South African Coast Research Articles

Shifts in Maritime Trade Routes as a Result of Red Sea Shipping Crisis Detected in TROPOMI NO2 Data

AbstractObservations from space‐borne spectrometers have been lately used to quantify shipping emissions of nitrogen oxides (ΝΟΧ). Here we present a method that enhances the shipping signal of NO2 TROPOspheric MOnitoring Instrument (TROPOMI) satellite sensor observations in order to assess the impact of the Red Sea ship attacks on NO2 levels in three important shipping routes along the Red Sea, the Cape of Good Hope, and the Gibraltar Strait. Major shipping carriers, sailing usually via the Red Sea, have responded to the attacks by transiting their fleet around the African continent. The shipping signal from TROPOMI declines by ∼55% in the Red Sea and ∼15% in the Gibraltar Strait while an increase of ∼40% is found off the South African coast between January–June 2024 and the same period in 2023. These changes correlate well with vessel statistics, demonstrating the ability to track abrupt changes in NO2 shipping levels with satellite measurements.

SNPs Analysis Indicates Non-Uniform Origins of Invasive Mussels (Mytilus galloprovincialis Lamarck, 1819) on the Southern African Coast.

Understanding the origins of invasive species is necessary to manage them and predict their potential for spreading. The mussel genus Mytilus forms an important component of coastal ecosystems in the northern and southern hemispheres. M. galloprovincialis is an important invasive species globally, first appearing on the South African coast in the 1970s. Studies using nuclear and mitochondrial DNA indicated that the invasion probably originated from the north-east Atlantic. We used fifty-five polymorphic SNPs to genotype mussels from sites across the coast of South Africa with reference samples from the Mediterranean, the Atlantic, and New Zealand to test for possible introgression of the northern and southern taxa. Low levels of genetic differentiation were confirmed, and all samples grouped with reference samples of the Atlantic form of M. galloprovincialis, supporting previous studies. The SNP genotyping, however, allowed the detection of some individuals with genotypes typical of the Mediterranean, indicating that introduced populations in South Africa do not have a uniform origin. The initial population introduced to South Africa may have been genetically heterogenous from the start, coming from a region influenced by both the Atlantic and Mediterranean. Alternatively, multiple introductions may have taken place, originating from different regions, specifically North Africa, southern Europe, and the Mediterranean, building up the final heterogeneity.

Life History Strategies Drive Meso-Scale Distribution Patterns in Coastal Benthic Macroinvertebrates.

The environment shapes the spatial distribution of species, but species also comprise suites of traits which may indicate their adaptability to a specific environment. This forms the basis of trait biogeography studies. We thus examined how a species distribution is not only influenced by its environment and traits, but by interactions among its traits. Trait information was collected for 150 intertidal macroinvertebrates along a 3000 km environmental and biogeographic gradient on the South African coast. This information was analysed, as functional entities (FEs) were species performing similar functions that have the same trait values and were further condensed into two trait domains (Reproduction and Lifestyle). We then defined Life History Strategies (LHS) as specific combinations of Lifestyle and Reproduction FEs. Seven combinations of Lifestyle and Reproduction formed LHS that dominated total biomass. Some of these LHS were ubiquitous, while others showed geographic patterns across our west-east environmental gradient. For Lifestyle, filter-feeders exhibited high abundances on the East (subtropical, oligotrophic) and West (cool-temperate, eutrophic) extremes of the biogeographic gradient, but differed between the two in size at reproductive maturity and larval development type. This similarity in functionality of feeding mechanism and mobility with different reproductive strategies suggests a trait trade-off (investment in one trait reduces resources for others) between the Reproduction and Lifestyle domains. Within the Reproduction domain, gonochoristic, annual planktotrophic reproduction was common across bioregions, reflecting spin-offs (investment in one trait facilitates another trait) among these traits. Gonochoristic investment in less frequent episodic reproduction is another trade-off, with investment in large size and delayed maturation being a trade-off for many reproductive cycles. Overall, although our data supports the habitat templet model (i.e., the importance of environmental drivers), it further indicates that species distribution patterns observed along the South African coast reflect strong trait interactions and biomass patterns related to their LHS.

Fronts divide diazotroph communities in the Southern Indian Ocean.

