Cyclone and bioturbation effects on sediments from coral reef lagoons

Despite the severity of tropical cyclone ‘Winifred’, which crossed the Great Barrier Reef on 1 February 1986, there were little long-term effects on lagoon surface sediments from reefs in its path. Short-term effects were apparent only at one particularly exposed area. These were: an increase in proportion of the coarse fraction, the establishment of sand ripples, and the destruction of the mounds produced by callianassid shrimps (normally the dominant topographic feature). Within six weeks this area was indistinguishable from a typical reef lagoon. This is probably the result of sediment reworking by callianassid shrimp, involving selective burial of the coarse fragments and transport to the surface of finer particles. Sediment turnover rates by callianassids are commensurate with change to the sediment within the relatively short period observed. The sediment fauna responded quickly to the changes in sediment type. Immediately after the cyclone the disturbed area supported a fauna typical of the coarse sediments on the shallow reef flat, as the sediment reverted to a more normal type so the fauna changed back to that typical of a reef lagoon.     

Anaerobic metabolism in lagoon sediments from Davies Reef,Great Barrier Reef

Sulphate reduction rates were measured in the lagoon sediments at Davies Reef, on the Great Barrier Reef, Australia. Sulphate reduction rates averaged 0·622 mmol sulphate m⁻² day⁻¹, over the 0–12 cm depth of sediment, compared to an average heterotrophic oxygen uptake rate by the sediment of 27 mmol oxygen m⁻² day⁻¹. Thus sulphate reduction to acid-volatile sulphide appeared to account for only about 5% of the total organic matter degradation, although the proportion may be greater if sulphate reduction to tin-reducible sulphide was taken into account. Although dissolved sulphate concentration in the sediment pore water was that of sea water, a large excess (equivalent to about 0·8% of the sediment dry weight) of precipitated sulphate was present in the sediment. This excess could not be attributed to precipitated strontium sulphate, and there was no exchange between the dissolved and precipitated sulphate. Methane formation in these superficial sediments was not detectable.     

Undisturbed Strata Succession Sampling Technology and the Engineering Geological Characteristics of an Atoll in the Southern South China Sea

Coral reef calcareous sediment, a special category of rock-soil material, has representative geological structure and environmental characteristics. It is widely distributed in shallow areas of the tropical ocean; therefore the exploration instruments and technologies for engineering geology studies of coral reef calcareous sediments are very different from those used in land or deep-sea. Obtaining undisturbed cores from the Holocene unconsolidated stratum of coral reefs has been a key problem in the field of marine geology and environment surveying. The authors have designed a novel floating drilling platform equipped with a drilling machine, and successfully achieved undisturbed cores from both reef flats (with water depth 0.5 to 2 m) and a enclosed lagoon (with water depth 2–12 m) of Yongshu Reef (9°32–9°42 N, 112°52–113°04 E), southern South China Sea. Based on the detailed observation on the cores and the analysis from engineering geology, Yongshu Reef was split into reef three engineering geological zones: leading edge, reef flat (including outer reef flat, middle reef flat and inner reef flat) and lagoon. The sediments are classified in the stratum as fine sand, medium sand, coarse sand, gravel and weak-cemented reef limestone.     

A process to design a network of marine no-take areas: Lessons from the Great Barrier Reef

In the absence of consensus on the quantity and level of zoning protection required for coral reef and lagoon ecosystems, which process can guide decision makers? The Great Barrier Reef Marine Park Authority (GBRMPA) worked with experts in a collaborative process to develop a set of Biophysical Operational Principles to guide the design of a network of no-take areas. First, 82 expert scientists were asked to provide data and advice on the physical, biological and ecological dimensions of the Great Barrier Reef ecosystem. They recommended that an independent Scientific Steering Committee (the Committee) was set up. How this Committee worked successfully with the GBRMPA staff is detailed here in a manner to enable other resource managers to adopt the process if they are working in data-limited marine environments.     

