2.2 Excellence
2.2.2 LTO-Ocean
their use for research and society. The scientific background and initial backbone on the specific platforms and protocols to be used will be ensured by the participation of the leading partners UP, RU, NMU, FH, SUN and UniSA as direct consortium partners or participants through the user forum (see Chapter 5).
● Space physics. SANSA operates an observational station at Marion Island base collecting long-term observations of the identified essential variables (Appendix C). The same considerations indicated for the SANAE IV long-term observations and activities apply here, and they will be implemented according to the specific logistics required for accessing the infrastructure on the island.
● Meteorology and atmospheric sciences. SAWS operates observational meteorological stations at Marion and Gough Islands, collecting long-term observations of the meteorological and climate essential variables (Appendix C). The research enabled by this infrastructure is similar to what was described for DML. The importance of PEI and Gough installations is further magnified due to the rapid spatial change which weather conditions exhibit at these dynamic remote sites and the relevance of having continuous datastream that would improve the forecasting on land. LTO-Land will work closely with SMCRI on PEI to ensure that data collected in this way will have short-term, tactical utility (e.g. navigation and planning), as well as long- term, hind-cast utility for climate research.
collect data, and the SA Agulhas II is an international model for multi-scale measurements of engineering data that can inform the design of polar vessels. Chapter 1 illustrated the complexity of large infrastructure management within the broad SANAP space. Science delivery and excellence is tightly linked to ease of access to these infrastructures and to proper logistics management. Over-the- side sampling operations, along with detailed sample analysis and extensive multi-faceted underway data acquisition, is only possible from a research vessel. In addition, the ship can host specialised container laboratories for sampling essential variables such as the micronutrient iron and sea ice features. Finally, nothing can replace a research vessel for training and inspiring early career scientists.
Where necessary and agreed on through the governing bodies, underway equipment will be combined and updated, and human resources will be provided through SAPRI. In addition, SAPRI will foster multi- disciplinary inclusion of teams and scientists, allowing for additional parameters to be collected during underway and over-the-side operations. This is a description of how the SAPRI will enhance the science activities on the vessel based on the existing infrastructure:
● Over-the-side operations, commonly identified as Conductivity, Temperature and Depth (CTD) operations. These can host multiple physics and optics instruments, seated on a frame called a rosette which holds specialised bottles for sample collection (Niskin). These samples are not limited to physics or biogeochemistry, but can be used for phytoplankton, microbe and microzooplankton sampling as well. A dedicated metal-free rosette for sampling trace metals is also available, with specialised GoFLO bottles. The DEFF and SOCCO already own these large CTD instruments acquired through national funding. In addition, SOCCO and UCT own an underway CTD which can be deployed from the aft of the vessel whilst steaming, providing relatively high-resolution profiles of Temperature and Salinity. Through this proposal, actions will be taken to combine the existing sparse national infrastructures and funding will be earmarked for additional Niskin/GoFLO bottles, sensor calibration and replacement/redundancy, as well as technical human resources required to operate these instruments at sea, process and archive data and maintain the instrumentation itself.
● Underway equipment that continuously collects water samples during navigation. The SA Agulhas II is equipped with a series of sensors that are permanently installed such as the thermosalinograph (TSG) which is maintained by DEFF as one of the ship’s assets, and a fluorometer and CO2 flux sensor (an underway General Oceanics pCO2 instrument) and pH, which is managed by SOCCO. In addition to this, there are a series of optical instruments that are not permanent features but can be installed on the vessel during specific scientific expeditions to measure optical characteristics of the phytoplankton community (backscatter, attenuation, absorption, multiple fluorescence). The instruments currently managed by SOCCO form part of the DSI infrastructural funding. The SAPRI set-up and design phase (Chapter 3) will establish a dedicated task team to assess the best options for managing the infrastructure.
● Specialised container laboratories that are loaded onto the ship prior to the science voyages.
Four container labs are currently maintained and operated by CSIR as part of the SOCCO national infrastructure: two certified trace metal-clean containers following GEOTRACES33 best practices, one radiotracer container laboratory certified for 14C and 55Fe and one general chemistry container with fume hood. Similar to the previous point, these instruments will be
33 https://www.geotraces.org/
considered for integration within SAPRI during the set-up phase and maintained/upgraded for longer term availability to the scientific community.
