Towards the validation of SeaWiFS in Southern African Waters: The effects of Gelbstoff

The effective application of future ocean colour data for southern African waters requires an in-depth assessment of bio-optical algorithm performance, given the productive and highly variable nature of the oceanographic region. Phytoplankton degradation products, commonly known as gelbstoff, represent a large potential error source to future remotely sensed chlorophyll data, particularly in highly productive regions, where there can be a dramatic lack of covariance between phytoplankton and gelbstoff concentrations. Data relevant to gelbstoff character in the Agulhas Bank and southern Benguela systems are examined to assess the variability of gelbstoff chromophoric structure in these regions. These take the form of gelbstoff absorption spectra, and fluorescence excitation-emission matrices, performed on filtered seawater samples. Modelled bio-optical data, using conditions typical of high biomass marine environments, are then used to assess the performance of a proposed SeaWiFS combined algorithm with respect to variations in the magnitude and nature of gelbstoff absorption. It is shown that expected algorithm performance can be poor in bloom type scenarios, and that an appreciation of algorithm application is needed for effective interpretation of ocean colour imagery

Anchovy biomass is linked to annual potential new production in the southern Benguela: support for the “Optimal environmental window” hypothesis

The hypothesis that physical forcing is related to tertiary production was tested by relating regional estimates of annual potential new production to certain pelagic fishery variables. The results show strong evidence of adome-shaped relationship between annual potential new production (x-axis) and anchovy spawner biomass (y-axis), providing further confirmation that both a paucity and surfeit of upwelling is detrimental to the fishery.Fish biomass was maximized by a median range of upwelling, which formed an “Optimal Environmental Window” either side of the dome apex. The relationship was described by a Gaussian Area curve

Carbon pathways and export associated with the Southern Benguela upwelling system: A re-appraisal

A network of six NO3-N-driven carbon pathways between the ocean, shelf and sediments was described in a paper published in 1992. A budgetary approach at the annual scale meant that, if three of the pathwayswere quantified, solutions could be found algebraically for those remaining. The network of pathways in the present study remains unchanged in principle, but in respect of long-term carbon sequestration, there hasbeen a shift in emphasis from ocean to continental shelf. This results from an adjusted estimate for carbon exported seawards of the continental shelf, mainly owing to a re-examination of the typical offshore penetrationof upwelling-derived water. Whereas the 1992 paper used a study based on grey-scale contrast, from Meteosat imagery, to designate a region up to and occasionally beyond the 2 000 m isobath where water of upwellingorigin was present on a quasi-permanent basis, the present study used actual sea surface temperatures (SSTs) from NOAA imagery and found comparatively little wate

Preliminary annual estimates of regional nitrate supply in the southern Benguela using coastal sea level fluctuations as a proxy for upwelling

First-order estimates of annual potential new production are presented for the southern Benguela upwelling region for the decade of the 1980s. Using satellite images of sea surface temperature and a 10-year record of sea level, preliminary estimates of potential new production for 12-month periods between May and June inclusive were made for the period 1980/81 to 1989/90. The annual period was selected so as to encompass the upwelling season (austral spring and summer) and to optimize the interaction betweenupwelling and biological response. The range of these estimates was 5.16 × 1013 to 6.19 × 1013 gC.year–1, with a mean of 5.60 × 1013 gC.year–1. The trend in the estimates was found to be consistent with related variablesand their validity, in terms of order of magnitude, was tested against 15NO3-N uptake rates measured in the southern Benguela and scaled to a regional level. In addition, they were subjected to an intra- and interregionalcomparison

Productivity of dinoflagellate blooms on the west coast of South Africa, as measured by natural fluorescence

