## 2 Methods: Modelling Approach
### The Requirement for a Biophysically Consistent PFT Optical Model
Empirically based phytoplankton abundance-type approaches, following observed relationships between phytoplankton assemblage taxonomic information (e.g., pigments) and biomass, show good results in low biomass conditions (i.e., where phytoplankton absorption dominates the phytoplankton IOP contribution), and where the covariability of the phytoplankton optical contribution with that of other in-water constituents generally holds [56], but do not address the sources of second order variability or optical causality [13], or the likelihood that these empirical relationships will not withstand the ecological shifts resulting from changing climatic conditions [6]. A biophysical approach to PFTs not only allows improved analysis of sensitivity and causality but is likely to have greater validity in a future ocean (see also [57]). The optical impact of a phytoplankton assemblage interacting with its aquatic environment is by no means straightforward, and a rigorous IOP model such as the EAP can systematically vary phytoplankton biogeophysical attributes in the context of likely additional non-algal absorption and scatter, and can examine the resulting effects on the light field when used in combination with a Radiative Transfer (RT) model. The value of this reductionist approach has been demonstrated [58; 59] (and furthermore by [PERSON] et al. [32]) for separating and understanding the effects of various phytoplankton groups and accompanying in-water constituents on the oceanic light field and emergent \(R_{rs}\). There is a bulk effect attributable simply to biomass, for which Chlorophyll \(a\) (Chl \(a\)) is used as a proxy, and which for the most part dominates the phytoplankton-related signal in Case 1 waters [60](It is acknowledged that Chl \(a\) concentration and biomass are not equivalent, as biomass includes non-pigmented biological matter in quantities which may not be proportional to pigmented matter. However, for the purposes of this study, biomass and Chl \(a\) concentration are used interchangeably, as this work is approached from a purely optical perspective and ignores non-pigmented biological matter.). PFT characteristics generally result in optical effects secondary to those of Chl _a_: accessory pigments dominate assemblage absorption characteristics [61], and particle size is usually the primary determinant of phytoplankton scattering characteristics [62] (excepting the influence of ultrastructure in certain species, e.g., highly scattering liths or vacuoles). Natural waters are also subject to non-algal absorption, the dissolved part of which is frequently referred to as Coloured Dissolved Organic Matter (CDOM) or gelbstoff, but which may also have a particulate component in addition to non-algal scatter that can include scatter by detrital matter, sediment, bacteria, and/or bubbles. These quantities absorb and scatter light with spectral signatures distinct from those of phytoplankton, and their subsequent optical interactions and resulting effect on the total water-leaving signal are highly complex. Understanding the interaction between cells' biophysical characteristics and the light field in the presence of these additional optically active constituents is central to determining which parts of the optical signal are useable for PFT diagnostics, and, likewise, where signal ambiguity is prohibitive.