A novel bio-optical model that allows incorporation of traditional plankton and remote sensing methods and observations and improves the assessment of biogeochemical processes

The CSIRO 3D-hydrodynamic- biogeochemical-sediment-wave model contributes to understanding of the coastal oceans and estuaries around Australia and Chile. The bio-optical model calculates phytoplankton absorption of individual cells with multiple pigment types and allows us to compare directly with HPLC pigments and remote sensing data to improve provide a more robust skill assessment. To calculate absorption due to each pigment we use a database of mass-specific wavelength-dependent absorption coefficients. HPLC pigment analysis is commonly used to quantitatively characterize major phytoplankton taxa. We compare microscopic observations and HPLC pigments with model phytoplankton groups and pigment concentrations in order to better assess representation of phytoplankton classes within the Great Barrier Reef, Chilean and Tasmanian models. We can also modify the spectral characteristics of the sediment and plankton traits within our optical model to suit water bodies with different spectral characteristics. We show several examples that take advantage of the novel bio-optical model to compare model output with chlorophyll extraction, HPLC, flow cytometry, microscopy, molecular analysis and remote sensing. Figure below shows transect of simulated Chl a from the eReefs model and extends from coast to off shelf in the Fitzroy Region of the Great Barrier Reef (Australia).