Seismic and stratigraphic evidence for reef expansion and onset of aridity on the Northwest Shelf of Australia during the Pleistocene

Modern reef (the Great Barrier Reef and Ryukyu Reef) distribution in the Indo-Pacific region is strongly controlled by warm currents (East Australian and Kuroshio Currents) that radiate from the Indo-Pacific Warm Pool. The modern distribution of reefs (south of 15°S) on the Western Australian shelf is related to the presence of the warm Leeuwin Current. However, the age of the reefs south of 15°S, and hence their temporal relationship to the Leeuwin Current, has been largely unknown. Seismic and subsurface stratigraphic data show that reef growth and expansion on the Northwest Shelf of Australia began in the Middle Pleistocene (∼0.5 Ma). The oldest ooids in the region are approximately synchronous with reef growth. We suggest a two stage process for the spread of reefs to higher latitudes on the Western Australian coast; first an increase in Leeuwin Current activity at approximately 1 Ma brought warm waters and a tropical biota to the region; and second, increased aridity after ∼0.6 Ma led to a decline in clastic input and increased alkalinity, triggering ooid formation and reef expansion to higher latitudes associated with the switch to higher amplitude glacio-eustatic cycles at the end of the Middle Pleistocene Transition. The timing and mechanisms for reef expansion south along the Western Australian coast has implications for the origin of the Eastern Australian Middle Pleistocene Great Barrier Reef, the New Caledonia Barrier Reef and Japanese Ryukyu Reef systems.     

Effect of agricultural activity on levels of organochlorine pesticides in hard corals, fish and molluscs from the Great Barrier Reef

An organochlorine baseline study of selected corals, fish and molluscs has established that lindane is the only consistently detectable persistent pesticide in Great Barrier Reef organisms sampled. Samples taken during 1976–1977 from twenty reefs between Heron Island and Lizard Island provide evidence from the distribution of lindane that the contamination is related to agricultural usage in the coastal sugar cane growing regions. Consideration is given to the possible mode of transport of lindane to the reef environment. No polychlorinated biphenyls were detected in any of the samples and only scattered samples contained levels of residues other than lindane. Inner marginal shelf reefs of the Great Barrier Reef may be the most pristine environment yet reported for organochlorine pollutants.     

The initiation of the southern central Great Barrier Reef: New multiproxy data from Pleistocene distal sediments from the Marion Plateau (NE Australia)

Significant synchronous shifts in the chemistry, mineralogy, grain sizes and color of the sediments at 6 m below sea floor (mbsf) at ODP Site 1195 on the Marion Plateau (NE Australia) are interpreted to reflect a major regional paleoceanographic change: the initiation of the southern province of the Great Barrier Reef (GBR). The onset of this massive carbonate production centre nearby resulted primarily in increased deposition of carbonate-rich sediments of neritic origin. Both sedimentation rate and terrigenous input record a coincident decline attributed to inshore trapping of materials behind the reefs. Our best estimate places the development of reef framework in the southern part of the GBR between 560 and 670 kyr B.P., based on an age model combining magnetostratigraphic and biostratigraphic data. The proposed estimation agrees with previous studies reporting an age between 500 and 930 kyr B.P., constraining more tightly their results. However, it does not support research placing the birth of the GBR in Marine Isotope Stage (MIS) 11 ( 400 kyr), nor the theory of a worldwide modern barrier reef development at that time.     

The wreck of the MV Rena: spatio-temporal analysis of ship-derived contaminants in the sediments and fauna of Astrolabe Reef

ABSTRACT

The October 2011 sinking of the container ship MV Rena on Astrolabe Reef, New Zealand, provided a rare opportunity to examine the fate of shipwreck-derived contaminants on an offshore rocky reef and food chain. Analyses of trace metals, polycyclic aromatic hydrocarbons (PAHs) and organotins indicated significant but localised contamination of Astrolabe Reef but not of nearby Mōtītī Island. Three years after the grounding, PAH concentrations were greater in sediments at Astrolabe (up to 131?mg kg^?1) than at control locations, while organotins from the ship's antifouling hull paint were found exclusively in Astrolabe Reef sediments and biota. Over 80% of Astrolabe sediment samples contained tributyltin at concentrations above guideline sediment levels (>0.07?mg kg^?1). Tributyltin and its decomposition products were also recorded in sea urchins, gastropods, lobster and fishes at concentrations up to 0.2?mg kg^?1. Wreck and cargo-derived metals, particularly copper, tin and zinc, were present in some Astrolabe sediment samples above Australia and New Zealand Environment and Conservation Council guideline concentrations. However, there appeared to be only limited transmission of metals through the food chain. Copper, tin and zinc were recorded at greater concentrations in Astrolabe sea urchins and gastropods compared to control specimens, while metal concentrations in other biota were comparable across impact and control sites. Despite over 3 years having passed since the Rena grounding, the data series does not show any upward or downward trends in contaminant concentrations on Astrolabe Reef. Consequently, there is uncertainty about the long-term implications of the Rena grounding for the ecology of Astrolabe Reef.     

