Stewart Bernard

Characterizing the Absorption Properties for Remote Sensing of Three Small Optically-Diverse South African Reservoirs

Characterizing the specific inherent optical properties (SIOPs) of water constituents is fundamental to remote sensing applications. Therefore, this paper presents the absorption properties of phytoplankton, gelbstoff and tripton for three small, optically-diverse South African inland waters. The three reservoirs, Hartbeespoort, Loskop and Theewaterskloof, are challenging for remote sensing, due to differences in phytoplankton assemblage and the considerable range of constituent concentrations. Relationships between the absorption properties and biogeophysical parameters, chlorophyll-a (chl-a), TChl (chl-a plus phaeopigments), seston, minerals and tripton, are established. The value determined for the mass-specific tripton absorption coefficient at 442 nm, a∗ (442), ranges from 0.024 to 0.263 m2·g−1. The value of the TChl-specific phytoplankton absorption coefficient (a∗ ) was strongly influenced by phytoplankton species, size, accessory pigmentation and biomass. a∗ (440) ranged from 0.056 to 0.018 m2·mg−1 in oligotrophic to hypertrophic waters. The positive relationship between cell size and trophic state observed in open ocean waters was violated by significant small cyanobacterial populations. The phycocyanin-specific phytoplankton absorption at 620 nm, a∗ (620), was determined as 0.007 m2·g−1 in a M. aeruginosa bloom. Chl-a was a better indicator of phytoplankton biomass than phycocyanin (PC) in surface scums, due to reduced accessory pigment production. Absorption budgets demonstrate that monospecific blooms of M. aeruginosa and C. hirundinella may be treated as “cultures”, removing some complexities for remote sensing applications. These results contribute toward a better understanding of IOPs and remote sensing applications in hypertrophic inland waters. However, the majority of the water is optically complex, requiring the usage of all the SIOPs derived here for remote sensing applications. The SIOPs may be used for developing remote sensing algorithms for the detection of biogeophysical parameters, including chl-a, suspended matter, tripton and gelbstoff, and in advanced remote sensing studies for phytoplankton type detection.

Dynamics of oxygen depletion in the nearshore of a coastal embayment of the southern Benguela upwelling system

Acquisition of high resolution time series of water column and bottom dissolved oxygen (DO) concentrations inform the dynamics of oxygen depletion in St Helena Bay in the southern Benguela upwelling system at several scales of variability. The bay is characterized by seasonally recurrent hypoxia (<1.42 ml l−1) associated with a deep pool of oxygen-depleted water and episodic anoxia (<0.02 ml l−1) driven by the nearshore (<20 m isobath) decay of red tide. Coastal wind forcing influences DO concentrations in the nearshore through its influence on bay productivity and the development of red tides; through shoreward advection of the bottom pool of oxygen-depleted water as determined by the upwelling-downwelling cycle; and through its control of water column stratification and mixing. A seasonal decline in bottom DO concentrations of ∼1.2 ml l−1 occurs with a concurrent expansion of the bottom pool of oxygen depleted water in St Helena Bay. Upwelling of this water into the nearshore causes severe drops in DO concentration (<0.2 ml l−1), particularly during end-of-season upwelling, resulting in a significant narrowing of the habitable zone. Episodic anoxia through the entire water column is caused by localized degradation of red tides within the confines of the shallow nearshore environment. Oxygenation of the nearshore is achieved by ventilation of the water column particularly with the onset of winter mixing. No notable changes are evident in comparing recent measures of bottom DO concentrations in St Helena Bay to data collected in the late 1950s and early 1960s.

