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An investigation into the ocean response to a protracted (>48 h) strong south-westerly wind event averaging 9.6 m/s on the eastern Agulhas Bank, South Africa, using in situ instrument data from Algoa Bay and a high resolution (dx ∼1 km) ROMS ocean model, is presented. A coastal trapped wave (CTW) was shown to be associated with the event, the peak amplitude of which increased as it travelled eastward through the domain. Alongshore current reversals to the full depth were seen in both the model and two acoustic doppler current profiler (ADCP) moorings (30 m bottom depth) as the CTW traversed the study domain, with strong currents exceeding 1 m/s developing directly to the south of Cape St Francis and Cape Recife at the peak of the wind event within the model. In a model run with wind forcing removed, the effects of remote wind forcing were shown to be a significant contributor to local circulation during strong wind events, suggesting that an estimated 61% of the total eastward transport of shelf water over the entire period of the event was due to remote forcing. In the no-wind model, a short lived anticyclonic rotating feature forms in the lee of Cape Recife in Algoa Bay shortly after the peak of the CTW, in contrast to the reference model, where instead a broad anticyclonic flow throughout the bay establishes.

Sea-level rise is a significant threat to salt marshes. However, these habitats can respond by increasing their relative elevation, or by migrating into adjacent areas. Here we provide the first re...

Net primary production (NPP) is indicative of the energy available to an ecosystem, which is central to ecological functioning and biological carbon cycling. The Southern Ocean’s Weddell Sea (WS) represents a point of origin where water masses form and exchange with the atmosphere, thereby setting the physical and chemical conditions of much of the global ocean. The WS is particularly understudied near Larsen C Ice Shelf (LCIS) where harsh sea-ice conditions persist year-round. We measured size-fractionated rates of NPP, nitrogen (N; as nitrate, ammonium, and urea) uptake, and nitrification, and characterized the phytoplankton community at 19 stations in summer 2018/2019, mainly near LCIS, with a few stations in the open Weddell Gyre (WG) and at Fimbul Ice Shelf (FIS). Throughout the study region, NPP and N uptake were dominated by nanophytoplankton (3-20 μm), with microphytoplankton (>20 μm) becoming more abundant later in the season, particularly at FIS. Here, we observed high phytoplankton biomass and diversity, and the community was dominated by diatoms known to enhance carbon export (e.g., Thalassiosira spp.). At LCIS, by contrast, the community comprised mainly Phaeocystis Antarctica. In the open WG, a population of small and weakly-silicified diatoms of the genus Corethron dominated the phytoplankton community. Here, euphotic zone-integrated uptake rates were similar to those at LCIS even though the depth-specific rates were lower. Mixed-layer nitrification was below detection at all stations such that nitrate uptake can be used as a proxy for carbon export potential sensu the new production paradigm – this was highest near FIS in late summer. Our observations can be explained by melting sea ice near the ice shelves that supplies iron and enhances water column stratification, thus alleviating iron and/or light limitation of phytoplankton and allowing them to consume the abundant surface macronutrients. That the sea ice melted completely at FIS but not LCIS may explain why late-summer productivity and carbon export potential were highest near FIS, more than double the rates measured in early summer and near LCIS. The early-to-late summer progression near the ice shelves contrasts that of the open Southern Ocean where iron is depleted by late summer, driving a shift towards smaller phytoplankton that facilitate less carbon export.

The summer of 2012/2013 signified the end of the dry phase in the St Lucia estuarine system that lasted for over a decade. The increased rainfall coupled with the partial re-connection of the Mfolozi River to the estuarine system shifted St Lucia to a new limnetic state. With the increased availability of habitat due to the higher water level, it was expected that microalgal biomass and abundance would rapidly increase through recruitment from refuge areas i.e. South Lake and new introductions. Microalgal and physico-chemical data were collected at three sites within the Mfolozi/Msunduzi River and at 23 sites within the St Lucia estuarine system between June 2014 and February 2015. Results from this study indicated low biomass for both phytoplankton ( −1 ) and microphytobenthos ( −2 ) because of local and external drivers. These included limited nutrient and light availability, variable water residence times, biomass dilution and heterogeneity of the sediment. The high spatio-temporal variability limits the effectiveness of using the microalgal communities to detect change in the estuarine lake. In addition, significant intrasystem differences were observed between the three main lake basins and Narrows, due to the influence of the freshwater input from the Mfolozi River. This study provides insight into the spatio-temporal variability of physico-chemical conditions and microalgal communities during the 2014–2015 limnetic state.

