3D morphological variability in foraminifera unravel environmental changes in the Baltic Sea entrance over the last 200 years

Human activities in coastal areas have intensified over the last 200 years, impacting also high-latitude regions such as the Baltic Sea. Benthic foraminifera, protists often with calcite shells (tests), are typically well preserved in marine sediments and known to record past bottom-water conditions. Morphological analyses of marine shells acquired by microcomputed tomography (µCT) have made significant progress toward a better understanding of recent environmental changes. However, limited access to data processing and a lack of guidelines persist when using open-source software adaptable to different microfossil shapes. This study provides a post-data routine to analyze the entire test parameters: average thickness, calcite volume, calcite surface area, number of pores, pore density, and calcite surface area/volume ratio. A case study was used to illustrate this method: 3D time series (i.e., 4D) of Elphidium clavatum specimens recording environmental conditions in the Baltic Sea entrance from the period early industrial (the 1800s) to present-day (the 2010 s). Long-term morphological trends in the foraminiferal record revealed that modern specimens have ∼28% thinner tests and ∼91% more pores than their historic counterparts. However, morphological variability between specimens and the BFAR (specimens cm−2 yr−1) in E. clavatum were not always synchronous. While the BFAR remained unchanged, morphological variability was linked to natural environmental fluctuations in the early industrial period and the consequences of anthropogenic climate change in the 21st century. During the period 1940–2000 s, the variations in BFAR were synchronous with morphological variability, revealing both the effects of the increase in human activities and major hydrographic changes. Finally, our interpretations, based on E. clavatum morphological variations, highlight environmental changes in the Baltic Sea area, supporting those documented by the foraminiferal assemblages

Ecology of benthic foraminifera, geochemical and biological interactions : multidisciplinary approach at different scales

The overall aim of this PhD thesis was to investigate sedimentary micro-environments and ecosystem functioning of two coastal areas. We combined different high spatial resolution methods and multivariate analyses at different spatio-temporal scales to reveal interactions between benthic faunal and geochemical compartments. Firstly, we investigated two stations with contrasted oxygen, nitrate and manganese conditions in the Gullmar Fjord (Sweden). We revealed the high contribution (50–100 %) of denitrifying benthic foraminifera to the nitrogen cycle in oxygenated and nitrate-rich micro–environments. Nitrogen and manganese cycles are closely related to oxygenation conditions of the ecosystem. Our results highlighted the high contribution (87 %) of macrofaunal bioirrigation to Mn release to the water column under hypoxic conditions. Secondly, we focused on a monthly monitoring of two ecological bioindicators groups; microphytobenthos (MPB) and foraminifera in the Bourgneuf Bay mudflat (France). We showed that foraminiferal reproduction events were modulated by unfavorable conditions (high hydrodynamic and winter conditions) versus favorable conditions (low hydrodynamic and summer conditions). We also demonstrated that foraminiferal species fed preferentially on diatom species based on their shape, size and life-forms. We further compared, with high spatial resolution methods, geochemical conditions at two contrasted months, which allowed to clarify the behavior of redox species and nutrients. Then, foraminiferal micro-distributions indicated the state of sediment instability versus stability. Finally, this doctoral research opens new perspectives in the use of high spatial resolution in 2D/3D to solve complex benthic ecology problemsL'objectif général de cette thèse est d'étudier les micro-environnements sédimentaires et le fonctionnement des écosystèmes de deux zones côtières. Nous avons combiné différentes méthodes à haute résolution spatiale et des analyses multivariées à différentes échelles spatio-temporelles pour révéler les interactions entre les compartiments de la faune benthique et géochimiques. Tout d'abord, nous avons étudié deux stations présentant des conditions contrastées en oxygène, nitrate et manganèse dans le Gullmar Fjord (Suède). Nous avons révélé la forte contribution (50-100 %) des foraminifères benthiques dénitrifiants au cycle de l'azote dans des micro-environnements oxygénés et riches en nitrate. Le cycle de l'azote et du manganèse sont étroitement liés aux conditions d'oxygénation de l'écosystème. Nos résultats ont mis en évidence la forte contribution (87 %) de la bioirrigation engendrée par la macrofaune au cycle du Mn dans des conditions hypoxiques. Deuxièmement, nous nous sommes concentrés sur un suivi mensuel de deux groupes de bio-indicateurs écologiques : le microphytobenthos (MPB) et les foraminifères dans la vasière en Baie de Bourgneuf (France). Nous avons montré que les événements de reproduction des foraminifères sont modulés par des conditions défavorables (hydrodynamisme plus fort en conditions hivernales) par rapport à des conditions favorables (hydrodynamisme plus faible en conditions estivales). Nos résultats suggèrent que les espèces de foraminifères se nourrissent préférentiellement des espèces de diatomées en fonction de leur forme, de leur taille et de leur mode de vie. Nous avons également comparé avec des méthodes à haute résolution spatiale les conditions géochimiques de deux mois contrastés, ce qui a permis de clarifier le comportement des espèces redox et des nutriments. De plus, les micro-distributions des foraminifères indiquent l'état d'instabilité versus stabilité des sédiments. Enfin, cette recherche doctorale ouvre de nouvelles perspectives dans l’utilisation des hautes résolutions spatiales en 2D/3D pour résoudre des problèmes d'écologie benthique complexes

