Wave-generated flow on coral reefs - an analysis for two-dimensional horizontal reef-tops with steep faces

Waves breaking on the seaward rim of a coral reef generate a flow of water from the exposed side of the reef to the sheltered side and/or to either channels through the reef-rim or lower sections of the latter. This wave-generated flow is driven by the water surface gradient resulting from the wave set-up created by the breaking waves. This paper reviews previous approaches to modelling wave-generated flows across coral reefs and discusses the influence of reef morphology and roughness upon these flows. Laboratory measurements upon a two-dimensional horizontal reef platform with a steep reef face provide the basis for extending a previous theoretical analysis for wave set-up on a reef in the absence of a flow [Gourlay, M.R., 1996b. Wave set-up on coral reefs. 2. Set-up on reefs with various profiles. Coastal Engineering 28, 1755] to include the interaction between a unidirectional flow and the wave set-up. The laboratory model results are then used to demonstrate that there are two basic reef-top flow regimes-reef-top control and reef-rim control. Using open channel flow theory, analytical relationships are derived for the reef-top current velocity in terms of the offreef wave conditions, the reef-top water depth and the physical characteristics of the reef-top topography. The wave set-up and wave-generated flow relationships are found to predict experimental values with reasonable accuracy in most cases. The analytical relationships are used to investigate wave-generated flows into a boat harbour channel on Heron Reef in the southern Great Barrier Reef. (c) 2005 Elsevier B.V. All rights reserved.

Recent developments on a nearshore, terrigenous-influenced reef: Low Isles Reef, Australia

Low Isles Reef is the most southerly located of 46 coral reef platforms unique to the inner shelf of the northern Great Barrier Reef Province, Australia, which support both sea grass and mangrove growth. Such reefs develop in areas that are influenced by river flood plumes and where interreef sediments are dominated by terrigenous mud. Low Isles Reef has long been a popular tourist destination. Informal reports of decreasing visibility, a decline in scleractinian corals, and increases in soft coral and macroalgae have sparked speculation that agricultural activities in coastal catchments are affecting the reef. Comparison of the modern surface of Low Isles Reef with historical surveys and photographs dating back to 1928 allows quantification of modern sedimentary processes, rates of change, and factors influencing reef development. Results indicate that changes on Low Isles Reef are related to remobilization of coarse sediment during storm events and gradual shoreline retreat associated with rising sea level. Retreat of shingle ramparts and elongate ridges of coral debris toward the reef interior has led to the infilling of subtidal ponds on the reef top, which supported hard coral colonies in 1928. The gradual development of a composite shingle rampart along the windward margin has promoted an increase (;150%) in the area of the reef top covered by mangroves. On the leeward margin, a decrease in hard corals since 1950 may reflect a rising contribution of organic debris from the expanding mangrove swamp. Results suggest that recent changes on Low Isles Reef can be explained in the context of natural processes. Further study is needed before the effects of agricultural activities in coastal catchments on reef health can be confirmed.

Spatial patterns of aerobic and anaerobic mineralization rates and oxygen penetration dynamics in coral reef sediments

Oxygen consumption rates (OCR), aerobic mineralization and sulfate reduction rates (SRR) were studied in the permeable carbonate reef sediments of Heron Reef, Australia. We selected 4 stations with different hydrodynamic regimes for this study. In situ oxygen penetration into the sediments was measured with an autonomous microsensor profiler. Areal OCR were quantified from the measured oxygen penetration depth and volumetric OCR. Oxygen penetration and dynamics (median penetration depths at the 4 stations ranged between 0.3 and 2.2 cm), OCR (median 57 to 196 mmol C m(-2) d(-1)), aerobic mineralization (median 24 to 176 mmol C m(-2) d(-1)) and SRR (median 9 to 42 mmol C m(-2) d(-1)) were highly variable between sites. The supply of oxygen by pore water advection was a major cause for high mineralization rates by stimulating aerobic mineralization at all sites. However, estimated bottom water filtration rates could not explain the differences in volumetric OCR and SRR between the 4 stations. This suggests that local mineralization rates are additionally controlled by factors other than current driven pore water advection, e.g. by the distribution of the benthic fauna or by local differences in labile organic carbon supply from sources such as benthic photosynthesis. Carbon mineralization rates were among the highest reported for coral reef sediments, stressing the role of these sediments in the functioning of the reef ecosystem.