The biomass and productivity of phytoplankton populations inshore on the west coast of South Africa were investigated towards the end of the upwelling season, a period when high-biomass dinoflagellate blooms arecommon. Productivity was estimated from natural fluorescence measurements (PNF), using photosynthesis (P) v. irradiance (E) relationships (PE) and by means of the in situ 14C-method (PC). A linear regression of PNF productivity against PC and PE productivities yielded a slope of 0.911 and an r2 of 0.83 (n = 41). Physical and biological variability was high inshore, reflecting alternating periods of upwelling and quiescence. Mean chlorophyll inshore (within a 12 m water column) ranged from 0.7 to 57.8 (mean = 8.9) mg.m-3, mean PNF productivity ranged from 8.4 to 51.0 (mean = 24.6) mgC.m-3.h-1 and daily integral PNF productivity from 0.8 to 4.8 (mean = 2.3) gC.m-2.day-1. Transects sampled during active and relaxation phases of upwelling had different chlorophyll distributions. High chlorophyll concentrations (sometimes >50 mg.m-3) were associated with surface blooms within the region of the upwelling front. Estimates of daily water-column PNF productivity within these frontal blooms ranged from 4.0 to 5.6 gC.m-2.day-1. With relaxation of wind stress, blooms dominated by dinoflagellates flooded shorewards and often formed red tides. Chlorophyll concentrations of>175 mg.m-3 and productivity rates > 500 mgC.m-3.h-1 and 12 gC.m-2.day-1 were measured during a particularly intense red tide. Offshore, the water column was highly stratified with a well-defined subsurface chlorophyll maximum layer within the pycnocline region. Estimates of daily water-column PNF productivity ranged from2.4 to 4.0 gC.m-2.day-1 offshore. The high productivity of shelf waters on the West Coast in late summer can be ascribed largely to dinoflagellate populations and their success in both upwelling systems and stratified conditions

Physical processes contributing to harmful algal blooms in Saldanha Bay, South Africa

The study synthesises current understanding of the predominant physical processes responsible for the seasonality of harmful algal blooms, notably Alexandrium catenella and Dinophysis spp., in the nearshore environmentof Saldanha Bay on the west coast of South Africa. Saldanha Bay is one of the few naturally sheltered areas on the South African coastline suitable for in situ shellfish farming and is the major site for the productionof black mussel Mytilus galloprovincialis in South Africa. Mussel farming started there in 1985 and the present level of production is some 2 700 tons per annum. Since 1994, disruption of harvesting as a result of the presence of harmful algal species has been a regular late-summer phenomenon. Toxic blooms that are ultimately advected into the bay develop on the continental shelf to the north between 32°S and St Helena Bay, a region characterized by favourable conditions for dinoflagellate growth and circulation patterns that facilitate build-up of intenseblooms during late summer. Offshore dinoflagellate populations are advected shorewards and polewards in response to relaxation of upwelling at the Namaqua cell to the north. Dinoflagellate blooms are advected south from the southern Namaqua shelf during upwelling relaxation. Under such conditions, the gyre south of Elands Bay moves offshore and a barotropic flow past Cape Columbine is established. Evidence suggests that the nearsurface component of the flow occurs as a sudden “flood” event. These dinoflagellate-containing shelf waters are in turn advected into Saldanha Bay when upwelling relaxes, when the density gradient between the bay and the shelf drives surface inflow and bottom water outflow. These flows are reversed with the resumption of upwellingover the shelf, resulting in intrusion and entrainment of bottom water and surface outflow. Entrainment dictates that the bay acts as a net importer of bottom water and net exporter of surface waters over a synoptic cycle. Thissystem of exchange between Saldanha Bay and the shelf curtails the duration and severity of toxic episodes in the bay relative to the shelf

Challenges for Australia's Bio/Nanopharma Policies: trade deals, public goods and reference pricing in sustainable industrial renewal

Industrial renewal in the bio/nanopharma sector is important for the long term strength of the Australian economy and for the health of its citizens. A variety of factors, however, may have caused inadequate attention to focus on systematically promoting domestic generic and small biotechnology manufacturers in Australian health policy

Estimates of new and total productivity in central Long Island Sound from in situ measurements of nitrate and dissolved oxygen

