Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region

Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly elevated during the sampled wet season with the influx of freshwater and agricultural run-off. Fish taxa richness significantly decreased in all three estuaries (F = 164.73, P = <0.001), along with pronounced changes in community composition (F = 46.68, P = 0.001) associated with environmental variables (largely salinity: 27.48% contribution to total variance). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Among the four sampled locations, variation in fish community composition was more pronounced within the wet season (F = 2.5, P = 0.001). Notably, variation in the wet season was significantly correlated with agricultural contaminants (phosphorus: 6.25%, pesticides: 5.22%) alongside environmental variables (salinity: 5.61%, DOC: 5.57%). Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects play a key role in shaping the community structure of fish in this region, agricultural contaminants are also important contributors in estuarine systems.

Shifts in bacterioplankton community structure between dry and wet seasons in a tropical estuary strongly affected by riverine discharge

Estuaries are among the most productive ecosystems in the world and are highly dynamic due to the interaction of freshwater and seawater, which results in strong spatial gradients in physico-chemical conditions. Bacterioplankton play a central role in these systems, driving the fluxes of carbon and energy, and being central for contaminant removal in human-impacted areas. Most studies on bacterioplankton dynamics have been carried out in temperate estuaries, and they show that salinity is a major factor driving bacterioplankton distribution. Tropical estuaries, although largely understudied, experience drastic variations in river discharge between the dry and the rainy seasons, influencing the spatial distribution of the salinity gradient and thus likely impacting bacterioplankton communities. Using Illumina sequencing of the 16S rRNA gene, here we studied bacterial communities from the Nicoya's Gulf (Costa Rica), a large tropical estuary characterized by high riverine discharge during the rainy season, to explore seasonal changes in the spatial distribution and connectivity of these communities along the Gulf. Our results show pronounced differences in bacterial diversity and community structure between seasons and zones within the estuary (the shallow upper Gulf, the middle zone and the lower zone, located in the marine end of the estuary). Bacterial communities from the different regions were more similar during the rainy season, suggesting a larger degree of microbial connectivity likely driven by the fast water circulation fueled by the riverine discharge. In the dry season, Enterobacteriales and Cyanobacteria dominated bacterial communities, whereas in the rainy season Alphaproteobacteria was the dominant group. These contrasting seasonal trends were consistent with the seasonal variations observed in bacterial assemblages during a year at a single station in the upper region of the Gulf. We conclude that the Gulf is highly dynamic in both the spatial and temporal scale and that bacterioplankton communities are strongly influenced by the riverine and tidal inputs during both seasons. This study sheds light on the sources of variability in the structure of bacterial communities in tropical estuarine systems, an understudied type of aquatic ecosystem, and sets the basis to design further comprehensive studies on their microbial diversity.

Ecological quality status assessment of tropical estuaries with benthic indices using differently derived reference conditions

Setting appropriate reference conditions (RCs) is critical for classifying the Ecological Quality Status (EcoQS) which is extremely challenging, considering the present-day estuaries. The EcoQS of three tropical estuaries was assessed by applying five different RCs to identify the best applicable method for the area. The AZTI's indices (AMBI and M-AMBI) categorised areas with sharper pollution gradient with ease, while classification of moderate-low polluted areas was ambiguous. Indices responded to chemical stressors more clearly in the impacted estuary compared to the less polluted estuaries. Ecological status assigned by the default RC (lowest AMBI and highest diversity and richness values) were more accurate than those obtained on application of other four types of RCs, owing to various estuarine constraints that are discussed herewith. Thus, prior to application, caution should be exercised while setting area-specific RCs. The inclusion of combination of AZTI's indices with professional judgment for successful appraisal of ecosystem is recommended.

