Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning

Monitoring biodiversity is essential to assess the impacts of increasing anthropogenic activities in marine environments. Traditionally, marine biomonitoring involves the sorting and morphological identification of benthic macro-invertebrates, which is time-consuming and taxonomic-expertise demanding. High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) represents a promising alternative for benthic monitoring. However, an important fraction of eDNA sequences remains unassigned or belong to taxa of unknown ecology, which prevent their use for assessing the ecological quality status. Here, we show that supervised machine learning (SML) can be used to build robust predictive models for benthic monitoring, regardless of the taxonomic assignment of eDNA sequences. We tested three SML approaches to assess the environmental impact of marine aquaculture using benthic foraminifera eDNA, a group of unicellular eukaryotes known to be good bioindicators, as features to infer macro-invertebrates based biotic indices. We found similar ecological status as obtained from macro-invertebrates inventories. We argue that SML approaches could overcome and even bypass the cost and time-demanding morpho-taxonomic approaches in future biomonitoring.

Sedimentation Pulse in the NE Gulf of Mexico following the 2010 DWH Blowout

The objective of this study was to investigate the impacts of the Deepwater Horizon (DWH) oil discharge at the seafloor as recorded in bottom sediments of the DeSoto Canyon region in the northeastern Gulf of Mexico. Through a close coupling of sedimentological, geochemical, and biological approaches, multiple independent lines of evidence from 11 sites sampled in November/December 2010 revealed that the upper ~1 cm depth interval is distinct from underlying sediments and results indicate that particles originated at the sea surface. Consistent dissimilarities in grain size over the surficial ~1 cm of sediments correspond to excess ²³⁴Th depths, which indicates a lack of vertical mixing (bioturbation), suggesting the entire layer was deposited within a 4–5 month period. Further, a time series from four deep-sea sites sampled up to three additional times over the following two years revealed that excess ²³⁴Th depths, accumulation rates, and ²³⁴Th inventories decreased rapidly, within a few to several months after initial coring. The interpretation of a rapid sedimentation pulse is corroborated by stratification in solid phase Mn, which is linked to diagenesis and redox change, and the dramatic decrease in benthic formanifera density that was recorded in surficial sediments. Results are consistent with a brief depositional pulse that was also reported in previous studies of sediments, and marine snow formation in surface waters closer to the wellhead during the summer and fall of 2010. Although sediment input from the Mississippi River and advective transport may influence sedimentation on the seafloor in the DeSoto Canyon region, we conclude based on multidisciplinary evidence that the sedimentation pulse in late 2010 is the product of marine snow formation and is likely linked to the DWH discharge.

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.

Marine biofouling organisms on beached, buoyant and benthic plastic debris in the Catalan Sea

Plastic debris provides long-lasting substrates for benthic organisms, thus acting as a potential vector for their dispersion. Its interaction with these colonizers is, however, still poorly known. This study examines fouling communities on beached, buoyant and benthic plastic debris in the Catalan Sea (NW Mediterranean), and characterizes the plastic type. We found 14 specimens belonging to two phyla (Annelida and Foraminifera) on microplastics, and more than 400 specimens belonging to 26 species in 10 phyla (Annelida, Arthropoda, Brachiopoda, Bryozoa, Chordata, Cnidaria, Echinodermata, Mollusca, Porifera and Sipuncula) on macroplastics. With 15 species, bryozoans are the most diverse group on plastics. We also report 17 egg cases of the catshark Scyliorhinus sp., and highlight the implications for their dispersal. Our results suggest that plastic polymers may be relevant for distinct fouling communities, likely due to their chemical structure and/or surface properties. Our study provides evidence that biofouling may play a role in the sinking of plastic debris, as the most abundant fouled plastics had lower densities than seawater, and all bryozoan species were characteristic of shallower depths than those sampled. More studies at low taxonomic level are needed in order to detect new species introduction and potential invasive species associated with plastic debris.

Comparison of benthic foraminifera and macrofaunal indicators of the impact of oil-based drill mud disposal

We compare foraminifera and macrofauna as bio-indicators of oil-based drill mud disposal site off Congo. The most polluted sites are characterized by poor faunas, dominated by some very tolerant taxa. Slightly further from the disposal site, there is an area with strongly increased densities, heavily dominated by opportunistic taxa. Still further, macrofauna appears to be similar to that at the reference area, but the foraminiferal meiofauna still suggests a slight environmental perturbation. The foraminiferal FIEI index, based on the species distribution in the study area, appears to be more discriminative than the macrofaunal ITI index, based on a priori definitions of the trophic guilds of the various taxa. Our comparative approach allows us to point out the benefits of (1) the use of macrofauna and foraminifera together and (2) the definition of the species groups used in biotic indices on the basis of observations made directly in the study area.

