Marlin J. Atkinson

Spectral reflectance of coral reef bottom-types worldwide and implications for coral reef remote sensing

Abstract Coral reef benthic communities are mosaics of individual bottom-types that are distinguished by their taxonomic composition and functional roles in the ecosystem. Knowledge of community structure is essential to understanding many reef processes. To develop techniques for identification and mapping of reef bottom-types using remote sensing, we measured 13,100 in situ optical reflectance spectra (400–700 nm, 1-nm intervals) of 12 basic reef bottom-types in the Atlantic, Pacific, and Indian Oceans: fleshy (1) brown, (2) green, and (3) red algae; non-fleshy (4) encrusting calcareous and (5) turf algae; (6) bleached, (7) blue, and (8) brown hermatypic coral; (9) soft/gorgonian coral; (10) seagrass; (11) terrigenous mud; and (12) carbonate sand. Each bottom-type exhibits characteristic spectral reflectance features that are conservative across biogeographic regions. Most notable are the brightness of carbonate sand and local extrema near 570 nm in blue (minimum) and brown (maximum) corals. Classification function analyses for the 12 bottom-types achieve mean accuracies of 83%, 76%, and 71% for full-spectrum data (301-wavelength), 52-wavelength, and 14-wavelength subsets, respectively. The distinguishing spectral features for the 12 bottom-types exist in well-defined, narrow (10–20 nm) wavelength ranges and are ubiquitous throughout the world. We reason that spectral reflectance features arise primarily as a result of spectral absorption processes. Radiative transfer modeling shows that in typically clear coral reef waters, dark substrates such as corals have a depth-of-detection limit on the order of 10–20 m. Our results provide the foundation for design of a sensor with the purpose of assessing the global status of coral reefs.

Spectral discrimination of coral reef benthic communities

Abstract 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.

Capabilities of remote sensors to classify coral, algae, and sand as pure and mixed spectra

Abstract We investigate the abilities of seven remote sensors to classify coral, algae, and carbonate sand based on 10,632 reflectance spectra measured in situ on reefs around the world. Discriminant and classification analyses demonstrate that full-resolution (1 nm) spectra provide very good spectral separation of the bottom-types. We assess the spectral capabilities of the sensors by applying to the in situ spectra the spectral responses of two airborne hyperspectral sensors (AAHIS and AVIRIS), three satellite broadband multispectral sensors (Ikonos, Landsat-ETM+ and SPOT-HRV), and two hypothetical satellite narrowband multispectral sensors (Proto and CRESPO). Classification analyses of the simulated sensor-specific spectra produce overall classification accuracy rates of 98%, 98%, 93%, 91%, 64%, 58%, and 50% for AAHIS, AVIRIS, Proto, CRESPO, Ikonos, Landsat-ETM+, and SPOT-HRV, respectively. Analyses of linearly mixed sensor-specific spectra reveal that the hyperspectral and narrowband multispectral sensors have the ability to discriminate between coral and algae across many levels of mixing, while the broadband multispectral sensors do not. Applying the results of the general mixing analyses to a specific spatial organization of coral, algae, and sand indicates that the hyperspectral sensors accurately estimate areal cover of the bottom-types regardless of pixel resolution. The narrowband multispectral sensors overestimate coral cover by 11–15%, while the broadband sensors underestimate algae cover by 7–29% and overestimate coral cover by 24–103%. We conclude that currently available satellite sensors are inadequate for assessment of global coral reef status, but that it is both necessary and possible to design a sensor system suited to the task.

Wave-Driven Circulation of a Coastal Reef–Lagoon System

Abstract The response of the circulation of a coral reef system in Kaneohe Bay, Hawaii, to incident wave forcing was investigated using field data collected during a 10-month experiment. Results from the study revealed that wave forcing was the dominant mechanism driving the circulation over much of Kaneohe Bay. As predicted theoretically, wave setup generated near the reef crest resulting from wave breaking established a pressure gradient that drove flow over the reef and out of the two reef channels. Maximum reef setup was found to be roughly proportional to the offshore wave energy flux above a threshold root-mean-square wave height of 0.7 m (at which height setup was negligible). On the reef flat, the wave-driven currents increased approximately linearly with incident wave height; however, the magnitude of these currents was relatively weak (typically <20 cm s−1) because of (i) the mild fore-reef slope of Kaneohe Bay that reduced setup resulting from a combination of frictional wave damping and its re...

