The humble bearded goby is a keystone species in Namibia's marine ecosystem

Marine ecosystems are dynamic and fluid environments. Sessile organisms must cope with the variable conditions delivered to them, whereas motile species either drift or move in response to local conditions. When the physical and chemical environment changes, there are numerous possible outcomes and responses by the constituent species. A focus of current marine ecosystem research is to understand how changes in driving variables (such as increases in fishing effort, warming sea temperatures and increased concentrations of pollutants, with concomitant decreases in pH and habitat degradation) will affect species composition and productivity. In the past two decades, studies of marine ecosystems under global change have received much attention.1 The goal of these studies is to predict how continuing changes might manifest in the face of global pressures. Organisms are able to adapt and evolve to accommodate changing environments, which might introduce unpredictable elements that can be responsible for further changes in those environments

Progress towards marine ecosystem observing systems in South Africa

Marine ecosystem observing systems combine measurements, observations and models through a data management and interpretation process to provide information on the status of marine ecosystems. Both biotic and abiotic aspects of the marine environment need to be considered. Single variables typically can be used to represent aspects of the physical and chemical environment, but ecosystem indicators are required for the living components. There are no true marine ecosystem observing systems globally, because most observing systems focus on the physical environment. In South Africa, some fledgling systems are being developed, using the knowledge base provided by focused marine ecosystem research over the past 30 years. Further development should be based on international guidelines, which highlight three interrelated elements : (i) Measurements, obtained directly from ships, drifters or buoys, or remotely from satellites. In South Africa, sustained, long-term measurements are hampered by limited available ship's time, lack of suitable instruments, and insufficient qualified personnel. (ii) Models and other analytical tools to augment observations. South Africa is making progress in marine modelling, but not in marine data assimilation; qualified persons need to be attracted, trained and retained. (iii) Archived and disseminated data generated from measurements and models. The infrastructure and human and institutional capacity for data management and communication in South Africa needs to be enhanced. Existing programmes contribute towards the development of an effective marine ecosystem observing system, but its sustainability requires support at an institutional level

A size-based model of carbon and nitrogen flows in plankton communities

Bibliography: pages 163-183.A generic, size-based simulation model is developed to investigate the dynamics of carbon and nitrogen flows in plankton communities. All parameters in the model are determined by body size using empirically-determined relationships calculated from published data. The model is robust with respect to most parameters and assumptions. Because the model is based on general ecological principles, it can be used to simulate microplankton community interactions in any planktonic ecosystem. Two coastal ecosystems from the southern Benguela region in South Africa are simulated; one typical of the relatively stable surface waters on the Agulhas Bank and one typical of upwelling plumes, usually found off the west coast of South Africa. Simulated communities compare well with field observations in terms of standing stocks and size composition, and simulation results indicate that the small-scale structure of the two ecosystems and the processes occurring within them are relatively well understood. Consequently, the dynamic functioning of the two systems is investigated at the ecosystem level, using the simulation results. Hypothetical carbon flow networks are constructed, and the average importance of different flow pathways at different times is assessed. In both ecosystems, the vast majority of carbon flows pass through short, efficient-transfer pathways, although longer pathways are potentially possible. Simulation analyses are extended from coastal to oceanic food webs, and the model results are consistent with the hypothesis that oceanic phytoplankton have rapid rates of primary production. At-sea sampling of a phytoplankton bloom is mimicked by "sampling" from simulation output, and interpretation of the data using standard techniques is compared with the model output. The dangers of extrapolating from snapshot measurements is highlighted, and the experiment emphasizes the importance of size-fractionated sampling of phytoplankton. A hypothetical pelagic food web is described, consisting of at least five different trophic pathways from phytoplankton to pelagic fish. It is suggested that coastal waters probably have all the different pathways, and the relative importance and efficiency of the different pathways will determine the total fish production in an ecosystem

Oxygen and temperature influence the distribution of deepwater Cape hake Merluccius paradoxus in the southern Benguela: a GAM analysis of a 10-year time-series

