Bathymetry,water optical properties,and benthic classification of coral reefs using hyperspectral remote sensing imagery

The complexity and heterogeneity of shallow coastal waters over small spatial scales provides a challenging environment for mapping and monitoring benthic habitats using remote sensing imagery. Additionally, changes in coral reef community structure are occurring on unprecedented temporal scales that require large-scale synoptic coverage and monitoring of coral reefs. A variety of sensors and analyses have been employed for monitoring coral reefs: this study applied a spectrum-matching and look-up-table methodology to the analysis of hyperspectral imagery of a shallow coral reef in the Bahamas. In unconstrained retrievals the retrieved bathymetry was on average within 5% of that measured acoustically, and 92% of pixels had retrieved depths within 25% of the acoustic depth. Retrieved absorption coefficients had less than 20% errors observed at blue wavelengths. The reef scale benthic classification derived by analysis of the imagery was consistent with the percent cover of specific coral reef habitat classes obtained by conventional line transects over the reef, and the inversions were robust as the results were similar when the benthic classification retrieval was constrained by measurements of bathymetry or water column optical properties. These results support the use of calibrated hyperspectral imagery for the rapid determination of bathymetry, water optical properties, and the classification of important habitat classes common to coral reefs.     

Pleistocene coral reefs associated with claystones, Southwestern Taiwan

 Scleractinian coral reefs, when coexistent with siliciclastic sediments, usually occur in association with deltaic or coastal sands. Nevertheless, Pleistocene reef limestones in southwestern Taiwan are developed in association with thick claystones that were deposited in a deeper-water environment. These reef limestones are characterized by: (1) rapid transition from underlying claystones upward to reefal limestones, (2) lateral interfingering with open-shelf claystones, (3) being overlain by terrestrial deposits or exposed with no covering strata, and (4) being located in close association with anticlines. The authors propose that these reef limestones developed on anticlinal ridges raised above the adjacent sea floor by thrust-front migration in a foreland setting. Accepted: 21 April 1998     

Increased sediment supply to the Great Barrier Reef will not increase sediment accumulation at most coral reefs

 The rate of terrigenous sediment supply to the central Great Barrier Reef (GBR) coastline has probably increased in the last 200 years due to human impact on the catchments of central Queensland. This has led some researchers and environmental managers to conclude that corals within the GBR are under threat from increased turbidity and sedimentation. Using geological data and information on sedimentary processes, we show that turbidity levels and sediment accumulation rates at most coral reefs will not be increased, because these factors are not currently limited by sediment supply. Accepted: 15 January 1999     

Optical spectra and pigmentation of Caribbean reef corals and macroalgae

 Coastal reef degradation and widespread bleaching of corals, i.e. loss of pigments and/or symbiotic zooxanthellae, is increasing globally. Remote sensing from boats, aircraft or satellites has great potential for assessing the extent of reef change, but will require ground-verified spectral algorithims characteristic of healthy and degraded reef populations. We collected seven species of Caribbean reef corals and also representative macroalgae from reefs near Lee Stocking Island, Bahamas and quantified their pigments using high performance liquid chromatography. We also measured the fluorescence and reflectance spectra of corals and macroalgae using an in situ benthic spectrofluorometer. In visibly pigmented (unbleached) coral from 4 to 5 m depth, the mean (±SD) surface density of pigments (3.0±1.3 μg chlorophyll-a cm^-2 and 2.1±0.7 μg peridinin cm^-2) was similar between colonies of the same species, but differed among species. The mean quantity of pigment per zooxanthella (1.8±0.9 pg chl-a cell^-1 and 1.4±0.7 pg peridinin cell^-1) also differed among species and sometimes between colonies of the same species. Chl-a and peridinin densities per surface area of coral were positively correlated. When excited with blue light (480 nm), macroalgae and corals had typical chlorophyll fluorescence with a peak at 680 nm and a smaller shoulder peak at 730 to 740 nm. Most corals, unlike macroalgae, also had distinct fluorescence peaks between 500 and 530 nm. In visibly bleached corals 680 nm fluorescence was greatly reduced in amplitude. Pigmented coral, under natural lighting conditions, had a reflected light peak at about 570 nm. Reflectance increased over all wavelengths in bleached corals, with the greatest increase at the wavelengths where chlorophyll and accessory pigments absorb light, i.e. 670 and 450 to 550 nm. Both fluorescence and reflectance spectra appear promising to remotely differentiate between pigmented and bleached coral and between coral and macroalgae. Accepted: 15 March 1999     