Seasonal coupling and de‐coupling of net calcification rates from coral reef metabolism and carbonate chemistry at Ningaloo Reef, Western Australia

Rates of net production, net calcification, and nutrient uptake were measured in a coral-dominated reef flat community on Ningaloo Reef in northwestern Australia under seasonally minimum and maximum light levels. Daily integrated light decreased twofold while water temperatures remained relatively constant increasing by only 1°C on average from summer to winter. Rates of daily community gross primary production (GPP) were only 33% ± 9% higher in summer than in winter (1400 ± 70 versus 1050 ± 60 mmol C m−2 d−1), far less than the twofold seasonal changes reported for most shallow reef communities. Rates of daily community net calcification (Gnet) were not significantly different between seasons (190 ± 40 mmol CaCO3 m−2 d−1 in summer versus 200 ± 10 mmol CaCO3 m−2 d−1 in winter). The average rate of total nitrogen uptake (dissolved + particulate) was also not significantly different between summer and winter (8.3 ± 3.8 versus 6.6 ± 3.4 mmol N m−2 d−1, respectively), despite evidence of sporadically high nitrate uptake in both seasons. In summer, rates of hourly net calcification (gnet) were linearly correlated with diurnal changes in net production, pH, and aragonite saturation state (Ωar); and were mostly correlated with light except at mid-day under heavy cloud cover. However, in winter,gnet was independent of diurnal changes in light, net production, pH, and Ωar indicating that the reef flat community had possibly reached a threshold above which rates of net calcification were insensitive to diurnal changes in their environment.

Detection of estradiol-17β during a mass coral spawn

The steroid estradiol-17β (E2) is associated with female gametogenesis in all vertebrates and many invertebrates. This is the first report of estrogens in scleractinian corals. Seawater and egg slicks were collected during a mass coral spawn at Ningaloo reef, Western Australia for the measurement of total phosphate (TP) and E2. Total P in the water column increased 600 times, from 0.5μM to 300μM. Concentrations of E2 increased nearly 8 fold during the spawn, from 55 to 420 pg/100 ml seawater. Coral eggs collected from egg slicks contained 368±40 pg E2/g dry wt of eggs. Estrogen may be a key hormone in a simple endocrine system of scleractinian corals that synchronizes growth and development of coral oocytes. Its potential role in triggering spawning via chemical messengers in the water column warrants further research.

Decorrelating remote sensing color bands from bathymetry in optically shallow waters

We have developed a simple technique to decorrelate remote sensing color band data from depth in optically shallow water. The method linearizes color band data with respect to depth by subtracting an optically deepwater value from the entire waveband under consideration and taking the natural logarithm of the result. Next, this linearized waveband is rotated about the model 2 regression line computed against a bathymetry band. The rotated color band is decorrelated from water depth. We demonstrate the technique for a small area of Kailua Bay, Oahu, HI, using Quickbird multispectral and Scanning Hydrographic Operational Airborne Lidar Survey LIDAR data. Results indicate that color band data are effectively decorrelated from depth, while bottom reflector variability is maintained, thus providing the basis for further analysis of the depth-invariant wavebands. The primary benefit of our technique is that wavebands are rotated independently, preserving relative spectral information.