Bedload sediment transport dynamics in a macrotidal embayment, and implications for export to the southern Great Barrier Reef shelf

Keppel Bay is a macrotidal embayment on a tectonically stable, tropical coast, which links the Fitzroy River with the Great Barrier Reef continental shelf. Estuaries and deltas act as conduits between catchments and inner shelf environments. Therefore, understanding sediment transport pathways in these complex systems is essential for the management of ecosystems such as coral-reefs that are potentially vulnerable to enhanced river sediment loads. Furthermore, the morphology and sediment dynamics of subtidal sand ridges and dunes are relatively poorly characterised in macrotidal estuaries, particularly in turbid, episodic systems such as the Fitzroy River and Keppel Bay. Our sedimentological analysis of seabed samples, shear-stress modelling and three-dimensional acoustic imaging reveals that Keppel Bay is a mixed wave- and tide-dominated estuarine system. Areas of sediment starvation and shoreward transport characterise the offshore zone, whereas a complex of both active and relict tidal sand ridges, and associated subaqueous dunes, dominate the relatively protected southern Keppel Bay. Transport within this region is highly dynamic and variable, with ebb-dominated sediment transport through tidal channels into the outer bay where there is a switch to wave-dominated shoreward transport. Ultimately, bedload sediments appear to be reworked back inshore and to the north, and are gradually infilling the bedrock-defined embayment. Our characterisation of the Keppel Bay system provides a detailed example of the physiography of the seaward portion of a tide-dominated system, and shows that sediment transport in these areas is influenced by a variable hydrodynamic regime as well as relict channels and bedrock topography.     

Aliphatic hydrocarbons in Great Barrier Reef organisms and environment

This investigation was undertaken to assess the chemical nature, occurrence, and possible origin of petroleum hydrocarbons in the Great Barrier Reef ecosystem. Aliphatic hydrocarbons in surface sediments, water, and a suite of seven species from widely separated coral reefs in the Great Barrier Reef area were analysed by gas chromatography, and by gas chromatography coupled with mass spectrometry. The hydrocarbons found were substantially of biogenic origin. The major components were n-pentadecane, n-heptadecane, pristane and mono-alkenes based on heptadecane, and were believed to originate from benthic algae and phytoplankton. There was no evidence to suggest that lipid content had any influence on hydrocarbon content. Hydrocarbons from the organisms and sediments have characteristic composition patterns which would be altered by the presence of petroleum hydrocarbons. An unresolved complex mixture, usually considered indicative of petroleum contamination, was found in greater than trace amounts only in Holothuria (sea cucumber) and Acropora (coral) from the Capricorn Group, and in some sediment samples from the Capricorn Group and Lizard Island area.     

Effective governance of a large and complex cross-jurisdictional marine protected area: Australia's Great Barrier Reef

Australia's Great Barrier Reef is the largest coral reef ecosystem on earth. The governance of such a large and iconic area is complex due to the overlapping federal and state (Queensland) jurisdictions. Since 1975 this globally significant area has been protected by pioneering federal legislation which enabled the ‘reasonable use’ of natural resources to co-exist with conservation, thus introducing the concept of a multiple-use marine park. In 1981 the Great Barrier Reef was listed as a UNESCO World Heritage Area. Today a federal multiple-use Marine Park covers 99% of the Great Barrier Reef Region and World Heritage Area, with the remaining areas under state jurisdiction. A close working partnership between the federal and state governments has evolved over 37 years and includes complementary legislation, joint field management and joint permits. In the face of increasing pressures, management of the Great Barrier Reef continues to be effective for a range of reasons, including a sound governance/legislative framework together with complementary federal/state legislation; integrated management with relevant federal and state agencies; and the application of ecosystem-based management principles both inside and outside the area of the marine park's jurisdiction. This integrated and comprehensive management model is widely regarded as effective by marine and coastal managers around the world.     

