Multidisciplinary study to monitor consequences of pollution on intertidal benthic ecosystems (Hauts de France, English Channel, France): Comparison with natural areas

Exploring the underwater life in transitional environments: Benthic foraminifera, ostracods, and dinoflagellate cysts - Biotic trends and EcoQS assessment in the Mar Piccolo of Taranto (Ionian sea, southern Italy)

Coastal areas have historically thrived as centers of human activities due to their resources, economic opportunities, and natural allure. The rapid growth of coastal populations has however brought forth a multitude of challenges to tackle, with pollution emerging as a significant and far-reaching issue. Our study focuses on the Mar Piccolo of Taranto (Ionian Sea, Southern Italy), a lagoon-like coastal basin (separated in two sub-basins) that, since decades, has been heavily affected by human activities and aquaculture, leading to environmental deterioration. Although past studies have looked at environmental conditions in the Mar Piccolo from a chemical perspective, the biological component (e.g., biological indicators) has been mostly neglected. In this study, we firstly aim to examine the distribution and diversity of foraminifera, ostracods, and dinoflagellate cysts in December 2016 and compare our findings with data collected in December 2011. Foraminiferal and ostracod communities exhibit similar patterns in the two sampling campaigns, while the communities of encysted dinoflagellates show differences concerning both densities and diversity. Then, we evaluate the Ecological Quality Status (EcoQS) using ecological indices. While the indices in the inner basin appear to reflect an actual ecological degradation, they yield conflicting results in the outer basin. In the outer basin, indeed, the indices overestimate the EcoQS. This study highlights the potential of these indices for characterizing the EcoQS but emphasizes the need for improvements in their reliability. This research also contributes to a more holistic understanding of environmental condition in the Mar Piccolo and underscores the importance of integrating biological quality elements into ecosystem management and remediation strategies.

Stormwater outlets: A source of microplastics in coastal zones of Cape Town, South Africa

The runoff from stormwater outlets are potential sources of microplastics (MPs) in coastal zones. The characteristics and concentrations of MPs in coastal water, sediment and biota (mussels, whelks and sea urchins) were measured in summer (2020/2021) (dry season) and winter (2021) (wet season) from three sites (Camps Bay, Mouille Point and Three Anchor Bay) in Cape Town. MPs were characterised visually using a stereo microscope and chemically using spectroscopy. MP concentrations were higher in water and sediment during winter, and higher in biota in summer. Compared to control sites, MPs were higher at all impact sites sampled. MPs extracted were mainly black polyester (PEST) fibres, 1000 to 2000 μm in length averaging 0.15 MPs/L in water, 52.11 MPs/kg dry weight in sediment and 1.35 MPs/g soft tissue wet weight in biota. The results indicate that coastal stormwater systems are potential sources of MPs in the coastal environment of Cape Town.

Sediment reworking of intertidal sediments by the benthic foraminifera Haynesina germanica: the importance of motion behaviour and densities

This study aimed to describe for the first time the vertical motion behaviour of the intertidal foraminifera Haynesina germanica and its contribution to bioturbation. Its infaunal behaviour leads to the creation of a one-end tube within the first centimetre of sediment. In addition, a vertical trail following behaviour was described for the first time in foraminifera, which may be linked to the sustainability of the biogenic sedimentary structures. As a consequence, H. germanica produces a vertical transport of both mud and fine sediment fractions similarly to the sediment reworking mode reported for gallery-diffusor benthic species. This finding allows us to refine the bioturbating mode of H. germanica, previously classified as surficial biodiffusor. Furthermore, sediment reworking intensity appeared to be dependent on the foraminiferal density. H. germanica would adapt its motion behaviour to deal with the intra-specific competition for food and space that may occur when density increases. Consequently, this behavioural modification would affect both the species and the individual contribution to sediment reworking processes. In fine, sediment reworking in H. germanica may further contribute to the bioirrigation of intertidal sediments, which has implications for oxygen availability in sediments and on aerobic microbial processes involved in carbon and nutrient cycling at the sediment-water interface.

