The capability for mapping two species of seagrass, Thalassia testudinium and Syringodium filiforme, by remote sensing using a physics based model inversion method was investigated. The model was based on a three-dimensional canopy model combined with a model for the overlying water column. The model included uncertainty propagation based on variation in leaf reflectances, canopy structure, water column properties, and the air-water interface. The uncertainty propagation enabled both a-priori predictive sensitivity analysis of potential capability and the generation of per-pixel error bars when applied to imagery. A primary aim of the work was to compare the sensitivity analysis to results achieved in a practical application using airborne hyperspectral data, to gain insight on the validity of sensitivity analyses in general. Results showed that while the sensitivity analysis predicted a weak but positive discrimination capability for species, in a practical application the relevant spectral differences were extremely small compared to discrepancies in the radiometric alignment of the model with the imagery-even though this alignment was very good. Complex interactions between spectral matching and uncertainty propagation also introduced biases. Ability to discriminate LAI was good, and comparable to previously published methods using different approaches. The main limitation in this respect was spatial alignment with the imagery with in situ data, which was heterogeneous on scales of a few meters. The results provide insight on the limitations of physics based inversion methods and seagrass mapping in general. Complex models can degrade unpredictably when radiometric alignment of the model and imagery is not perfect and incorporating uncertainties can have non-intuitive impacts on method performance. Sensitivity analyses are upper bounds to practical Hedley et al.Remote Sensing of Seagrasses capability, incorporating a term for potential systematic errors in radiometric alignment may be advisable. While T. testudinium and S. filiforme were too spectrally similar to be discriminated purely on spectral grounds, mapping of these, and other species may be achievable by exploiting co-incident factors based on ecological zonation.

The analysis of the variation of the capacity and efficiency of photosynthetic tissues to collect solar energy is fundamental to understand the differences among species in their ability to transform this energy into organic molecules. This analysis may also help to understand natural changes in species distribution and/or abundance, and differences in species ability to colonize contrasting light environments or respond to environmental changes. Unfortunately, the challenge that optical determinations on highly dispersive samples represent has strongly limited the progression of this analysis on multicellular tissues, limiting our knowledge of the role that optical properties of photosynthetic tissues may play in the optimization of photosynthesis and growth of benthonic primary producers. The aim of this study is to stimulate the use of optical tools in marine eco-physiology, offering a succinct description of the more convenient tools and also solutions to resolve the more common technical difficulties that arise while performing optical determinations on highly dispersive samples. Our study focuses on two-dimensional (2D-) parameters: absorptance, transmittance, and reflectance, and illustrates with correct and incorrect examples, specific problems and their respective solutions. We also offer a general view of the broad variation in light absorption shown by photosynthetic structures of marine primary producers, and its low association with pigment content. The ecological and evolutionary functional implications of this variability deserve to be investigated across different taxa, populations, and marine environments.

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The distinction between shallow coral reefs and mesophotic coral ecosystems (MCEs) has not been fully clarified yet. The original definition of MCEs, by depths of 30–150 m, fixes their bathymetrical limits and fails to accommodate environmental and biological variation. Recent studies have indicated that water transparency and light availability may explain why MCEs do not occur at fixed depths but vary among localities. This study aimed to evaluate the presence and distribution of MCEs, along the central coast of Oaxaca, through optical depths and the associated benthic community. Using MODIS-Aqua satellite data (Kd490), we estimated the mesophotic optical depths monthly (z10%, z1%, z0.1%), over the last four years. In addition, to characterize benthic community structure, we conducted underwater photo quadrat surveys at two locations on the southern Mexican Pacific coast from 10 to 55 m depth. Significant differences between depths and locations were found in benthic communities. Furthermore, the lower distribution of photosynthetic taxa was different between the two locations but indicative to the z10% and z1% in both cases. Those differences were associated with the upwelling season, which reduces, drastically and differentially, the light availability for benthic communities between the two locations and limits the development of MCEs on the central coast of Oaxaca.