Publications
Below are some of our recent publications.
2019 - 2023
Featured Publications
Nursery function of red-algal dominated reef in temperate Algoa Bay, South Africa
Nicola C. James, Aidan Jacobs, Mihle Gayiza, Lucienne Human, Paul-Pierre Steyn, Anthony Bernard, Gavin Rishworth | preprint
Structurally complex macroalgae within coastal seascapes are important as nursery areas for many marine fish species. This study examines the nursery role of a mosaic of red algae dominated habitats in a shallow (< 5 m), sheltered rocky cove in warm-temperate Algoa Bay, South Africa. As an indicator of nursery function within the cove we assessed and mapped macroalgal communities, the resource seascape (epiphytes and invertebrates), as well as fish assemblages (abundance, size structure and species richness) in different subtidal habitat patches. We also looked at the trophic ecology of dominant juvenile fish species within the cove. Red algae, particularly canopy forming Plocamium spp. and lower growing Laurencia spp. dominated subtidal high and low profile reef respectively, with the lower intertidal dominated by coralline turf. Algal complexity (canopy height) was negatively correlated with the biomass of resources, with the biomass of epiphytic algae highest on coralline turf and the abundance of amphipods and polychaetes highest on low growing Laurencia and corralline turf. Laurencia, epiphytes, polychaetes and amphipods were important food sources for juvenile sparids. Although results from this study indicate that lower complexity algae likely provide more food for juvenile sparids, the high abundance of juvenile sparids in Plocamium dominated high profile reef indicates that canopy-forming Plocamium likely provides more shelter from predation than lower complexity algal reef habitats. This shows that macroalgal habitats comprising several functional forms have the potential to support higher juvenile diversity and abundance through both food provision and protection.
Response of demersal fishes to low dissolved oxygen events in two eutrophic estuaries
Coastal ecosystems serve as important nursery areas, yet they are facing many challenges. For example, eutrophication-induced hypoxia is one of the major threats to the functioning of coastal ecosystems, particularly estuaries. The Sundays and Swartkops estuaries both experience persistent eutrophic conditions, with frequent phytoplankton blooms (>20 μg Chl-a l-1) that result in instances of bottom-water oxygen depletion (<4 mg/l). Bi-seasonal sampling of both physico-chemical parameters and demersal fishes between February 2018 and September 2019 in the Swartkops and Sundays estuaries allowed for the quantification of low dissolved oxygen (<4 mg/l) and hypoxic (<2 mg/l) events in both estuaries and the impact of low dissolved oxygen (DO) and hypoxic events on overall fish species abundance, richness and distribution. Low DO conditions were typically observed in the bottom waters of the vertically-stratified meso-to polyhaline middle and upper reaches of the Sundays and Swartkops estuaries, respectively. Hypoxic conditions ( DO = 0.5 mg/l) were recorded in the Sundays Estuary during the study, whereas in the Swartkops Estuary the lowest DO recorded was 2.4 mg/l. Low DO events resulted in a decrease in fish species richness and overall abundance in the Sundays Estuary, while in the Swartkops Estuary fish species richness declined during low DO events, with little effect on fish abundance. Fish only completely avoided areas where DO was <1 mg/l or >10 mg/l. As such, the low DO concentrations recorded in the Swartkops Estuary did not have a noticeable impact on fish distribution, although the abundance of Rhabdosargus holubi and Caffrogobius gilchristi declined in the upper reaches of the Swartkops Estuary when DO was <3 mg/l. The results from this study provide much-needed insights into the impact of low DO and hypoxic conditions on the spatial distribution of demersal fish species.