● Various types and sizes of phyto- and zooplankton net systems. These are towed from a particular depth to the surface either vertically or obliquely. Similarly, surface tows are undertaken for microplastic and surface plankton research. The equipment needed for polar research of plankton is the same as that used for coastal research by SMCRI and DEFF. SAPRI will enhance the availability and efficient use of existing netting and frames for plankton acquisition, flow-meters and technical human resources for sample collection and analysis (using sample analysis techniques and imaging technology such as Zooscan and Underwater Vision Profiler (UVP)), data archiving and maintenance.
● A number of monitoring lines are undertaken each year (Figure 4): The Good Hope Line , the SAMBA and ASCA CTD lines (all of which augment data along these transects for additional parameter sampling), CTD monitoring lines between and around the Prince Edward Islands and the Crossroads CTD and XBT line which extends across the Agulhas Return and Agulhas Currents from Marion Island back to the South African coast each year. These monitoring lines are established but not guaranteed. SAPRI will foster multi-disciplinary inclusion of teams and scientists, allowing for additional parameters to be collected during underway and over-the- side CTD operation work and tows with phyto- and zooplankton nets. Moorings in association with these lines need addressing.
● The ship herself is a measuring platform, which is already used to provide real-time data on her performances. The Digital Antarctic facility in SAPRI will contribute to make the ship a full- scale monitoring system and create the digital twin DIGSAAII for downstream exploitation.
This will happen thanks to existing and additional platforms mounted to the vessel, such as automatic weather stations, underway PAR, wave radar, automatic cameras for real-time ocean state acquisition (sea ice and surface roughness), echosounders used for plankton and fish density descriptions, and multibeam echosounders for seafloor characterisation.
Critically, the SA Agulhas II is not equipped with a multibeam echosounder, side-scan sonar technology or a wave radar to estimate wave conditions. These should be key instruments for acquisition for the vessel through SAPRI. Prior agreements and coordination with DEFF will be essential due to them being permanently installed on the vessel. Ship-based personnel will require training in running these systems. Marine geophysical data can be processed and archived at the CGS.
● The ship is equipped with facilities for deep-sea sediment coring and its crew have demonstrated capability of deploying coring equipment during science voyages with international teams. However, the existing coring equipment available in the country is not usable and needs replacement. Sediment cores and samples provide fundamental data on seabed character, sedimentation, benthic community composition and ecosystem functioning. Southern Ocean sediment cores are highly sought-after because of the potential for reconstructing the Southern Ocean’s role in past climate. SAPRI will make available funding to procure the proper coring equipment as decided during the technical design phase and maintain it as part of the seafloor observation platforms (Section 2.2.2.4).
Autonomous platforms
Research vessels cannot be maintained at sea indefinitely. Autonomous platforms have been developed over the last 30-40 years with major developments in the field over the last decade specifically. The DSI-funded programme SOCCO hosted at CSIR pioneered ocean robotics in South Africa by investing in a fleet of ocean and wave gliders and engineering capacity building and 2.2.2.2
creating the South African Robotics Ocean Technology Innovation Centre (SA-RobOTIC), currently hosted at the DEFF premises in Cape Town. South African oceanography is now recognised as a global leader in ocean robotics, particularly with respect to long term deployments that reduce the cost and sparseness of ship-based observations and observe ocean physics and biogeochemical dynamics scales that cannot be done using ships. SAPRI will expand on the infrastructure model successfully developed at SOCCO to provide the necessary set of operational technological services as well as expand its HCD and R&D roles in ocean robotics. Since SOCCO is a parallel national infrastructure funded through DSI, the details on the infrastructure development will be agreed during the implementation phase (Section 3.1.2.2). Local engineering developments have also indicated the opportunity for developing innovative biogeochemical instrumentation such as sensors for measuring carbon in the water. The proposed infrastructure will focus on the following ocean robotics and Lagrangian instrumentation in general, as well as the related technical capacity:
● Wave and buoyancy gliders, capable of undertaking very high-resolution scientific expeditions. These are ideal for process studies and seasonal studies as they need to be retrieved and maintained periodically. Gliders can also be maintained in pseudo-mooring mode as demonstrated by several SANAP science projects and have contributed to critical high-frequency time series of essential variables.
