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

Assessing the potential of nematode metabarcoding for benthic monitoring of offshore oil platforms

Environmental DNA metabarcoding is gaining momentum as a time and cost-effective tool for biomonitoring and environmental impact assessment. Yet, its use as a replacement for the conventional marine benthic monitoring based on morphological analysis of macrofauna is still challenging. Here we propose to study the meiofauna, which is much better represented in sediment DNA samples. We focus on nematodes, which are the most numerous and diverse group of meiofauna. Our aim is to assess the potential of nematode metabarcoding to monitor impacts associated with offshore oil platform activities. To achieve this goal, we used nematode-optimized marker (18S V1V2-Nema) and universal eukaryotic marker (18S V9) region to analyse 252 sediment DNA samples collected near three offshore oil platforms in the North Sea. For both markers, we analysed changes in alpha and beta diversity in relation to distance from the platforms and environmental variables. We also defined three impact classes based on selected environmental variables that are associated with oil extraction activities and used random forest classifiers to compare the predictive performance of both datasets. Our results show that alpha- and beta-diversity of nematodes varies with the increasing distance from the platforms. The variables directly related to platform activity, such as Ba and THC, strongly influence the nematode community. The nematode metabarcoding data provide more robust predictive models than eukaryotic data. Furthermore, the nematode community appears more stable in time and space, as illustrated by the overlap of nematode datasets obtained from the same platform three years apart. A significative negative correlation between distance and Shannon diversity also advocates for higher performance of the V1V2-Nema over the V9. Overall, these results suggest that the sensitivity of nematodes is higher compared to the eukaryotic community. Hence, nematode metabarcoding has the potential to become an effective tool for benthic monitoring in marine environment.

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.

Measuring ecological quality status in low-diversity Arctic intertidal foraminiferal assemblages using a diversity-based index

EcoQS assessment of the marine intertidal zone based on its fauna is challenging because the assemblages have a low diversity and consist of stress tolerant species. The new approach we propose is to pool foraminiferal diversity (effective number of species exp(H'bc)) across the whole intertidal zone including the salt marsh and tidal flat. In seven fjordheads studied in northern Fennoscandia, polycyclic aromatic hydrocarbon (PAH) concentrations indicated low levels of pollution (EcoQSPAH Excellent to Moderate). Jadammina or Balticammina dominated the salt marsh, Elphidium albiumbilicatum, Elphidium williamsoni, Elphidium clavatum, and Buccella frigida occurred in the tidal flat. Ovammina opaca thrived in both belts. While foraminiferal test abnormalities are often proposed to measure pollution impacts, we did not detect any correlation with PAHs. EcoQS based on foraminiferal diversity (EcoQSforam Excellent to Good) matched EcoQS based on PAHs suggesting that pooled foraminiferal diversity reliably measures intertidal EcoQS.

Deciphering the impact of decabromodiphenyl ether (BDE-209) on benthic foraminiferal communities: Insights from Cell-Tracker Green staining and eDNA metabarcoding

This study investigates the ecotoxicological effects of BDE-209, a persistent organic pollutant (POP) prevalent in Kuwait's coastal-industrial areas, on benthic foraminiferal communities. We conducted a mesocosm experiment in which we exposed benthic foraminiferal communities sampled from the coastal-industrial areas of Kuwait to a gradient of BDE-209 concentrations (0.01 to 20 mg/kg). The impact of exposure was assessed using live-staining and metabarcoding techniques. Despite the significantly different taxonomic compositions detected by the two techniques, our results show that BDE-209 significantly affects foraminiferal communities, with moderately high concentrations leading to reduced α-diversity and considerable taxonomic shifts in both molecular and morphological assemblages. At concentrations of 10 and 20 mg/kg, no living foraminifera were detected after 8 weeks, suggesting a threshold for their survival under BDE-209 exposure. The parallel responses of molecular and morphological communities confirm the reliability of both assessment methods. This study is the first to investigate the reaction of eukaryotic communities, specifically foraminifera, to POPs such as BDE-209, generating valuable insights that have the potential to enhance field studies and aid the refinement of sediment quality guidelines.

Assessment of the ecological quality status of the Sepetiba Bay (SE Brazil): When metabarcoding meets morphology on foraminifera

In recent years, the region surrounding Sepetiba Bay (SB; SE Brazil) has become a hub of intense urban expansion and economic exploitation in response to ore transport and industrial and port activities. As a result, contaminants have been introduced into the bay, leading to an overall worsening of the environmental quality. The present work applies for the first time a foraminiferal morphology-based approach (M) and eDNA-based metabarcoding sequencing (G), along with geochemical data to assess the ecological quality status (EcoQS) in the SB. Principal component analysis shows that the eDNA and morphospecies diversity as well as most of the taxa relative abundance decline in response to the environmental stress (ES) gradient related to total organic carbon (TOC) and metal pollution. Based on ecological indices, Exp(H'bc) (G), Exp(H'bc) (M), foraminifera ATZI marine biotic index (Foram-AMBI), Foram Stress Index (FSI), and geochemical indices (TOC and Potential Ecological Risk Index), the lowest values of EcoQS (i.e., bad to moderate) are inferred in the innermost part of the SB. Despite minor discrepancies among the six EcoQS indices, an agreement has been found for 63% of the stations. To improve the agreement between the ecological indices, it is necessary to fill the gap in species ecology; information on the ecology of many species is still unknown. This work reinforces the importance of molecular analysis and morphological methods in environmental impact studies and confirms the reliability of foraminiferal metabarcoding in EcoQS assessment. This is the first study evaluating the EcoQS in the South Atlantic by using combined foraminiferal eDNA metabarcoding with morphological data.

Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity

Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.

Unlocking foraminiferal genetic diversity on estuarine mudflats with eDNA metabarcoding

Environmental biomonitoring is a prerequisite for efficient evaluation and remediation of ecosystem degradation due to anthropogenic pressure or climate change. Estuaries are key habitats subject to multiple anthropogenic and natural stressors. Due to these multiple stressors, the detection of anthropogenic pressure is challenging. The fact that abundant natural stressors often lead to negative quality assessments has been coined the "estuarine quality paradox". To solve this issue, the application of molecular approaches with successful bioindicators like foraminifera is promising. However, sampling protocols, molecular procedures and data analyses need to be validated before such tools can be routinely applied. We conducted an environmental DNA survey of estuarine mudflats along the French Atlantic coast, using a metabarcoding approach targeting foraminifera. Our results demonstrate that estuarine environments have only a few active OTUs dominating the community composition and a large stock of dormant or propagule stages. This last genetic diversity components constitute an important reservoir, with different species which can potentially develop in response to the temporal variability of the multiple stressors. In fact, different OTUs were dominant in the studied estuaries. Our statistical model shows that the physical and chemical characteristics of the sediment and the climatic conditions explain only 43 % of the community composition variance. This suggests that other, less easily quantifiable factors, such as the history and use of the estuaries or the ecological drift could play an important role as well. Environmental DNA biomonitoring opens new perspectives to better characterize the genetic diversity in estuaries.

Assessment of environmental parameters effect on potentially toxic elements mobility in foreshore sediments to support marine-coastal contamination prediction

Potentially toxic elements (PTEs) presence in marine sediments can significantly affect the environmental quality and negatively influence economy and recreational activities in related areas. Accordingly, contamination monitoring and control in the marine environment is a fundamental task. In this work, four PTEs behavior (i.e. As, Hg, Pb, and Zn) in sandy foreshore sediments (SFSs) was thoroughly investigated at different pH, redox potential and temperature conditions of the marine water. For all the tests, the released As was 2.7-6 times higher than its initial concentration in water. Nonetheless, final mass balances showed that preferential release in the liquid phase occurred for Pb and Hg (up to 10 % and 9.1 %, respectively). Moreover, final Zn and Hg content increase in SFSs labile fractions indicated their higher bioavailability after the tests. The obtained results outline an approach useful to predict the contaminants behavior in marine matrices and support environmental monitoring and preservation strategies.

Inferring the ecological quality status based on living benthic foraminiferal indices in transitional areas of the Guanabara bay (SE Brazil)

Using benthic foraminifera, we evaluate the ecological quality status (EcoQS) of transitional waters of the Guanabara Bay (SE Brazil) by applying the diversity-based index exp (H'_bc) and the sensitivity-based Foram-AMBI for the first time in South America. The Guanabara Bay was selected for this study as it is one of the largest transitional ecosystems in the State of Rio de Janeiro and has been severely impacted by anthropogenic activities. Concentrations of potentially toxic elements (PTEs) were assessed by sequential chemical extraction in three phases (i.e., dissolved in water, adsorbed on organic matter, and Mn oxy-hydroxides). Total organic carbon, total nitrogen, and stable isotope (δ¹³C and δ¹⁵N) signatures of organic matter were analyzed to trace environmental stress. The Ammonia/Elphidium ratio suggests hypoxic conditions at most of the sampled sites. Principal component analysis identifies the first component as environmental stress underlying organic matter and PTE enrichment (in all three phases), which is positively related to Foram-AMBI and negatively to exp (H'_bc). The exp (H'_bc) and Foram-AMBI indices reveal that stations near the Governador Island and Niterói margin have the worst EcoQS, showing medium to extreme pollution. Additionally, Foram-AMBI and exp (H'_bc) provide a congruent EcoQS classification for ∼64% of the sites. Although these results are promising, they suggest that a significant effort should be made to obtain better knowledge of foraminiferal ecological requirements to employ benthic foraminifera as a biomonitoring and management method.

Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites

The Anthropocene is characterized by dramatic ecosystem changes driven by human activities. The impact of these activities can be assessed by different geochemical and paleontological proxies. However, each of these proxies provides only a fragmentary insight into the effects of anthropogenic impacts. It is highly challenging to reconstruct, with a holistic view, the state of the ecosystems from the preindustrial period to the present day, covering all biological components, from prokaryotes to multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing all trophic levels of biodiversity to reconstruct the two century-natural history in Bagnoli-Coroglio (Gulf of Pozzuoli, Tyrrhenian Sea), one of the most polluted marine-coastal sites in Europe. The site was characterized by seagrass meadows and high eukaryotic diversity until the beginning of the 20th century. Then, the ecosystem completely changed, with seagrasses and associated fauna as well as diverse groups of planktonic and benthic protists being replaced by low diversity biota dominated by dinophyceans and infaunal metazoan species. The sedaDNA analysis revealed a five-phase evolution of the area, where changes appear as the result of a multi-level cascade effect of impacts associated with industrial activities, urbanization, water circulation and land-use changes. The sedaDNA allowed to infer reference conditions that must be considered when restoration actions are to be implemented.

