Demersal fish distribution in the shallow marine nearshore and estuarine seascape of Algoa Bay : Nursery areas and the effect of environmental drivers
Authors:   , Nodo Phakama 
Published: April 2022

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. Assessing fish distribution across estuarine and marine nearshore habitats is important to identify ecologically important habitats and develop effective management strategies for coastal fishes, many of which are important fishery species. Despite this, only a few studies have focussed on fish community patterns across an estuary and marine nearshore gradient concurrently, particularly including early life history stages, to determine the nursery value of both environments, and to examine whether these two coastal environments have distinct fish assemblages in relation to physical factors. The main aim of this study was to assess the environmental drivers of demersal fish communities in soft-bottom benthic habitats in two permanently open estuaries and adjacent marine nearshore areas (5 – 10 m) of Algoa Bay, South Africa, as well as to assess the relative roles of these two habitats as settlement and nursery areas for demersal fish species. A 1.5 m, conical shoeless beam trawl net was used to sample the demersal fish community concurrently in each habitat between July 2017 and September 2019. Sampling was conducted in July 2017, February, March, May, July, August, October and November 2019 and February, April and September 2019. DNA barcoding was used to verify identification of the early life history stages of fish caught in the estuarine and marine nearshore areas of Algoa Bay. In addition, since the two estuaries (Swartkops and Sundays) are heavily polluted, the effect of low dissolved oxygen and hypoxia and associated shifts in spatial distribution of demersal species was investigated. The two sampled estuaries had a higher abundance of demersal fishes, with a total of 6437 fishes (28 species) caught (3752 and 2685 individuals with 24 and 20 species recorded in the Sundays and Swartkops estuaries, respectively). Species richness was higher in the marine nearshore of Algoa Bay, with 29 species (797 individuals) caught. Of the 7234 individuals caught, the identification of 100 specimens, in either a larval or early juvenile phase, were uncertain and therefore DNA barcoding was used to verify their identification. Of these 100 individuals, 86 were positively identified to species level using COI sequences. Fourteen failed to amplify by PCR and could only be identified morphologically. The marine nearshore sites were dominated by species which spawn in the marine environment and are not dependent on estuaries (marine species and marine estuary-opportunists), whilst the estuaries were dominated by estuarine spawners or marine spawners dependent on estuaries to some degree. Two discrete demersal fish assemblages were identified representing the marine nearshore and the estuary, with no significant differences observed between the two estuaries (Sundays and Swartkops). The differences observed between the marine nearshore and estuary were mostly driven by salinity, turbidity, silt and organic content of the sediment. These distinct fish assemblages might be considered as indicators for the respective environments they inhabit. Both habitats were dominated by early life history stages (larvae to juveniles), indicating the nursery function of both habitats. Early life stages collectively comprised 97% of the catch in the marine nearshore and 68% in the estuary. Young-of-the-year (YOY) juveniles (< 1-year-old juveniles) and transformation stages (when changes in body shape and pigment pattern occur) dominated the total catch in the marine nearshore, while YOY juveniles dominated the estuarine fish assemblages. Ariidae Galeichthys feliceps, Haemulidae Pomadasys olivaceus, Sciaenidae Argyrosomus inodorus and Cynoglossidae Cynoglossus zanzibarensis, comprised the largest proportion of YOY juveniles in the marine nearshore. The transformation stage in the marine nearshore was numerically dominated by P. olivaceus and G. feliceps. In the estuarine environment, YOY juveniles were mostly dominated by Sparidae Rhabdosargus holubi, Soleidae Heteromycteris capensis and Gobiidae Caffrogobius gilchristi. The greatest abundance of early life stage fishes was observed in the lower reaches of the Sundays Estuary and the upper reaches of the Swartkops Estuary, as well as nearshore sites located in close proximity to the estuary mouths, particularly during spring and summer. Despite the fact that these coastal ecosystems are important nursery areas, they are threatened by a number of factors, including habitat loss and modification due to urban development, intensification of agriculture and subsequent eutrophication, climate change, and overfishing, all of which reduce ecosystem functioning and reduce the ecological and economic value of these habitats around the world. 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). During the present study in the Sundays Estuary, low oxygen waters were recorded in the middle reaches (Site S5) mostly during summer (four months of low DO conditions). In the Swartkops Estuary, low dissolved oxygen was recorded in the upper reaches during spring. The lowest dissolved oxygen concentration recorded was 0.5 mg/l and 2.4 mg/l in the bottom waters of the Sundays and Swartkops estuaries, respectively. Selected dominant species were only absent from areas where dissolved oxygen was < 1 mg/l and present in the adjacent sites (for example Site S4, and S3) where DO was higher mostly during January 2019. As such, the low dissolved oxygen concentrations recorded in the Swartkops Estuary did not have a noticeable impact on fish distribution, although the total abundance of species did show a slight decline when dissolved oxygen was < 3 mg/l. This study demonstrates the importance of concurrently examining estuarine and nearshore marine habitats in order to identify ecologically important habitats, which has important implications for the development of effective management strategies for coastal fish populations, particularly in the light of anthropogenic change. In addition, in order to identify nursery hotspots it is crucial to correctly identify all the species occupying these areas. As such, this study confirms the importance of also using DNA barcoding for fish identification, particularly for the early life history stages of cryptic species (e.g. Argyrosomus inodorus and Argyrosomus japonicus).