Spectral reflectance of coral

Spectral reflectance (R) of corals is a fundamental parameter to coral reef remote sensing. We explore general trends as well as geographic and taxonomic variabilities of coral R using a data set consisting of 5,199 Rs measured in situ at depths of up to 15 m for 195 coral colonies at 11 sites worldwide. Coral R ranges in magnitude from ~0.5% at 400 nm to near 100% at 700 nm; mean coral R rises from ~2.5% at 400–500 nm to ~8% between 550 and 650 nm. All corals measured in this study exhibit one of two basic shapes of R, which we label the brown and blue modes. We postulate that brown-mode R is determined by pigment absorption solely by zooxanthellae, while blue-mode R arises through expression of a non-fluorescing coral-host pigment. Taxonomic and geographic variabilities are approximately equal to global variability, both in magnitude and shape, indicating that coral R is independent of taxonomic or geographic differences. We reason that this is to be expected, since R is determined by pigments that are conservative across geographic and taxonomic boundaries.     

Macroborers within coral framework at Discovery Bay, north Jamaica: species distribution and abundance, and effects on coral preservation

 Macroboring organisms are recognised as key agents of reef framework modification and destruction, and while recent studies in the Pacific have improved understanding of spatial variations in macroboring community structure, and rates of macroboring within individual reefs, comparable studies from the Caribbean are largely lacking. This study assesses the distribution of macroboring species and the degree of framework infestation across the reefs at Discovery Bay, north Jamaica. Although individual species of borers exhibit variable distributions across the reef, relative abundances of the main groups of macroborers (sponges, bivalves, worms) illustrate clear distributional trends. Sponges are dominant at fore-reef sites, while sipunculan and polychaete worms are only of importance at back-reef/lagoon and shallow fore-reef sites. Bivalves are locally important within back-reef and lagoon patch reef framework. Average percentages of internal bioerosion (macroboring) vary between sites, but are highest at back-reef and deep fore-reef sites. No systematic pattern of variation occurs within back-reef/lagoon samples, but a significant trend of increased macroboring is recognised with increased water depth on the fore-reef. In addition, significant differences in terms of the susceptibility of individual coral species are recognised. These factors are likely to result in biasing of the fossil record, with variable styles of preservation evident both between sites (i.e. with depth/environment) and within sites (i.e. between coral species). Accepted: 1 June 1998     

Estimates of species diversity of free-living marine isopod crustaceans on coral reefs

 A core group of isopod crustacean genera appears to be present at many coral reef sites. Within these genera, however, species show high local endemicity. Based on the estimated percentage of endemism for the Atlantic (19% for individual sites, 90% for the tropical western Atlantic as a unit), the Indian Ocean (50%), the eastern-central Pacific (80%), and the western Pacific (40%), it is estimated that there are some 5,000 to 13,000 isopod species in the world’s coral reefs, and that some 2,000 to 6,000 of these are endemics. (At present, approximately 4,400 species of marine and 560 species of freshwater isopods have been described.) Based on the crudely estimated relative abundances of other peracaridan crustaceans in coral reefs (compared to isopods), the total diversity of reef amphipods, tanaidaceans, cumaceans, and mysidaceans is approximately 54,500 species. Accepted: 29 August 1997     

An appraisal of methods used in coral recruitment studies

 A new method for attaching individual artificial settlement plates directly to the reef surface using small stainless steel base plates is described. Recruitment of corals to settlement plates attached to the reef substratum and to steel mesh racks is compared. The effects of differences in depth, settlement plate angle, and local topography on recruitment of corals were also investigated. No significant difference in mean recruit density was found between settlement plates deployed using the two attachment methods. Small differences in depth and plate angle among replicate plates explained less than 6% of the variability in coral recruitment on replicate settlement plates. The direct-attachment method is less obtrusive, more cost and time efficient, and settlement plates can be deployed at precise locations. Additionally, because settlement plates are deployed individually rather than grouped on racks or frames, the direct-attachment method avoids complications associated with assumptions of independence implicit in most statistical procedures. Accepted: 24 November 1999     

