Optical closure in highly absorptive coastal waters: significance of inelastic scattering processes.

In hydrological optics, "optical closure" means consistency between the apparent optical properties (AOPs) determined from radiometric measurements and those derived from radiative transfer modelling based on concurrently measured inherent optical properties (IOPs) and boundary conditions (sea and sky states). Good optical closure not only provides confidence in the data quality but also informs on the adequacy of the radiative transfer parameterization. Achieving optical closure in highly absorptive coastal waters is challenging due to the low signal-to-noise ratio of radiometric measurements and uncertainties in the measurements of IOPs, namely the spectral absorption and backscattering coefficients. Here, we present an optical closure assessment using a comprehensive set of in situ IOPs acquired in highly absorptive coastal waters optically dominated by chromophoric dissolved organic matter (CDOM). The spectral remote sensing reflectance, Rrs(λ), was modeled using the software HydroLight (HL) with measured IOPs and observed boundary conditions. Corresponding in-water in situ Rrs(λ) was derived from radiometric measurements made with a Compact Optical Profiling System (C-OPS; Biospherical). The assessment revealed that the inclusion of inelastic scattering processes in the model, specifically sun-induced CDOM fluorescence (fDOM) and sun-induced chlorophyll fluorescence (SICF) from Chlorophyll-a ([chl]), significantly improved the optical closure and led to good agreement between measured and modeled Rrs (i.e., for 440 ≤ λ ≤ 710 nm with no inelastic processes: R2=0.90, slope=0.64; with inelastic processes: R2=0.96, slope=0.90). The analysis also indicated that fDOM and SICF contributed a substantial fraction of the green-red wavelength Rrs in these waters. Specifically, fDOM contributed ∼18% of the modeled Rrs in the green region and SICF accounted for ∼20% of the modeled Rrs in the red region. Overall, this study points out the importance of accounting for fDOM in remote sensing applications in CDOM-dominated waters.

Optical backscattering and linear polarization properties of the colony forming cyanobacterium Microcystis.

Light scattering characteristics of the cyanobacterium Microcystis are investigated with numerical models for sphere aggregates. During summer bloom seasons, Microcystis is prevalent in many inland waters across the globe. Monitoring concentrations with remote sensing techniques requires knowledge of the inherent optical properties (IOPs), especially the backscattering properties of Microcystis cells and colonies in natural settings. In situ measurements in waters dominated by Microcystis blooms have previously detected extremely high backscattering ratios, i.e., bb/b>0.043 at 443 nm [1], the highest to our knowledge in the natural environment. These highbb/bvalues could hold promise as a diagnostic tool in identifying and monitoring Microcystis using optical approaches. However, it has been unclear how this type of optically 'soft' organic particle can generate such highbb/bvalues. In this study, the Multiple Sphere T-matrix (MSTM) model is used to calculate the IOPs of model colonies, including bb/b. Colony sizes in the model ranged from several cells to several hundred and both colony packing density and cell gas vacuole content were varied. Results are compared with model results for equivalent-volume spheres (EVS) and direct in situ measurements. Colony formation was required in the modeling to reproduce the high bb/bconsistent with in situ measurements. The combination of moderate to very dense colony (packing density >30%) and high gas vacuole content in individual cells (volume percentage >20%) was the most favorable condition leading to rapid increases in bb/bwith increasing number of cells Ncell of the colony. Significant linear correlations were observed betweenbb/b and Ncell1/3 for these colonies, wherebb/b increased beyond 0.04 once cell number reached about 1000 cells in the case with the most densely packed cells and highest gas vacuole content. Within commonly observed colony sizes (Ncell <106), colonies with high gas vacuole content exhibited bb/bvalues up to 0.055, consistent with direct measurements from Lake Erie. Polarized scattering was also of interest as a diagnostic tool, particularly with future Earth-orbiting polarimeters being deployed for the NASA Plankton, Aerosols, Cloud, ocean Ecosystem (PACE) mission. The Degree of Linear Polarization (DoLP), expressed by the ratio of two Mueller matrix elements-P12/P11, decreased with increasing colony cell number for Microcystis. Another ratio of two Mueller matrix elementsP22/P11, an index for nonsphericity, also decreased with increasing colony size. In addition to higher relative backscattering, greater colony packing density and larger gas vacuole sizes both led to lower DoLP peak magnitude and lowerP22/P11. An optical opposition feature due to constructive phase interference that was observed previously for cosmic dusts is also present for these modeled colonies, manifested by a narrow intensity peak and negative polarization dip near exact backscattering direction, gradually forming as colony size increases.