● Argo floats, capable of standard operations (2000 m profiles), biogeochemical studies (such as the Southern Ocean Carbon and Climate Observations and Modeling - SOCCOM - project) and deep Argo profilers capable of 4000-6000 m profiles (instrument dependent) contribute to a larger global program and can be effective in ultimately providing long term information over large areas of the ocean.
● Satellite tracked ocean and sea ice drifters can be used to track surface water movement and when deployed on ice floes, their movement within the Marginal Ice Zone (MIZ) and related ice features. SAPRI will coordinate with SAWS for the routine deployment of ocean drifters and by joint coordination between LTO-Ocean and the Polar Lab will work to consolidate the prototype array of low-cost expendable buoys for long-term sea ice monitoring.
● Animal tracking devices that allow measurement of ocean properties are logistically included in LTO-Land, but their technology is related to the engineering development done in the ocean space.
Moorings
The existing long-term observations funded by national research programs have also been maintained by means of subsurface moorings deployed to the sea floor.
● South Africa plays host to three subsurface mooring systems: the South Atlantic Meridional Overturning Circulation Basin-scale Array (SAMBA) out into the South Atlantic Ocean (along 34.5° S), the Agulhas System Climate Array (ASCA) across the Agulhas Current (currently not deployed) and the Marion Island moorings. These three mooring systems, all endorsed by international bodies, share similar instrumentation which allows for sharing of instrumentation and consumables, technical skills, communication costs, data processing techniques and interpretation methods. SAPRI will facilitate the harmonisation of existing infrastructures and the sharing of equipment and personnel through LTO-Ocean.
● The high source levels of baleen whale vocalisations make the acoustic monitoring of populations possible over a wider area and with greater efficiency than visual detection.
Passive Acoustic Monitoring (PAM) is now widely used to monitor seasonal abundance by latitude and therefore seasonal migration patterns. South Africa has carried out PAM within 2.2.2.3
SANAP, during which deep-water automated acoustic recorder moorings were deployed on the Maud Rise (65°00’S; 2°30’E) and off the west coast of South Africa providing significant information on seasonal migration patterns of Antarctic blue and fin whales. PAM is more efficient than ship-based visual monitoring and can provide significant understandings of stock structure, distributions, and migration patterns required for stock status assessments. The mooring equipment with the array of acoustic hydrophones was initially developed by the University of Pretoria’s Mammal Research Institute Whale Unit and the equipment has been transferred to CPUT. SAPRI will promote the use of acousting moorings in combination with the cost-effective mooring deployment of oceanographic instrumentation from other disciplines. Ship-time is minimal in relation to long-term data that can be collected over the mooring soak period. These data will contribute to the International Whaling Commission Southern Ocean Research Partnership and their international Southern Ocean Hydrophone Network (as was carried out with previous data) to contribute to a global array of Southern Ocean PAM of baleen whale migrations.
These infrastructures are in some cases already existing at partner institutions. For instance, mooring equipment is owned by DEFF and by SAEON, and PAM devices are available at CPUT. The details of the sharing, continued maintenance and additional acquisitions are further given in Section 3.1.2.
Land based Laboratories
Most of the biogeochemical, nutrient, trace metal, and sensor validation samples collected at sea are not processed at sea due to time and space constraints. Thus, effective and efficient state-of-the-art laboratories and sample analysis instrumentation are required to ensure these data are accurately acquired. A major national breakthrough has been achieved with the establishment of a dedicated RI for biogeochemistry (BIOGRIP). Through the new Water and Soil Biogeochemistry Node that will be established at SUN, BIOGRIP will provide a range of high-quality water analyses, as well as facilities for experimental work that will be of great support for oceanic polar research. This will be especially relevant for the measurement of macronutrients in the ocean and within sea ice. SAPRI will undertake an agreement with BIOGRIP management to ensure that samples from the designated LTO-Ocean sites and cruises will be processed through the BIOGRIP facility at convenient costs and will contribute with expertise to make certain that the most appropriate techniques are used. SAPRI will likewise partner with SMCRI and DEFF for the processing and analysis of phytoplankton and zooplankton samples collected by LTO-Ocean. This will be detailed in dedicated agreements that will provide the necessary complementary resources, both in terms of consumables or technical personnel.