Natural inducers for coral larval metamorphosis

 Coral gametes from Acropora millepora (Ehrenberg, 1834) and from multi-species spawning slicks provided larvae for use in metamorphosis assays with a selection of naturally occurring inducer chemicals. Four species of crustose coralline algae, one non-coralline crustose alga and two branching coralline algae induced larval metamorphosis. However, one additional species of branching coralline algae did not produce a larval response. Metamorphosis was also observed when larvae were exposed to skeleton from the massive coral Goniastrea retiformis (Lamarck, 1816) and to calcified reef rubble, demonstrating metamorphosis is possible in the absence of encrusting algae. Chemical extracts from these algae and the coral skeleton, obtained using either decalcification or simple methanol extraction procedures, also contained active inducers. These results extend the number of crustose algal species known to induce coral metamorphosis, suggest that some inducers may not necessarily be strongly associated with the calcified algal cell walls, and indicate that inducer sources in reef habitats may be more diverse than previously reported. Accepted: 21 May 1999     

Spectral discrimination of coral reef benthic communities

Effective identification and mapping of coral reef benthic communities using high-spatial and -spectral resolution digital imaging spectrometry requires that the different communities are distinguishable by their spectral reflectance characteristics. In Kaneohe Bay, Oahu, Hawaii, USA, we collected in situ a total of 247 spectral reflectances of three coral species (Montipora capitata, Porites compressa, Porites lobata), five algal species (Dictyosphaeria cavernosa, Gracilaria salicornia, Halimeda sp., Porolithon sp., Sargassum echinocarpum) and three sand benthic communities (fine-grained carbonate sand, sand mixed with coral rubble, coral rubble). Major reflectance features were identified by peaks in fourth derivative reflectance spectra of coral (at 573, 604, 652, 675 nm), algae (at 556, 601, 649 nm) and sand (at 416, 448, 585, 652, 696 nm). Stepwise wavelength selection and linear discriminant function analysis revealed that spectral separation of the communities is possible with as few as four non-contiguous wavebands. These linear discriminant functions were applied to an airborne hyperspectral image of a patch reef in Kaneohe Bay. The results demonstrate the ability of spectral reflectance characteristics, determined in situ, to discriminate the three basic benthic community types: coral, algae and sand. Accepted: 12 January 2000     

Maintenance of fish diversity on disturbed coral reefs

Habitat perturbations play a major role in shaping community structure; however, the elements of disturbance-related habitat change that affect diversity are not always apparent. This study examined the effects of habitat disturbances on species richness of coral reef fish assemblages using annual surveys of habitat and 210 fish species from 10 reefs on the Great Barrier Reef (GBR). Over a period of 11 years, major disturbances, including localised outbreaks of crown-of-thorns sea star (Acanthaster planci), severe storms or coral bleaching, resulted in coral decline of 46–96% in all the 10 reefs. Despite declines in coral cover, structural complexity of the reef framework was retained on five and species richness of coral reef fishes maintained on nine of the disturbed reefs. Extensive loss of coral resulted in localised declines of highly specialised coral-dependent species, but this loss of diversity was more than compensated for by increases in the number of species that feed on the epilithic algal matrix (EAM). A unimodal relationship between areal coral cover and species richness indicated species richness was greatest at approximately 20% coral cover declining by 3–4 species (6–8% of average richness) at higher and lower coral cover. Results revealed that declines in coral cover on reefs may have limited short-term impact on the diversity of coral reef fishes, though there may be fundamental changes in the community structure of fishes.     

