A South African commitment to having a much greater role in both regional and global science has been articulated by the Global Change Grand Challenge science plan prepared by the science community at the request of DST. Key to gaining new knowledge depends on enhancing our observational technological skills, including numerical modelling. The commitment by DST, Treasury and DEA: SANAP to invest in advanced cluster computing facilities (CHPC and SANReN) and a new research vessel (SA Agulhas II) were catalytic in giving significant encouragement to the SA science community to invest research energy in the Southern Ocean domain. These together with the Global Change Grand Challenge were the context that let CSIR-NRE to place the Southern Ocean into its strategic research plans.

A number of new research facilities (Fig. 1) are already operational and each has been located and developed at institutions that are identifiably strong in the field so that this investment is strongly leveraged by a sustained research interest and HCD plans.
New interdisciplinary research facilities in support of SANAP and the Global Climate Grand ChallengeFig. 1. New interdisciplinary research facilities in support of SANAP and the Global Climate Grand Challenge

  • SO Observational Engineering R&D facility
  • Robotics and Ocean profiling (CSIR-STS-Universities)
  • Iron (Fe) clean analytical experimental facility (Stellenbosch University)
  • High precision CO2 and pCO2 Facility (CSIR)
  • Bio-optics Research Facility (CSIR)
  • High precision Nutrient and Oxygen biogeochemistry (UCT)
  • Ocean productivity and biogeochemistry facility (UCT)

 
Integrated earth systems scale climate research in the Southern HemisphereFig.2. Integrated earth systems scale climate research in the Southern Hemisphere

All these facilities are set up to interface with the new polar research ship and the Centre for High Performance computing to grow a 21st century Ocean research capability in South Africa (Fig. 2)

Autonomous ocean robots are the future of marine research and environmental monitoring. This is because of the high costs and man-power associated with ‘snapshot’ observations made by ships and because today we require high quality, high-frequency sampling to support on-going world class oceanographic and climate research. The CSIR-led South Africa Marine Engineering & Robotics Centre (SAMERC) in Cape Town presents a state-of-the-art facility that (1) provides a glider-port for maintaining and piloting both profiling and surface gliders, (2) services and calibrates ship-based equipment and sensors for ocean profiling (e.g., CTD, UCTD, XBT), and (3) serves as a platform to grow technological R&D and marine engineering innovation in South Africa. This facility functions in collaboration with Sea Technology Services (STS) and is hosted by DEA-SANAP

This DST-supported world class facility is under the leadership of Dr Seb Swart and Dr Pedro Monteiro of the CSIR. The Centre currently houses long-endurance, deep- profiling (1000m) ocean gliders that consist of 4 Seagliders and 1 Webb-Teledyne Slocum Glider. These gliders are capable of sampling a range of physical and biogeochemical parameters including temperature, salinity, pressure, dissolved oxygen, bio-optics (incl. chl-a) and PAR. In addition there are long-endurance surface wave gliders that consist of 2 SV2 Liquid Robotics Wave Gliders with pCO2 systems and weather stations, and 2 new generation SV3 Liquid Robotics Wave Gliders. The wave gliders are suited to measure atmospheric CO2 fluxes, dissolved oxygen, pH, temperature, salinity and surface weather (wind, RH, air temperature, etc.). The Slocum glider and SV3 Wave Gliders perform as R&D platforms for sensor integration, power utilization testing and experimental design.

The Centre also maintains specially adapted biogeochemical profiling floats, ship-mounted heat flux sensors and the profiling equipment deployed from ships. The profiling equipment includes a full standard and Geotraces CTD carousel with 24 x 20 litre Niskin Bottles and auxiliary sensors for measuring key physical, biogeochemical and bio-optical properties of the water column. An underway-CTD (UCTD) for acquiring temperature and salinity profiles of the ocean to 500m depth, while the ship is steaming, is also part of the Centre’s gadgets.