Developing a long-term outlook for the Great Barrier Reef,Australia: A framework for adaptive management reporting underpinning an ecosystem-based management approach

The Great Barrier Reef Outlook Report 2009 was the first produced in response to a newly legislated requirement for five-yearly reports on the status of and outlook for the Great Barrier Reef. It adopted an ecosystem approach, assessing all habitats and species, ecosystem processes and major uses. By then considering the factors affecting the ecosystem, coupled with an assessment of management effectiveness, it provided a risk-based forward-looking projection for the ecosystem. Rarely has such a comprehensive, ecosystem-based report been produced to guide government action. With no pre-determined path to follow for interpreting the legislative requirements, the Great Barrier Reef Marine Park Authority (GBRMPA) developed a repeatable structure and method for Great Barrier Reef Outlook Reports that impartially and consistently considers the evidence and clearly presents the findings. The GBRMPA worked closely with relevant Australian and Queensland Government agencies as well as researchers, industry representatives and the community while developing the report. That such a report must be produced every five years allows an overview of the effectiveness of management responses to be regularly assessed. It also provides a transparent means of highlighting and tracking emerging risks facing the Great Barrier Reef.     

Abundance and Photosynthetic Characteristics of Trichodesmium spp. Along the Atlantic Barrier Reef at Carrie Bow Cay, Belize

Abstract. Trichodesmium abundance and photosynthetic rates were determined across a transect of the Atlantic Barrier Reef at Carrie Bow Cay, Belize in May 1993 and May-June 1994. A fore reef station receiving oceanic water had a Trichodesmium abundance characteristic of the open Caribbean Sea (≤ 10² colonies m^-3 and 10⁴-^-10⁵ trichomes m^-3). Several species were present; however, in all cases a sharp decrease in abundance occurred across the reef to the coastal lagoon. At this latter site, virtually no Trichodesmium was present, although a substantial bloom of the diatom Proboscia alata occurred in 1994.
Maximum photosynthetic rates and the initial light-limited slope a were significantly lower in offshore stations than in reef top populations. The increased photosynthetic rates and light-harvesting ability in reef-top populations, as well as the lack of significant photoinhibition, indicated that the Trichodesmium abundance decrease was probably not due to a decline in photosynthetic capacity. Grazing and physical removal rather than a physiological decline were likely mechanisms operating to reduce Trichodesmium abundance in these regions. These data suggest that the Belizean barrier reef is a sink for Trichodesmium transported in from offshore regions.     

A wave model for the Great Barrier Reef

A new wind wave generation model, WAMGBR, is presented that has been adapted from WAM especially for use in the complex geometry of the Great Barrier Reef. A technique (reef parameterization) has been presented that incorporates sub-grid scale dissipation caused by coral reefs. Three other improvements to WAM have been proposed. An explicit/implicit finite difference scheme has been implemented that allows for more efficient modelling (longer time steps) while maintaining diffusive characteristics that are at least as good as those of WAM. An offset in discrete angles creates more uniform diffusive characteristics. And, a transformed spherical coordinate system allows for more efficient grid sizes and smaller grid dependent refraction. Comparisons between modelling techniques and between model and measured data show that WAMGBR produces very good results in the difficult challenge of modelling both non-cyclonic and tropical cyclone waves in the geographically complex environment of the Great Barrier Reef.     

Ontogenetic patterns of concentration indicate lagoon nurseries are essential to common grunts stocks in a Puerto Rican bay