The use of equivalent size distributions of natural phytoplankton assemblages for optical modeling

The effective cell size is expected to be one of the principal causes of variability in the inherent optical properties (IOPs) of a phytoplankton population. However, establishing simple size descriptors is complicated by the typically complex particle size distributions of natural phytoplankton assemblages. This study compares the use of measured and equivalent particle size distributions on the modeled IOPs of a wide range of natural phytoplankton assemblages. It demonstrates that several equivalent size distributions, using simple parameterizations of complex size distributions based on the effective radius or diameter, are capable of modeling phytoplankton IOPs with sufficient accuracy for further use in marine bio-optical models. The results offered here are expected to be of use in bio-optical studies of phytoplankton dynamics e.g. harmful algal bloom oriented inverse reflectance models.

Sensitivity in reflectance attributed to phytoplankton cell size: forward and inverse modelling approaches

Synoptic scale knowledge of the size structure of phytoplankton communities can offer insight in to primary ecosystem diversity and biogeochemical variability from operational to the decadal scales. Accordingly, obtaining estimates of size and other phytoplankton functional type descriptors within known confidence limits from remotely sensed data has become a major objective to extend the use of ocean colour data beyond chlorophyll a retrievals. Here, a new forward and inverse modelling structure is proposed to determine information about the cell size of phytoplankton communities using Standard size distributions of two layered spheres to derive a full suite of algal inherent optical properties for a coupled radiative transfer model. This new capability allows explicit quantification of the remote sensing reflectance signal attributable to changes in phytoplankton cell size. Inversion of this model reveals regions within the parameter space where ambiguity may limit potential of inversion algorithms. Validation of the algorithm within the Benguela upwelling system using independent data shows promise for ecosystem applications and further investigation of the interaction between phytoplankton functional types and optical signals. The results here suggest that the utility of assemblage related signals in spectral reflectance is highly sensitive to algal biomass, the presence of other absorbing and scattering constituents and the resultant constituent-specific inherent optical property budget. As such, optimal methods for determining phytoplankton size from (in situ or satellite) ocean colour data will likely rely on appropriately spectrally dense and optimised sensors, well characterised measurement errors including those from atmospheric correction, and an ability to appropriately limit ambiguity within the context of regional inherent optical properties.

Real-time monitoring of harmful algal blooms in the southern Benguela

The southern Benguela Current region off South Africa is subject to frequent harmful algal blooms (HABs), which can have serious impacts — both through the introduction of toxins into the ecosystem and the collapse of high-biomass blooms leading to anoxia. As part of the Benguela Current Large Marine Ecosystem Programme, a bio-optical buoy has been developed for monitoring HABs in the region, providing both real-time and time-series data. Considerations in developing the buoy were that it should be small, cost effective and robust, allowing for field calibration of the sensors and servicing from a small boat. The instrument package on the buoy consists of two hyperspectral radiometers (providing remote sensing reflectance), a thermistor chain, a fluorometer and an Acoustic Doppler Current Profiler. A half-hourly acquisition regime collects data from the instruments, which are transmitted in real time using cellular phone telemetry. A website is updated with these data, when available, along with satellite data and shellfish warnings, to provide near real-time information on conditions in the area. Demonstration data from the buoy, related to observed blooms of dinoflagellates and the ciliate Mesodinium rubrum, are presented.

Ocean Colour Remote Sensing of Harmful Algal Blooms in the Benguela System

The Benguela, as a highly productive upwelling system, suffers from the occurrence of a variety of harmful algal blooms, most of which are associated with elevated biomass; a feature common to the shelf environment of upwelling systems. Most harmful blooms have in the past been attributed to one or another dinoflagellate species, but more recently harmful impacts have also been ascribed to other groups of phytoplankton, including diatom and autotrophic ciliate species. Typical bloom assemblages, forcing mechanisms and harmful impacts are outlined, and bloom types most amenable to detection with ocean colour radiometry are identified. Inherent and apparent optical properties of these algal assemblage types are described, and a preliminary evaluation is made of the suitability of available ocean colour data and algorithms. The evolution of several bloom events is described using various algorithms applied to ocean colour data from the Medium Resolution Imaging Spectrometer (MERIS), and recommendations are made about optimal ocean colour usage for high biomass algal blooms in coastal zones.