The relative roles of multiple drivers on benthic ciliate communities in an intertidal zone

Intertidal biodiversity is being severely disrupted as a result of increased anthropogenic activity. However, our knowledge about how natural gradients, human induced disturbance and biotic interactions affect biodiversity is limited. So, we investigated how three facets of alpha diversity and community composition of benthic ciliates responded to environmental and biological gradients in the intertidal zone of Zhejiang, China. The key determinants and their relative effects on ciliate communities were identified using structural equation modeling, distance-based redundancy analysis and variation partitioning analysis. Our results revealed that sediment grain size was the most important factor affecting alpha diversity and community composition. Human induced eutrophication had significant effects on phylogenetic alpha diversity and community composition. However, the effects of biotic interactions on ciliate communities were relatively small. Moreover, we found community composition was more sensitive to human disturbance than alpha diversity, thus, more suitable for indicating human-induced eutrophication.

Environmental impact of removal of a large-scale sluice gate on Nakaumi Lagoon and adjacent coastal waters, southwest Japan: Evidence from long-term foraminiferal monitoring

A large-scale sluice gate, which was built in southwest Japan as a national project to reclaim and desalinate lagoon water in 1974, was removed between 2005 and 2009. To examine the impact of this removal on both Nakaumi Lagoon and the nearby coastal waters, we analyzed the foraminiferal assemblages of a coastal sediment core and of samples obtained during 10 years of lagoon monitoring (2001-2010). Detailed 210Pb(ex) dating of the sediment core revealed an increased sediment accumulation rate in the coastal waters, implying that discharge of fine-grained materials, including organic matter, was facilitated by removal of the sluice gate. The observed increase in agglutinated foraminifera and decrease in calcareous species was related to the sediment accumulation rate, and these changes occurred close to 2005, when sluice-gate removal began. In Nakaumi Lagoon, the sporadic presence of the coastal species Quinqueloculina seminula within the 6-m water column and the decline in the lagoon-adapted Ammonia "beccarii" have occurred since 2005. The removal of the sluice gate, plus the sea-level rise, allowed greater seawater inflow and stabilized the monthly deep-water salinity fluctuations in Nakaumi Lagoon.

Benthic foraminifera as proxies for the environmental quality assessment of the Kuwait Bay (Kuwait, Arabian Gulf): Morphological and metabarcoding approaches

The rapid urbanization and industrialization of Kuwait and the consequent effluent discharges into marine environments have resulted in a degradation of water and sediment quality in the coastal marine ecosystems such as in the Kuwait Bay. This study investigates the ecological response of benthic foraminifera (protists) to environmental stress in the Kuwait Bay. The traditional morphological approach was compared to the innovative environmental DNA (eDNA) metabarcoding to evaluate the ecological quality status (EcoQS). Forty-six surface sediment samples were collected from selected stations in the Kuwait Bay. To detect the pollution gradient, environmental parameters from water (e.g., salinity, pH, dissolved oxygen) and sediment (e.g., grain-size, trace metals, total organic carbon, total petroleum hydrocarbons) were measured at each station. Although the foraminiferal assemblages were different in the morphological and molecular datasets, the species turnover was congruent and statistically significant. Diversity-based biotic indices derived from both morphological and metabarcoding approaches, reflect the environmental stress gradient (i.e., organic and metal contaminations) in the Kuwait Bay. The lowest values of EcoQS (i.e., bad to poor) are found in the innermost part (i.e., Sulaibikhat Bay and Ras Kazmah), while higher EcoQS values occur in the outer part of the bay. This study constitutes the first attempt to apply the foraminiferal metabarcoding to assess the EcoQS within the Arabian Gulf and presents its advantages compared to the conventional morphological approach.

Responses of the copepod Eurytemora affinis to trace metal exposure: A candidate for sentinel to marine sediment resuspension effects

Our study reports the ability of Eurytemora affinis to indicate certain responses in 96 h when exposed to resuspended sediment from a polluted site (PS, Seine estuary, France), less polluted site (LPS, Canche estuary, France) and dissolved trace metals. Mortality from dissolved trace metal was highest (57.5 %) followed by PS (38.59 %) > LPS (24.04 %). The exposure to PS sediment resulted in significantly lower no. of early larval stage (nauplii < 2), sex-ratio (39.24 % of males) and higher ovigerous female (>10). Eurytemora affinis bioaccumulated high concentrations of copper (27.3 mg/kg), nickel (12.8 mg/kg), lead (21.8 mg/kg) and arsenic (13.7 mg/kg) from PS exposure with significantly lower bioaccumulation of metals from LPS. The bioconcentration factor (BCF) was highest from dissolved toxicity (>2000) followed by PS that showed significantly higher BCF for Nickel and Copper, compared to LPS. The responses of E. affinis to different matrices exemplify its role as a sentinel.