Morphological differences among three species of newly settled pocilloporid coral recruits

 Investigation of the life history of corals is hampered by an inability to identify early recruits. In this study, the pattern of formation and morphology of the juvenile skeletons of three laboratory-reared pocilloporids, Seriatopora hystrix, Stylophora pistillata and Pocillopora damicornis, were compared to determine whether they could be reliably distinguished. The pattern of skeleton formation, including the origin and structure of the septa, columella and corallite wall was similar in all species. Following the completion of the primary corallite wall after 4–5 days, these species could be identified by differences in the diameter of the primary corallite. The mean diameter (±SE) of each species differed markedly: S. hystrix 400 ± 2.7 μm, range 325–450 μm; S. pistillata 505 ± 3.5 μm, range 400–550 μm; P. damicornis 697 ± 7.5 μm, range 492–885 μm. Values for the primary corallite diameter overlapped in only 3% of samples, demonstrating the potential utility of this feature as a tool for classifying recruits obtained from the field. Accepted: 4 January 2000     

A 200-year coral stable oxygen isotope record from a high-latitude reef off Western Australia

 A core from a coral colony of Porites lutea was analysed for stable oxygen isotopic composition^*. A 200-year proxy record of sea surface temperatures from the Houtman Abrolhos Islands off west Australia was obtained from coral δ¹⁸O. At 29′S, the Houtman Abrolhos are the southernmost major reef complex of the Indian Ocean. They are located on the path of the Leeuwin Current, a southward flow of warm, tropical water, which is coupled to Indonesian throughflow. Coral δ¹⁸O primarily reflects local oceanographic and climatic variability, which is largely determined by spatial variability of the Leeuwin Current. However, coherence between coral δ¹⁸O and the current strength itself is relatively weak. Evolutionary spectral and singular spectrum analyses of coral δ¹⁸O demonstrate a high variability in spectral composition through time. Oscillations in the 5–7-y, 14–15-y, and quasi-biennial bands reflect teleconnections of local sea surface temperature (SST) to tropical Pacific climate variability. Deviations between local (coral-based) and regional (instrument) SST contain a cyclic component with a period of 15 y. Coral δ¹⁸O suggests a rise in SST by 0.6 ′C since AD 1944, consistent with available instrumental SST records. A long-term warming by 1.4 ′C since AD 1795 is inferred from the coral record. Accepted: 3 July 1998     

Satellite observation of Keppel Islands (Great Barrier Reef) 2002 coral bleaching using IKONOS data

An examination of IKONOS satellite imagery of the Keppel Islands (Great Barrier Reef) acquired before and during a coral bleaching event indicates that severe bleaching of reefs can be detected as an increase in brightness in the band 1 (blue) and band 2 (green) IKONOS spectral bands (4-m resolution). The bleaching was not detected in band 3 (red), band 4 (near-infrared), or in the 1-m panchromatic band data. A total of 0.74 km² of bleached coral was identified, with detection occurring in waters as deep as 15 m. The procedure requires that one of the scenes be radiometrically normalized to match the reference scene prior to image differencing. A relative radiometric normalization was used in this case because variable cloud cover present in the image acquired during the bleaching event prevented reliable modeling of atmospheric effects. The success at coral bleaching detection at Keppel Islands represents both a best-case and a cloud-challenged scenario. It was a best-case scenario in that coral cover was extensive (70–90% live coral cover, mostly acroporids) and the bleaching level was extreme (92–95% of coral cover white bleached). It was a cloud-challenged scenario in terms of having extensive and highly variable cloud cover present in the image acquired during the bleaching event. Color difference images reveal extensive areas of bleached coral at sites away from our study area, indicating that this platform and methodology may be a valuable tool for mapping high coral cover areas during bleaching events. Additional studies and technique refinements would be required to test the detection limits of bleaching with IKONOS imagery or to develop a spectrally based bleaching detection index.An erratum to this article can be found at     

Coral calcification: autoradiography of a scleractinian coral Galaxeafascicularis after incubation in 45Ca and 14C