Are genomic indices effective alternatives to morphology based benthic indices in biomonitoring studies? Perspectives from a major harbour and marine protected area

Ecological assessments are currently being conducted by traditional morpho-taxonomical identification techniques that are time-consuming and often inaccurate. Biomonitoring programs are increasingly being complemented by the more rapid and efficient DNA barcoding approach. We compared the congruency of morpho-taxonomic (AMBI - AZTI's Marine Biotic Index) and genomic (gAMBI) benthic indices in ecological quality status (EcoQS) assignation in Mumbai harbour and Malvan Marine Protected area (MPA). The study, first of its kind to adopt the gAMBI tool in the selected milieu, contributed substantial number of macrobenthic cytochrome c oxidase subunit I gene (COI) sequences that were previously unavailable in the reference library, adding sufficient genetic resources for establishing ecostatus. AMBI and gAMBI values based on presence/absence data related significantly with those derived from abundance data matrices. Taxonomic and genomic indices derived ecostatus corresponded sufficiently well despite minor discrepancies, underscoring the viability of gAMBI as a superior alternative to AMBI in monitoring studies.

Spatial distribution of pollution levels and assessment of benthic foraminifera in Apapa-Badagry Creek, Nigeria

The Apapa and Badagry creeks in Nigeria are a corridor of long-term anthropogenic activities, including mangrove removal, urban expansion, and industrialization. Consequently, this uncontrolled development led to the release of untreated effluents and wastes, which resulted in sediment and water quality degradation. This area has the highest degree of pollution (Enrichment and Contamination Factors) especially north of Tincan Island where potentially toxic element (PTE) depocenters occur. Our data shows that salinity and pH are the two main factors favoring foraminiferal distributions, but the sediments in the depocenters with the highest degree of PTE pollution are barren of foraminifera. Bioavailable sediment-bound PTEs have been found to negatively impact the assemblage distribution and diversity. It is important to highlight that dissolved phosphorous was the only PTE that negatively impacted species richness. This study highlights the significance of implementing PTE bioavailability as an integral part of ecosystem functioning in all nearshore environments.

Assessing sediment organic pollution via machine learning models and resource performance

Due to the potential ecological risks of organic pollution in sediments, aquatic ecosystems are currently facing substantial environmental threats. Assessing and controlling sediment pollution has become a huge challenge. Therefore, this study proposes a novel strategy for predicting organic pollution indicators for sediment, as well as an effective resource-utilization method. Contaminated sediments were converted into catalysts for sulfate radical advanced oxidation technologies by a one-step calcination method. The results revealed that the catalyst excelled in activating peroxymonosulfate to degrade tetracycline via a non-radical pathway. Most importantly, a predictive model of organic pollution indicators was established by machine learning. This study provides a novel approach for resource utilization and a strategy for assessing organic pollution in sediments.

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.

Environmental RNA outperforms eDNA metabarcoding in assessing impact of marine pollution: A chromium-spiked mesocosm test

Environmental (e)DNA metabarcoding holds great promise for biomonitoring and ecotoxicological applications. However, few studies have compared the performance of eDNA versus eRNA metabarcoding in assessing organismal response to marine pollution, in experimental conditions. Here, we performed a chromium (Cr)-spiked mesocosm experimental test on benthic foraminiferal community to investigate the effects on species diversity by analysing both eDNA and eRNA metabarcoding data across different Cr concentrations in the sediment. Foraminiferal diversity in the eRNA data showed a significant negative correlation with the Cr concentration in the sediment, while a positive response was observed in the eDNA data. The foraminiferal OTUs exhibited a higher turnover rate in eRNA than in the eDNA-derived community. Furthermore, in the eRNA samples, OTUs abundance was significantly affected by the Cr gradient in the sediment (Pseudo-R² = 0.28, p = 0.05), while no significant trend was observed in the eDNA samples. The correlation between Cr concentration and foraminiferal diversity in eRNA datasets was stronger when the less abundant OTUs (<100 reads) were removed and the analyses were conducted exclusively on OTUs shared between eRNA and eDNA datasets. This indicates the importance of metabarcoding data filtering to capture ecological impacts, in addition to using the putatively active organisms in the eRNA dataset. The comparative analyses on foraminiferal diversity revealed that eRNA-based metabarcoding can better assess the response to heavy metal exposure in presence of subtle concentrations of the pollutant. Furthermore, our results suggest that to unlock the full potential for ecosystem assessment, eDNA and eRNA should be studied in parallel to control for potential sequence artifacts in routine ecosystem surveys.

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.

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.