The stability of P in coral reef fishes

The constancy of phenotypic variation and covariation is an assumption that underlies most recent investigations of past selective regimes and attempts to predict future responses to selection. Few studies have tested this assumption of constancy despite good reasons to expect that the pattern of phenotypic variation and covariation may vary in space and time. We compared phenotypic variance-covariance matrices (P) estimated for Populations of six species of distantly related coral reef fishes sampled at two locations on Australia's Great Barrier Reef separated by more than 1000 km. The intraspecific similarity between these matrices was estimated using two methods: matrix correlation and common principal component analysis. Although there was no evidence of equality between pairs of P, both statistical approaches indicated a high degree of similarity in morphology between the two populations for each species. In general, the hierarchical decomposition of the variance-covariance structure of these populations indicated that all principal components of phenotypic variance-covariance were shared but that they differed in the degree of variation associated with each of these components. The consistency of this pattern is remarkable given the diversity of morphologies and life histories encompassed by these species. Although some phenotypic instability was indicated, these results were consistent with a generally conserved pattern of multivariate selection between populations.

High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

Background: Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. Results: We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Conclusion: Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown.

Acclimatization of the tropical reef coral Acropora millepora to hyperthermal stress

The demise of reef-building corals potentially lies on the horizon, given ongoing climate change amid other anthropogenic environmental stressors. If corals cannot acclimatize or adapt to changing conditions, dramatic declines in the extent and health of the living reefs are expected within the next half century. The primary and proximal global threat to corals is climate change. Reef-building corals are dependent upon a nutritional symbiosis with photosynthetic dinoflagellates belonging to the group Symbiodinium. . The symbiosis between the cnidarian host and algal partner is a stress-sensitive relationship; temperatures just 1°C above normal thermal maxima can result in the breakdown of the symbiosis, resulting in coral bleaching (the loss of Symbiodinium and/or associated photopigments) and ultimately, colony death. As ocean temperatures continue to rise, corals will either acclimatize or adapt to changing conditions, or will perish. By experimentally preconditioning the coral Acropora millepora via sublethal heat treatment, the coral acquired thermal tolerance, resisting bleaching during subsequent hyperthermal stress. The complex nature of the coral holobiont translates to multiple possible explanations for acclimatization: acquired thermal tolerance could potentially originate from the host itself, the Symbiodinium, or from the bacterial community associated with the coral. By examining the type of in hospite Symbiodinium and the bacterial community prior acclimation and after thermal challenge, it is shown that short-term acclimatization is not due to a distinct change in the dinoflagellate or prokaryote community. Though the microbial partnerships remain without considerable flux in preconditioned corals, the host transcriptome is dynamic. One dominant pattern was the apparent tuning of gene expression observed between preconditioned and non-preconditioned treatments, showing a modulated transcriptomic response to stress. Additionally several genes were upregulated in association with thermal tolerance, including antiapoptotic genes, lectins, and oxidative stress response genes. Upstream of two of these thermal tolerance genes, inhibitor of NFκB and mannose-binding lectin, DNA polymorphisms were identified which vary significantly between the northern and southern Great Barrier Reef. The impact of these mutations in putative promoter regions remains to be seen, but variation across thermally-disparate geography serves to generate hypotheses regarding the role of regulatory element evolution in a coral adaptation context.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

GPS linked photos of benthic cover transect surveys in Heron Reef

Underwater photo-transect surveys were conducted on September 23-27, 2007 at different sections of the reef flat, reef crest and reef slope in Heron Reef. This survey was done by swimming along pre-defined transect sites and taking a picture of the bottom substrate parallel to the bottom at constant vertical distance (30cm) every two to three metres. 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 transect surveys. Approximation of the coordinates for each benthic photo was based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software. Coordinates of each photo were interpolated by finding the the gps coordinates that were logged at a set time before and after the photo was captured. The output of this process was an ArcMap point shapefile, a Google Earth KML file and a thumbnail of each benthic photo taken. The data in the ArcMap shapefile and in the Google Earth KML file consisted of the approximated coordinate of each benthic photo taken during the survey. Using the GPS Photo Link extension within the ArcMap environment, opening the ArcMap shapefile will enable thumbnail to be displayed on the associated benthic cover photo whenever hovering with the mouse over a point on the transect. By downloading the GPSPhotoLink software from the www.geospatialexperts.com, and installing it as a trial version the ArcMap exstension will be installed in the ArcMap environment.