Understanding the contribution of phytoplankton phase functions to uncertainties in the water colour signal

The accurate description of a water bodys volume scattering function (VSF), and hence its phase functions, is critical to the determination of the constituent inherent optical properties (IOPs), the associated spectral water-leaving reflectance, and consequently the retrieval of phytoplankton functional type (PFT) information. The equivalent algal populations (EAP) model has previously been evaluated for phytoplankton-dominated waters, and offers the ability to provide phytoplankton population-specific phase functions, unveiling a new opportunity to further understanding of the causality of the PFT signal. This study presents and evaluates the wavelength dependent, spectrally variable EAP particle phase functions and the subsequent effects on water-leaving reflectance. Comparisons are made with frequently used phase function approximations e.g. the Fournier Forand formulation, as well as with phase functions inferred from measured VSFs in coastal waters. Relative differences in shape and magnitude are quantified. Reflectance modelled with the EAP phase functions is then compared against measured reflectance data from phytoplankton-dominated waters. Further examples of modelled phytoplankton-dominated waters are discussed with reference to choice of phase function for two PFTs (eukaryote and prokaryote) across a range of biomass. Finally a demonstration of the sensitivity of reflectance due to the choice of phase function is presented. The EAP model phase functions account for both spectral and angular variability in phytoplankton backscattering i.e. they display variability which is both spectral and shape-related. It is concluded that phase functions modelled in this way are necessary for investigating the effects of assemblage variability on the ocean colour signal, and should be considered for model closure even in relatively low scattering conditions where phytoplankton dominate the IOPs.

Bilko and African capacity development in coastal and marine remote sensing

In much of Africa barriers still exist to the effective use of Earth observation in marine and coastal research and management. To remedy this, the development of data access and processing capacity must go hand in hand with hands-on training in the use of satellite data. The Bilko project has been providing training resources suitable for this for 25 years. In recent years marine scientists from Africa and Europe have been using Bilko to develop lessons based on African examples taken from image data disseminated via GEONETCast in two EC funded projects. The work is part of current efforts to develop MSc level and professional training courses for use in Africa, and shows how the contribution of African experts in the development of new lessons contributes to making these more relevant.

Calibration of an in-water multi-excitation fluorometer for the measurement of phytoplankton chlorophyll-a fluorescence quantum yield

A multi-excitation fluorometer (MFL, JFE Advantech Co., Ltd.), originally designed to discriminate between phytoplankton species present within a population, has been redirected for use in fluorescence quantum yield (FQY) determination. While this calibration for apparent FQY requires no modification of the MFL, it is necessary to have an independent measurement of the spectral absorption coefficient of the subject fluid. Two different approaches to calibration were implemented. The primary method made use of reference fluorescent dye solutions of known quantum yield. The second method made use of acrylic fluorescent plaques and films. The two methods yielded consistent results, except in the 570 and 590 nm LED channels of the MFL. Application of the MFL in FQY determination is illustrated with an in situ Southern Ocean sample.

In situ Measurements and Model Estimates of NO3 and NH4 Uptake by Different Phytoplankton Size Fractions in the Southern Benguela Upwelling System

Bulk measurements can be made of phytoplankton standing stocks on a quasi-synoptic scale but it is more difficult to measure rates of production and nutrient uptake. We present a method to estimate nitrogen uptake rates in productive coastal environments. We use observed phytoplankton cell size distributions and ambient nitrogen concentrations to calculate uptake rates of nitrate, ammonium and total nitrogen by different size fractions of diverse phytoplankton communities in a coastal upwelling system. The data are disaggregated into size categories, uptake rates are calculated and these uptake rates are reaggregated to obtain bulk estimates. The calculations are applied to 72 natural assemblages for which nitrogen uptake rates and particle size distributions were measured \textit{in situ}. The calculated values of total N uptake integrated across all size classes are similar to those of \textit{in situ} bulk measurements (N slope=0.90), (NH