Earth observation and machine learning reveal the dynamics of productive upwelling regimes on the Agulhas Bank

The combined application of machine learning and satellite observations offers a new way for analysing complex ocean biological and physical processes. Here, an unsupervised machine learning approach, Self Organizing Maps (SOM), is applied to discover links between surface current variability and phytoplankton productivity during seasonal upwelling over the Agulhas Bank (South Africa), from 23 years (November-March 1997-2020) of daily satellite observations (surface current, sea surface temperature, chlorophyll-a). The SOM patterns extracted over this dynamically complex region, which is dominated by the Agulhas Current (AC), revealed 4 topologies/modes of the AC system. An AC flowing southwestward along the shelf edge is the dominant mode. An AC with a cyclonic meander near shelf is the second most frequent mode. An AC with a cyclonic meander off shelf and AC early retroflection modes are the least frequent. These AC topologies influence the circulation and the phytoplankton productivity on the shelf. Strong (weak) seasonal upwelling is seen in the AC early retroflection, the AC with a cyclonic meander near shelf modes and in part of the AC along the shelf edge mode (the AC with a cyclonic meander off shelf mode and in part the AC along the shelf edge mode). The more productive patterns are generally associated with a strong southwestward flow over the central bank caused by the AC intrusion to the east Bank or via an anticyclonic meander. The less productive situations can be related to a weaker southwest flow over the central bank, strong northeast flow on the eastern bank, and/or to a stronger northwest flow on the central bank. The SOM patterns show marked year-to-year variability. The high/low productivity events seem to be linked to the occurrence of extreme phases in climate variability modes (El Niño Southern Oscillation, Indian Ocean Dipole)

Absence of the Great Whirl giant ocean vortex abates productivity in the Somali upwelling region

Somali upwelling is the fifth largest upwelling globally with high productivity, attracting tuna migratory species. A key control on the upwelling productivity is its interaction with one of the world’s largest oceanic eddies, the Great Whirl inducing a strong downwelling signal. Here, we use satellite-derived observations to determine the Great Whirl impact on the extent of the upwelling-driven phytoplankton bloom. We find that following decreases in upwelling intensity, productivity has declined by about 10% over the past two decades. The bloom extent has also been diminishing with an abrupt decrease around 2006–2007, coinciding with an abrupt increase in the downwelling effect. Absent or weak Great Whirl leads to the occurrence of smaller anticyclonic eddies with a resulting downwelling stronger than when the Great Whirl is present. We suggest that 2006–2007 abrupt changes in the bloom and downwelling extents’ regimes, are likely driven by Indian Ocean Dipole abrupt shift in 2006

Retention properties of the Agulhas bank and their relevance to the chokka squid life cycle

Retention is thought to be a crucial component required to create a favourable habitat for coastal pelagic species. It is vital for the survival of ‘chokka’ squid (Loligo reynaudii), which is a fishery that supports thousands of people living in the Eastern Cape of South Africa. After chokka spawn, retention on the Agulhas Bank is crucial to prevent starvation in the early life stages. Using a high-resolution ocean model, this study quantifies retention properties of the Agulhas Bank most relevant to the chokka squid. We estimate the proportion of virtual Lagrangian particles, representing paralarvae, that are retained on the Agulhas Bank within 30 days after being released from the main chokka squid spawning sites. Over an 18-year period (1995–2013), considerable variability is found on seasonal and interannual timescales, with the greatest retention occurring for particles released further to the west. The greater losses for the easternmost release sites are due to increased interaction with the Agulhas Current. While 90–100% retention is the most common scenario, high loss (>50%) events are also apparent and are associated with different variability modes of the Agulhas Current. These variability modes include i) meanders that cause offshore flow at the northeast edge of the Bank, ii) the presence of a fast, onshore branch of the Agulhas Current rapidly advecting the particles off the Bank further west (associated with a Natal Pulse) and iii) an Agulhas Current positioned further south of the Bank leading to an offshore flow from the eastern Agulhas Bank. The third variability mode usually occurs 1–2 months after the passage of a Natal Pulse or meander. However, 1–2 weeks after the passage of a Natal Pulse, retention increases, so the timing of these events relative to particle release is crucial. This shows that the key to understanding paralarvae retention lies both in the occurrence of these dynamic features and in their timing relative to the spawning events