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Estuaries and Coasts 36 (2013): 74-97, doi:10.1007/s12237-012-9560-5.Biogeochemical cycles in estuaries are regulated by a diverse set of physical and biological variables that operate over a variety of time scales. Using in situ optical sensors, we conducted a high-frequency time-series study of several biogeochemical parameters at a mooring in central Long Island Sound from May to August 2010. During this period, we documented well-defined diel cycles in nitrate concentration that were correlated to dissolved oxygen, wind stress, tidal mixing, and irradiance. By filtering the data to separate the nitrate time series into various signal components, we estimated the amount of variation that could be ascribed to each process. Primary production and surface wind stress explained 59% and 19%, respectively, of the variation in nitrate concentrations. Less frequent physical forcings, including large-magnitude wind events and spring tides, served to decouple the relationship between oxygen, nitrate, and sunlight on about one-quarter of study days. Daytime nitrate minima and dissolved oxygen maxima occurred nearly simultaneously on the majority (> 80%) of days during the study period; both were strongly correlated with the daily peak in irradiance. Nighttime nitrate maxima reflected a pattern in which surface-layer stocks were depleted each afternoon and recharged the following night. Changes in nitrate concentrations were used to generate daily estimates of new primary production (182 ± 37 mg C m-2 d-1) and the f-ratio (0.25), i.e., the ratio of production based on nitrate to total production. These estimates, the first of their kind in Long Island Sound, were compared to values of community respiration, primary productivity, and net ecosystem metabolism, which were derived from in situ measurements of oxygen concentration. Daily averages of the three metabolic parameters were 1660 ± 431, 2080 ± 419, and 429 ± 203 mg C m-2 d-1, respectively. While the system remained weakly autotrophic over the duration of the study period, we observed very large day-to-day differences in the f-ratio and in the various metabolic parameters.This work was supported by the Yale Institute for Biospheric Studies, the Sounds Conservancy of the Quebec-Labrador Foundation, and the Yale School of Forestry and Environmental Studies Carpenter-Sperry Fund.2014-01-0

Seasonal and sub-seasonal oxygen and nutrient fluctuations in an embayment of an eastern boundary upwelling system: St Helena Bay

Seasonal, sub-seasonal and spatial fluctuations in bottom dissolved oxygen (DO) were examined in St Helena Bay, South Africa’s largest and most productive embayment, between November 2013 and November 2014. Alongshore bay characteristics were assessed through comparison of variables along the 50-m depth contour. A mean coefficient of variation of 0.35 provided a measure of the relative variability of near-bottom DO concentrations along this contour. Consistently lower DO concentrations in the southern region of the bay in summer and autumn are attributed to enhanced retention. Across-shelf transects captured the seasonal development of hypoxia in relation to the distribution of phytoplankton biomass. Exceptional dinoflagellate blooms form extensive subsurface thin layers preceding the autumn DO minima in the south of the bay, prior to winter ventilation of the bottom waters. The seasonal decline in DO concentrations in the bottom waters was marked by sub-seasonal events of hypoxia, and ultimately anoxia linked to episodic deposition of organic matter, as indicated by increases in bottom chlorophyll-a concentrations. Seasonal changes in bottom water macronutrient concentrations followed trends in apparent oxygen utilisation (AOU), both of which mirrored DO concentrations. In the south of the bay, nitrogen loss through denitrification/anammox in suboxic waters was indicated by a dissolved inorganic N deficit in the bottom waters, which was most pronounced in autumn.Keywords: anoxia, apparent oxygen utilization, dinoflagellate blooms, dissolved oxygen, hypoxia, intensive sampling, nitrogen deficit, seasonal fluctuation

Water quality characteristics of Vanderkloof Dam and its potential for rainbow trout farming

Vanderkloof Dam was periodically sampled between November 2014 and April 2016 for a range of water quality parameters to assess the potential for cage culture of rainbow trout, Oncorhyncus mykiss.  The dam is strongly stratified in summer and autumn, although upper water column temperatures remain relatively cool, largely <25°C. The dam is considered oligotrophic, characterised by phosphorus limitation of primary production, particularly during summer. Light is strongly attenuated in the epilimnion and heterotrophic community metabolism is observed through much of the water column. Surface nutrients are depleted through the summer with phytoplankton assemblages dominated by the green algae, Oocystis lacustris, Desmodesmus bicaudatus and Coelastrum microporum. The water column turns over during the winter and the nearly isothermal impoundment approaches 11°C. Nutrients are re-introduced into surface waters following winter mixing coincident with an increase in diatoms. The preferred environmental window for rainbow trout becomes severely contracted during the summer in that epilimnion temperatures exceed 21°C and thermocline/hypolimnion oxygen concentrations fall below 3 mg‧L−1. The coincidence of relatively high pH >9.5 could exacerbate these physiological challenges. Hydrological conditions for fish farming are most suitable in the proximity of the dam wall as opposed to further upstream. Here the hypoxic conditions that develop in the thermocline/hypolimnion during summer and autumn are less pronounced, particularly towards the southern bank, where concentrations of total suspended solids are generally <10 mg‧L−1 and water clarity is more favourable for visual feeders such as fish. Although rainbow trout may survive the adverse conditions prevalent during the summer, growth is likely to be compromised and susceptibility to disease may increase