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

The intertidal areas of the Hauts-de-France (English Channel - France) stand out for the occurrence of fragile ecosystems that are exposed to natural and human-induced stress. Over the last two centuries, the northern part of this region has experienced a strong human pressure, with the settlement of numerous activities (i.e., metallurgic factories, harbors, embankments). On the contrary, the southern part includes mostly natural areas. The whole region is influenced by a macrotidal regime. A multidisciplinary approach based on sedimentological (grain-size), geochemical (trace metals, biomarkers) and biological (foraminifera) proxies was used to unravel the contrasting environmental conditions in the Hauts-de-France. Three foraminiferal-types communities, which reflect different ecological characteristics at regional scale, were identified: 1) estuarine macrotidal assemblages (Haynesina germanica associated to Elphidiidae) in low impacted estuaries; 2) industrial-perturbed assemblages (H. germanica and Cribroelphidium excavatum) in harbor areas; and 3) infaunal-dominant assemblages (Bolivina variabilis and B. pseudoplicata) in embankment areas. The outcomes of this study show that a multiproxy procedure needs to be adopted for properly characterizing intertidal ecosystems, where human impacts and natural stresses overlap and are hard to disentangle.

ForCenS, a curated database of planktonic foraminifera census counts in marine surface sediment samples

Census counts of marine microfossils in surface sediments represent an invaluable resource for paleoceanography and for the investigation of macroecological processes. A prerequisite for such applications is the provision of data syntheses for individual microfossil groups. Specific to such syntheses is the necessity of taxonomical harmonisation across the constituent datasets, coupled with dereplication of previous compilations. Both of these aspects require expert knowledge, but with increasing number of records involved in such syntheses, the application of expert knowledge via manual curation is not feasible. Here we present a synthesis of planktonic foraminifera census counts in surface sediment samples, which is taxonomically harmonised, dereplicated and treated for numerical and other inconsistencies. The data treatment is implemented as an objective and largely automated pipeline, allowing us to reduce the initial 6,984 records to 4,205 counts from unique sites and informative technical or true replicates. We provide the final product and document the procedure, which can be easily adopted for other microfossil data syntheses.

Benthic foraminifera assemblages as elemental pollution bioindicator in marine sediments around fish farm (Vrgada Island, Central Adriatic, Croatia)

Effects on sediments of fish farming activity near Vrgada Island was analysed through living and total foraminiferal assemblages and concentration of major, minor and trace elements from three sediment cores. Elemental concentrations of sediments are in accordance with carbonate characteristics of the surrounding area and show mostly natural element variations between sampling locations and throughout the cores, with no significant increases due to fish farming activity. Only phosphorus concentration shows elevate values below the fish cage, assigned to fish pellets. Foraminiferal communities are dominated by epifaunal and stress tolerant species, while diversity indices point to normal marine conditions. The type of substrate and phosphorus content in sediments principally influence foraminiferal community composition, while other elemental concentrations have no perceptible effect on the assemblages. Some foraminiferal species Ammoniatepida, Ammoniabeccarii, Elphidiumcrispum, Elphidiummacellum and genus Haynesina are confirmed to be tolerant to elevated nutrient (phosphorus) content, while Ammonia parkinsoniana shows sensitivity to pollution. Postmortem processes cause decrease of foraminiferal density and species richness with core depth. All results point to negligible influence of fish farming and relatively stable environmental conditions at all sampling locations.

Cigarette butts, a threat for marine environments: Lessons from benthic foraminifera (Protista)

Cigarette butts are the most common form of litter in the world and their environmental impact is related to both persistence and potential toxic effects for chemical composition. The objective of this study was to assess the acute toxicity (LC₅₀-48 h) of human-smoked cigarette butts leachate on 3 cultured genera of benthic foraminifera: the calcareous perforate Rosalina globularis, the calcareous imperforate Quinqueloculina spp., and the agglutinated Textularia agglutinans. The specimens were exposed to 16, 8, 4, 2, and 1 cigarette butts/L concentrations that prove to be acutely toxic to all taxa. Starting from 4 cigarette butts/L, both calcareous genera showed shell decalcification, and death of almost all the individuals, except for the more resistant agglutinated species. These results suggest the potential harmfulness of cigarette butts leachate related to pH reduction and release of toxic substances, in particular nicotine, which leads to physiology alteration and in many cases cellular death.