Coastal wetlands are vulnerable to sea-level rise (SLR) but are also valued for their potential to provide effective nature-based solutions to climate change mitigation and adaptation. Ecological benefits from these ecosystems can be constrained under urban settings by anthropogenic disturbances and pressures, so restoration activities are promoted as a management approach. Here we report on the potential for restoration of disused commercial salt extraction pans to enhance carbon (C) sequestration in the urban Swartkops Estuary, South Africa. We also considered the impact of SLR to 2100 on the distribution of estuarine habitats, the vulnerability of built infrastructure to tidal flooding, and how C sequestration is projected to change over time using the Sea-Level Affecting Marshes Model (SLAMM). Potential restoration of all salt pans (320 ha) to estuarine habitat was estimated to result in a gain of 67 850 Mg C. Establishing tidal connectivity was investigated as a potential restoration action, but most of the salt pan area was above the elevation of the current tidal range and would require excavation. Although conversion of the salt pans to estuarine habitat was predicted to occur without intervention under SLR, 44% of the original area would remain unchanged. Restoring hydrological connectivity to the estuary for these salt pans would significantly increase the extent of transitional/floodplain marsh, even under SLR to 2100. C sequestration was predicted to be 15% higher (54 614.8 Mg C) by 2100 if the salt pans could be restored, compared to if no action is taken. Overall, restoration of the salt pans has the potential to enhance C sequestration, but SLR will still cause large losses of supratidal marsh due to ‘coastal squeeze’ and extensive tidal flooding of developed areas by 2100 in the lower reaches of the estuary. A full-scale restoration approach for the Swartkops Estuary could use C sequestration potential to fund the project through carbon offsetting if the revenue exceeds the cost of the restoration activities, but additional social and ecological goals also need to be incorporated if the outcome is to be holistic and beneficial.

Marine epilithic diatom abundance and species richness are highly variable along the South African coastline. To determine the variability in spatial diversity and benthic–pelagic​ exchanges, we conducted a baseline study of the Bird Island ecosystem in Algoa Bay. Diatom samples were collected from the rocky substrate and the adjacent water column in conjunction with physico-chemical variables at five localities around the island. Species belonging to Achnanthes, Cocconeis, Licmophora and Navicula genera were found to be widely distributed around the island. Diatom species abundance and diversity varied around the island and a dominance of typically benthic species in the surf zone, coupled with a low abundance of truly planktonic species, was evident. The low number of planktonic diatoms in the water column and their absence in benthic samples in this study suggests an intertidal system driven largely by benthic diatoms. Elevated dissolved inorganic nitrogen (DIN), indicative of the guano influence from resident seabirds, along with temperature and turbidity, influenced the observed diatom composition and distribution. This study reveals an interplay between benthic and planktonic diatoms in the nearshore environment providing some insight into their contribution to the intertidal and subtidal food web. It further provides important information for future comparisons of benthic diatoms on Bird Island in light of their ecological indicator properties under global environmental change scenarios for this region.

Living peritidal stromatolites forming at the interface of coastal groundwater seepage and regular marine input are known from only a few locations globally, including South Africa, Western Australia and Northern Ireland. In contrast to modern stromatolites from exclusively fresh or marine waters, which persist due to high calcium carbonate saturation states or hypersaline and erosive conditions (which exclude organisms that might disrupt or out-compete the stromatolite-forming benthic microalgae), the factors supporting stromatolite formation at peritidal locations have not been well-documented. Therefore, the aim of this study was to investigate the fine-scale physico-chemical parameters in terms of pool temperature, salinity and nutrient dynamics at three representative sites along the coastline near Port Elizabeth, South Africa. These parameters were assessed with reference to potential physical, meteorological and ocean drivers using a linear or linear mixed-effects modelling approach. Results demonstrate that nutrient inputs into the pools supporting the majority of stromatolite accretion (barrage pools) are driven by groundwater seepage site-specific properties related to anthropogenic occupation (dissolved inorganic nitrogen; DIN) as well as marine water incursion (dissolved inorganic phosphorus; DIP). Pool temperature is a function of seasonal ambient variability while salinity reflects regular state shifts from fresh to marine conditions, which are related to tidal amplitude and swell height. The regular marine incursions likely promote benthic primary biomass in the phosphorus-limited stromatolite pools, as well as preclude organisms which might otherwise outcompete or disrupt the stromatolite microalgae due to intolerances to extreme (~ 1.5 to ≥ 30) salinity variability.

A survey of six seamounts and two transects through the subtropical convergence zone (SCZ) in the South Indian Ocean in November and December 2009 showed a strong latitudinal gradient from the subtropics to the Sub-Antarctic Front. Concentrations of oxygen, nitrate, nitrite, soluble reactive phosphorous as well as phytoplankton biomass (measured as chlorophyll a ) increased while salinity and temperature decreased with an increase in latitude. These differences resulted in significant differences between seamounts. The chlorophyll a maximum became shallower at higher latitudes, changing from a depth of ~85 m in the subtropics to ~35 m over the seamounts and in the SCZ. The mixed layer depth also increased from ~50 m in the subtropics to ~100 m at higher latitude stations. The N:P and N:Si ratio indicated that NO 3 - was limiting at all the seamounts except one, at which SiO 4 was the limiting nutrient. The phytoplankton community also showed a latitudinal gradient with decreasing diversity and a change in dominance from dinoflagellates in the tropics to diatoms towards the SCZ. The dominant diatom genus of the survey (>50% of the cell counts) was Pseudo-nitzschia . Nutrients exhibited an inverse linear relationship with temperature and salinity. The oligotrophic subtropical areas differed from the mesotrophic seamounts in temperature while waters over seamounts north and south of the Agulhas Return Current (ARC) differed in salinity. The phytoplankton (148 taxa) responded to these differences, showing three communities: subtropical seamount phytoplankton (Atlantis Seamount, Walters Seamount and off-mount samples), phytoplankton of the waters north of the ARC (Melville Bank, Sapmer Bank, Middle of What Seamount) and phytoplankton south of the ARC (Coral Seamount, SCZ1) characterised by a bloom of Phaeocystis antarctica. The environmental drivers most strongly linked to these observed differences were nitrate, temperature and oxygen. These environmental drivers displayed a clear latitudinal gradient unaffected by mesoscale variability of the ARC eddy field and allowing the three phytoplankton communities to persist. Phytoplankton biomass was enhanced in the shallow (