Bio-optical modeling of photosynthetic pigments in corals

The spectral reflectance of coral is inherently related to the amounts of photosynthetic pigments present in the zooxanthellae. There are no studies, however, showing that the suite of major photosynthetic pigments can be predicted from optical reflectance spectra. In this study, we measured cm-scale in vivo and in situ spectral reflectance for several colonies of the massive corals Porites lobata and Porites lutea, two colonies of the branching coral Porites compressa, and one colony of the encrusting coral Montipora flabellata in Kaneohe Bay, Oahu, Hawaii. For each reflectance spectrum, we collected a tissue sample and utilized high-performance liquid chromatography to quantify six major photosynthetic pigments, located in the zooxanthellae. We used multivariate multiple regression analysis with cross-validation to build and test an empirical linear model for predicting pigment concentrations from optical reflectance spectra. The model accurately predicted concentrations of chlorophyll a, chlorophyll c2, peridinin, diadinoxanthin, diatoxanthin and β-carotene, with correlation coefficients of 0.997, 0.941, 0.995, 0.996, 0.980 and 0.984, respectively. The relationship between predicted and actual concentrations was 1:1 for each pigment, except chlorophyll c2. This simple empirical model demonstrates the potential for routine, rapid, non-invasive monitoring of coral-zooxanthellae status, and ultimately for remote sensing of reef biogeochemical processes.

Multi-scale remote sensing of microbial mats in an atoll environment

Microbial mats are encountered in many coastal environments. They are generally constituted by stratified layers produced by the development of various micro-organisms. A current research programme aims to assess the biotechnological potential of the microbial communities in South Pacific atolls. As part of this project, the characterisation of mats was examined in Rangiroa atoll (French Polynesia) using high resolution (20-30 m) multi-spectral images (SPOT HRV and Landsat ETM+), hyperspectral imagery (CASI (Compact Airborne Spectrographic Imager), 27 bands, 5.5 2 1 m) and in situ reflectance spectra. At atoll scale, mats are successfully inventoried among different geomorphological environments by fuzzy classification/segmentation of the 20-30 m resolution multi-spectral data. Laboratory biochemical analysis (not described here) highlighted and identified the most promising mats for their biotechnological potential. The spectral signatures of these remarkable mats are described at two scales. Major reflectance features of the microbial community were identified by peaks in fourth-derivatives analysis, discriminating the surface layers dominated by the cyanobacteria Schizothrix sp. (orange mats), Scytonema sp. (grey-black mats) and Phormidium sp. (green mats). At mat scale, CASI-derived spectral signatures from heterogeneous 5.5m 2 pixels including various microbial communities, vegetation, sand and water did not provide fine optical distinctions between mats because of mixing effects. This multi-scale analysis provides optical and geomorphological criteria to locate interesting stratified mats in other atolls.

Alkalinity to calcium flux ratios for corals and coral reef communities: variances between isolated and community conditions

Calcification in reef corals and coral reefs is widely measured using the alkalinity depletion method which is based on the fact that two protons are produced for every mole of CaCO3 precipitated. This assumption was tested by measuring the total alkalinity (TA) flux and Ca2+ flux of isolated components (corals, alga, sediment and plankton) in reference to that of a mixed-community. Experiments were conducted in a flume under natural conditions of sunlight, nutrients, plankton and organic matter. A realistic hydrodynamic regime was provided. Groups of corals were run separately and in conjunction with the other reef components in a mixed-community. The TA flux to Ca2+ flux ratio (ΔTA: ΔCa2+) was consistently higher in the coral-only run (2.06 ± 0.19) than in the mixed-community run (1.60 ± 0.14, p-value = 0.011). The pH was higher and more stable in the mixed-community run (7.94 ± 0.03 vs. 7.52 ± 0.07, p-value = 3 × 10−5). Aragonite saturation state (Ωarag) was also higher in the mixed-community run (2.51 ± 0.2 vs. 1.12 ± 0.14, p-value = 2 × 10−6). The sediment-only run revealed that sediment is the source of TA that can account for the lower ΔTA: ΔCa2+ ratio in the mixed-community run. The macroalgae-only run showed that algae were responsible for the increased pH in the mixed-community run. Corals growing in a mixed-community will experience an environment that is more favorable to calcification (higher daytime pH due to algae photosynthesis, additional TA and inorganic carbon from sediments, higher Ωarag). A paradox is that the alkalinity depletion method will yield a lower net calcification for a mixed-community versus a coral-only community due to TA recycling, even though the corals may be calcifying at a higher rate due to a more optimal environment.