Ecological quality status of the NE sector of the Guanabara Bay (Brazil): A case of living benthic foraminiferal resilience

The ecological quality status of the NE region of the Guanabara Bay (SE Brazil), one of the most important Brazilian embayments, is evaluated. For this purpose, sediment samples from in the inner of the Guanabara Bay (GB) were collected and analyzed (grain-size, mineralogy, geochemistry and living foraminifera). In this study, it is hypothesized that the potentially toxic elements (PTEs) concentrations, in solution and associated with organic matter (_OMPTEs, potential nutrient source), may represent two potential pathways to impact benthic foraminifers. A multiproxy approach applied to complex statistical analyses and ecological indexes shows that the study area is, in general, eutrophic (with high organic matter and low oxygen content), polluted by PTEs and oil. As a consequence, foraminifera are not abundant and their assemblages are poorly diversified and dominated by some stress-tolerant species (i.e., Ammonia tepida, Quinqueloculina seminula, Cribroelphidium excavatum). The results allow us to identify a set of species sensitive to eutrophication and _OMPTEs. Factors such as the increase of organic matter contents and _OMPTEs and, in particular of Zn, Cd and Pb, the oxygen depletion and the presence of oil, altogether contribute to a marked reduction in the abundance and diversity of foraminifera. Ammonia-Elphidium Index and the Foram Stress Index confirm that the NE zone of GB is, in general, "heavily polluted", with "poor ecological quality status" and experiences suboxic to anoxic conditions. In light of it, special attention from public authorities and policymakers is required in order to take immediate actions to enable its environmental recovery.

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.

Shell Growth of Large Benthic Foraminifera under Heavy Metals Pollution: Implications for Geochemical Monitoring of Coastal Environments

This study was promoted by the recent efforts using larger benthic foraminiferal (LBF) shells geochemistry for the monitoring of heavy metals (HMs) pollution in the marine environment. The shell itself acts as a recorder of the ambient water chemistry in low to extreme HMs-polluted environments, allowing the monitoring of recent-past pollution events. This concept, known as sclerochronology, requires the addition of new parts (i.e., new shell) even in extreme pollution events. We evaluated the physiological resilience of three LBF species with different shell types and symbionts to enriched concentrations of Cd, Cu, and Pb at levels several folds higher than the ecological criteria maximum concentration (CMC) (165-166, 33-43, 1001-1206 µg L^-1, respectively), which is derived from aquatic organisms' toxicity tests. The physiological response of the holobiont was expressed by growth rates quantified by the addition of new chambers (new shell parts), and by the chlorophyll a of the algal symbionts. The growth rate decrease varied between 0% and 30% compared to the unamended control for all HMs tested, whereas the algal symbionts exhibited a general non-fatal but significant response to Pb and Cu. Our results highlight that shell growth inhibition of LBF is predicted in extreme concentrations of 57 × CMC of Cu and 523 × CMC of Cd, providing a proof of concept for shell geochemistry monitoring, which is currently not used in the regulatory sectors.

Disentangling natural vs. anthropogenic induced environmental variability during the Holocene: Marambaia Cove, SW sector of the Sepetiba Bay (SE Brazil)