Salt marshes are highly productive and biologically diverse coastal wetlands that are threatened by rising sea-level. Salt marsh habitats within the Swartkops Estuary were examined to determine their structure along an elevation gradient and how this structure has changed over the past seven decades, what the primary drivers of this structure were and whether the salt marsh surface is stable, rising or declining relative to current and future sea-level rise. Relative sea-level has been rising by 1.82 mm·year − 1 over the past 36 years, with a short-term trend of 7.48 mm·year − 1 measured during the study period. GIS analyses showed that during the last 70 years, losses of floodplain, intertidal and supratidal salt marsh are mainly attributed to developmental pressure. The main environmental drivers influencing salt marsh distribution were soil moisture and elevation. Elevation dictates tidal inundation periodicity and frequency, and thus acts to influence all edaphic factors influencing vegetation distribution. Rod Surface Elevation Table results for the past six years indicate that the salt marsh surface elevation is keeping pace (2.98 ± 2.34 mm·year − 1 ) with historic relative sea-level rise (RSLR), but at an accelerated RSLR, only two of the eight RSET stations show an elevation rate surplus. These results should be interpreted with caution though because of the short time-series (RSET and RSL) and the high likelihood that the current ratio of sediment elevation change will be accelerated in response to the increased sea-level rise.

Contrary to global production, most fibers floating in the ocean are not synthetic but natural fibers of animal or plant origin., Microfibers are ubiquitous contaminants of emerging concern. Traditionally ascribed to the “microplastics” family, their widespread occurrence in the natural environment is commonly reported in plastic pollution studies, based on the assumption that fibers largely derive from wear and tear of synthetic textiles. By compiling a global dataset from 916 seawater samples collected in six ocean basins, we show that although synthetic polymers currently account for two-thirds of global fiber production, oceanic fibers are mainly composed of natural polymers. µFT-IR characterization of ~2000 fibers revealed that only 8.2% of oceanic fibers are synthetic, with most being cellulosic (79.5%) or of animal origin (12.3%). The widespread occurrence of natural fibers throughout marine environments emphasizes the necessity of chemically identifying microfibers before classifying them as microplastics. Our results highlight a considerable mismatch between the global production of synthetic fibers and the current composition of marine fibers, a finding that clearly deserves further attention.

Spring and summer Southern Ocean phytoplankton communities have been well characterized, but winter communities are often overlooked. Diatoms are a major contributor to Southern Ocean particulate organic carbon (POC) production and export, and exert a strong control on Antarctic surface and Subantarctic thermocline nutrient concentrations, thus influencing the low-latitude nutrient supply. Understanding diatom distribution, seasonal community progression, and diatom-nutrient interactions is vital for improving biogeochemical models, particularly as climate change alters polar phytoplankton communities. We investigated the distribution of nanophytoplankton (≥3 μm) and their associated biogeochemical environments along 30°E across the Indian Southern Ocean (Subtropical Zone; STZ to Antarctic Zone; AZ) in July 2017. Phytoplankton productivity inferred from chlorophyll-a was low compared to previously-published summertime values. Mixed-layer nitrate (NO3−) and phosphate (PO43−) concentrations were similar to existing summer measurements, likely due to a combination of deep mixing and biological uptake, while silicic acid (Si(OH)4) was high relative to summer, particularly south of the Polar Front (PF). The PF emerged as an important biogeochemical boundary separating relatively high chlorophyll-a, flagellate-dominated northern waters from southern waters characterized by low chlorophyll-a and diatom-dominated communities. Mixed layer-integrated biogenic silica (bSi) decreased 12-fold from the southern AZ to the STZ, resulting in a strong south-north gradient in bSi-per-chl-a (from 3.6 to 0.1 mol/g) and bSi-per-POC (from 0.22 to 0.016 mol mol−1). We attribute this to a high abundance of heavily-silicified diatom species (e.g., Fragilariopsis spp., which dominated the AZ diatom community) and a limited contribution of other phytoplankton to chlorophyll-a and POC to the south – indeed, diatoms constituted 5–67% of the total POC south of the PF and only 3–7% to the north. While mixed-layer Si(OH)4 concentrations decreased more than NO3− across the PF, likely due to preferential Si(OH)4 consumption by iron-limited diatoms, our data imply a lower ratio of Si(OH)4 to NO3− uptake compared to summer. This suggests that iron limitation may be less severe in the AZ in winter, at least in the west Indian sector. We conclude that AZ diatoms impact the low-latitude nutrient supply and are potentially important for carbon export in winter, despite the lower productivity of the Southern Ocean during this season.