Assessing tropical coastal dynamics across habitats and seasons through different dimensions of fish diversity

Coastal habitat mosaics are among the most productive ecosystems around the globe, with many ecological and social-economic services provided. Their natural challenging conditions have always been a subject of concern for ecologist and conservationist, with a particular interest in understanding how its spatial and temporal dynamics influence ecosystem functioning. In this context, we aimed to assess tropical coastal dynamics using an integrative approach, measuring the different facets of fish diversity across space (habitats) and time (seasons). Three different estuarine systems and their adjacent areas in the southwestern Atlantic were monthly sampled between July 2017 and June 2018, in a sampling design that encompassed three different coastal mosaics with three habitat types (mangroves, seagrass and sandy beaches), and both seasons of the studied region (dry and rainy). Taxonomic, phylogenetic, and functional diversity were then evaluated with equivalent diversity measures to allow comparisons between them. Different patterns of species occurrence and distribution were found between habitats and seasons, which resulted in different effects on the abundance-weighted diversity dimensions. Although taxonomic diversity of habitats was greater during the rainy season (p = 0.03), a seasonal increase in phylogenetic diversity was only observed in the sandy beach habitat (p = 0.04). In contrast for the functional diversity, no significant differences were found among habitats in both seasons (p = 0.15), indicating high levels of redundancy. Our results showed that patterns in the occurrence and abundance of tropical fish species among habitats that comprise a coastal mosaic have different effects on distinct diversity dimensions. More precisely, for tropical coastal systems with marked seasonality, both habitats and season appear to play a synergic role in the maintenance of ecosystem functioning by enhancing functional and phylogenetic redundancy.

Seasonal variation of oxidative biomarkers in gills and digestive glands of the clam Anomalocardia flexuosa and the mangrove oyster Crassostrea rhizophorae

We determined values of antioxidant biomarkers catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), glutathione S-transferase (GST) and malondialdehyde (MDA) in two bivalve species from a subtropical system in Brazil. Differences in the biomarkers activities measured in digestive glands and gills sampled at two seasons and in sites with different levels of contamination were tested using univariate and multivariate analyses. Seasonality was the main factor accounting for overall variability. Significant SOD and GPx activities and increased levels of lipid peroxides were detected in summer, while CAT activity was higher in winter. However, biomarkers respond to complex environmental settings as indicated by the significant interaction between season and contamination level. We propose A. flexuosa as a candidate for monitoring studies with sampling occurring at a yearly timescale, and using C. rhizophorae is better suited for designs that include both seasons.

Thermal exposure risks to mobile tropical marine snails: Are eco-engineered rock pools on seawalls scale-specific enough for comprehensive biodiversity outcomes?

To test the model that eco-engineering plant boxes on seawalls sustain water temperatures within thermal tolerance to maximize tropical marine biodiversity, we conducted acute thermal effects (AET) experiments using intertidal gastropods (Nerita albicilla and Littoraria articulata). The AET₅₀ (50th percentile) for N. albicilla (39.6 °C) was higher than L. articulata (32.8 °C). Loggers (Hobo) in boxes on a seawall positioned for full exposure to air temperature at mean sea level (<1.1 m) recorded temperature every 20 min during summer months. Temperature frequency distribution plots were generated for day and night, above and below 1.1 m (which is proximal to mean tide level for the region). Using the AET₅₀, N. albicilla would need to thermoregulate for a lower percentage of time compared to L. articulata regardless of day and night. It is likely that designing eco-engineering improvements to include microclimate refugia are particularly relevant in tropical areas, where extreme environmental conditions mean that scale-specific actions are important components for climate adaptation.

Factors structuring spatio-temporal dynamics of macrobenthic communities of three differently modified tropical estuaries

Tropical estuaries of industrialized northwest coast of India, subject to seasonal and multifarious anthropogenic interventions, are poorly studied. Three estuaries, Ulhas, Amba and Savitri were investigated seasonally to identify the principal factors among natural and anthropic stressors that shaped spatio-temporal macrobenthic patterns. The macrobenthic community structure and chemical parameters differed significantly between estuaries, zones and seasons. Multivariate dispersions were significant between the estuaries whereas for the zones and seasons, significant variability was nonexistent. Multivariate regression analysis indicated that both natural and anthropogenic drivers influenced the spatio-temporal variability of macrobenthos of Ulhas and Amba. In Savitri, no anthropogenic factor was significantly influential. Salinity explained a greater proportion of the variability of macrobenthic structure than other factors in all estuaries. The pollution tolerant species responded largely to salinity changes and were observed to inhabit specific salinity zones. Thus, the spatio-temporal patterns of the estuarine macrobenthos were primarily dictated by the salinity.