Multiproxy approach based on textural, mineralogical, geochemical, and microfaunal analyses on a 176-cm-long core (SP8) has been applied to reconstruct the Holocene paleoenvironmental changes and disentangling natural vs. anthropogenic variability in Marambaia Cove of the Sepetiba Bay (SE Brazil). Sepetiba Bay became a lagoonal system due to the evolution and development of the Marambaia barrier island during the Holocene and the presence of an extensive river basin. Elemental concentrations from pre-anthropogenic layers from the nearby SP7 core have been used to estimate the baseline elemental concentrations for this region and to determine metals enrichment factors (EF), pollution load index (PLI), and sediment pollution index (SPI). Record of the core SP8 provides compelling evidence of the lagoon evolution differentiating the effects of potentially toxic elements (PTEs) under natural vs. anthropic forcing in the last ~ 9.5 ka BP. The study area was probably part of coastal sand ridges between ≈ 9.5 and 7.8 ka BP (radiocarbon date). Events of wash over deposited allochthonous material and organic matter between ≈ 8.6 and 7.8 ka. Climatic event 8.2 ka BP, in which the South American Summer Monsoon was intensified in Brazil causing higher rainfall and moisture was scored by an anoxic event. Accumulation of organic matter resulted in oxygen depletion and even anoxia in the sediment activating biogeochemical processes that resulted in the retention of potentially toxic elements (PTEs). After ≈ 7.8 ka BP at the onset of the Holocene sea-level rise, a marine incursion flooded the Marambaia Cove area (previously exposed to subaerial conditions). Environmental conditions became favorable for the colonization of benthic foraminifera. The Foram Stress Index (FSI) and Exp(H'bc) indicate that the environmental conditions turned from bad to more favorable since ≈ 7.8 ka BP, with maximum health reached at ≈ 5 ka BP, during the mid-Holocene relative sea-level highstand. Since then, the sedimentological and ecological proxies suggest that the system evolved to an increasing degree of confinement. Since ≈ 1975 AD, a sharp increase of silting, Cd, Zn, and organic matter also induced by anthropic activities caused major changes in foraminiferal assemblages with a significant increase of Ammonia/Elphidium Index (AEI), EF, and SPI values and decreasing of FSI and Exp(H'bc) (ecological indicators) demonstrating an evolution from "moderately polluted" to "heavily polluted" environment (bad ecological conditions), under variable suboxic conditions. Thus, core SP8 illustrates the most remarkable event of anthropogenic forcing on the geochemistry of the sediments and associated pollution loads and its negative effect on benthic organisms.

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.

The response of benthic foraminifera to heavy metals and grain sizes: A case study from Hainan Island, China

Benthic foraminifera, heavy metals, and sediment grain sizes were studied in three bays of Hainan Island, and canonical correspondence analysis (CCA) and nonparametric regression were used to reveal the relationship between foraminifera and their environment. According to our survey, the three bays were moderately contaminated by Mo and As and uncontaminated to moderately contaminated by Pb, Zn, Cr, Sb, and Hg. The spatial pattern of heavy metals was comparable to sediment transport trends, indicating that their distribution was determined by sediment transport. Both living and dead foraminiferal assemblages were analyzed, and their compositions were similar, although the latter had a higher density and diversity. Based on the CCA method, species were divided into three groups, each of which responded differently to heavy metals and grain sizes. The response curves of individual species to heavy metals and grain sizes were obtained by using the Loess (locally weighted regression) method.

Defining ecological reference conditions in naturally stressed environments - How difficult is it?

The present study performed in Horten Inner Harbor (southern Norway) shows that foraminifera link the present-day Ecological Quality Status (EcoQS) to EcoQS of former times and, this way, bridge an important knowledge gap concerning determination of reference conditions, even in naturally stressed environments such as transitional waters and oxygen depleted habitats. In Horten Inner Harbor, geochemical data in the oldest deposits showed stable background concentrations for about 200 years (from about 1600 to 1800) before human activity became noteworthy, reflecting 'good' to 'high' status. Hence, it is reasonable that organisms, which lived in the area during the same nearly un-impacted time interval, represent the biologically defined reference conditions, irrespectively of whether the biotic indices are classified as 'good' or 'bad'. The present paper illustrates, with a conceptual model, how the retrospective foraminiferal biomonitoring method can be used to detect environmental perturbations in estuaries and meet the difficulties of the Estuarine Quality Paradox.

First record of microplastic in the environmental matrices of a Mediterranean marine cave (Bue Marino, Sardinia, Italy)

This study investigates for the first time the presence of microplastics in sediment, water, and benthic organisms (foraminifera) of a marine cave in the Gulf of Orosei (Sardinia, Italy). Microplastics were found in all water, and sediment samples with similar shapes, sizes, and compositions; identified items were mainly fragments and fibers constituted by PVC and polyethylene. Their provenance was supposed to be predominantly from the sea than from the seasonal freshwater supplies from the karst system. Foraminiferal assemblages were mainly constituted by calcareous hyaline taxa in the outer station, while in the inner ones, the agglutinated Eggerelloides advenus was dominant. FTIR analyses on agglutinated shells identified polyethylene. Microplastic items are collected by the foraminifers and sediment grains building the shell chambers. This is the first study providing evidence that marine caves may be collectors of microplastics and that, in these habitats, microplastics enter the biotic matrix at the protist's level.