These new capabilities have begun to attract a number of engineering students that complete their in-service training and BTech projects at the Centre. This advances human resource development in scarce skills in the fields of marine technology, robotics engineering and scientific sensor development that contributes to innovation in South Africa.

Follow our gliders on twitter

  • Robotic Seagliders and Wave Gliders housed in the Southern Ocean Engineering Centre, Cape Town.
  • Engineering interns, Sinekhaya Bilana and JP Smit work on sensors of the Wave Glider before deployment from the polar ship SA Agulhas II.
  • A Liquid Robotics Wave Glider with CO2, O2, pH and CTD sensors with a backdrop of Cape Town.
  • CTD carousel being deployed in sublime Southern Ocean conditions by engineering BTech student, Sinekhaya Bilana.
  • Dr Seb Swart, in collaboration with the Institute of Maritime Technology (IMT), deploys a Seaglider into False Bay, Cape Town - the first deployment of a glider in African waters.
  • Engineering interns of the Southern Ocean Engineering Centre in Cape Town work on a Rutgers Slocum Glider (RU29). This glider was deployed in Cape Town on route to Rio de Janeiro, as part of the Challenger Mission.
  • A Wave Glider is deployed into the Southern Ocean - a first for science and robotics engineering. This glider experiment lasted 4.5 months where both Seagliders and Wave Gliders were used to sample the spring to summer physics and gas fluxes in the Subantarctic region.
  • Engineering BTech student, JP Smit, works on the IOP system before installation on South Africa’s polar research ship, the SA Agulhas II.
Related News and Publications

Autonomous ocean robots are the future of marine research and environmental monitoring. This is because of the high costs and man-power associated with ‘snapshot’ observations made by ships and because today we require high quality, high-frequency sampling to support on-going world class oceanographic and climate research. The CSIR-led South Africa Marine Engineering & Robotics Centre (SAMERC) in Cape Town presents a state-of-the-art facility that (1) provides a glider-port for maintaining and piloting both profiling and surface gliders, (2) services and calibrates ship-based equipment and sensors for ocean profiling (e.g., CTD, UCTD, XBT), and (3) serves as a platform to grow technological R&D and marine engineering innovation in South Africa. This facility functions in collaboration with Sea Technology Services (STS) and is hosted by DEA-SANAP

This DST-supported world class facility is under the leadership of Dr Seb Swart and Dr Pedro Monteiro of the CSIR. The Centre currently houses long-endurance, deep- profiling (1000m) ocean gliders that consist of 4 Seagliders and 1 Webb-Teledyne Slocum Glider. These gliders are capable of sampling a range of physical and biogeochemical parameters including temperature, salinity, pressure, dissolved oxygen, bio-optics (incl. chl-a) and PAR. In addition there are long-endurance surface wave gliders that consist of 2 SV2 Liquid Robotics Wave Gliders with pCO2 systems and weather stations, and 2 new generation SV3 Liquid Robotics Wave Gliders. The wave gliders are suited to measure atmospheric CO2 fluxes, dissolved oxygen, pH, temperature, salinity and surface weather (wind, RH, air temperature, etc.). The Slocum glider and SV3 Wave Gliders perform as R&D platforms for sensor integration, power utilization testing and experimental design.

The Centre also maintains specially adapted biogeochemical profiling floats, ship-mounted heat flux sensors and the profiling equipment deployed from ships. The profiling equipment includes a full standard and Geotraces CTD carousel with 24 x 20 litre Niskin Bottles and auxiliary sensors for measuring key physical, biogeochemical and bio-optical properties of the water column. An underway-CTD (UCTD) for acquiring temperature and salinity profiles of the ocean to 500m depth, while the ship is steaming, is also part of the Centre’s gadgets.

These new capabilities have begun to attract a number of engineering students that complete their in-service training and BTech projects at the Centre. This advances human resource development in scarce skills in the fields of marine technology, robotics engineering and scientific sensor development that contributes to innovation in South Africa.