Estuarine ecocline function and essential habitats for fish larvae in tropical South Western Atlantic estuaries

Estuarine gradients rule the dispersal of larval fishes leading to community replenishment and the recruitment of juveniles to adult populations. Here, the variations in density and diversity of fish larvae communities were assessed to understand whether the seasonal variability of environmental forcings in two tropical estuaries express the estuarine function for larvae. Spatial differences ruled larval dispersal. Larval recruitment to the Caeté Estuary occurs in the upper estuary in the late-dry season. Species richness is higher when temperature, salinity and precipitation increase, while changes in diversity is more pronounced in the lower estuary due to salinity variability. Larval recruitment to the Goiana Estuary occurs in the lower estuary, with peaks during wet warmer conditions. Species richness and diversity are also higher seawards. Thus, the seasonal fluctuation of the salinity ecocline had a greater power to predict larvae distribution and diversity by retaining larvae in essential habitats with suitable environmental conditions.

Factors controlling organic matter composition and trophic state in seven tropical estuaries along the west coast of India

To understand the organic matter (OM) sources and trophic states, spatial and seasonal (post-monsoon and pre-monsoon) variation in sedimentary OM compositions was investigated in seven tropical estuaries of the state of Maharashtra along the central west coast of India. Based on the result of cluster analysis, estuaries were segregated into two distinct groups: Northern Maharashtra and Southern Maharashtra owing to dissimilarity in OM characteristics potentially constrained by geomorphology and catchment properties. Enrichment of C_org and major biochemical compounds (lipids, carbohydrates and proteins) in the middle zone of most estuaries highlighted towards the addition of allochthonous OM. Results of principal component analysis highlighted the similar source of OM in most of the estuaries during both seasons and their distribution largely constrained by grain size change. The benthic trophic state indicated the prevalence of eutrophic state in the middle zone of the investigated estuaries, which may be sporadic and dependent upon anthropogenic activities in the study area.

Emerging and traditional organic markers: Baseline study showing the influence of untraditional anthropogenic activities on coastal zones with multiple activities (Ceará coast, Northeast Brazil)

Molecular markers are useful tools to characterize natural and anthropogenic impacts on coastal zones. Distribution of n-alkanes showed that the Pacoti River was predominantly influenced by terrigenous input. Distribution of polycyclic aromatic hydrocarbon (PAH) indices showed a mix of natural sources, especially pyrogenic influences. Sterol and hormone levels showed sewage discharge. Integrated geographic assessment showed that pyrogenic process and sewage discharge are predominant along the river because of natural and different anthropogenic activities. The upstream region is influenced by rural activities such as livestock and discharge from the sewage treatment plant, whereas the estuarine region is influenced by urban and industrial activities, predominantly the discharge of treated or untreated sewage, vehicle traffic, and manufacture of red ceramics. On the other hand, on the river mouth, there is the predominance of aquaculture activities. Traditional anthropogenic markers are not sufficient for producing a comprehensive assessment of anthropogenic impacts in areas with multiple activities.

Functional diversity of zooplankton communities in two tropical estuaries (NE Brazil) with different degrees of human-induced disturbance

This study assessed the functional diversity (FD) of copepod communities along the environmental gradient of two tropical estuaries with different intensities of human impact - the environmentally protected "Mamanguape" and the urbanised "Paraiba". Different trait-based approaches were used: functional groups identification and description, and FD indices estimation. The results showed similar functional groups and functional indices between the two estuaries with some variability attributed to seasonality. Copepods in each estuary seemed to perform similar functions. Overall, biomass was more evenly distributed among groups, and mean total biomass and FD indices were slightly higher in the Mamanguape. Nevertheless, both estuaries presented comparable FD, indicating that environmental filters may be the main driver of species coexistence within systems. Results also pointed towards anthropogenic disturbance, despite the protection status of the Mamanguape.