Geochemical signatures of benthic foraminiferal shells from a heat-polluted shallow marine environment provide field evidence for growth and calcification under extreme warmth

Shallow marine calcifiers play an important role as marine ecosystem engineers and in the global carbon cycle. Understanding their response to warming is essential to evaluate the fate of marine ecosystems under global change scenarios. A rare opportunity to test the effect of warming acting on natural ecosystems is by investigation of heat-polluted areas. Here, we study growth and calcification in benthic foraminifera that inhabit a thermally polluted coastal area in Israel, where they are exposed to elevated temperatures reaching up to ~42°C in summer. Live specimens of two known heat-tolerant species Lachlanella sp. 1 and Pararotalia calcariformata were collected over a period of 1 year from two stations, representing thermally polluted and undisturbed (control) shallow hard bottom habitats. Single-chamber element ratios of these specimens were obtained using laser ablation, and the Mg/Ca of the most recently grown final chambers were used to calculate their calcification temperatures. Our results provide the first direct field evidence that these foraminifera species not only persist at extreme warm temperatures but continue to calcify and grow. Species-specific Mg/Ca thermometry indicates that P. calcariformata precipitate their shells at temperatures as high as 40°C and Lachlanella sp. 1 at least up to 36°C, but both species show a threshold for calcification at cold temperatures: calcification in P. calcariformata only occurred above 22°C and in Lachlanella sp. 1 above 15°C. Our observations from the heat-polluted area indicate that under future warming scenarios, calcification in heat-tolerant foraminifera species will not be inhibited during summer, but instead the temperature window for their calcification will be expanded throughout much of the year. The observed inhibition of calcification at low temperatures indicates that the role of heat-tolerant foraminifera in carbonate production will most likely increase in future decades.

Plastics, (bio)polymers and their apparent biogeochemical cycle: An infrared spectroscopy study on foraminifera

To understand the fate of plastic in oceans and the interaction with marine organisms, we investigated the incorporation of (bio)polymers and microplastics in selected benthic foraminiferal species by applying FTIR (Fourier Transform Infrared) microscopy. This experimental methodology has been applied to cultured benthic foraminifera Rosalina globularis, and to in situ foraminifera collected in a plastic remain found buried into superficial sediment in the Mediterranean seafloor, Rosalina bradyi, Textularia bocki and Cibicidoides lobatulus. In vitro foraminifera were treated with bis-(2-ethylhexyl) phthalate (DEHP) molecule to explore its internalization in the cytoplasm. Benthic foraminifera are marine microbial eukaryotes, sediment-dwelling, commonly short-lived and with reproductive cycles which play a central role in global biogeochemical cycles of inorganic and organic compounds. Despite the recent advances and investigations into the occurrence, distribution, and abundance of plastics, including microplastics, in marine environments, there remain relevant knowledge gaps, particularly on their effects on the benthic protists. No study, to our knowledge, has documented the molecular scale effect of plastics on foraminifera. Our analyses revealed three possible ways through which plastic-related molecules and plastic debris can enter a biogeochemical cycle and may affect the ecosystems: 1) foraminifera in situ can grow on plastic remains, namely C. lobatulus, R. bradyi and T. bocki, showing signals of oxidative stress and protein aggregation in comparison with R. globularis cultured in negative control; 2) DEHP can be incorporated in the cytoplasm of calcareous foraminifera, as observed in R. globularis; 3) microplastic debris, identified as epoxy resin, can be found in the cytoplasm and the agglutinated shell of T. bocki. We hypothesize that plastic waste and their associated additives may produce modifications related to the biomineralization process in foraminifera. This effect would be added to those induced by ocean acidification with negative consequences on the foraminiferal biogenic carbon (C) storage capacity.

Foraminifera as bioindicators of water quality: The FoRAM Index revisited

Coral reefs worldwide are degrading at alarming rates due to local and global stressors. There are ongoing needs for bioindicator systems that can be used to assess reef health status, the potential for recovery following destructive events such as tropical storms, and for the success of coral transplants. Benthic foraminiferal shells are ubiquitous components of carbonate sediment in reef environments that can be sampled at minimal cost and environmental impact. Here we review the development and application of the FoRAM Index (FI), which provides a bioindicator metric for water quality that supports reef accretion. We outline the strengths and limitations of the FI, and propose how it can be applied more effectively across different geographical regions.