Microbial mats were the dominant habitat type in shallow marine environments between the Palaeoarchean and Phanerozoic. Many of these (termed ‘microbialites’) calcified as they grew but such lithified mats are rare along modern coasts for reasons such as unsuitable water chemistry, destructive metazoan influences and competition with other reef-builders such as corals or macroalgae. Nonetheless, extant microbialites occur in unique coastal ecosystems such as the Exuma Cays, Bahamas or Lake Clifton and Hamelin Pool, Australia, where limitations such as calcium carbonate availability or destructive bioturbation are diminished. Along the coast of South Africa, extensive distributions of living microbialites (including layered stromatolites) have been discovered and described since the early 2000s. Unlike the Bahamian and Australian ecosystems, the South African microbialites form exclusively in the supratidal coastal zone at the convergence of emergent groundwater seepage. Similar systems were documented subsequently in southwestern Australia, Northern Ireland and the Scottish Hebrides, as recently as 2018, revealing that supratidal microbialites have a global distribution. This review uses the best-studied formations to contextualise formative drivers and processes of these supratidal ecosystems and highlight their geological, ecological and societal relevance. Dynamic interchanges between salinity states both exclude many destructive metazoans and competitors and provides optimal nutrient conditions for benthic microbial and microalgal growth. The outflowing groundwater seeps are alkaline and rich in calcium carbonate, which reflects local catchment geological processes. These habitats support a diverse microbial community dominated by Cyanobacteria as well as some metazoan species previously unknown to science, or unknown for the region. Several taxa (from invertebrates to fish) utilise this environment as refugia. Supratidal microbialites are important coastal features because of the organisms they support and the ecological processes that they facilitate, such as habitat connectivity. Culturally and socially, the value of these habitats is increasingly being appreciated, for example as traditional freshwater supply points or as an unrealised geotourism opportunity. This review also frames new information about threats, opportunities for future research and conservation trajectories for these unique geobiological habitats.

Recently-discovered peritidal stromatolite ecosystems in South Africa form at the interface of freshwater seeps and the ocean intertidal zone, sharing several similarities with both tidal pool and estuarine ecosystems. While the overall ecology of tidal rock pools has been well studied, the dynamics of the phytoplankton assemblage have been comparatively neglected. In addition, there are no studies to date which describe the dynamics of phytoplankton within a habitat associated with stromatolites. The aim of this study was to investigate the coarse-scale phytoplankton community composition of a series of peritidal pools associated with living stromatolites, using a spectral fluorescence analysis tool, in relation to source-specific drivers related to both freshwater and marine forces. Three sites were sampled monthly from January to December 2014. Physico-chemical, biotic and meteorological parameters were recorded to assess some of the factors which might influence the phytoplankton size-fractionation and community composition using a generalised linear modelling approach. Results indicate that fresh or marine pool state, temporal differences associated with season, macronutrients (N and P), and benthic microalgal biomass are important drivers of the phytoplankton assemblages. Specifically, a transition from fresh to marine pool conditions resulted in an increased abundance of smaller phytoplankton size fractions and a shift from Chlorophyta and Cyanophyta to Bacillariophyta and Cryptophyta. Overall, the community was dominated by Chlorophyta and Bacillariophyta. There was consistency between the drivers and composition of the phytoplankton community compared to those from the few other comparable published studies. Furthermore, this study demonstrates a system which is dominated by benthic rather than pelagic microalgae in terms of biomass, thereby supporting the persistence of actively accreting stromatolites.

The South African coastline is just over 3000 km in length yet it covers three major biogeographic regions, namely subtropical, warm temperate and cool temperate. In this review we examine published information to assess the possible role of climate change in driving distributional changes of a wide variety of organisms around the subcontinent. In particular we focus on harmful algal blooms, seaweeds, eelgrass, mangroves, salt marsh plants, foraminiferans, stromatolites, corals, squid, zooplankton, zoobenthos, fish, birds, crocodiles and hippopotamus, but also refer to biota such as pathogens, coralline algae, jellyfish and otters. The role of pioneers or propagules as indicators of an incipient range expansion are discussed, with mangroves, zoobenthos, fishes and birds providing the best examples of actual and imminent distributional changes. The contraction of the warm temperate biogeographic region, arising from the intrusion of cool upwelled waters along the Western Cape shores, and increasingly warm Agulhas Current waters penetrating along the eastern parts of the subcontinent, are highlighted. The above features provide an ideal setting for the monitoring of biotic drivers and responses to global climate change over different spatial and temporal scales, and have direct relevance to similar studies being conducted elsewhere in the world. We conclude that, although this review focuses mainly on the impact of global climate change on South African coastal biodiversity, other anthropogenic drivers of change such as introduced alien invasive species may act synergistically with climate change, thereby compounding both short and long-term changes in the distribution and abundance of indigenous species.

Extant marine stromatolites act as partial analogues of their Achaean counterparts, but are rare due to depleted ocean calcium carbonate levels and suppression by eukaryotic organisms. Unique, peritidal tufa stromatolites at the interface between marine and freshwater inputs were discovered in South Africa in the past decade. Our aim was to investigate the benthic microalgal community (green algae, diatoms and cyanobacteria) of these stromatolites to assess succession and dominance patterns using real-time, in situ measurements of algal concentrations and composition. These biological measurements were modelled using generalized linear modelling (GLM) multivariate statistics against water physical and chemical parameters measured at regular monthly intervals, from January to December 2014. Salinity peaked and temperature dipped in winter, with both correlated to microalgal community change (GLM: P < 0.01). Diatoms and cyanobacteria, which construct the stromatolites, were consistently the dominant groups within the algal community, with minimal green algae present throughout the year. Importantly, this demonstrates a unique, relatively stable microalgal stromatolite community as opposed to those of other marine stromatolites, which likely require seasonal and stochastic disturbance to persist. This has implications in terms of interpreting community succession and differential layering in modern and fossilized stromatolites respectively.