Unraveling Anthropocene Paleoenvironmental Conditions Combining Sediment and Foraminiferal Data: Proof-of-Concept in the Sepetiba Bay (SE, Brazil)

The Sepetiba Bay (SB), located in the state of Rio de Janeiro (SE Brazil), is a transitional ecosystem highly anthropized. Because of its great environmental, economic, and social importance, the SB has been the target of several studies to investigate the sources of pollution and their environmental impact. However, studies on the response of foraminifera to pollution are rare. This study applies for the first time in the SB the Ecological Quality Ratio (EQR) based on the biotic index exp(H’bc), related to foraminiferal diversity, coupled with granulometric, mineralogical, and geochemical data and a robust age model (based on 210Pb and 137Cs activity). This study aims to evaluate the paleo-ecological quality status (PaleoEcoQS) along core SP5, collected in the inner central region of the SB. In the sedimentary record of the first half of the 20th century, no foraminifera were found, and the moderate enrichment in lithogenic elements was probably related not only to weathering and erosion of rocks but also to mining activities in the region. From the second half of the 20th century, the study area was under higher marine influence. Progressive siltation took place because of anthropogenic interventions in river courses, eutrophication, and metal pollution. Weak hydrodynamic conditions favored the accumulation of fine-grained sediments and organic matters. In the same period, low diversified benthic foraminiferal assemblages, including mainly opportunist species, were developed. Paleo-ecological conditions inferred by the biotic index exp(H’bc) were poor around 1970 and worsened after the metal spill released by Companhia Ingá Mercantil (a zinc ore processing plant). After that, progressively recovery has led to good ecological conditions in 2015. This study shows how benthic foraminiferal methods could represent a very useful tool to track changes in the evaluation of PaleoEcoQS.

Occurrence, sources, and risk assessment of unconventional polycyclic aromatic compounds in marine sediments from sandy beach intertidal zones

This study investigated the concentrations of polycyclic aromatic compounds (PACs), including parent polyaromatic hydrocarbons (PAHs) and their nitrated and oxygenated derivatives, in 48 sediment samples from the intertidal region of sandy beaches in Baía de Todos os Santos (BTS), Salvador, State of Bahia, Brazil. The total PAH (∑PAH) concentration, total nitro-PAH (∑nitro-PAH) concentration, and total oxy-PAH (∑oxy-PAH) concentration ranged from 2.11 μg g^-1 dry weight (dw) to 28.0 μg g^-1 dw, 2.58 μg g^-1 dw to 30.2 μg g^-1 dw, and 0.34 μg g^-1 dw to 3.65 μg g^-1 dw, respectively. Elevated concentrations of parent PAHs and nitro-PAHs were found in samples from two sites in BTS, which were also characterized by high percentages of fine-medium sand and low organic matter contents. Potent mutagenic 3-nitrobenzanthrone (3-NBA) was found in 86% of the samples at concentrations ranging from 0.200 μg g^-1 dw to 0.690 μg g^-1 dw. Furthermore, calculations of the benzo[a]pyrene toxicity equivalency (BaPTEQ) indicated that three carcinogenic high-molecular-weight PAHs accounted for 98.7% of the total maximum PAH concentration. Finally, we assessed the possible environmental risks posed to benthic species living in the sediments of BTS. The results showed that the risk quotient for PAHs (RQ_PAHs) was ≥1. In turn, the summed RQ for all PACs (∑RQ_mixture) ranged from 1 to 30, but did not exceed the maximum allowable threshold; thus, the risks posed to benthic species were moderate for all sediment samples.

Investigating the impact of remediation efforts on Hedistediversicolor in the Seine estuary using multiple levels of biological organization

The Seine Estuary is historically one of the most contaminated estuaries in Europe. In 2002 the estuary underwent major redevelopment which emphasized environmental remediation to measure biological effects. The present study investigated the health status of the sentinel species Hediste diversicolor in the Seine estuary by comparing data from a sampling campaign immediately after the Seine underwent reconstruction and 10 years afterward. Both studies implemented multiple levels of biological organization ranging from enzymatic biomarkers to population density. Integrative modeling was used to establish a holistic status assessment for H. diversicolor in the Seine. H. diversicolor populations in the Seine estuary were impacted in both campaigns suggesting no significant improvements over the 10-year period. This interpretation however can be improved by increasing the number of reference sites used to establish the baseline natural variation, integrating additional environmental parameters into the model and measuring additional biological endpoints, such as reproductive status.