Dinitrogen (N2) fixation represents a key source of reactive nitrogen in marine ecosystems. While the process has been rather well-explored in low latitudes of the Atlantic and Pacific Oceans, other higher latitude regions and particularly the Indian Ocean have been chronically overlooked. Here, we characterize N2 fixation and diazotroph community composition across nutrient and trace metals gradients spanning the multifrontal system separating the oligotrophic waters of the Indian Ocean subtropical gyre from the high nutrient low chlorophyll waters of the Southern Ocean. We found a sharp contrasting distribution of diazotroph groups across the frontal system. Notably, cyanobacterial diazotrophs dominated north of fronts, driving high N2 fixation rates (up to 13.96nmol N l-1 d-1) with notable peaks near the South African coast. South of the fronts non-cyanobacterial diazotrophs prevailed without significant N2 fixation activity being detected. Our results provide new crucial insights into high latitude diazotrophy in the Indian Ocean, which should contribute to improved climate model parameterization and enhanced constraints on global net primary productivity projections.

Occurrence of Selected Pharmaceuticals in the East London Coastline Encompassing Major Rivers, Estuaries, and Seawater in the Eastern Cape Province of South Africa.

This study investigated the occurrence of ibuprofen, naproxen, sulfamethoxazole, trimethoprim, and efavirenz in water resources (river, estuarine, and sea waters) of the East London coastline, South Africa. These pharmaceuticals were previously reported to be dominant in wastewater and inland rivers of South Africa. Hence, it is important to monitor their occurrence in the coastal and marine environment. The pharmaceuticals of interest were extracted with a solid-phase extraction method and analyzed by using a liquid chromatography-quadrupole time-of-flight mass spectrometry instrument. The analytical method was validated by spiking the environmental samples with a mixture of pharmaceuticals at two concentration levels (5 and 15 μg L-1). The analytical method yielded acceptable recoveries ranging from 75 to 107%, with method quantitation limits from 0.16 to 9.44 ng of L-1. All five targeted pharmaceuticals were detected in seawater samples, with ibuprofen recording the highest concentration of 90 ng L-1. However, it was efavirenz and sulfamethoxazole with the highest concentrations of 572 and 60 ng L-1, respectively, in the Gonubie River that showed high ecotoxicological risks toward the aquatic organisms. There were no risks associated with the occurrence of other targeted pharmaceuticals. The suspect screening showed the occurrence of 57 additional pharmaceuticals in samples, with antibiotics being more dominant. The results of the present study demonstrate a need to perform a more robust investigation on the occurrence of a wide range of pharmaceuticals along the South African coasts.

Fouling communities from the South African west coast are vulnerable to cooling and ocean acidification

Changing temperature and ocean acidification are well-recognised consequences of climate change in marine systems. In contrast to global trends, the South African west coast is experiencing cooling due to increased frequency and intensity of upwelling. The implications of concurrent cooling and acidification for marine biota are poorly understood, particularly at the community level. This laboratory study assessed how cooling and acidification might affect fouling communities along the South African west coast. Communities were experimentally exposed to two temperatures, 13℃ (current) and 9℃ (cooling), and three pH treatments, 7.9 (current), 7.6 and 7.4, for 18 days. Cooling and acidification altered community structure. Species diversity declined in response to acidification but was not affected by cooling. This was driven by greatest loss of species at 7.4 pH. Notably, acidification reduced the abundance of both calcifying and soft-bodied taxa, highlighting the vulnerability of taxa like ascidians to acidification. Overall, these results highlight the dominant threat posed by acidification, even for alien taxa that are often perceived as resilient to climate change. Additionally, in regions experiencing cooling, acidification may pose a greater threat to fouling communities than thermal changes.

A new MIS 5 to MIS 2 speleothem record from Sandkraal Cave on the South African Cape south coast

AbstractWe present new stable oxygen and carbon isotope composite records (δ18O, δ13C) of speleothems from Sandkraal Cave 1 (SK1) on the South African south coast for the time interval between 104 and 18 ka (with a hiatus between 48 and 41 ka). Statistical comparisons using kernel-based correlation analyses and semblance analyses based on continuous wavelet transforms inform the relationships of the new speleothem records to other proxies and their changes through time. Between 105 and ~70 ka, changes of speleothem δ18O values at SK1 are likely related to rainfall seasonality. Variations of δ13C values are associated with changes of vegetation density, prior carbonate precipitation (PCP), CO2 degassing in the cave, and possibly variations of the abundance of C3 and C4 grasses in the vegetation. The relationships of δ18O with other proxies shift between ~70 and 48 ka (Marine Isotope Stages 4–3) so that both stable isotope records now reflect CO2 degassing, evaporation, and PCP. Similar relationships also continue after the hiatus for the deposition phase between 42 and 18 ka. Our findings support modeling results suggesting drier conditions in the study area when the Southern Hemisphere westerlies are shifted north and the paleo–Agulhas Plain is exposed.