Not all the essential variables required for polar research are however considered within the BIOGRIP implementation plan. Two main laboratories have been established as part of previous national initiatives funded by DSI. The SOCCO infrastructure holds a dedicated laboratory for measuring oceanic carbon variables. This laboratory is fully functional and equipped, and currently located at the CSIR Stellenbosch premises. SAPRI will integrate this laboratory in the LTO IF to expand their accessibility to a wider community and improve the exchange with other facilities. The Centre for Trace and Experimental Biogeochemistry (TracEx) is a virtual centre located in Stellenbosch and brings in researchers from SUN and other local and international institutions together with an aim to gain an improved understanding on biogeochemical cycling of bioactive trace elements in marine environments. The Centre promotes the mandate of international GEOTRACES program and runs the 2.2.2.4
laboratory on trace metal analyses34, which is an international excellence due to the paucity of these specialised metal-clean facilities. This facility is considered a crucial component of the long-term monitoring of the Southern Ocean, given the role played by trace nutrients in the functioning of the planktonic system.
Seafloor observation platforms
Much of our existing knowledge of the structure and functioning of benthic ecosystems comes from data collected in tropical and temperate environments and from depths shallower than 100 m.
Relatively little benthic research has been conducted in high latitudes (>40° N or S) and in the deep- sea. Within South Africa’s territories, the shelves shallower than 250 m only cover 16.6 % and 1.4 % of the exclusive economic zones around South Africa and the PEI, respectively (Figure 4). As such, we have a very limited understanding of the structure, functioning and services provided by the deep-sea system.
The SAPRI seafloor is a novel structure within LTO-Ocean that will spin-off from the recognised experience of both SAEON and SAIAB in benthic research. These platforms will permit research that directly addresses the knowledge gap on deep-sea systems, enhancing our ability to manage resources and providing globally standardised data to report against national and global development and biodiversity targets. This thematic study area would directly address the following biology and geology essential ocean variables (Appendix C):
● seabed mapping, sampling geomorphology and benthic habitat delineation;
● fish abundance and distribution;
● hard coral cover and composition;
● invertebrate abundance and distribution.
The consortium partner SAEON has established baseline data and imagery in the PEI from which indices can be developed to detect future changes. To continue and advance this monitoring programme, it would be best placed as a component within a larger, more formally supported research platform, through which the seabed biodiversity can continue to be observed.
The seafloor thematic study area in LTO-Ocean will do this through three embedded infrastructure units focussed on mapping, biodiversity monitoring (with the primary method being underwater imaging systems) and biogeochemistry (the latter in collaboration with the SMCRI and BIOGRIP RIs).
The first two will build on three existing infrastructure platforms funded through the National System of Innovation; namely the Marine Remote Imagery Platform, the Geophysics and Mapping Platform both based at SAIAB, and the Offshore Invertebrate Observing Program from SAEON. Through SAPRI, these partners’ facilities that now operate in the shallow ocean will be integrated with LTO-Ocean in phase 1 and further expanded to enable research in the shallow and deep sea of polar environments.
This equipment will provide fundamental data on seabed character, sedimentation, benthic community composition and ecosystem functioning, and enable research into climate change and the role of benthic organisms in carbon cycling and other biological processes. The sampling techniques and data they provide will align with the GEBCO Seabed2030 project35, Global Ocean Observing System (GOOS), Scientific Community for Oceanographic Research (SCOR) and the Intergovernmental
34 https://tracexsite.wordpress.com/laboratory-facilities/
35 https://seabed2030.gebco.net/southern_ocean/
2.2.2.5
Oceanographic Commission (IOC) for the reporting against Sustainable Development Goals and Aichi targets.