Disentangling the relative roles of natural and anthropogenic-induced stressors in shaping benthic ciliate diversity in a heavily disturbed bay

Coastal areas are facing biodiversity loss and degradation of habitats due to intensified human activities. However, our understanding of the relative contribution of natural gradients and human induced disturbance to biodiversity is limited. Here, we investigated the response of three facets of alpha and beta diversity of benthic ciliates to environmental gradients in a highly disturbed estuarine bay in China. We used linear regression and distance-based redundancy analysis to determine the key driving factors for biodiversity. Variation partitioning was further used to examine the relative influence of natural gradients and anthropogenic disturbances on ciliate communities. Our results revealed that ciliate alpha diversity and functional composition remained similar despite notable variation in species composition along salinity gradient. Sediment grain size, together with heavy metals were the strongest determinants in shaping both alpha and beta diversity. After controlling for the effect of natural factors, heavy metals still had significant impacts on beta diversity. Human induced nitrogen enrichment was positively correlated with algivorous functional group with possible impacts on benthic food webs. These results suggest that beta diversity is overall more sensitive to anthropogenic stressors than alpha diversity and give important insights into the role of anthropogenic disturbance on coastal diversity, being also useful for developing ecosystem protection and conservation strategies.

Testing the applicability of random forest modeling to examine benthic foraminiferal responses to multiple environmental parameters

The main environmental variables controlling benthic foraminiferal distributions were identified and used to assess their influence on ecological indices developed as predictors of Ecological Quality Status (EcoQS) in marine ecosystems. Gradient forest and random forest models were applied to assess the predictive value of a selection of abiotic (environmental) and biotic (foraminifera) variables in a costal marine area in the central Adriatic Sea (Italy). This approach yields evidence that the predictor variables sand, silt, Pollution Load Index, and TN have the greatest influence on the distribution of benthic foraminifera in this area. In addition, we identify thresholds for the most important environmental variables that influence ecological indices. These findings contribute to efforts to determine how to best improve sediment quality and environmental stability for marine conservation. Further application of these approaches represents a useful tool for policymakers to survey the diversity of marine organisms and to improve the ability to protect and restore marine ecosystems by identifying predictors of diversity and identifying key thresholds in these predictors.

Distribution Patterns of Benthic Foraminifera in Fish Farming Areas (Corsica, France): Implications for the Implementation of Biotic Indices in Biomonitoring Studies

Corsican marine aquaculture is one of the highest contributors of fish production in France, which may result in environmental perturbations caused by organic matter (OM) accumulation under fish farms and impacting natural communities. This study aimed to (1) characterise the environmental conditions at two different fish farms, (2) monitor the response of benthic foraminiferal species to this activity, and (3) assess the accuracy of existing foraminiferal biotic indices. In 2017, sea floor sediment was sampled in transects from two Corsican fish farms for living foraminiferal and sedimentary analyses. Four indices were calculated and compared: exp(H′bc), Foram-AMBI, Foram Stress Index and TSI-Med. A significant increase in total organic carbon (TOC) has been shown, mainly below the fish cages. Communities were characterized by a shift from high density, opportunistic and tolerant species under the cages to lower densities and more sensitive species further away. According to their distribution patterns along the TOC gradient, we propose to update the ecological group classification of seven species to improve Foram-AMBI’s accuracy and sensitivity: Triloculina oblonga and Quinqueloculina lamarckiana to Ecological Group (EG) I; Rosalina bradyi to EGIII; and Bolivina dilatata, Bulimina aculeata and Quinqueloculina stalkeri to EGIV. We recommend prioritising the use of TSI-Med and Foram-AMBI with the updated list to assess ecological quality in coastal waters of the Mediterranean Sea.