Generalised additive models (GAMs) were applied to survey data to assess the influence of dissolved oxygen, water temperature and year of sampling upon the presence/absence of small (≤15 cm TL), medium (16–34 cm TL) and large (≥35 cm TL) size classes of deepwater Cape hake Merluccius paradoxus captured off the west coast of South Africa. Data were obtained from surveys using the RV Dr Fridtjof Nansen conducted in 2003 and from 2005 to 2013 during summer (January–February). Among the variables investigated, oxygen was the most important for the small size class (juveniles), with both low and high constraints (two-sided, ‘just right’ option), whereas for the medium and large size classes the oxygen effects were one-sided (avoiding lows). This finding, in combination with other published information, suggests that the Orange Banks is a nursery ground for juvenile M. paradoxus and that the area covered by this nursery ground can vary with the optimal oxygen concentration. The temperature constraint was generally wider and weaker than that for oxygen, being two-sided for the small and medium hake and one-sided (avoiding highs) for the large hake. The medium hake displayed the greatest tolerance to the investigated variables, which resulted in the widest distribution for this size class. Temperature, oxygen and sampling year play an important role in determining the distribution of M. paradoxus, but details of the biology (life cycle) of the species, such as its pelagic–demersal transition and associated movements, are no less important.publishedVersio

Combined fishing and climate forcing in the southern Benguela upwelling ecosystem: an end-to-end modelling approach reveals dampened effects

The effects of climate and fishing on marine ecosystems have usually been studied separately, but their interactions make ecosystem dynamics difficult to understand and predict. Of particular interest to management, the potential synergism or antagonism between fishing pressure and climate forcing is analysed in this paper, using an end-to-end ecosystem model of the southern Benguela ecosystem, built from coupling hydrodynamic, biogeochemical and multispecies fish models (ROMS-N 2 P 2 Z 2 D 2 -OSMOSE). Scenarios of different intensities of upwelling-favourable wind stress combined with scenarios of fishing top-predator fish were tested. Analyses of isolated drivers show that the bottom-up effect of the climate forcing propagates up the food chain whereas the top-down effect of fishing cascades down to zooplankton in unfavourable environmental conditions but dampens before it reaches phytoplankton. When considering both climate and fishing drivers together, it appears that top-down control dominates the link between top-predator fish and forage fish, whereas interactions between the lower trophic levels are dominated by bottom-up control. The forage fish functional group appears to be a central component of this ecosystem, being the meeting point of two opposite trophic controls. The set of combined scenarios shows that fishing pressure and upwelling-favourable wind stress have mostly dampened effects on fish populations, compared to predictions from the separate effects of the stressors. Dampened effects result in biomass accumulation at the top predator fish level but a depletion of biomass at the forage fish level. This should draw our attention to the evolution of this functional group, which appears as both structurally important in the trophic functioning of the ecosystem, and very sensitive to climate and fishing pressures. In particular, diagnoses considering fishing pressure only might be more optimistic than those that consider combined effects of fishing and environmental variability

South African research in the Southern Ocean: New opportunities but serious challenges

South Africa has a long track record in Southern Ocean and Antarctic research and has recently invested considerable funds in acquiring new infrastructure for ongoing support of this research. This infrastructure includes a new base at Marion Island and a purpose-built ice capable research vessel, which greatly expand research opportunities. Despite this investment, South Africa's standing as a participant in this critical field is threatened by confusion, lack of funding, lack of consultation and lack of transparency. The research endeavour is presently bedevilled by political manoeuvring among groups with divergent interests that too often have little to do with science, while past and present contributors of research are excluded from discussions that aim to formulate research strategy. This state of affairs is detrimental to the country's aims of developing a leadership role in climate change and Antarctic research and squanders both financial and human capital

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 _ 4 slope=0.96) indicating dependence of NH _ 4 and total N uptake on ambient N concentrations and cell size distributions of the phytoplankton assemblages. NO _ 3 uptake was less well explained by cell size and ambient concentrations, but regressions between measured and estimated rates were still significant. The results suggest that net nitrogen dynamics can be quantified at an assemblage scale using size dependencies of Michaelis-Menten uptake parameters. These methods can be applied to particle size distributions that have been routinely measured in eutrophic systems to estimate and subsequently analyse variability in nitrogen uptake