Novel insights into the genetics, morphology, distribution and hosts of the global fish parasitic digenean Proctoeces maculatus (Looss, 1901) (Digenea: Fellodistomidae).

Larval stages of the widely distributed digenean species Proctoeces maculatus (Looss, 1901) were reported 40 years ago from South Africa in the common octopus, Octopus vulgaris Cuvier (Octopodidae). However, the absence of adult specimens and molecular data from this region has hindered a comprehensive understanding of its distribution. In this study, we collected three species of intertidal and near-shore marine fishes [Clinus superciliosus (L.) (Clinidae), Diplodus capensis (Smith) (Sparidae) and Sparodon durbanensis (Castelnau) (Sparidae)] along the South African coast and discovered adult specimens of P. maculatus at five localities. By employing a combination of morphological and molecular techniques, including 28S rDNA, 18S rDNA and COI mtDNA analyses, the first report of adult P. maculatus from South Africa is presented. The findings encompass a comprehensive morphological description and molecular data, illuminating the true distribution of this species in the region.

The value of multibeam bathymetry in marine spatial planning in South Africa: A review

Given a growing global population and shift to embrace the blue economy, a need for marine spatial planning (MSP) has emerged in South Africa to sustainably resolve the rising conflicts over the use of marine and seabed resources and services. A well-developed marine spatial plan yields numerous ecological, social and economic benefits. These are achieved through mediating between spatially conflicting economic drivers’ interests (e.g. commercial fishing, tourism, mining), preventing their activities from compromising thresholds of an environment’s sustainability. Within the MSP framework, high-resolution geospatial datasets are required to document and describe the seabed in the highest possible detail. At any scale, integrated analysis of seabed geomorphology and habitats is anticipated to greatly improve the understanding of ecosystem functioning from a multidisciplinary perspective, whilst improving MSP procedures and management of marine space. South Africa is the first of few African countries to have an approved and implemented MSP framework, but is still somewhat behind globally in implementing large-scale regional hydroacoustic surveys to cover the country’s vast offshore territory. The deficiency of hydroacoustic surveys is perhaps due to a relative lack of funds and poor communication about the value of multibeam echo-sounder (MBES) derived data, whilst marine geoscience remains a scarce skill in the country. This review paper presents a geological perspective of MSP and explores (1) the value that seabed mapping offers MSP specifically and (2) the need to increase seabed mapping with MBES, using a recently initiated project from the South African east coast as a case study. Significance: The collected MBES data (our case study) provides unprecedented seabed detail of the complex reef habitat and adjacent areas within specific management zones of the uThukela Banks Marine Protected Area. We reveal seabed features and their spatial distribution at a scale not possible using earlier (singlebeam) seabed mapping techniques. These high-resolution data will enable a better understanding of east coast marine habitats whilst contributing to improved spatial management of areas within and around the uThukela Banks Marine Protected Area.

Integrating environmental, evolutionary, and socioeconomic vulnerability to future-proof coastal conservation planning

Conservation of biodiversity remains a challenge as changing climate and other anthropogenic threats alter species distributions. Assessing vulnerability to future changes often takes solely a species- or environment-centred perspective, with few conservation plans integrating different vulnerability objectives, especially within a marine context. We evaluated conservation trade-offs associated with vulnerability measures reflecting a range of environmental, evolutionary, and socioeconomic objectives, based on contemporary and future timeframes. Using the South African coastline and three rocky shore invertebrates as a study system, we developed a framework to estimate cumulative biodiversity impacts across space and time. We compared conservation solutions obtained with the prioritizr decision support tool for individual scenarios to assess how priority areas differ between objectives and timeframes. We found that scenario solutions were more similar with a shared objective rather than timeframe. There were also no common priority areas selected across all scenarios, but most scenarios had overlapping solutions along the South African southwest coast. This study highlights the importance of integrating multiple vulnerability components, and how these are likely to have different trajectories into the future. Further, using a multi-objective approach increases the likelihood of capturing differences within objectives between now and the future, offering empirical evidence that multi-objective conservation plans can counteract uncertainties associated with future vulnerabilities.