Assessing the ecological quality status of the highly polluted Bagnoli area (Tyrrhenian Sea, Italy) using foraminiferal eDNA metabarcoding

Morphology-based benthic foraminifera indices are increasingly used worldwide for biomonitoring the ecological quality of marine sediments. The recent development of foraminiferal eDNA metabarcoding offers a reliable, time-, and cost-effective alternative to morphology-based foraminiferal biomonitoring. However, the practical applications of these new tools are still highly limited. In the present study, we evaluate the response of benthic foraminifera and define the ecological quality status (EcoQS) in the Bagnoli area (Tyrrhenian Sea, Italy) based on a traditional morphology-based approach and eDNA metabarcoding. The geochemical data show that several sites in front of the former industrial plant contain higher concentrations of potentially toxic elements than the effect range median and are characterized by the highest total organic carbon (TOC) content, whereas the distantly located sites can be considered relatively low- to unpolluted. Significant differences (i.e., diversity and assemblage composition) in both morphological and molecular datasets were found between the relatively low- to unpolluted and the most polluted areas. Similarly, the selected ecological indices of both morphological and molecular datasets strikingly and congruently resulted in a clear separation following the environmental stress gradient. The molecular indices (i.e., g-exp(H'_bc), g-Foram AMBI, and g-Foram AMBI-MOTUs) reliably identified poor-to-bad EcoQS in the polluted area in front of the former industrial plant. On the other hand, the Foram-AMBI based on morphology well identified an overall trend but seemed to overestimate the EcoQS if the traditional class boundaries were considered. The congruent and complementary trends between morphological and metabarcoding data observed in the case of the Bagnoli site further support the application of foraminiferal metabarcoding in routine biomonitoring to assess the environmental impacts of heavily polluted marine areas.

Benthic Foraminiferal Indices and Environmental Quality Assessment of Transitional Waters: A Review of Current Challenges and Future Research Perspectives

Transitional waters straddle the interface between marine and terrestrial biomes and, among others, include fjords, bays, lagoons, and estuaries. These coastal systems are essential for transport and manufacturing industries and suffer extensive anthropogenic exploitation of their ecosystem services for aquaculture and recreational activities. These activities can have negative effects on the local biota, necessitating investigation and regulation. As a result of this, EcoQS (ecological quality status) assessment has garnered great attention as an essential aspect of governmental bodies’ legislative decision-making process. Assessing EcoQS in transitional water ecosystems is problematic because these systems experience high natural variability and organic enrichment and often lack information about their pre-human impact, baseline, or “pristine” reference conditions, knowledge of which is essential to many commonly used assessment methods. Here, foraminifera can be used as environmental sentinels, providing ecological data such as diversity and sensitivity, which can be used as the basis for EcoQS assessment indices. Fossil shells of foraminifera can also provide a temporal aspect to ecosystem assessment, making it possible to obtain reference conditions from the study site itself. These foraminifera-based indices have been shown to correlate not only with various environmental stressors but also with the most common macrofaunal-based indices currently employed by bodies such as the Water Framework Directive (WFD). In this review, we firstly discuss the development of various foraminifera-based indices and address the challenge of how best to implement these synergistically to understand and regulate human environmental impact, particularly in transitional waters, which have historically suffered disproportionate levels of human impact or are difficult to assess with standard EcoQS methods. Further, we present some case studies to exemplify key issues and discuss potential solutions for those. Such key issues include, for example, the disparate performance of multiple indices applied to the same site and a proper assignment of EcoQS class boundaries (threshold values) for each index. Disparate aptitudes of indices to specific geomorphologic and hydrological regimes can be leveraged via the development of a site characteristics catalogue, which would enable the identification of the most appropriate index to apply, and the integration of multiple indices resulting in more representative EcoQS assessment in heterogenous transitional environments. In addition, the difficulty in assigning threshold values to systems without analogous unimpacted reference sites (a common issue among many transitional waters) can be overcome by recording EcoQS as an ecological quality ratio (EQR). Lastly, we evaluate the current status and future potential of an emerging field, genetic biomonitoring, focusing on how these new techniques can be used to increase the accuracy of EcoQS assessment in transitional systems by supplementing more established morphology-based methods.