Benthic and substrate cover data derived from photo-transect surveys in Lizard Island Reef conducted on December 10-15, 2011

Underwater georeferenced photo-transect surveys were conducted on December 10-15, 2011 at various sections of the reef at Lizard Island, Great Barrier 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 GPS in a surface float which logged the 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 the position as it floated at the surface while being towed by the photographer. A total of 5,735 benthic photos were taken. A floating GPS setup connected to the swimmer/diver by a line enabled recording of coordinates of each benthic photo (Roelfsema 2009). Approximation of coordinates of each benthic photo was conducted 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 for Microsoft Excel program (Kohler and Gill, 2006). Each point was then assigned to 1 of 78 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 55 South.

Seawater carbonate chemistry during a Ishigaki Island (Japan) coral reef seasonal observations, 2005

Monitoring seawater CO2 for a full year with seasonal observations of community metabolism in Ishigaki Island, Japan, revealed seasonal variation and anomalous values owing to the bleaching event in 1998. The daily average pCO2 showed a seasonal pattern on an annual scale, 280 to 320 ?atm in winter and 360 to 400 ?atm in summer, which was determined primarily by the seasonal change in seawater temperature. By contrast, the range in the diel variation in pCO2, 400 to 500 ?atm in summer 200 to 300 ?atm in winter, was attributed to the seasonal variation in community metabolism: Gross primary production (P g ) and respiration (R) were high in summer and low in winter. During the 1998 bleaching event, although P g and R increased, community excess organic production (E) decreased by three quarters compared with the same month in 1999, when the coral community showed high recovery. This change in metabolism led to large diel range and increased average value of pCO2 levels in the seawater on the reef flat. The decrease in the range and increase in the average value of pCO2 were observed by monitoring the Palau barrier reef flat, where overall mortality of corals occurred after the bleaching. All the metabolic parameters, P g , R, E and calcification (G) were reduced by half after the bleaching, which increased the average pCO2 value by 10 ?atm and decreased its diel range from 200-400 ?atm to 100-200 ?atm. Bleaching and resultant mortality of coral reefs led to degradation of their metabolic performance, and thus resulted in the loss of their active interaction with the carbon cycle.

Seawater carbonate chemistry and calcification during tropical reef studies at Moorea (French Polynesia), 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.

Seawater carbonate chemistry and reproduction of a coral reef fish in a laboratory experiment

Ocean acidification is predicted to negatively impact the reproduction of many marine species, either by reducing fertilization success or diverting energy from reproductive effort. While recent studies have demonstrated how ocean acidification will affect larval and juvenile fishes, little is known about how increasing partial pressure of carbon dioxide (pCO2) and decreasing pH might affect reproduction in adult fishes. We investigated the effects of near-future levels of pCO2 on the reproductive performance of the cinnamon anemonefish, Amphiprion melanopus, from the Great Barrier Reef, Australia. Breeding pairs were held under three CO2 treatments [Current-day Control (430 µatm), Moderate (584 µatm) and High (1032 µatm)] for a 9-month period that included the summer breeding season. Unexpectedly, increased CO2 dramatically stimulated breeding activity in this species of fish. Over twice as many pairs bred in the Moderate (67% of pairs) and High (55%) compared to the Control (27%) CO2 treatment. Pairs in the High CO2 group produced double the number of clutches per pair and 67% more eggs per clutch compared to the Moderate and Control groups. As a result, reproductive output in the High group was 82% higher than that in the Control group and 50% higher than that in the Moderate group. Despite the increase in reproductive activity, there was no difference in adult body condition among the three treatment groups. There was no significant difference in hatchling length between the treatment groups, but larvae from the High CO2 group had smaller yolks than Controls. This study provides the first evidence of the potential effects of ocean acidification on key reproductive attributes of marine fishes and, contrary to expectations, demonstrates an initially stimulatory (hormetic) effect in response to increased pCO2. However, any long-term consequences of increased reproductive effort on individuals or populations remain to be determined.