Structural complexity governs seagrass acclimatization to depth with relevant consequences for meadow production, macrophyte diversity and habitat carbon storage capacity.

Analyses of the integrated seagrass response to depth support the previously documented low plasticity and consistent shade-adapted leaf physiology of a habitat-builder that dominates well-illuminated reef environments. Two structural responses, "canopy-opening" and "below-ground-mass-depletion", govern the photoacclimatory response and facilitate, respectively, light penetration within the canopy and functional adjustments in whole-plant carbon balances. Conversely, "canopy-closing" may also explain dense canopies formed close to the waterline, as they provide shade and photoprotection to a susceptible leaf physiology under high-light. Canopy light attenuation is primarily regulated by the leaf area index (LAI), which is governed by changes in shoot size and density. Shoot density diminishes non-linearly with depth, while shoot size increases to a maximum followed by a decline. The initial increase in shoot size, which resembles a self-thinning response, increases LAI and meadow production in shallow depths. These seagrass structural adjustments have relevant ecological implications. Canopy-thinning allows macrophyte diversity to increase with depth, while seagrass production and carbon storage diminish exponentially, and are maximal only in a shallow coastal fringe. The results support the universality of plant self-thinning, from phytoplankton to complex canopies, likely the consequence of simple physical laws related to light limitation and pigment self-shading within photosynthetic structures and communities.

Seagrass canopy photosynthetic response is a function of canopy density and light environment: a model for Amphibolis griffithii.

A three-dimensional computer model of canopies of the seagrass Amphibolis griffithii was used to investigate the consequences of variations in canopy structure and benthic light environment on leaf-level photosynthetic saturation state. The model was constructed using empirical data of plant morphometrics from a previously conducted shading experiment and validated well to in-situ data on light attenuation in canopies of different densities. Using published values of the leaf-level saturating irradiance for photosynthesis, results show that the interaction of canopy density and canopy-scale photosynthetic response is complex and non-linear, due to the combination of self-shading and the non-linearity of photosynthesis versus irradiance (P-I) curves near saturating irradiance. Therefore studies of light limitation in seagrasses should consider variation in canopy structure and density. Based on empirical work, we propose a number of possible measures for canopy scale photosynthetic response that can be plotted to yield isoclines in the space of canopy density and light environment. These plots can be used to interpret the significance of canopy changes induced as a response to decreases in the benthic light environment: in some cases canopy thinning can lead to an equivalent leaf level light environment, in others physiological changes may also be required but these alone may be inadequate for canopy survival. By providing insight to these processes the methods developed here could be a valuable management tool for seagrass conservation during dredging or other coastal developments.

Modeling the mean Mueller matrix of randomly orientated nonspherical particles.

A fast graphics processing unit implementation of the finite-difference time-domain model was used to determine the computational effort required to accurately characterize the mean scattering functions of randomly orientated aspherical particles. The influence of the number of randomized rotational positions on the accuracy of the mean scattering phase function curve was appraised. In general, multiplying the number of orientations by 100 gives increased accuracy of factor 10. Dependent on particle shape, certain regions of the phase function were insensitive to particle orientation. In addition, an error in a key previous publication on scattering by aspherical particles was identified.

Modeling the beta diversity of coral reefs.