Estimates of abundance and size of three commercially exploited grunt species indicate ontogenetic changes in habitat utilization concentrate their juveniles within the lagoon of the Bay of La Parguera, Puerto Rico. Eleven biotopes, defined by four benthic structures (reef, mangrove, vegetation beds and unconsolidated sediments) and three geographic zones (inner lagoon, outer lagoon and bank shelf) were sampled randomly by visual surveys. French, bluestriped and white grunt (Haemulon flavolineatum, Haemulon sciurus and Haemulon plumeri) were common in the bay and appeared to exhibit similar life history patterns of cross-shelf migration and habitat selection. Recently settled grunts were dispersed over vegetated and unconsolidated soft-bottom sediments of the bay. The juvenile stage occurred in highest densities in shallow lagoon biotopes among the submerged prop-roots of mangrove stands and on inshore reefs. Length data indicates that grunts migrate offshore to adult habitat via increasingly deep reefs. Indices of biotope nursery function based on standing stock estimates of juveniles identified three biotopes, all within the inner lagoon as essential habitat for juveniles of 5–10 cm length interval. This concentration of juveniles within biotopes of the lagoon could represent a bottleneck to recruitment for grunt stocks. Evidence that quantity and quality of lagoon nurseries may limit recruitment indicates that these areas represent a key component of a marine protected area designed to restore fisheries within the bay.     

Carbon-isotope composition of sediments from the Gulf of Papua

Rivers draining into the Gulf of Papua (GOP) from the Papua New Guinea mainland deliver approximately 340 × 10⁶ t yr^–1 of sediment to the marine environment. The terrestrially derived sediment contains 1.1 ± 0.2% particulate organic carbon with a carbon-isotope composition of –26.5 ± 0.2, and amounts to 3.7 ± 0.7 × 10⁶ t yr^–1. The carbon-isotope composition of sediments in the Gulf of Papua indicates that 40% of the sediment cover contains 75% or more terrestrially derived carbon. Suspended sediments that are transported beyond the delta complex of the Fly River are transported north and northwest, augmented by sediments from other rivers along the coast of the GOP. The carbon-isotope results suggest that a significant quantity of terrestrially derived sediment escapes from the GOP, either along the coastlines to east and west or into the deep ocean via the Moresby and Pandora troughs. Little sediment travels south onto the Great Barrier Reef shelf. Extrapolating the results from this study to the region of Oceania suggests a total flux of particulate organic carbon to the world's oceans from the islands of Oceania of ~ 90 × 10⁶ t yr^–1 or twice the flux of riverine POC from the major rivers of North America, South America, and Africa combined. While such a calculation must be considered illustrative only, the similar tectonic, geomorphologic, and climatic features of the islands of Oceania suggest that the calculation is unlikely to be grossly in error and that the rivers of Oceania therefore represent a major but poorly documented source of sediment and organic carbon to the global ocean.     

Tidally incised valleys on tropical carbonate shelves: An example from the northern Great Barrier Reef, Australia

The formation of incised valleys on continental shelves is generally attributed to fluvial erosion under low sea level conditions. However, there are exceptions. A multibeam sonar survey at the northern end of Australia's Great Barrier Reef, adjacent to the southern edge of the Gulf of Papua, mapped a shelf valley system up to 220 m deep that extends for more than 90 km across the continental shelf. This is the deepest shelf valley yet found in the Great Barrier Reef and is well below the maximum depth of fluvial incision that could have occurred under a − 120 m, eustatic sea level low-stand, as what occurred on this margin during the last ice age. These valleys appear to have formed by a combination of reef growth and tidal current scour, probably in relation to a sea level at around 30–50 m below its present position.

Tidally incised depressions in the valley floor exhibit closed bathymetric contours at both ends. Valley floor sediments are mainly calcareous muddy, gravelly sand on the middle shelf, giving way to well-sorted, gravely sand containing a large relict fraction on the outer shelf. The valley extends between broad platform reefs and framework coral growth, which accumulated through the late Quaternary, coincides with tidal current scour to produce steep-sided (locally vertical) valley walls. The deepest segments of the valley were probably the sites of lakes during the last ice age, when Torres Strait formed an emergent land-bridge between Australia and Papua New Guinea. Numerical modeling predicts that the strongest tidal currents occur over the deepest, outer-shelf segment of the valley when sea level is about 40–50 m below its present position. These results are consistent with a Pleistocene age and relict origin of the valley.