Follow our gliders on twitter

A South African commitment to having a much greater role in both regional and global science has been articulated by the Global Change Grand Challenge science plan prepared by the science community at the request of DST. Key to gaining new knowledge depends on enhancing our observational technological skills, including numerical modelling. The commitment by DST, Treasury and DEA: SANAP to invest in advanced cluster computing facilities (CHPC and SANReN) and a new research vessel (SA Agulhas II) were catalytic in giving significant encouragement to the SA science community to invest research energy in the Southern Ocean domain. These together with the Global Change Grand Challenge were the context that let CSIR-NRE to place the Southern Ocean into its strategic research plans.

A number of new research facilities are already operational and each has been located and developed at institutions that are identifiably strong in the field so that this investment is strongly leveraged by a sustained research interest and HCD plans.

  1. SO Observational Engineering R&D facility: Robotics and Ocean profiling (CSIR-STS-Universities)
  2. Iron (Fe) clean analytical experimental facility (Stellenbosch University)
  3. High precision CO2 and pCO2 Facility (CSIR)
  4. Bio-optics Research Facility (CSIR)
  5. High precision Nutrient and Oxygen biogeochemistry (UCT)
  6. Ocean productivity and biogeochemistry facility (UCT)

All these facilities are set up to interface with the new polar research ship and the Centre for High Performance computing to grow a 21st century Ocean research capability in South Africa.

  • CO2 lab
  • Underway pCO2
  • Underway pCO2
Related News and Publications

A South African commitment to having a much greater role in both regional and global science has been articulated by the Global Change Grand Challenge science plan prepared by the science community at the request of DST. Key to gaining new knowledge depends on enhancing our observational technological skills, including numerical modelling. The commitment by DST, Treasury and DEA: SANAP to invest in advanced cluster computing facilities (CHPC and SANReN) and a new research vessel (SA Agulhas II) were catalytic in giving significant encouragement to the SA science community to invest research energy in the Southern Ocean domain. These together with the Global Change Grand Challenge were the context that let CSIR-NRE to place the Southern Ocean into its strategic research plans.

A number of new research facilities are already operational and each has been located and developed at institutions that are identifiably strong in the field so that this investment is strongly leveraged by a sustained research interest and HCD plans.

  1. SO Observational Engineering R&D facility: Robotics and Ocean profiling (CSIR-STS-Universities)
  2. Iron (Fe) clean analytical experimental facility (Stellenbosch University)
  3. High precision CO2 and pCO2 Facility (CSIR)
  4. Bio-optics Research Facility (CSIR)
  5. High precision Nutrient and Oxygen biogeochemistry (UCT)
  6. Ocean productivity and biogeochemistry facility (UCT)

All these facilities are set up to interface with the new polar research ship and the Centre for High Performance computing to grow a 21st century Ocean research capability in South Africa.

For the iron chemistry project, seawater samples are collected during our annual relief voyages to Antarctica on board RV Agulhas II. A GEOTRACES trace metal clean 24 x 12L GoFlo carousel and Kevlar cable winch (Figure 1) is used to collect seawater along a vertical profile. Subsampling is conducted inside a certified trace metal clean container lab equipped with circulating HEPA filters for clean air supply (Figures 2 and 3). Concentrations for total dissolvable Fe (TDFe, unfiltered), dissolved Fe (DFe, filtered through 0.22 µm) and soluble Fe (SFe, filtered through 0.02µm) are measured using a Flow Injection Analyser (FIA; Figures 3 and 4) with chemiluminescence detection inside a trace metal clean class 100 laboratory at Stellenbosch University. An ICP-MS is also available at Stellenbosch University.