Spatial and temporal variability of net primary production on the Agulhas Bank, 1998–2018

Despite the importance of Agulhas Bank (AB) marine productivity in supporting South African coastal fisheries and shelf ecosystems, there are relatively few regional-scale assessments of its spatial and temporal variability, and most productivity studies have been limited in scale. Here we use satellite-derived Net Primary Production (NPP) rates calculated using the Vertically Generalized Production Model (VGPM) to examine the spatial and temporal dynamics of NPP over the 21-year satellite record (1998–2018) on the AB. In calculating VGPM NPP we used the OCCI Chlorophyll-a product, SST from Operational-Sea-Surface-Temperature-and-Sea-Ice-Analysis (OSTIA) and PAR from GlobColour level-3 mapped products as these represent the longest datasets that fit our extended study period. We examine spatial trends between the eastern and central AB, as well as three areas of the bank (around Port Alfred, the Tsitsikamma coast, and the ‘cold ridge’) that have been previously identified as contributing significantly to the overall productivity of the AB. The AB shows only a moderate degree of seasonality in NPP calculated from the VGPM, with NPP being highest in austral summer (1.7–1.8 g C m−2 d−1) and lowest in winter (0.9–1.0 g C m−2 d−1), and remains relatively high (>1 g C m−2 d−1) throughout the year, contrasting sharply with other shelf systems. Considered annually, NPP on the bank was 516 g C m−2 yr−1 (38 Mt C yr−1 when scaled to the total shelf area) which is higher than many other shelf systems though lower than the neighbouring Benguela system and is indicative of a moderately productive shelf system fuelled by perennial NPP. Comparing different sections of the AB from east to central bank, and including the three upwelling areas, highlighted that spatial differences in NPP were relatively limited; that these three upwelling areas made similar contributions to their relative proportion of the total shelf area, and that average rates of NPP are spatially similar across the bank, though notable high rates occur in some coastal upwelling areas. Interannual variability in NPP was relatively modest, varying between years by only ∼15% over the two decades assessed. Over the 21-year data set, there was a slight (∼0.26% yr−1) statistically-significant decline in calculated NPP over time for the AB as a whole, which, when examined on a pixel-by-pixel basis, indicated that most of the decline was on the central bank between 100 m and 200 m isobaths. In summer, an increase in NPP occurred on the EAB (26.5–28°E). In conclusion, the AB is a significant site of perennial moderate levels of NPP, varying little interannually and with only a slight decline in NPP over time. These factors lead to a stable environment in terms of ecosystem productivity so that the AB makes a significant contribution to the productivity of South African regional fisheries

Interannual monsoon wind variability as a key driver of East African small pelagic fisheries

Small pelagic fisheries provide food security, livelihood support and economic stability for East African coastal communities—a region of least developed countries. Using remotely- sensed and field observations together with modelling, we address the biophysical drivers of this important resource. We show that annual variations of fisheries yield parallel those of chlorophyll-a (an index of phytoplankton biomass). While enhanced phytoplankton biomass during the Northeast monsoon is triggered by wind-driven upwelling, during the Southeast monsoon, it is driven by two current induced mechanisms: coastal “dynamic uplift” upwelling; and westward advection of nutrients. This biological response to the Southeast monsoon is greater than that to the Northeast monsoon. For years unaffected by strong El-Niño/La-Niña events, the Southeast monsoon wind strength over the south tropical Indian Ocean is the main driver of year-to-year variability. This has important implications for the predictability of fisheries yield, its response to climate change, policy and resource management

Unravelling links between squid catch variations and biophysical mechanisms in South African waters