 The uptake of ⁴⁵Ca and/or ¹⁴C by the skeleton of coral colonies has been commonly used to investigate the processes of calcification. This study reports the differential uptake of these tracers within different regions of the skeleton and tissues of individual corallites and polyps of the hermatypic coral Galaxea fascicularis. Incubation in ⁴⁵Ca in the light resulted in 80 percent of the ⁴⁵Ca taken up being deposited in the skeleton. Autoradiography of transverse and longitudinal slices of freeze-substituted polyps and corallites showed that in the light ⁴⁵Ca was incorporated into the exsert septa, the outside of the thecal walls of the corallite and the inner edges of the septa. Incorporation did not occur in the costae. The radioactivity in the skeleton was considerably greater than in the tissues. In the dark, or in the presence of the photosynthetic inhibitor Diuron, ⁴⁵Ca was taken up by the exsert septa and was patchily distributed in the corallite walls which suggests that it was not a result of isotopic exchange. The differential incorporation of ⁴⁵Ca onto the exsert septa was confirmed by scintillation counting. Negligible radioactivity remained in the extrathecal coelenteron after a brief 5 min rinse in non-radioactive seawater. Only 0.1% of ¹⁴C taken up in the light was incorporated into the skeleton and this was confirmed by autoradiography. In the presence of Diuron or in the dark, very little ¹⁴C was incorporated into tissues or skeleton and in autoradiographs was either not evident in the skeleton or the distribution was similar to that seen in autoradiographs of ⁴⁵Ca uptake. These results show that the deposition of ⁴⁵Ca, and therefore calcium carbonate, occurs at specific loci on the skeleton of a corallite. In the dark, deposition occurs specifically at the growing points of the corallite. Differential deposition of calcium carbonate within individual corallites has not been previously reported. Accepted: 27 May 1997     

Spatio-temporal variation in coral recruitment at different scales on Heron Reef, southern Great Barrier Reef

 Recruitment of scleractinian corals on settlement plates at Heron Island, Great Barrier Reef, was examined over four years (September 1991–September 1995) to quantify spatio-temporal patterns at different scales and to assess post settlement mortality. Recruitment was dominated by pocilloporid corals which accounted for 80.1% of the 8627 spat counted, whereas non-isoporan acroporids represented only 16.4%. Poritids, faviids and isoporan acroporids rarely recruited to the plates (3.5%), despite their obvious abundance as adults on the reef. Recruitment patterns on the plates indicate strong space-time interactions as evidenced by patchy recruitment of both pocilloporid and acroporid spat. Interactions were found between space (on the scale of 10² m, i.e. sites within zones, and 10¹ m, i.e. racks within sites) and time (on the scale of years) for pocilloporids and between space (on the scale of 10³ m, i.e. zones, and 10² m) and time (on the scale of years) for acroporids. Post-recruitment mortality of acroporid spat in the period 3–10 months after their major spawning was dependent on their initial recruitment density, but pocilloporid mortality was either independent of initial recruitment density or, more likely, obscured by additional recruitment of pocilloporids to plates between late February and September. High rates of recruitment and growth by other sessile organisms, particularly bryozoans and oysters, appear to result in increased post-recruitment mortality and limit recruitment of scleractinian corals on settlement plates. The work reinforces an emerging picture that coral recruitment patterns are determined by mechanisms that manifest over a large range of spatial scales. Accepted: 1 September 1997     

The role of colony morphology and substratum inclination in the success of Millepora alcicornis on shallow coral reefs