Seawater samples are also collected from the GoFlo bottles for the incubation experiments (Figure 6). Phytoplankton physiological parameters are measured using a Chelsea Fast Repetition fluorimeter (FRRf; Figure 4), dissolved Fe using the dedicated FIA in the trace metal clean laboratory at Stellenbosch University, and macro-nutrients using FIA at CSIR. The culture experiments are also conducted inside the trace metal clean class 1000 laboratory at Stellenbosch University

  • Figure 4: Dr. Thato Mtshali setting up the Fast Repetition Rate Fluorometer (FRRf) inside a trace metal clean laboratory container.
  • Figure 2: Dr. Thato Mtshali setting up the FIA system inside a trace metal clean laboratory container for Fe concentration measurements in seawater during field work at sea.
  • Figure 3: Prof Alakendra Roychoudhury and Natasha van Horsten inside a trace metal clean laboratory at SUN, showing the Flow Injection Analyzer for measuring Fe concentration in seawater on land (photo credit: Wiida Fourie-Basson, Stellenbosch University).
  • Figure 1: Trace metal GEOTRACES CTD rosette equipped with 24 12L GoFlo bottles.
  • Figure 5: Dr. Thato Mtshali holding certified certificates for two trace metal clean container laboratories.
  • Figure 6: Three incubators for growing phytoplankton community at sea under different dFe supply and light regimes (Bioassay experiments).
Related News and Publications

For the iron chemistry project, seawater samples are collected during our annual relief voyages to Antarctica on board RV Agulhas II. A GEOTRACES trace metal clean 24 x 12L GoFlo carousel and Kevlar cable winch (Figure 1) is used to collect seawater along a vertical profile. Subsampling is conducted inside a certified trace metal clean container lab equipped with circulating HEPA filters for clean air supply (Figures 2 and 3). Concentrations for total dissolvable Fe (TDFe, unfiltered), dissolved Fe (DFe, filtered through 0.22 µm) and soluble Fe (SFe, filtered through 0.02µm) are measured using a Flow Injection Analyser (FIA; Figures 3 and 4) with chemiluminescence detection inside a trace metal clean class 100 laboratory at Stellenbosch University. An ICP-MS is also available at Stellenbosch University.

Seawater samples are also collected from the GoFlo bottles for the incubation experiments (Figure 6). Phytoplankton physiological parameters are measured using a Chelsea Fast Repetition fluorimeter (FRRf; Figure 4), dissolved Fe using the dedicated FIA in the trace metal clean laboratory at Stellenbosch University, and macro-nutrients using FIA at CSIR. The culture experiments are also conducted inside the trace metal clean class 1000 laboratory at Stellenbosch University

The biogeochemistry laboratory in the Oceanography department at UCT performs routine hydrographic measurements such as nutrient concentrations (NO3, NO2, NH4, SiO4, PO4, urea), dissolved oxygen, chlorophyll and pH. An automated system (flow injection auto-analyser) is available for NO3, SiO4 and PO4 analyses while NH4 is determined fluorometrically. All of the above nutrient concentrations can be determined manually using a colourimetric method.

The following equipment is available:

  1. Lachat QuikChem 8500 series 2 – 3 channels : currently set-up for the automated determination of NO3, SiO4 and PO4
  2. Turner fluorometer
  3. Metrohm 848 Titrino+
  4. Digital burette
  5. Crison pH meter
  6. Spectrophotometers (UV/vis)
  7. Access to mass spectrometer for 15N analyses
  • Dissolved oxygen titrino
  • Flow injection autoanalyser fluorometer
  • Incubators
Related News and Publications

The biogeochemistry laboratory in the Oceanography department at UCT performs routine hydrographic measurements such as nutrient concentrations (NO3, NO2, NH4, SiO4, PO4, urea), dissolved oxygen, chlorophyll and pH. An automated system (flow injection auto-analyser) is available for NO3, SiO4 and PO4 analyses while NH4 is determined fluorometrically. All of the above nutrient concentrations can be determined manually using a colourimetric method.