The use of fish parasitic isopods as element accumulation indicators in marine pollution monitoring

Marine ecosystems are continuously under threat due to pollutants, which endanger marine biodiversity. The present study determines the potential use of the parasitic isopod, Cinusa tetrodontis Schjödte et Meinert, 1884, together with its fish host, Amblyrhynchotes honckenii (Bloch) for marine bioaccumulation monitoring. The concentrations of As, Cd, Cu, Mn, Ni, Pb, Se, and Zn were determined in muscle and liver tissues of infested and uninfested fish, and male and female parasites on the South African temperate south coast. The concentrations of Cu and Ni in C. tetrodontis differed significantly between two sampling sites, a near-pristine (Breede River Estuary, Witsand) and a more polluted site (harbour area in Mossel Bay). Mossel Bay isopods had higher concentrations of Ni, while Witsand isopods had higher concentrations of Cu. In contrast to fish hosts, parasitic isopods accumulated significantly higher levels of all elements except Cd. Most significant relationships between elements accumulated by C. tetrodontis and an increase of elements in fish tissues were seen in liver, rather than muscle tissue samples. Specimens of C. tetrodontis can be defined as good bioindicators for elements such as As, Cu, Mn, Ni, Pb, Se, and Zn, as they possess high bioaccumulation capabilities. This study addresses one of several future directions needed within environmental parasitology and highlights the importance of studying and utilising this host-ectoparasite model system.

Acoustic telemetry reveals the drivers behind estuary–sea connectivity of an important estuarine-dependent fishery species, Pomadasys commersonnii, in the Breede Estuary, South Africa

The spotted grunter Pomadasys commersonnii is an important estuarine-dependent fishery species known to spawn along the east coast (KwaZulu-Natal Province) of South Africa. However, recent evidence suggests that this species also spawns along the southwest coast in the Western Cape Province (WC), which has necessitated the investigation of estuary–sea movements of adult P. commersonnii in the WC, and their link with spawning season and changing environmental conditions. Seasonal gonad maturation of adult P. commersonnii (n = 112) was investigated using histology and the gonadosomatic index. Seven adult P. commersonnii were acoustically tagged and monitored in the Breede Estuary (WC) between November 2016 and March 2020. Tagged individuals spent more time in the estuary (83.5%) than in the adjacent marine environment. Sea trips (n = 90) lasted on average 3.23 (SD 4.55) days (range 1–37 days), with most sea trips (82.6%) having a duration of less than 5 days. The majority of sea trips (>50%) occurred in austral summer, which coincided with the peak spawning season. Increases in estuary water temperatures in summer and river inflow in winter also influenced the presence of tagged fish in the sea. The high degree of residency of P. commersonnii in the Breede Estuary and short sea trips, along with increased frequency of reproductively ripe fish during summer months, supports the conclusion that regional spawning is occurring along the southwest coast. We suggest that management strategies should be put in place to protect the P. commersonnii population along the South African southwest coast, especially during summer, for the recovery of this population.

Using ecological infrastructure to comprehensively map ecosystem service demand, flow and capacity for spatial assessment and planning

Ecosystem services provide substantial benefits to people, but the underlying ecosystems are under unprecedented pressure, compromising service delivery. Therefore, ecosystem services need to be integrated into conservation and management processes to secure their benefits for current and future generations. A key first step is a robust method to map ecosystem services for spatial planning. We aimed to develop and apply a broadly applicable, flexible and spatially accurate method for comprehensive ecosystem services mapping using Ecological Infrastructure, abbreviated to PROPSER. We evaluated the demand, flow, and capacity of three ecosystem services (sports events, recreation, and coastal protection) along the South African coast using causal relationships, including ecological condition of the EI, and approximated EI performance as a measure of its importance to society. This resulted in a high-resolution map of EI performance per service and a cumulative map of multiple-service performance created by integrating the three single-service maps. Altogether, there were 5127 EI sites, with EI close to urban nodes being most important. Post-hoc tests confirmed the spatial accuracy of the output maps, and the sensitivity of PROPSER to the variables and components of the indicator models. PROSPER is a comprehensive and innovative method for mapping ecosystem services that is flexible and can be widely applied. The outputs from this study have been taken up in a national spatial planning process, with several other applications discussed. We identify seven ways in which PROSPER can be advanced, and encourage further testing and application of our approach.