Juvenile sparids (Rhabdosargus holubi) consistently select structurally dense vegetated habitat in nursery seascapes
Seagrass habitats provide structural complexity in coastal estuarine and marine environments, which offer fish optimal foraging grounds and refuge from predation. However, seagrasses are some of the most threatened ecosystems globally, with anthropogenic activities such as population growth and environmental degradation leading to the fragmentation, thinning, and loss of these habitats. Rhabdosargus holubi is one of only a few vegetation-associated marine fish species in South African estuaries. Although field studies have shown a strong association with seagrass over other aquatic vegetation for the juveniles of this species, habitat choice has never been empirically tested. Here, we used artificial vegetation units to test habitat choice (different structural complexities) for this species. We also tested whether habitat choice is influenced by a predatory threat, with fish preferentially selecting dense habitat in the presence of a predator and whether this effect may be more apparent in smaller individuals. We found that R. holubi significantly prefer greater
structural complexity over less complex habitats, in both the absence and presence of a predator and for both small and large juveniles, showing that R. holubi actively choose more complex structures and are attracted to the structure per se irrespective of the threat of predation. This study highlights the importance of dense seagrass as nursery areas for this species and demonstrates how the loss of these habitats could impact the nursery function of estuaries.
The role of macroalgal habitats as ocean acidification refugia within coastal seascapes
Ocean acidification (OA) refers to a global decline in the average pH of seawater driven by the absorption of atmospheric carbon dioxide (CO2). Marine macroalgae, while affected by this pH change, are also able to modify seawater pH through their own interaction with inorganic carbon in the carbonate system. Through this action, macroalgae-dominated habitats are potential refugia from OA for associated marine species. This review summarises the most prominent literature on the role of macroalgae in OA mitigation and the potential of macroalgal habitats to serve as OA refugia. It includes a brief overview of macroalgal distribution in an effort to illustrate where such refugia might be most prevalent. Macroalgae influence seawater carbonate chemistry through the absorption of CO2 and HCO3− during photosynthesis, raising surrounding seawater pH in the process. This transient effect on seawater chemistry could provide some respite from the negative effects of OA for many marine species. This refuge role varies over a range of scales along with macroalgal architecture, which varies in size from low-growing turfs to large canopy-forming stands. The associated pH changes can range over various temporal (daily and seasonal) and spatial (from centimetre to kilometre) scales. Areas of high macroalgal biomass are likely to play an important role as significant OA refugia. Such communities are distributed widely throughout the globe. Large brown macroalgae (Laminariales) dominated communities are common in temperate regions, while members of the Fucales are responsible for substantial macroalgal stands in warmer tropical regions. These marine fields and forests have great potential to serve as localised refuges from OA. While more work needs to be done to clarify the effect of macroalgal communities on seawater pH on a large scale, such refuge areas could become important considerations for the management of marine resources and in protected area selection.
The nursery function of shallow nearshore and estuarine benthic habitats for demersal fishes
Estuaries and shallow marine nearshore areas are highly productive and valuable ecosystems, which provide numerous habitats for fish and support fundamental ecological links with other environments. Yet only a few studies have focussed on fish community patterns across an estuary and marine nearshore gradient concurrently to determine the nursery value of both environments. This research gap is particularly apparent in southern Africa. The main aim of this study was to assess the relative roles of two permanently open estuaries and the adjacent marine nearshore areas of Algoa Bay, on the south coast of temperate South Africa, as settlement and nursery areas for demersal fishes. Soft-bottom habitats in both the estuaries and the nearshore were dominated by early-life stages (postflexion larvae, settlement stage and young-of-the-year fishes), but a significantly greater density of early-life stage fishes was found in the estuarine environment, highlighting the importance of estuarine habitats for demersal fishes within the Algoa Bay nursery seascape. Settlement and nursery habitats also differed by estuarine-association, with the marine nearshore environment dominated by marine and marine estuarine-opportunists, with core settlement and nursery areas for these species located close to estuary mouths, freshwater outlets and harbours. In contrast, the estuarine environment was dominated by marine estuarine-dependent and estuarine and marine species. This highlights the importance of concurrently sampling habitats in marine nearshore and estuarine environments, which allows for a better understanding of the degree of estuarine dependency of marine fish as well as an understanding of the nursery function of coastal habitats.