Managing the Yongala Historic Shipwreck

The Yongala Historic Shipwreck lies within the Great Barrier Reef Marine Park in northeastern Australia. A draft management plan, produced by the Queensland Museum in 1992, provided primarily for the management of the historical and archaeological values of the wreck. The plan did not outline comprehensive strategies for management of either the special ecological values of the site or an increasing demand by recreational divers to dive the wreck This article will outline the processes involved in integrating management of the social, ecological, and historical values of the wreck into a format that is acceptable to all stakeholders associated with the site.

Two new genera, Provitellus and Ovipusillus, and four new species of Monorchiidae (Digenea) from carangid fishes of queensland, Australia

Two new genera and four new species of monorchiid digeneans are described from the Great Barrier Reef and Moreton Bay, Queensland. Provitellus turrum n. g., n. sp. from Pseudocaranx dentex and Trachinotus coppingeri is characterised by the presence of vitelline follicles in the forebody, a single testis, a unipartite terminal organ and filamented eggs. Ovipusillus mayu n. g., n. sp. from Gnathanodon speciosus is characterised by the presence of two testes, vitelline follicles overlapping the ventral sucker and a large, complex cirrus-sac that contains a coiled eversible ejaculatory duct joined by the pars prostatica halfway along its length. Paramonorcheides pseudocaranxi n. sp. from Pseudocaranx dentex differs from other species described in this genus in the longer flatter forebody, entire ovary and the well-developed cirrus-sac. Chrisomon gaigai n. sp. from Trachinotus coppingeri and T botla is characterised by the unflattened forebody and transversely oval pharynx. Chrisomon is redefined to include species of Lasiotocus with a vitellarium composed of clusters of tubular acini, creating the following new combinations: C. albulae n. comb. for L. albulae Overstreet, 1969, C. ulua n. comb, for L. ulua Yamaguti, 1970 and C. weke n. comb, for L. weke Yamaguti, 1970. The diagnosis of Lasiotocus is amended accordingly and the new combinations, L. polynemi n. comb. and L. sunderbanensis n. comb., are created for C.polynemi Dutta, Hafeezullah & Manna, 1994 and C. sunderbanensis Dutta, Hafeezullah B Manna, 1994, respectively. Extrapolation of our collection data suggests that there may be as many as 80 species of monorchiids infecting carangid fishes in Australia and 180 species infecting carangids in all oceans of the world. The latter figure greatly exceeds the number of monorchiids described from all host families to date.

A sponge/dinoflagellate association in the haplosclerid sponge Haliclona sp.: cellular origin of cytotoxic alkaloids by Percoll density gradient fractionation

Light-microscopic and electron-microscopic studies of the tropical marine sponge Haliclona sp. (Or der: Haplosclerida Family: Haliclonidae) from Heron Island, Great Barrier Reef, have revealed that this sponge is characterized by the presence of dinoflagellates and by nematocysts. The dinoflagellates are 7-10 mu m in size, intracellular, and contain a pyrenoid with a single stalk, whereas the single chloroplast is branched, curved, and lacks grana. Mitochondria are present, and the nucleus is oval and has distinct chromosomal structure. The dinoflagellates are morphologically similar to Symbiodinium microadriaticum, the common intracellular symbiont of corals, although more detailed biochemical and molecular studies are required to provide a precise taxonomic assignment. The major sponge cell types found in Haliclona sp, are spongocytes, choanocytes, and archaeocytes; groups of dinoflagellates are enclosed within large vacuoles in the archaeocytes. The occurrence of dinoflagellates in marine sponges has previously been thought to be restricted to a small group of sponges including the excavating hadromerid sponges; the dinoflagellates in these sponges are usually referred to as symbionts. The role of the dinoflagellates present in Haliclona sp. as a genuine symbiotic partner requires experimental investigation. The sponge grows on coral substrates, from which it may acquire the nematocysts, and shows features, such as mucus production, which are typical of some excavating sponges. The cytotoxic alkaloids, haliclonacyclamines A and B, associated with Haliclona sp. are shown by Percoll density gradient fractionation to be localized within the sponge cells rather than the dinoflagellates. The ability to synthesize bioactive compounds such as the haliclonacyclamines may help Haliclona sp. to preserve its remarkable ecological niche.