Based on these observations, we propose a new conceptual model for the formation of tidally incised shelf valleys. Tidal erosion on meso- to macro-tidal, rimmed carbonate shelves is enhanced during sea level rise and fall when a tidal, hydraulic pressure gradient is established between the shelf-lagoon and the adjacent ocean basin. Tidal flows attain a maximum, and channel incision is greatest, when a large hydraulic pressure gradient coincides with small channel cross sections. Our tidal-incision model may explain the observation of other workers, that sediment is exported from the Great Barrier Reef shelf to the adjacent ocean basins during intermediate (rather than last glacial maximum) low-stand, sea level positions. The model may apply to other rimmed shelves, both modern and ancient.     

Determination of pteridines and flavins in seawater by reverse-phase,high-performance liquid chromatography with fluorometric detection

Methods are described for routine analyses of individual pteridines and flavins from marine waters at picomolar concentrations. Samples were concentrated by adsorption on bonded-phase, C₁₈ silica and Florisil Sep-Pak extraction columns connected in series. Sample extracts derived from Sep-Pak eluates were analysed by reverse-phase liquid chromatography with fluorometric detection. These methods proved sensitive for the quantitative identification of pterin, xanthopterin, isoxanthopterin, 6-biopterin, pterin-6-carboxylic acid, 6-hydroxymethylpterin, riboflavin, riboflavin-5′-phosphate, lumiflavin and lumichrome in reef waters at Davies Reef, Great Barrier Reef, Australia.Preliminary experiments were conducted to test the application of these methods to the measurement of pterin and flavin excretion from several reef-dwelling, benthic organisms. Results from these experiments suggest that the benthic community contributes these compounds to the coral reef environment.     

Population biology and recruitment of a vulnerable sea cucumber,Stichopus herrmanni,on a protected reef

Populations of tropical sea cucumbers, harvested for bêche‐de‐mer, are in a perilous state of conservation, yet there remains a paucity of information on the biology of many harvested species. We examined the population biology of the commercially important curryfish, Stichopus herrmanni, across 2 years on Heron Reef, a protected zone in the Great Barrier Reef (GBR) Marine Park. Stichopus herrmanni, a species recently listed as vulnerable to extinction, is a major target species for the fishery operating in the GBR. The size class distribution and density of S. herrmanni were documented for six sites across Heron Reef. There was distinct spatial variation in the size and density of S. herrmanni across sites, with no significant difference between the 2 years. The smallest individuals found were 10 cm long, some of the only juvenile S. herrmanni documented in nature. Juvenile and sub‐adult populations were found along the leeward reef edge of Heron Reef, a habitat characterized by shallow channels of sand between inter‐tidal coral reef and crustose coralline algae (CCA). Juvenile nurseries of sea cucumbers are rarely observed in nature, making this an important observation for understanding the recruitment and population biology of S. herrmanni. The presence of juveniles in the consolidated CCA habitat each year in autumn following the summer spawning period, and the absence of small individuals several months later in spring, suggests an ontogenetic migration or displacement of these individuals to adult habitat. The distribution of larger S. herrmanni suggests intra‐reef connectivity and migration into deeper lagoon areas. This study contributes to understanding the population dynamics of this vulnerable species, a consideration for fisheries management in light of increasing global harvest.     

Methane sources,sinks and fluxes in a temperate tidal Lagoon: The Arcachon lagoon (SW France)

The Arcachon lagoon is a 156 km² temperate mesotidal lagoon dominated by tidal flats (66% of the surface area). The methane (CH₄) sources, sinks and fluxes were estimated from water and pore water concentrations, from chamber flux measurements at the sediment–air (low tide), sediment–water and water–air (high tide) interfaces, and from potential oxidation and production rate measurements in sediments. CH₄ concentrations in waters were maximal (500–1000 nmol l⁻¹) in river waters and in tidal creeks at low tide, and minimal in the lagoon at high tide (<50 nmol l⁻¹). The major CH₄ sources are continental waters and the tidal pumping of sediment pore waters at low tide. Methanogenesis occurred in the tidal flat sediments, in which pore water concentrations were relatively high (2.5–8.0 μmol l⁻¹). Nevertheless, the sediment was a minor CH₄ source for the water column and the atmosphere because of a high degree of anaerobic and aerobic CH₄ oxidation in sediments. Atmospheric CH₄ fluxes at high and low tide were low compared to freshwater wetlands. Temperate tidal lagoons appear to be very minor contributor of CH₄ to global atmosphere and to open ocean.