The following equipment is available:

  1. Lachat QuikChem 8500 series 2 – 3 channels : currently set-up for the automated determination of NO3, SiO4 and PO4
  2. Turner fluorometer
  3. Metrohm 848 Titrino+
  4. Digital burette
  5. Crison pH meter
  6. Spectrophotometers (UV/vis)
  7. Access to mass spectrometer for 15N analyses

The establishment of a national bio-optical research competency that will allow multi-ecosystem observations. SOCCO have recently set up a CapEx funded world-class bio-optical research facility under the leadership of Dr Sandy Thomalla. To date SOCCO have put in place new IOP sensors on the CTD’s, a multi-spectral profiling radiometre (C-OPS) and a Beckman Multisizer 4 for characterising the size distribution of the phytoplankton community. In Addition, SOCCO have developed an underway IOP system that can be set up to run in both underway mode (using the ships underway water supply) and bench top mode (using discreet water samples from CTD’s, bio-assay incubation experiments and cultures. The observational objectives of the underway IOP system are as follows: 1) Calibration‐independent hyperspectral measurements of particulate absorption ap(λ) and attenuation cp(λ) via periodic measurements of total (unfiltered) and 0.2 m filtered absorption at(λ) – aCDOM(λ), and attenuation ct(λ) – cCDOM(λ) 1,2 [WET Labs AC-S], 2) Supporting hyperspectral measurements of filtered absorption aCDOM(λ) using long pathlength (integrating cavity) absorption meter [TriOS OSCAR], 3) Multi-λ measurements of particulate backscattering bbp(λ) [WET Labs BB-9], 4) In‐line acidification of seawater for bbbp(λ), supporting PIC estimates, 5) simultaneous feeds of de-bubbled flow-through seawater to other flow-through instruments [e.g., Fast repetition rate fluorometry, Multi-λ excitation fluorometry]. The new bio-optics facility also includes autonomous platforms such as Gliders (with fluorescence and backscattering at two wavelengths) and specialised bio-optics floats with florescence, backscattering and beam attenuation sensors with the additional capability of measuring carbon export.

  • The underway IOP system on the SA Agulhas that measures Hyperspectral particulate and dissolved absorption a(λ) and attenuation c(λ), supporting hyperspectral measurements of dissolved absorption aCDOM(λ), multi-λ measurements of particulate backscattering bbp(λ), in‐line acidification of seawater for bbp(λ) supporting PIC estimates, simultaneous feeds of de-bubbled flow-through seawater for Fast Repetition Rate Fluorometry and Multi-λ excitation fluorescence
  • Two bio-optics floats with sensors for measuring temperature, salinity, dissolved oxygen, fluorescence, backscattering and beam attenuation at two wavelengths (red and blue).
  • The dry laboratory on the SA Agulhas II showing the Beckmann Coulter counter for characterising the size distribution and the SHIMADZU spectrophotometre for measuring spectral absorption.
  • The underway IOP system and accessory instruments in the wet laboratory on the SA Agulhas II.
  • Deploying the profiling radiometer C-OPS from Biospherical
  • The profiling radiometer C-OPS from Biospherical gets deployed over the side of the SA Agulhas
Related News and Publications

The establishment of a national bio-optical research competency that will allow multi-ecosystem observations. SOCCO have recently set up a CapEx funded world-class bio-optical research facility under the leadership of Dr Sandy Thomalla. To date SOCCO have put in place new IOP sensors on the CTD’s, a multi-spectral profiling radiometre (C-OPS) and a Beckman Multisizer 4 for characterising the size distribution of the phytoplankton community. In Addition, SOCCO have developed an underway IOP system that can be set up to run in both underway mode (using the ships underway water supply) and bench top mode (using discreet water samples from CTD’s, bio-assay incubation experiments and cultures. The observational objectives of the underway IOP system are as follows: 1) Calibration‐independent hyperspectral measurements of particulate absorption ap(λ) and attenuation cp(λ) via periodic measurements of total (unfiltered) and 0.2 m filtered absorption at(λ) – aCDOM(λ), and attenuation ct(λ) – cCDOM(λ) 1,2 [WET Labs AC-S], 2) Supporting hyperspectral measurements of filtered absorption aCDOM(λ) using long pathlength (integrating cavity) absorption meter [TriOS OSCAR], 3) Multi-λ measurements of particulate backscattering bbp(λ) [WET Labs BB-9], 4) In‐line acidification of seawater for bbbp(λ), supporting PIC estimates, 5) simultaneous feeds of de-bubbled flow-through seawater to other flow-through instruments [e.g., Fast repetition rate fluorometry, Multi-λ excitation fluorometry]. The new bio-optics facility also includes autonomous platforms such as Gliders (with fluorescence and backscattering at two wavelengths) and specialised bio-optics floats with florescence, backscattering and beam attenuation sensors with the additional capability of measuring carbon export.