Using satellite observations, this study uncovers the biophysical drivers of the lucrative chokka squid fishery in South Africa over the last two decades (1998–2017) and addresses their potential links with low squid catches. Chokka squid fishing is crucial to the economic wellbeing of local communities. However, the squid biomass is prone to considerable fluctuations, including abrupt declines with negative socio-economic impacts. We show that the squid catch is significantly and positively correlated with satellite-derived chlorophyll-a (Chl-a, an index of phytoplankton biomass) from year to year in South African coastal waters. Two main phytoplankton blooms are observed to occur seasonally in the austral spring and autumn, peaking in October and April, respectively. From October to April, phytoplankton abundance is influenced by the occurrence of wind-driven upwelling over the South African west coast (southern Benguela) and the central Agulhas Bank (so-called Cold Ridge upwelling), while the surface currents appear more important for shelf edge processes and advection along the Cold Ridge on shorter timescales. Low squid catches are observed in 2001 and 2013 and linked to declines in Chl-a induced by weak winds and relaxed negative wind stress curl over the southwest coast in 2001, and over the southwest coast and the central Agulhas Bank in 2013. Phytoplankton phenology (bloom timing) analysis reveals absent, or shorter and delayed blooms, over the Benguela upwelling region in 2001 and both the Benguela and Cold Ridge upwelling areas in 2013. In contrast, the high catch years of 2004 and 2009, associated with elevated Chl-a, coincide with early and/or prolonged seasonal blooms. These are induced by strong winds over the Benguela upwelling and Cold Ridge areas in 2004, and by intensified negative wind stress curl over the Benguela upwelling area in 2009. These results show that the squid catch fluctuations are potentially predictable and could support policymakers seeking to improve their planning of adaptation strategies and risk mitigation

Variability of mackerel fish catch and remotely-sensed biophysical controls in the eastern pemba channel

Advances in satellite remote sensing of environmental perturbations have become important in understanding variations of ocean productivity and small pelagic fish catches. This marine resource is vital for coastal populations dependent on artisanal fishing for their income and food security, such as in coastal East Africa. In this region, the eastern Pemba Channel (Tanzania) represents a hotspot area, for a variety of marine species including small pelagics and coral reef associated species. This study examines the links between mackerel fish catch, one of the important small pelagic fish for direct consumption in the region, and changes in environmental oceanographic parameters over the period 2012–2018. The fisheries catch data is a rare local dataset, consisting of daily mackerel landings (from 2012 onwards) and supplemented by qualitative information on the mackerel fishery obtained through interviews with local stakeholders. The physical factors influencing phytoplankton biomass, and in turn, mackerel fisheries yield is investigated, using remotely-sensed chlorophyll-a (Chl-a) and Sea Surface Temperature (SST), together with Mixed Layer Depth (MLD) data from the high-resolution ocean model NEMO. We show that seasonal variations in mackerel landings are positively (negatively) correlated with Chl-a (SST) with a 1-month time lag (i.e., biophysical factors change first, mackerel stocks follow one month later). On the eastern side of the Pemba Channel, cooler SST and higher Chl-a are observed during the Southeast monsoon accompanied by increased mackerel landings, suggestive of enhanced productivity. Interannually, these relationships remain valid both for monthly and annual means, which confirms the close link between the variations of mackerel and biophysical conditions. Analysis of the Chl-a and MLD anomalies, relative to the mean, reveals that the phytoplankton blooms observed on the eastern side of the Pemba Channel, during the Southeast monsoon, are likely due to the deepening of the mixed layer, which tends to entrain cold and nutrient rich waters from greater depths to the surface. We conclude that upper ocean mixing contributes to the observed enhanced productivity along with other environmental factors. Additionally, we show how our results can be applied in the management of the mackerel resource in the Pemba Channel