Quantifying the beta diversity (species replacement along spatiotemporal gradients) of ecosystems is important for understanding and conserving patterns of biodiversity. However, virtually all studies of beta diversity focus on one-dimensional transects orientated along a specific environmental gradient that is defined a priori. By ignoring a second spatial dimension and the associated changes in species composition and environmental gradients, this approach may provide limited insight into the full pattern of beta diversity. Here, we use remotely sensed imagery to quantify beta diversity continuously, in two dimensions, and at multiple scales across an entire tropical marine seascape. We then show that beta diversity can be modeled (0.852 > or = r2 > or = 0.590) at spatial scales between 0.5 and 5.0 km2, using the environmental variables of mean and variance of depth and wave exposure. Beta diversity, quantified within a "window" of a given size, is positively correlated to the range of environmental conditions within that window. For example, beta diversity increases with increasing variance of depth. By analyzing such relationships across seascapes, this study provides a framework for a range of disparate coral reef literature including studies of zonation, diversity, and disturbance. Using supporting evidence from soft-bottom communities, we hypothesize that depth will be an important variable for modeling beta diversity in a range of marine systems. We discuss the implications of our results for the design of marine reserves.

Biological and remote sensing perspectives of pigmentation in coral reef organisms.

Coral reef communities face unprecedented pressures on local, regional and global scales as a consequence of climate change and anthropogenic disturbance. Optical remote sensing, from satellites or aircraft, is possibly the only means of measuring the effects of such stresses at appropriately large spatial scales (many thousands of square kilometres). To map key variables such as coral community structure, percentages of living coral or percentages of dead coral, a remote sensing instrument must be able to distinguish the reflectance spectra (i.e. "spectral signature", reflected light as a function of wavelength) of each category. For biotic classes, reflectance is a complex function of pigmentation, structure and morphology. Studies of coral "colour" fall into two disparate but potentially complementary types. Firstly, biological studies tend to investigate the structure and significance of pigmentation in reef organisms. These studies often lack details that would be useful from a remote sensing perspective such as intraspecific variation in pigment concentration or the contribution of fluorescence to reflectance. Secondly, remote sensing studies take empirical measurements of spectra and seek wavelengths that discriminate benthic categories. Benthic categories used in remote sensing sometimes consist of species groupings that are biologically or spectrally inappropriate (e.g. merging of algal phyla with distinct pigments). Here, we attempt to bridge the gap between biological and remote sensing perspectives of pigmentation in reef taxa. The aim is to assess the extent to which spectral discrimination can be given a biological foundation, to reduce the ad hoc nature of discriminatory criteria, and to understand the fundamental (biological) limitations in the spectral separability of biotic classes. Sources of pigmentation in reef biota are reviewed together with remote sensing studies where spectral discrimination has been effectively demonstrated between benthic categories. The basis of reflectance is considered as the sum of pigmented components, such as zooxanthellae, host tissues and skeletons of corals. Problems in the empirical in situ measurement of reflectance are identified, such as the differing types of reflectance which can be measured, the interaction of the light field with morphology, and depth-dependent variability of measured reflectance due to fluorescence. The latter is estimated in some cases to introduce an error of up to 20% when depth differs by 8 m. Spectral features useful in discriminating reef benthos are identified and related to pigmentation. The slope in the reflectance spectra between 650 and 690 nm is dependent on chlorophyll-a concentration and can be used to discriminate bare sand with no algal component from chlorophyll-a containing benthos (algae, corals). The slope in reflectance at various locations between 500 and 560 nm can be useful in discriminating bleached and unbleached corals, possibly due to reduced peridinin concentration. Rhodophyta may be discernible by the presence of a dip in reflectance at 570 nm, due to a phycoerythrin absorption peak. However, the utility of some discriminatory criteria in deeper waters is mitigated by the relatively poor transmission of light through water at longer wavelengths (especially > 600 nm). Contrary to suggested categorizations of fluorescent pigments in coral host tissues, it is shown that these pigments form an almost continuous distribution with respect to their excitation and emission peaks. Remote sensing by induced fluorescence is a promising approach, but further details about the variation and distribution of these pigments are required. It is hoped that this review will promote cross-disciplinary collaboration between pigment biologists and the reef remote sensing community. Where possible, the discriminative criteria adopted in remote sensing should be related to biological phenomena, thus lending an intuitive, process-orientated basis for interpreting spectral data. Similarly, remote sensing may provide a novel scaling perspective to biological studies of pigmentation in reef organisms.