Supersized Potholes Discovered off South African Coast

Curious circular pits off South Africa’s Eastern Cape coast are larger than any similar feature previously recorded. Their origin remains a morphological mystery.

Euryalida (Echinodermata, Ophiuroidea) from Northwest Africa

From 2004 to 2012, ten multidisciplinary oceanographic surveys were conducted along the coast of Northwest Africa, between the Strait of Gibraltar and the northern border of Sierra Leone. A total of five species of Euryalida Lamarck, 1816 belonging to three families were captured at 29 of the 1298 stations sampled in the area. Among them, Astrodendrum juancarlosi sp. nov. is described and figured in this paper. Ophiocreas oedipus Lyman, 1879 is recorded for the first time on West African continental margin and Gorgonocephalus pustulatum (H.L. Clark, 1916), an Indo-Pacific species only known from South African coast in the Atlantic, is reported off Guinea-Bissau, greatly extending to the North its Atlantic distribution. In addition, Asteroschema inornatum Koehler, 1906, a northeast Atlantic species, is recorded for the first time in African waters, off Western Sahara, extending its range of distribution to the south. Our data also extend the bathymetric distribution of A. inornatum to shallower waters and of G. pustulatum to deeper waters. The association of some euryalids with certain species of pennatulaceans and gorgonians is also described.

Assessing the application of the revised Remane Model to fish species in a fluvially dominated cool-temperate southern African coastal system

Estuaries are ecologically important areas which support a variety of aquatic species, particularly marine and estuarine fish species. This study represents a case study of the Orange River and Estuary (ORE) to understand patterns in fish assemblages and diversity trends that were compared to the revised Remane Model predictions in an estuary with poor marine fish species richness. A total of 30 species were recorded in the River continuum that comprised 14 freshwater, 10 marine and six estuarine species. Species diversity revealed seasonal variation in fish assemblages during the high-flow and low-flow seasons but not inter-annually. The results revealed that species diversity is lower in higher salinity areas when compared to low salinity areas. These patterns are consistent with the biogeographical trend of decreasing species richness along the South African coast from east to west, however, inconsistent with Remane predictions. The extremely low marine fish richness at its lower end and the extremely large freshwater influx at its upper end are the primary causes of the inconsistency. This may reflects the unsuitability of the Remane model for the Orange Estuary. In comparison to similar river-dominated South African estuaries, the ORE has a low marine species richness. When compared to more conventional South African estuaries, the ORE has a unique biotic environment with low fish species richness of estuarine-associated marine species adjacent to the Benguela upwelling zone and therefore the region does not offer suitable habitat for such species. As a result, the ORE is not a good candidate to test the Remane Model. The data does, however, confirm the left-hand part of the Remane model, which shows a decline in the fish species richness of freshwater fish species as salinity rises towards mesohaline and polyhaline levels.

The reinstatement of Plocamium robertiae (Rhodophyta, Plocamiales) and an updated species inventory of the genus in South Africa

ABSTRACT The morphologically diverse and widespread red algal genus Plocamium has recently emerged as a source of bioactive compounds with potential application in the pharmaceutical industry. However, species identification and the taxonomy of the group remains problematic. An initial contribution to the taxonomy of Plocamium in South Africa was therefore carried out using combined morphological and molecular approaches and existing literature. Plocamium robertiae is reinstated as a distinct species based on molecular and morphological evidence, while Plocamium raphelisianum, a species from Spain, is placed in synonymy with P. suhrii. Along the South African coast, individuals of P. suhrii were genetically divergent in different bioregions and will require further investigation. Contrary to previous reports, we confirm the absence in South Africa of two Australasian species, P. microcladioides and P. mertensii, which were previosuly misidentified. The latter species likely represents a new, undescribed species in South Africa. Two additional species were also identified based on DNA but require further morphological assessment. We now recognize P. robertiae, along with eight other named species, plus five additional taxa, with varying levels of taxonomic confidence, and exclude P. microcladioides and P. mertensii from the South African flora. This study doubles the number of species recognized since the last biodiversity assessment of Plocamium and expands the distributional range of P. suhrii. Although our findings contribute an initial assessment assisted by DNA data, a full understanding of the taxonomy of Plocamium in South Africa is far from complete.