 Millepora species are conspicuous members of shallow coral reefs where they occupy a variety of substrata and produce morphologically complex skeletons. This study focuses on the roles of growth on vertical and horizontal surfaces and the production of encrusting bases and branches (a “sheet-tree” morphology) for the success of the Millepora alcicornis on coral reefs. The effects of inclination were investigated by comparing the size and growth rates of M. alcicornis on vertical and horizontal surfaces at 3–5 m depth, in St. John, US Virgin Islands. The consequences of morphological complexity were investigated by comparing polyp density, chlorophyll content and biomass between encrusting bases and branches; the role of branches in asexual reproduction was also quantified. Colonies on vertical surfaces had larger encrusting bases, longer perimeters and lower densities of branches compared to those on horizontal surfaces. Growth rates also varied significantly between surfaces, largely because colonies on horizontal surfaces shrank in area while those on vertical surfaces increased in area, albeit slowly. Branches were not specialized in comparison to encrusting bases in terms of the density of dactylozooids and gastrozooids, chlorophyll content and biomass, but they were effective asexual propagules. During one storm, 79% of the branches were removed from colonies of M. alcicornis, and 4% attached to the substratum to produce new colonies at a density of ≈0.5 colonies.m^-2. Anecdotal observations suggest that such storms rarely damaged encrusting bases on vertical surfaces, but often destroyed those on horizontal surfaces. Thus, the encrusting bases on vertical surfaces are likely to be large because of greater age rather than faster growth, while those on horizontal surfaces are likely to be small because they are relatively young and short lived. These findings suggest that the success of M. alcicornis is a result, in part, of the beneficial consequences of their “sheet-tree” morphology, that supports: (a) slow growth and resistance to wave damage of encrusting bases on vertical surfaces, and (b) the use of branches as asexual propagules. Accepted: 24 November 1998     

Using satellite and real-time weather data to predict maize production

 Large-scale assessments of crop conditions prior to harvest are critical for providing early estimates of production. Satellite and weather information provide the opportunity for near real-time crop monitoring. The objective of this research was to develop an operational assessment system for crop production utilizing data from these sources. Maize (Zea mays) production was assessed in 42 Crop Reporting Districts (CRDs) across the United States Corn Belt, which produce 60% of all maize grown in the United States. Satellite, climatolocal, and agricultural data were collected for 8 years, 1985–1992, and aggregated into CRDs. A model predicting the normalized maize yields for each CRD was developed that included as independent variables a satellite data variable, the Vegetation Condition Index, and a climatological variable, the Crop Moisture Index. This model explained approximately three-quarters (R ²=0.73) of the variation observed in the normalized yields, and was examined both for its accuracy and its timeliness in providing production estimates. Predicted seasonal yields were summed to provide a maize production estimate for the entire Corn Belt study region. Production estimates deviated from the final USDA statistics, which become available several months after harvest, by less than 10% for all eight growing seasons. In addition, the production estimates were available approximately 2 months prior to the completion of the maize harvest. This system has the potential for providing timely in-formation to organizations monitoring regional or global agricultural production for humanitarian or economic benefits. Received: 23 July 1997 / Accepted: 17 February 1998     

Importance of foraminifera for the formation and maintenance of a coral sand cay: Green Island, Australia

 CaCO₃ production by reef-building organisms on Green Island Reef in the Great Barrier Reef of Australia is estimated and compared with the contribution of benthic foraminifera to the sediment mass of the vegetated sand cay. Major constituents of the cay are benthic foraminifera (mainly Amphistegina lessonii, Baculogypsina sphaerulata, and Calcarina hispida), calcareous algae (Halimeda and coralline algae), hermatypic corals, and molluscs. Among these reef-building organisms, benthic foraminifera are the single most important contributor to the sediment mass of the island (ca. 30% of total sediments), although their production of CaCO₃ is smaller than other reef-building organisms. Water current measurements and sediment traps indicate that the velocity of the current around Green Island is suitable for transportation and deposition of foraminiferal tests. Abundant foraminifera presently live in association with algal turf on the shallow exposed reef flat, whose tests were accumulated by waves resulting in the formation and maintenance of the coral sand cay. Accepted: 30 June 1999     

Multiple criteria analysis integrates economic, ecological and social objectives for coral reef managers

 Managing a coral reef in a small island state is a difficult task. Apart from having conflicting objectives and few data there is the added problem of how to evaluate the less tangible benefits of management. This study reports the successful use of multiple criteria analysis to help the managers of a coral reef to make “good” decisions. “Good” decisions are consistent with the community’s desires to, in this case, preserve social and ecological values while simultaneously maintaining the economic benefits of dive tourism and maintaining the park as a global model of successful management. Multiple criteria analysis provides a systematic framework for evaluating management options. This study presents one of the first times multiple criteria analysis has been used in coral reef management, let alone in a non-industrialised setting. The results suggest that the method may be more widely useful than previously thought. Accepted: 20 July 1999