predator-prey interactions cannot be reliably estimated from molecular signals obtained from the faeces of benthic predators. At a broad semi-quantitative level, the approach is useful to identify relative magnitudes of predation and temporal and spatial variability in predation.

Spatial distribution of surgeonfish and parrotfish in the north sector of the Mesoamerican Barrier Reef System

AbstractSurgeonfish and parrotfish play an important role in structuring the benthic communities of coral reefs. However, despite their importance, little is known about their distribution patterns in the north sector of the Mesoamerican Reef System. This study evaluated the distribution of these fish in 34 sites in four habitats (lagoon, front, slopes and terrace) along a depth gradient (c 0.5–20 m). These herbivorous fish were assessed by visual censuses. Species dominance was evaluated for each habitat using SIMPER analysis. Habitat characteristics data were collected to determine the relationship between habitat conditions and spatial variations in herbivorous fish (using abundance and biomass as a proxy) via redundancy analysis. The herbivorous fish assemblage had a low density (fish per 100 m2) and biomass (g·100 m−2) in comparison with assemblages in similar studies. In contrast, species richness was high compared with other studies in the Caribbean. Spatial variation of the abundance, biomass and size of herbivorous fish was strongly related to coral and seagrass cover, as well as to depth and rugosity. These four variables were critical in controlling the distribution patterns of the herbivorous fish assemblages. No associations were found between fish and macroalgae or any other benthic group. The present study indicates that the species richness of surgeonfish and parrotfish was not regionally affected by the dominance of macroalgae in the habitats studied. Seagrass beds and the coral reef matrix need to be preserved for the herbivorous fish assemblages to remain healthy and capable of controlling excess macroalgae growth.