The knowledge on the composition and spatial distribution of marine benthic diatoms around the coast of South Africa remains limited. Epilithic diatom assemblages from natural intertidal rocky substrate and physico-chemical variables were investigated during July–August in 2016 and 2017 along the South African coastline. A total of 85 diatom taxa from 31 genera were observed at 15 sites along the coast. Taxa with the highest contribution included Nitzschia (9 species), Cocconeis (7 species) and Achnanthes (6 species) and the observed Shannon–Wiener diversity (H’) during the study varied from 0.44 (Kraalbaai) to 2.09 (Bird Island). Non-metric multidimensional scaling ordination (nMDS) separated the diatom assemblages into three groups with 20% similarity among sites (grouped according to coastal sections) and PERMANOVA analysis revealed a significant difference between the coastal sections. The observed diatom composition was shown to be influenced by both nutrient concentrations along the west coast and temperature along the east coast. This study provides insights on the abundance and distribution patterns of marine littoral diatoms along the coastline and the potential environmental drivers. The observed variations in diatom composition and distribution warrant further investigations if they are to be considered as potential indicator species of change.

New molecular and morphological insights are presented on Campylosira africana and two new species, Extubocellulus cupola sp. nov. and Plagiogrammopsis castigatus sp. nov. Species descriptions were based on LM/SEM micrographs and a data set with concatenated sequences of SSU, rbcL and psbC loci constructed from 56 cymatosiroid strains isolated from global geographic locations. Extubocellulus cupola is distinguished by a mesh-like marginal ridge and dome-shaped areolation, and P. castigatus, by a prominent marginal extension at the valve center. Campylosira africana, a species from South Africa described by Professor Malcolm Giffen, has never been documented through LM or SEM, which led some authors to place it in synonymy under Campylosira cymbelliformis. We confirm that C. africana is a distinct species and provide microphotographic documentation and DNA sequences. We present morphological evidence for the well-known cymatosiroid species Extubocellulus spinifer possessing complete pili, and we emend the generic description of Extubocellulus.

Six large solitary meanders in the Agulhas Current, so-called Natal Pulses, propagated down the eastern coast of South Africa between 2009 and 2011. Their influence on the coastal waters between Port Alfred and Algoa Bay, on the far eastern Agulhas Bank, was measured by thermistor strings moored at 30–80 m bottom depths and two current metres (30 m bottom depth) located at both sides of Algoa Bay. During all events active upwelling lasting 1–3 weeks was observed over the inner shelf and in Algoa Bay. During upwelling the isotherms ascended at an average rate of 1.8 m day −1 as the cold bottom layer increased in thickness to 40–60 m, although upwelled water did not break the surface in all cases. Cold water remained in the area for a further 2–3 weeks. During three Natal Pulses the water temperatures at the outer moorings initially increased as the plume of the leading edge (crest) of the meander moved onshore. During one Natal Pulse upwelling was recorded before the warm water plume impacted the moorings. At the onset of upwelling currents switched to the southwest in the case of Bird Island and southward at the Cape Recife inner-bay site and reached a maximum speed of 80 cm s −1 . During all Natal Pulses cold bottom water (10–12 °C) flooded over the 80 m bottom depth moorings as the crest of the meander moved onshore, but also around the same time the core of the Agulhas Current began to move offshore. In all cases upwelling was wide-spread.

The family Cymatosiraceae, composed of two subfamilies (Cymatosiroideae and Extubocelluloideae), are elongate, non-pennate diatoms and are commonly reported in marine planktonic and benthic assemblages all over the world. The combination of the gross bilateral symmetry of the frustule and radial symmetry of the valve poration, distinct pore fields at the valve apices and DNA sequence data place this family in the controversial diatom class Mediophyceae, sister to the pennate diatoms. The relationships of the Cymatosiraceae within the Mediophyceae, and the monophyly of the two cymatosiroid subfamilies, have become less stable with the addition of new DNA sequence data. In this paper, we examine 24 cymatosiraceaen strains, including the new taxa Lambertocellus africana (Dąbek & Witkowski) Dąbek, Witkowski & Ashworth comb. nov., Leyanella probus Ashworth, Dąbek & Witkowski sp. nov., and Leyanella pauciporis Ashworth, Dąbek & Park sp. nov. to create the most complete molecular phylogeny of the Cymatosiraceae to date, using a three-gene (SSU, rbcL and psbC) dataset. The results of the phylogenetic analysis support the monophyly of the Cymatosiraceae, but not the monophyly of the subfamilies Cymatosiroideae and Extubocelluloideae. The phylogenetic analysis also suggests a close relationship of the Cymatosiraceae to the family Eupodiscaceae. The phylogenetic results have lead us to re-evaluate the taxonomy of Lambertocellus africana, which is sister to Cymatosira lorenziana rather than Minutocellus as suggested in the original description. This article is protected by copyright. All rights reserved.