A baseline assessment of coastal pH variability in a temperate South African embayment: implications for biological ocean acidification research
Compared with the open ocean, knowledge of pH variability in coastal waters is rudimentary, especially in Africa. This is concerning as quantifying local pH conditions is critical when assessing the response of coastal species to future ocean acidification scenarios. The objective of this study was to capture some of the variability in pH at scales and sites relevant to coastal marine organisms in a South African temperate embayment (Algoa Bay, Indian Ocean). We used a sampling approach that captured spatial (at a resolution of ∼10 km), monthly and diel (24-hour) variability in pH and associated physical and biological parameters at offshore and shallow inshore sites in Algoa Bay. We found that pH and associated parameters (temperature, calculated pCO2, chlorophyll a) varied over space and time in Algoa Bay. The range in pH was 0.30 units at offshore sites and 0.46 at inshore sites, and the average pH was 8.10 (SD 0.06) and 8.10 (SD 0.13) at these sites, respectively, which is typical for coastal environments. Our results showed that both biological factors (at the offshore sites) and salinity (at the inshore sites) may influence temporal and spatial variability in pH. We also identified a shallow inshore site with high levels of macroalgal growth that had consistently higher average daytime pH levels (8.33 [SD 0.07]), which may serve as an ocean acidification refuge for coastal marine species. This is the first comprehensive pH-monitoring study to be implemented in a nearshore coastal area in Africa and provides recommendations for monitoring in other understudied regions.
The role of macroalgae as nursery areas for fish species within coastal seascapes
Nicola C. James, Alan K. Whitfield | 2022
One of the most critical ecosystem functions provided by shallow coastal habitats is as nurseries for the juveniles of fish. Many of the studies that have assessed the nursery function of structurally complex coastal habitats have compared seagrass with unstructured sand and mud and as such, seagrass has emerged as the most important coastal nursery habitat for juvenile fishes. Although considerably less work has focussed on the nursery provision of structurally complex macroalgae within coastal nursery seascapes, recent work has started to highlight that the nursery provision of canopy forming macroalgae may in fact be comparable with that of seagrass. This review collates research published on the important nursery role of macroalgae within both tropical and temperate coastal seascapes and highlights the importance of smaller canopy forming brown algae from the Fucalean genera (particularly Sargassum spp). as core nursery areas for juvenile fishes, particularly emperors (Lethrinidae), rabbitfishes (Siganidae), wrasse and parrotfishes (Labridae), goatfishes (Mullidae), groupers (Serranidae), surgeonfish (Acanthuridae) and damselfish (Pomacentridae) within tropical back-reef systems. Similarly, in temperate nursery seascapes, fucoid (Cystoseira spp.) and macroalgae dominated reef were important nursery habitats for damselfish (Chromis chromis), groupers and numerous species of wrasse and sparids (Sparidae). Although the overall density of juvenile fish was not shown to be higher in kelp relative to other temperate nursery habitats, kelp was important in the recruitment of Notolabrus celiodotus (wrasse), Paralabrax clathrus (Serranidae), Brachyistius frenatus (Embiotocidae), Heterostichus rostratus (Clinidae) and Sebastes spp. (Scorpaenidae). Although not interchangeable (fish communities were often different), the nursery function of structurally complex macroalgae was found to be similar to that of seagrass in both temperate and tropical seascapes.