Test deformation and chemistry of foraminifera as response to anthropogenic heavy metal input

Benthic foraminifera are sensitive to environmental changes and widely used as tools to monitor pollution. Rising numbers of deformed tests are often used as indicator for elevated levels of heavy metals, but little is known about the relation between heavy metal incorporation into foraminiferal tests and the formation of test deformities. Here, two sediment cores from the south-eastern North Sea are compared, regarding the occurrence of deformed foraminiferal tests, foraminiferal test chemistry (ICP-MS) and bulk sediment Pb content (XRF). The total abundance of deformed foraminiferal tests seems not to align temporarily with historical heavy metal pollution. Therefore, we suggest that foraminifera react with test deformation to other environmental stressors than the studied heavy metals. Test chemistry reflects historical increased bulk sediment heavy metal content, despite a slight temporal offset. We propose that Pb (and Cd) are only incorporated into foraminiferal tests above a yet to be defined threshold of pollution.

Sensitivity of foraminiferal-based indices to evaluate the ecological quality status of marine coastal benthic systems: A case study of the Gulf of Manfredonia (southern Adriatic Sea)

This paper aims to compare two foraminiferal based biotic indices generally used to evaluate the ecological quality status (EcoQS): the Foram-AMBI and the Foram Stress Index (FSI). For this purpose, we report the distribution and diversity of living foraminiferal assemblages and the environmental variables from a bathymetric transect in the Southern Adriatic Sea. The two indices agree well with the detected organic enrichment but indicate conflicting EcoQS as the Foram-AMBI detects good environmental conditions, whereas the FSI describes a poor-moderate quality. Many species not assigned (including soft-shelled foraminifera) are to blame for the different results. Also, both foraminiferal-based indices neglect the heavy metal increase encountered in the deepest stations. These findings suggest the need for a more in-depth analysis to improve the ecological status evaluation of marine benthic systems, including other descriptors as chemical pollutants in combination with biotic indices sensitive to organic matter enrichment.

Strategies in times of crisis-insights into the benthic foraminiferal record of the Palaeocene-Eocene Thermal Maximum

Climate change is predicted to alter temperature, carbonate chemistry and oxygen availability in the oceans, which will affect individuals, populations and ecosystems. We use the fossil record of benthic foraminifers to assess developmental impacts in response to environmental changes during the Palaeocene-Eocene Thermal Maximum (PETM). Using an unprecedented number of µ-computed tomography scans, we determine the size of the proloculus (first chamber), the number of chambers and the final size of two benthic foraminiferal species which survived the extinction at sites 690 (Atlantic sector, Southern Ocean, palaeodepth 1900 m), 1210 (central equatorial Pacific, palaeodepth 2100 m) and 1135 (Indian Ocean sector, Southern Ocean, palaeodepth 600-1000 m). The population at the shallowest site, 1135, does not show a clear response to the PETM, whereas those at the other sites record reductions in diameter or proloculus size. Temperature was similar at all sites, thus it is not likely to be the reason for differences between sites. At site 1210, small size coincided with higher chamber numbers during the peak event, and may have been caused by a combination of low carbonate ion concentrations and low food supply. Dwarfing at site 690 occurred at lower chamber numbers, and may have been caused by decreasing carbonate saturation at sufficient food levels to reproduce. Proloculus size varied strongly between sites and through time, suggesting a large influence of environment on both microspheric and megalospheric forms without clear bimodality. The effect of the environmental changes during the PETM was more pronounced at deeper sites, possibly implicating carbonate saturation.This article is part of a discussion meeting issue 'Hyperthermals: rapid and extreme global warming in our geological past'.

A baseline investigation of benthic foraminifera in relation to marine sediments parameters in western parts of the Arabian Gulf

This baseline paper discusses the distribution and abundance of living benthic foraminifera in relation to Potentially Toxic Elements (PTEs) such as As, Al, Fe Cd, Co, Cr, Cu, V, Ni, Hg, Pb, and Zn in marine sediments collected from 30 stations in the offshore Arabian Gulf to define baseline environmental conditions for the implementation of future biomonitoring programs. A total of 271 living benthic foraminiferal species were identified belonging to 66 genera, 37 families and 6 orders. Data from this work suggest that PTEs are within the range of background values, and the sediments support highly diversified and stable benthic foraminiferal communities adapted to the unique environmental conditions in the Gulf. Thus, the effect of anthropogenic activities is deemed negligible. This study is expected to provide a baseline dataset for PTE levels in sediment, benthic foraminiferal communities, and identify endemic species adapted to extremes of temperature and saline conditions typical of the Gulf.