Spartina alterniflora Loisel., widely recognised as an aggressive invader of estuaries and salt marshes around the world, was discovered growing in the temporarily open/closed Great Brak Estuary on the southern Cape coast of South Africa in 2004. This is the first record of this invasive plant in Africa as well as its first occurrence in an estuary that closes to the sea. Plant traits and sediment characteristics were measured in 2009 and 2011 and found to be comparable to those reported elsewhere. Prior to the 2011 sampling, S. alterniflora stands had been flooded for almost eight months. As a result, sediment redox potential (-268 + 4 mV) was significantly lower in 2011. Sediments were mostly clay in 2009 (71 ± 0.01%) compared to a predominance of sand in 2011 (40 ± 0.02%). These differences were related to the artificial breaching of the estuary one month prior to sampling in March 2011. The grass currently occupies 1.1 ha in the salt marsh, sandflat and mudflat habitats of the estuary where its cover is expanding at a rate of 0.162 ha y–1. Individual stands numbered about 12 in 2006, but have increased to 24 in 2011. These stands are expanding laterally at 0.9 m y–1 although the long period of inundation during 2010 reduced this to 0.6 m y–1. Expansion is due to vegetative spread as an analysis of the sediment seed bank showed no S. alterniflora seeds and very few salt marsh seeds (1 132 seeds m–2). If left unchecked, S. alterniflora has the potential to replace 42.9 ha or 41% of the total estuary habitat in the Great Brak Estuary, but also has the potential to invade other estuaries in South Africa, especially those with extensive intertidal habitat and containing S. maritima (19 estuaries in total). This study illustrates the adaptive potential of this invasive marsh plant and indicates the possibility of invasion in seasonally closed estuaries in other locations around the world.Keywords: biomass, closed estuary, cordgrass, expansion rate, habitat loss, intertidal habitatAfrican Journal of Marine Science 2012, 34(3): 313–322

The Orange Estuary lost 27% (276 ha) of its wetland area near the mouth as a result of bad management practices during the 1980s. The salt marsh has been unable to recover over the last 20 years because of the persistently high soil and groundwater salinity. In 2006, a 1 in 5 year flood occurred that completely covered the desertified salt marsh and floodplain with freshwater. The flood was followed by an above average (>45 mm) winter rainfall. Soil and groundwater sampled in April and August 2004 were compared with 2006 data to quantify the impact of the flood and rainfall event. It was hypothesised that the two freshwater events would significantly reduce the soil and groundwater salinity. However, the results showed no significant difference in sediment electrical conductivity throughout the soil profile over the four sampling periods. Soil moisture and organic content however increased significantly after these events in the surface soil layer. The flood deposited silt and scoured sand from the surface layers in significant quantities. The depth to groundwater in the desertified marsh retained a similar pattern after the flood despite 15 cm changes in depth in places. In 2004 a clear groundwater electrical conductivity gradient was present extending from the less saline north part of the marsh (0–15 mS cm −1 ) to the central part (120–135 mS cm −1 ) and decreasing again towards the south (60–75 mS cm −1 ). The flood served to even out the groundwater salinity across the desertified marsh (60–90 mS cm −1 ). The flood and high rainfall had a limited impact on the soil and groundwater characteristics. The few significant changes that were recorded were mostly restricted to the surface soil layers and on a small spatial scale. The rainfall did however create numerous pools of low salinity ( −1 ) water on the marsh surface that provided a brief opportunity for salt marsh seeds to germinate. A further benefit of the flood was the increased tidal reach into the desertified marsh importing freshwater from the river mouth and exporting salt. Despite these responses it is unlikely that the hypersaline salt marsh will revegetate naturally. Human intervention is needed to ensure the rehabilitation of this important Ramsar site.

The Olifants Estuary is one of only three permanently open estuaries on the West Coast and is ranked third in terms of conservation importance of all estuaries in South Africa. It has the largest supratidal (143 ha) and floodplain (797.1 ha) salt marshes in the country. Intertidal salt marsh covers 91.94 ha, reeds and sedges 60.05 ha and the submerged macrophyte Zostera capensis 47.72 ha. Correspondence analysis revealed intertidal, supratidal, floodplain and terrestrial plant community types within the studied estuary. The species composition of these communities was the same for the lower, middle and upper reaches of the Olifants Estuary, with the exception of the supratidal community type in the upper reaches that consisted of halophytes with a lower salinity tolerance range rather than the typical dense monospecific stands of Sarcocornia pillansii. The environmental variables that had the greatest influence on the distribution of the dominant salt marsh species, S. pillansii, included soil moisture, distance from the estuary, elevation above mean sea level, and depth to the water table. The most important ecological driver for salt marsh vegetation, especially along the arid West Coast of southern Africa, is moisture. The low rainfall and irregular occurrence of advection sea fog increases the importance of a shallow (