Turbidity influences the recruitment of Argyrosomus japonicus to estuarine nurseries
Nicola C. James, Amber-Robyn Childs, Justin O.G. Kemp, Shannon Wilsnagh and Carla Edworthy | 2022
Estuaries serve as important nursery habitats for several coastal fishery species. The successful recruitment of larvae and early juveniles into estuaries is paramount for population persistence and maintenance. Several factors have been proposed as stimuli that could elicit a recruitment response in estuary-associated fish species. Larvae and early juveniles may trace land-based cues back to an estuary by following the olfactory concentration gradient or use other visual or acoustic stimuli. Argyrosomus japonicus is an iconic estuarine-associated species. Due to overfishing, reduced freshwater input and habitat degradation in their estuarine nursery habitat, the South African population has suffered severe stock declines. Turbidity associated with high freshwater input is thought to promote recruitment into estuaries. We used choice-chamber laboratory experiments to test the hypothesis that settlement-stage A. japonicus are attracted to turbidity rather than olfactory gradients when recruiting into estuaries. Three choice experiments (with three replicate trials each) were performed over three consecutive days. Each experiment used paired combinations of six estuarine/seawater types with varying turbidity and olfactory characteristics. For each experiment, three trials were repeated in succession with six new fish for each trial. Settlement-stage A. japonicus showed a significant preference for turbid water (with and without olfactory cues) over seawater (no olfactory cues) and clear estuary water (with olfactory cues). No clear choice was made between clear estuary water (with olfactory cues) and clear artificial seawater (without olfactory cues), suggesting that turbidity gradients are most likely the primary factor governing the recruitment of settlement-stage A. japonicus into estuaries.
The Last Two Remaining Populations of the Critically Endangered Estuarine Pipefish Are Inbred and Not Genetically Distinct
Sven-Erick Weiss, Arsalan Emami-Khoyi, Horst Kaiser, Paul D. Cowley, Nicola C. James, Bettine Jansen van Vuuren, Alan K. Whitfield and Peter R. Teske | 2022
The critically endangered estuarine pipefish, Syngnathus watermeyeri, is one of Africa’s rarest fish species and currently faces a significant risk of extinction. A combination of anthropogenic and natural factors threaten submerged macrophyte beds in the two South African estuaries (Bushmans and Kariega) in which the species’ only two known remaining populations reside. Here, we genotyped 34 pipefish from both populations using genome-wide data to determine whether the two estuaries harbour distinct genetic diversity, such that translocating individuals between them might improve the genetic health of both. Our results show that both populations are highly inbred, and no statistically significant genetic structure was found between them. Moreover, individuals both within and between estuaries were very closely related to each other. These results indicate that the remaining populations of the estuarine pipefish suffer from the adverse genetic effects of small population sizes. Even though recent surveys have estimated population sizes in the order of thousands of individuals, these may fluctuate considerably. Although the translocation of genetically similar individuals between habitats will not increase local genetic diversity, the creation of additional populations across the species’ historical range may be a suitable conservation strategy to prevent further loss of genetic diversity, and to minimise the overall extinction risk posed by environmental stochasticity.
Effects of Experimental Ocean Acidification on the Larval Morphology and Metabolism of a Temperate Sparid, Chrysoblephus laticeps
Ocean acidification is predicted to have widespread impacts on marine species. The early life stages of fishes, being particularly sensitive to environmental deviations, represent a critical bottleneck to recruitment. We investigated the effects of ocean acidification (∆pH = −0.4) on the oxygen consumption and morphometry during the early ontogeny of a commercially important seabream, Chrysoblephus laticeps, up until flexion. Hatchlings appeared to be tolerant to hypercapnic conditions, exhibiting no difference in oxygen consumption or morphometry between treatments, although the yolk reserves were marginally reduced in the low-pH treatment. The preflexion stages appeared to undergo metabolic depression, exhibiting lower metabolic rates along with lower growth metrics in hypercapnic conditions. However, although the sample sizes were low, the flexion-stage larvae exhibited greater rates of metabolic and growth metric increases in hypercapnic conditions. This study shows that the effects of OA may be stage specific during early ontogeny and potentially related to the development of crucial organs, such as the gills. Future studies investigating the effects of climate change on fish larvae should endeavour to include multiple developmental stages in order to make more accurate predictions on recruitment dynamics for the coming decades.