Modulation of the cGAS-STING DNA sensing pathway by gammaherpesviruses

Kaposi’s sarcoma-associated herpesvirus (KSHV) is a DNA virus that is linked to several human malignancies. The cGMP-AMP synthase (cGAS) and stimulator of interferon genes (STING) pathway is able to detect KSHV during primary infection and regulates the reactivation of KSHV from latency. We screened KSHV proteins for their ability to inhibit this pathway and block IFN-β activation. One KSHV protein, vIRF1, inhibited this pathway by preventing STING from interacting with TBK1 and inhibiting STING’s phosphorylation and concomitant activation. Moreover, depletion of vIRF1 in the context of KSHV infection prevented efficient viral reactivation and replication, and increased the host IFN response to KSHV. Collectively, our results demonstrate that the modulation of this pathway is important for viral transmission and the lifelong persistence of gammaherpesviruses in the human population

Productivity driven by Tana river discharge is spatially limited in Kenyan coastal waters

The Tana River is the longest river system in Kenya (~1000 km) and contributes ~ 50% of the total river discharge to Kenyan coastal waters. The river discharges significant amounts of nutrients and sediments, reaching ~24,000 tons per day during the rainy season (March–April), into Ungwana Bay (North Kenya Banks). The bay is an important habitat for high-value Panaeid prawn species which sustain important small-scale fisheries, semi-industrial bottom trawl prawn fisheries, and is the livelihood mainstay in the surrounding counties. In this study we analysed >20 years of satellite-derived chlorophyll-a observations (Chl-a, an index of phytoplankton biomass), along with in situ river discharge and rainfall data, to investigate if the Tana River discharge is a major driver of local phytoplankton biomass in Ungwana Bay and for the neighbouring Kenyan shelf. We find that during the rainy inter-monsoon (March–April), a significant positive relationship (r = 0.63, p < 0.0001) exists between river discharge and phytoplankton biomass. There is a clear time-lag between rainfall, river discharge (1-month lag) and local chlorophyll biomass (2-months lag after discharge). Unlike offshore waters which exhibit bi-annual chl-a peaks (0.22 mg m−3 in February, and 0.223 mg m−3 in August/September), Ungwana Bay displays a single peak per annum in July (2.51 mg m−3), with indications that river discharge sustains phytoplankton biomass for several months. Satellite-derived observations and Lagrangian tracking simulations indicate that higher Chl-a concentrations remain locally within the bay, rather than influencing the broader open waters of the North Kenya Banks that are mainly impacted by the wider oceanic circulation

A Major Ecosystem Shift in Coastal East African Waters During the 1997/98 Super El Niño as Detected Using Remote Sensing Data

Under the impact of natural and anthropogenic climate variability, upwelling systems are known to change their properties leading to associated regime shifts in marine ecosystems. These often impact commercial fisheries and societies dependent on them. In a region where in situ hydrographic and biological marine data are scarce, this study uses a combination of remote sensing and ocean modelling to show how a stable seasonal upwelling off the Kenyan coast shifted into the territorial waters of neighboring Tanzania under the influence of the unique 1997/98 El Niño and positive Indian Ocean Dipole event. The formation of an anticyclonic gyre adjacent to the Kenyan/Tanzanian coast led to a reorganization of the surface currents and caused the southward migration of the Somali–Zanzibar confluence zone and is attributed to anomalous wind stress curl over the central Indian Ocean. This caused the lowest observed chlorophyll-a over the North Kenya banks (Kenya), while it reached its historical maximum off Dar Es Salaam (Tanzanian waters). We demonstrate that this situation is specific to the 1997/98 El Niño when compared with other the super El-Niño events of 1972,73, 1982–83 and 2015–16. Despite the lack of available fishery data in the region, the local ecosystem changes that the shift of this upwelling may have caused are discussed based on the literature. The likely negative impacts on local fish stocks in Kenya, affecting fishers’ livelihoods and food security, and the temporary increase in pelagic fishery species’ productivity in Tanzania are highlighted. Finally, we discuss how satellite observations may assist fisheries management bodies to anticipate low productivity periods, and mitigate their potentially negative economic impacts