The Orange River estuary is a Ramsar site that has been placed on the Montreux Record following the degradation of 300 ha of salt marsh. The groundwater and surface sediments are hypersaline and above the tolerance range of the dominant plant Sarcocornia pillansii. This study measured the sediment characteristics in 2005 (dry conditions) and in 2006 (flood and high rainfall). The sediment EC ranged from 120.9±4.7 mS cm−1 in 2005 to 52.5±4.8 mS cm−1 in 2006 with sediment moisture content sufficient for the germination of seed during both years (9.7±0.7%). The small areas of remaining S. pillansii have the potential to produce 40 billion seeds, which would be sufficient to revegetate the desertified marsh, but due to hypersaline sediment conditions the successful establishment and survival of the seedlings remain low. Many seeds (3616 m−2) and seedlings (1296 m−2) were found in drift lines in 2006. Microhabitats created by the adult vegetation also provided favourable conditions for seed germination. Laboratory studies indicated that seeds of S. pillansii germinate best in freshwater (40% at 0 psu compared to 5% at 35 psu). Exposure to hypersaline conditions (70 psu) decreased the viability of the seeds. The potential of the marsh to rehabilitate naturally therefore depends on sufficient freshwater entering the marsh.

Extant marine stromatolites act as partial analogues of their Achaean counterparts, but are rare due to depleted ocean calcium carbonate levels and suppression by eukaryotic organisms. Unique, peritidal tufa stromatolites at the interface between marine and freshwater inputs were discovered in South Africa in the past decade. Our aim was to investigate the benthic microalgal community (green algae, diatoms and cyanobacteria) of these stromatolites to assess succession and dominance patterns using real-time, in situ measurements of algal concentrations and composition. These biological measurements were modelled using generalized linear modelling (GLM) multivariate statistics against water physical and chemical parameters measured at regular monthly intervals, from January to December 2014. Salinity peaked and temperature dipped in winter, with both correlated to microalgal community change (GLM: P0.01). Diatoms and cyanobacteria, which construct the stromatolites, were consistently the dominant groups within the algal community, with minimal green algae present throughout the year. Importantly, this demonstrates a unique, relatively stable microalgal stromatolite community as opposed to those of other marine stromatolites, which likely require seasonal and stochastic disturbance to persist. This has implications in terms of interpreting community succession and differential layering in modern and fossilized stromatolites respectively.

The distribution of Sarcocornia pillansii (Moss) A.J. Scott was determined by water-table depth and electrical conductivity (EC) of the groundwater. Where the groundwater was accessible ( −1 ), S . pillansii extended its roots down to the water-table where a suitable water potential gradient was shown to exist between the soil and roots. In areas where the groundwater was too deep and/or hypersaline, the plants grew on hummocks. The unconfined aquifer below the floodplain is linked to the estuary and although diurnal tidal waves were dampened, water-table level fluctuations were recorded between tidal events. The complex geomorphology of the floodplain influences groundwater flow, in turn affecting the distribution of the salt marsh vegetation.

The desertified floodplain of the Orange River Mouth (ORM) is characterised by large areas completely devoid of vegetation. Although barren areas are a natural feature of salt marshes on the west coast of southern Africa, more than 70 ha of salt marsh have been lost through bad management practices. Salt marsh plants have adapted to the low rainfall, high evaporative demand and hypersaline topsoil by accessing the uppermost layer of groundwater (i.e. that below the water table), which can be saline rather than hypersaline. This study demonstrated that although the water table was shallow enough to be accessible to the dominant salt marsh species, Sarcocornia pillansii, it was too saline and had too low a water potential to be of use to the plant. The hypersaline groundwater in turn controls the edaphic salinity and this effect - combined with the low rainfall and a lack of backflooding - prevents seedling recruitment. Rehabilitation of the desertified marsh can succeed only if the groundwater salinity is reduced. Then the establishment of favourable physico-chemical conditions is expected to result in the natural recolonisation of the bare areas by S. pillansii.

When rivers are impounded, the reduction in downstream flow can produce important and often adverse effects, especially in the estuarine environment. One or more dams have been proposed for the Olifants River system in the Western Cape, South Africa. This estuary has an extensive area of salt marsh that was examined to see whether it required occasional flooding with freshwater to wash out accumulated salts. The dominant salt marsh species,Sarcocornia pillansii, occurred in supratidal and floodplain areas where the water table was shallowest, the soil moisture highest, and the soil electrical conductivity lowest. Aerial photographs and simulated runoff data showed that no flood had covered the floodplain during the previous 80 years. The data indicate that salt marsh plants use saline groundwater during the dry months of the year in order to survive, but use the short season winter rainfall period with low salinity conditions to grow and reproduce. This study demonstrated that live roots ofS. pillansii reached the water table during the dry season. Tissue and soil water potentials, the relationship between vegetation cover, depth to the water table, and electrical conductivity of the groundwater support the conclusion that saline groundwater is the only source of water during the drier months of the year. Freshwater flooding of the river in winter may be important because it covers the supratidal area with less saline water and reduces the depth to the water table on the floodplain. This makes the groundwater more accessible to the halophytes growing on the floodplain.