Indicative value of benthic foraminifera for biomonitoring: Assignment to ecological groups of sensitivity to total organic carbon of species from European intertidal areas and transitional waters

This work contributes to the ongoing work aiming at confirming benthic foraminifera as a biological quality element. In this study, benthic foraminifera from intertidal and transitional waters from the English Channel/European Atlantic coast and the Mediterranean Sea were assigned to five ecological groups using the weighted-averaging optimum with respect to TOC of each species. It was however not possible to assign typical salt marsh species due to the presence of labile and refractory organic matter that hampers TOC characterization. Tests of this study species' lists with Foram-AMBI on two independent datasets showed a significant correlation between Foram-AMBI and TOC, confirming the strong relation between foraminifera and TOC. For one of the validation datasets, associated macrofaunal data were available and a significant correlation was found between the foraminiferal Foram-AMBI and the macrofaunal AMBI. The here proposed lists should be further tested with sensitivity-based indices in different European regional settings.

Effects of temperature on the behaviour and metabolism of an intertidal foraminifera and consequences for benthic ecosystem functioning

Heatwaves have increased in intensity, duration and frequency over the last decades due to climate change. Intertidal species, living in a highly variable environment, are likely to be exposed to such heatwaves since they can be emerged for more than 6 h during a tidal cycle. Little is known, however, on how temperature affects species traits (e.g. locomotion and behaviour) of slow-moving organisms such as benthic foraminifera (single-celled protists), which abound in marine sediments. Here, we examine how temperature influences motion-behaviour and metabolic traits of the dominant temperate foraminifera Haynesina germanica by exposing individuals to usual (6, 12, 18, 24, 30 °C) and extreme (high; i.e. 32, 34, 36 °C) temperature regimes. Our results show that individuals reduced their activity by up to 80% under high temperature regimes whereas they remained active under the temperatures they usually experience in the field. When exposed to a hyper-thermic stress (i.e. 36 °C), all individuals remained burrowed and the photosynthetic activity of their sequestered chloroplasts significantly decreased. Recovery experiments subsequently revealed that individuals initially exposed to a high thermal regime partially recovered when the hyper-thermic stress ceased. H. germanica contribution to surface sediment reworking substantially diminished from 10 mm³ indiv^-1 day^-1 (usual temperature) to 0 mm³ indiv^-1 day^-1 when individuals were exposed to high temperature regimes (i.e. above 32 °C). Given their role in sediment reworking and organic matter remineralisation, our results suggest that heatwaves may have profound long-lasting effects on the functioning of intertidal muddy ecosystems and some key biogeochemical cycles.

Reconstruction of the palaeo-ecological quality status in an impacted estuary using benthic foraminifera: The Santos Estuary (São Paulo state, SE Brazil)

The Santos Estuary (SE Brazil) is a coastal ecosystem with a high ecological importance and has been strongly impacted by human activities over the last century. A multiproxy analysis of sediment core dated by ¹³⁷Cs, ²¹⁰Pb and ²²⁶Ra activities and based on sediment geochemistry and benthic foraminifera is here used to reconstruct the environmental changes and the variations of the Palaeo-Ecological Quality Status (Palaeo-EcoQS) during the last ~120 years. The Palaeo-EcoQS was reconstructed by applying the diversity index Exp(H'_bc) based on the benthic foraminiferal fauna. Specifically, the Ecological Quality Ratio (EQR) allowed to assess the Palaeo-EcoQS during the last ~120 years using local reference conditions. Based on our data, the pre-industrial period (~1883-1902) represents the reference conditions with "Good" Palaeo-EcoQS. The ~1902-1972 period coincides with the beginning of industrial operations and intensification of coastal urbanization leading to a deterioration of the environmental quality and Palaeo-EcoQS shifting to "Moderate" conditions. Dredging operations in 1972 led to increase the influences of adjacent sea that ultimately resulted in a "Good" Palaeo-EcoQS persisting up to the 1990s. Despite the preservation actions and recovery programs, the 1993-2012 period was characterized by an overall deterioration of the environmental conditions. Indeed, the reconstructed "Poor" to "Bad" Palaeo-EcoQS suggest the ineffectiveness of the remediation actions. This work confirmed that benthic foraminifera are reliable to evaluate EcoQS and Palaeo-EcoQS in estuarine ecosystems. Based on the present findings and previous studies showing the potential of fossil foraminifera to define in situ reference conditions, we recommend the inclusion of foraminifera in the list of biological quality elements within legislations concerning transitional and marine habitats.