Thermal tolerance, safety margins and vulnerability of coastal species: Projected impact of climate change induced cold water variability in a temperate African region
Anthropogenic induced climate change is predicted to increase the thermal variability in coastal waters, which can have strong physiological effects on individuals and populations of marine ectotherms. The magnitude and direction of these thermal effects varies depending on species, life stage, biogeography, habitat and season. This study aimed to compare the thermal tolerance of a range of juvenile fish and adult macro-invertebrates from intertidal and estuarine habitats in a warm-temperate, thermally variable region on the south-east coast of South Africa. Seasonal variability in thermal tolerance was compared between species, taxonomic groups, biogeographical distribution and habitat affinity and related to existing and projected water temperature data to gauge the local vulnerability of each species. Critical thermal maximum (CTmax), critical thermal minimum (CTmin), thermal breadths and scopes, and the thermal safety margins of each species were quantified. The greatest differences in thermal tolerance patterns were based on taxonomy, with macro-invertebrates having broader thermal tolerance compared to fish, with the exception of the Cape sea urchin, in both summer and winter. Relatively narrow lower breadths in tolerance and safety margin values for transient juvenile sub-tropical and temperate fish species from the intertidal rocky low-shore habitat were observed in both summer and winter. This indicates that these fish species and the Cape sea urchin may be more vulnerable to projected increases in cold temperature (upwelling in summer) than warm temperature variability in this warm-temperate region if they are unable to seek thermal habitat refuge.
High flow variability and storm events shape the ecology of the Mbhashe Estuary, South Africa
The possible impacts of extreme events on the ecology of selected aquatic biota within the Mbhashe Estuary were investigated during a four year (2010–2013) spring sampling programme. During periods of low to average flow conditions the estuary is shallow, turbid and characterised by the presence of fluid mud and the build-up of mud and clay deposits. During these conditions, extremely high biomasses of intertidal microalgae and zooplankton are present. Fish and macroinvertebrate abundance and diversity are also highest during low-flow conditions. Flood events can reset, or partially disrupt, the sediment erosion/depositional cycle and decrease the biomass and diversity of plankton, fish and macroinvertebrate species. The Mbhashe Estuary’s unique fluid mud habitat is therefore subjected to regular resetting, which potentially contributes to the fluid nature of the muds. A storm surge in 2011 resulted in the temporary dieback of an area of mangroves, as a result of the deposition of marine sediment. Although extreme events seem to play an important role in the deposition and erosion cycle of the estuary, an increased frequency of both types of extreme events may ultimately result in estuarine habitat loss, which will adversely affect the biota of the estuary.
The importance of different juvenile habitats as nursery areas for a ubiquitous estuarine-dependent marine fish species
Estuarine-dependent marine fish species rely on shallow, sheltered and food rich habitats for protection from predators, growth and ultimately recruitment to adult populations. Hence, habitats within estuaries function as critical nursery areas for a variety of fish species. Results from stomach content analysis and dietary diatom composition of a ubiquitous estuarine-dependent species Rhabdosargus holubi (Steindachner, 1881) in the main vegetated and un-vegetated habitats in the Bushmans Estuary, South Africa, were interpreted along with published information on habitat complexity, relative abundance and behaviour of this species. Although the complexity of seagrass, together with the higher abundance and behaviour of R. holubi in seagrass suggests that this is the main nursery habitat (in terms of both feeding and protection from predation), the dominance of red filamentous algae and the presence of some invertebrates mainly in the diet of fish from un-vegetated habitats indicates that this species is using a mosaic of habitats, including un-vegetated areas, for foraging. Based on the above findings, and results from other studies, it is concluded that juvenile R. holubi in permanently open estuaries makes use of a range of habitats according to macrophyte shelter from predators, the availability of preferred food resources and physical drivers such as water depth and tidal phase. This study demonstrated that a multi-method approach, as opposed to a single method approach (diet alone) is useful to assess the nursery value of juvenile fish habitats.