Magellan mussels Aulacomya atra from the South African coast show high diversity within populations but a lack of geographic differentiation

The Magellan mussel Aulacomya atra is a bivalve mollusc found along parts of the South African and Namibian coastline. Its numbers were low historically compared with other indigenous species but have decreased further since the 1970s owing to habitat invasion by Mediterranean mussels Mytilus galloprovincialis. We studied sequences of the mitochondrial cytochrome oxidase subunit 1 (CO1) and the nuclear internal transcribed spacer (ITS1) of A. atra to determine patterns of differentiation among three localities on the South African coastline and the phylogenetic position of these populations relative to other populations of Aulacomya species in the Southern Hemisphere. Results from both mitochondrial and nuclear genes revealed a high level of diversity within South African populations from the west and south coast, with little to no geographic differentiation among these populations. Phylogenetic trees constructed using maximum likelihood and haplotype network analysis show that individuals from all three regions sampled are intermingled in groups with low bootstrap support. Our CO1 sequences exhibited a phylogeographic structure concordant with the spatial distribution in South Africa, Argentina, Chile and New Zealand. However, results for ITS1 showed a lack of differentiation over a large spatial scale stretching from South Africa to New Zealand. Future studies should include additional samples from across the species’ distributional range and the examination expanded to include genetic markers with adaptive significance.

April 2022 Floods over East Coast South Africa: Interactions between a Mesoscale Convective System and a Coastal Meso-Low

Extreme rainfall occurred over the South African east coast during 10–12 April 2022, leading to over 500 deaths and massive damage. This study seeks to understand a key feature, namely the progression of the rainfall maxima from the northern KwaZulu-Natal (KZN) coast during the night of 10–11 April by ~550 km to the Eastern Cape coast about 48 h later. The large-scale circulation was dominated by a cut-off low over the South African interior with a strong ridging anticyclone southeast of the country in the South Indian Ocean. Satellite, rain gauge, and ERA5 reanalysis are used to show that the timing and location of the heaviest rainfall are closely tied to, firstly, the formation of a Mesoscale Convective System (MCS) at ~0300UTC April 11 on the northern KZN coast which tracked south and then offshore, and secondly, a meso-trough which formed a coastal meso-low by ~2100 UTC April 11. The meso-low tracked south over the warm waters of the Agulhas Current before strengthening into Subtropical Depression Issa. Mesoscale interaction between the MCS and coastal meso-low determined the positioning and timing of the strongest onshore low-level jet, moisture convergence and uplift, and hence the progression of the heavy rainfall down the coast. Such mesoscale interaction has not previously been documented in southern Africa or the Southern Hemisphere.

Making Points: The Middle Stone Age lithic industry of the Makgadikgadi Basin, Botswana

Studies of early human occupation of Africa over recent decades have profoundly changed how we understand our early ancestors, their inventiveness and adaptability. The spread of Homo sapiens to new environmental settings, the expansion of diet breadth, the development of more complex technology and the use of personal ornaments have all been recognized at well-documented Middle Stone Age (MSA) cave and shelter sites, particularly along the South African coast. This paper addresses two under-represented aspects of MSA research: open-air sites and the African interior. We present here recent surveys and excavations in Ntwetwe Pan, Botswana, a remote, open landscape, that formerly contained a vast palaeolake. The five excavated sites yielded assemblages composed exclusively of silcrete, a locally available raw material. The lithic industry at these sites was deposited during dry periods following palaeolake high stands dating to c.128–81 ka and c. 72–57 ka. This industry, characterized by a limited toolkit dominated by highly retouched unifacial and bifacial points, is not previously documented but shows similarities to dated MSA sites of equivalent age in north-western Botswana and Zimbabwe. Combined, these exposed open-air sites document the successful MSA adaptation to a hydrologically dynamic, interior landscape and arguably display MSA behavioural patterns that complement and balance the more well-documented perspectives from coastal cave and shelter sites.