The Centre for High Performance Computing provides high performance computing to support scientific research and the private sector’s needs in South Africa. Based in Rosebank, Cape Town, the CHPC represents South Africa as a world-class facility and has been ranked in the world’s top 500 supercomputers. At the CHPC, over 5000 cpu cores are shared by users to conduct research.

The modelling goal of SOCCO is to have a suite of ocean-ice-biogeochemistry models which we can use to understand the surface-ocean processes and ocean-atmosphere carbon exchange in the Southern Ocean. Starting at coarse-resolution global models to regional high-resolution models, the increasing complexity and resolution requires increasing computing power. Currently, out high-resolution 1/12 South Atlantic Sector model uses over 1200 cpus. For this, SOCCO modelling research depends on the infrastructure as well as the technical staff provided by the CHPC.

  • The CHPC boardroom
  • The Tsessebe cluster of the CHPC with over 5000 cores.
Related News and Publications

The Centre for High Performance Computing provides high performance computing to support scientific research and the private sector’s needs in South Africa. Based in Rosebank, Cape Town, the CHPC represents South Africa as a world-class facility and has been ranked in the world’s top 500 supercomputers. At the CHPC, over 5000 cpu cores are shared by users to conduct research.

The modelling goal of SOCCO is to have a suite of ocean-ice-biogeochemistry models which we can use to understand the surface-ocean processes and ocean-atmosphere carbon exchange in the Southern Ocean. Starting at coarse-resolution global models to regional high-resolution models, the increasing complexity and resolution requires increasing computing power. Currently, out high-resolution 1/12 South Atlantic Sector model uses over 1200 cpus. For this, SOCCO modelling research depends on the infrastructure as well as the technical staff provided by the CHPC.

The Southern African Data Centre for Oceanography (SADCO) stores, retrieves and manipulates multi-disciplinary marine information from the areas around southern Africa.

SADCO has been in existence since the 1960’s, and in its present configuration is hosted by the South African CSIR and located in Stellenbosch, about 50 km east of Cape Town.

SADCO is funded by a number of marine organisations, namely

  • CSIR
  • Oceans and Coasts, Department of Environmental Affairs
  • Namibian Ministry for Fisheries and Marine Resources
  • South African Environmental Observation Network
  • South African Navy

These and other participating organisations are represented on a Steering Committee, along with a representative from the maritime industry. The role of the Steering Committee is to advise on strategic and other issues, review SADCO’s operational progress and decide on work list priorities.

Historic data can be accessed through www.sadco.csir.co.za

  • Image Caption Needed
  • Image Caption Needed
Related News and Publications

The Southern African Data Centre for Oceanography (SADCO) stores, retrieves and manipulates multi-disciplinary marine information from the areas around southern Africa.

SADCO has been in existence since the 1960’s, and in its present configuration is hosted by the South African CSIR and located in Stellenbosch, about 50 km east of Cape Town.

SADCO is funded by a number of marine organisations, namely

  • CSIR
  • Oceans and Coasts, Department of Environmental Affairs
  • Namibian Ministry for Fisheries and Marine Resources
  • South African Environmental Observation Network
  • South African Navy

These and other participating organisations are represented on a Steering Committee, along with a representative from the maritime industry. The role of the Steering Committee is to advise on strategic and other issues, review SADCO’s operational progress and decide on work list priorities.

Historic data can be accessed through www.sadco.csir.co.za

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