Following the first description of living marine stromatolites along the South African east coast, new investigations along the south coast have revealed the occurrence of extensive fields of actively calcifying stromatolites. These stromatolites have been recorded at regular distances along a 200-km stretch of coastline, from Cape Recife in the east to the Storms River mouth in the west, with the highest density found between Schoenmakerskop and the Maitland River mouth. All active stromatolites are associated with freshwater seepage streams flowing from the dune cordon, which form rimstone dams and other accretions capable of retaining water in the supratidal platform. Resulting pools can reach a maximum depth of about 1 m and constitute a unique ecosystem in which freshwater and marine organisms alternate their dominance in response to vertical mixing and the balance between freshwater versus marine inflow. Although the factors controlling stromatolite growth are yet to be determined, nitrogen appears to be supplied mainly via the dune seeps. The epibenthic algal community within stromatolite pools is generally co-dominated by cyanobacteria and chlorophytes, with minimal diatom contribution.

Gridded SST products developed particularly for offshore regions are increasingly being applied close to the coast for biogeographical applications. The purpose of this paper is to demonstrate the dangers of doing so through a comparison of reprocessed MODIS Terra and Pathfinder v5.2 SSTs, both at 4 km resolution, with instrumental in situ temperatures taken within 400 m from the coast. We report large biases of up to +6°C in places between satellite-derived and in situ climatological temperatures for 87 sites spanning the entire ca . 2 700 km of the South African coastline. Although biases are predominantly warm (i.e. the satellite SSTs being higher), smaller or even cold biases also appear in places, especially along the southern and western coasts of the country. We also demonstrate the presence of gradients in temperature biases along shore-normal transects -- generally SSTs extracted close to the shore demonstrate a smaller bias with respect to the in situ temperatures. Contributing towards the magnitude of the biases are factors such as SST data source, proximity to the shore, the presence/absence of upwelling cells or coastal embayments. Despite the generally large biases, from a biogeographical perspective, species distribution retains a correlative relationship with underlying spatial patterns in SST, but in order to arrive at a causal understanding of the determinants of biogeographical patterns we suggest that in shallow, inshore marine habitats, temperature is best measured directly.

The polar regions are more critically affected by climate change than any other region on our planet. On the Antarctic continent and in its surrounding oceans, the effects of climate change are likely to be dramatic, and include largescale catastrophic ice melt, loss of habitat and biodiversity, and global sea level rise. The 'Southern Ocean' refers to the region where Atlantic, Indian and Pacific Ocean waters come together to encircle Antarctica. These waters connect the different ocean basins by linking the shallow and deep limbs of the global ocean current system ('overturning circulation') and play a critical role in storing and distributing heat and carbon dioxide (CO2). The Southern Ocean thus regulates not only the climate of the Antarctic, but of the entire earth system. By extension, the capacity of the global ocean to ameliorate earth's changing climate is strongly controlled by the Southern Ocean. Marine phytoplankton (microscopic plants inhabiting the sunlit upper ocean) convert CO2 (an inorganic form of carbon) dissolved in surface waters into organic carbon through photosynthesis. This organic carbon fuels upper trophic levels such as fish, mammals and birds, and a portion sinks into the deep ocean where it remains stored for hundreds to thousands of years. This mechanism, which lowers the atmospheric concentration of CO2, is termed the 'biological pump'. The efficiency of the global ocean's biological pump is currently limited by the Southern Ocean, where the macronutrients (nitrate and phosphate) required for photosynthesis are never fully consumed in surface waters. In theory, increased consumption of these nutrients could drive higher organic carbon removal to the deep ocean, enhancing the oceanic uptake of atmospheric CO2. Indeed, more complete consumption of Southern Ocean nutrients is a leading hypothesis for the decrease in atmospheric CO2 that characterised the ice ages. Despite the global importance of the Southern Ocean, knowledge of the controls on and interactions among the physical, chemical and biological processes operating in Antarctic ecosystems is limited, largely because of a scarcity of in-situ observational data, compounded by the challenge of integrating siloed scientific fields. Given predictions that diverse aspects of Southern Ocean physics and carbon biogeochemistry are likely to change in the coming decades, a transdisciplinary approach to studying Antarctic systems is critical.

The Atlantic Ocean receives warm, saline water from the Indo-Pacific Ocean through Agulhas leakage around the southern tip of Africa. Recent findings suggest that Agulhas leakage is a crucial component of the climate system and that ongoing increases in leakage under anthropogenic warming could strengthen the Atlantic overturning circulation at a time when warming and accelerated meltwater input in the North Atlantic is predicted to weaken it. Yet in comparison with processes in the North Atlantic, the overall Agulhas system is largely overlooked as a potential climate trigger or feedback mechanism. Detailed modelling experiments-backed by palaeoceanographic and sustained modern observations-are required to establish firmly the role of the Agulhas system in a warming climate. © 2011 Macmillan Publishers Limited. All rights reserved.

In 2005/2006 a multidisciplinary research programme that included studies on the hydrodynamics, sediment dynamics, macronutrients, microalgae, macrophytes, zoobenthos, hyperbenthos, zooplankton, ichthyoplankton, fish and birds of the temporarily open/closed East Kleinemonde Estuary was conducted. Particular attention was given to the responses of the different ecosystem components to the opening and closing of the estuary mouth and how this is driven by both riverine and marine events. Using a complementary dataset of daily estuary mouth conditions spanning a 14-year period, five distinct phases of the estuary were identified, including closed (average = 90% of the days), outflow (