Ecology of benthic foraminifera, geochemical and biological interactions : multidisciplinary approach at different scales

The overall aim of this PhD thesis was to investigate sedimentary micro-environments and ecosystem functioning of two coastal areas. We combined different high spatial resolution methods and multivariate analyses at different spatio-temporal scales to reveal interactions between benthic faunal and geochemical compartments. Firstly, we investigated two stations with contrasted oxygen, nitrate and manganese conditions in the Gullmar Fjord (Sweden). We revealed the high contribution (50–100 %) of denitrifying benthic foraminifera to the nitrogen cycle in oxygenated and nitrate-rich micro–environments. Nitrogen and manganese cycles are closely related to oxygenation conditions of the ecosystem. Our results highlighted the high contribution (87 %) of macrofaunal bioirrigation to Mn release to the water column under hypoxic conditions. Secondly, we focused on a monthly monitoring of two ecological bioindicators groups; microphytobenthos (MPB) and foraminifera in the Bourgneuf Bay mudflat (France). We showed that foraminiferal reproduction events were modulated by unfavorable conditions (high hydrodynamic and winter conditions) versus favorable conditions (low hydrodynamic and summer conditions). We also demonstrated that foraminiferal species fed preferentially on diatom species based on their shape, size and life-forms. We further compared, with high spatial resolution methods, geochemical conditions at two contrasted months, which allowed to clarify the behavior of redox species and nutrients. Then, foraminiferal micro-distributions indicated the state of sediment instability versus stability. Finally, this doctoral research opens new perspectives in the use of high spatial resolution in 2D/3D to solve complex benthic ecology problemsL'objectif général de cette thèse est d'étudier les micro-environnements sédimentaires et le fonctionnement des écosystèmes de deux zones côtières. Nous avons combiné différentes méthodes à haute résolution spatiale et des analyses multivariées à différentes échelles spatio-temporelles pour révéler les interactions entre les compartiments de la faune benthique et géochimiques. Tout d'abord, nous avons étudié deux stations présentant des conditions contrastées en oxygène, nitrate et manganèse dans le Gullmar Fjord (Suède). Nous avons révélé la forte contribution (50-100 %) des foraminifères benthiques dénitrifiants au cycle de l'azote dans des micro-environnements oxygénés et riches en nitrate. Le cycle de l'azote et du manganèse sont étroitement liés aux conditions d'oxygénation de l'écosystème. Nos résultats ont mis en évidence la forte contribution (87 %) de la bioirrigation engendrée par la macrofaune au cycle du Mn dans des conditions hypoxiques. Deuxièmement, nous nous sommes concentrés sur un suivi mensuel de deux groupes de bio-indicateurs écologiques : le microphytobenthos (MPB) et les foraminifères dans la vasière en Baie de Bourgneuf (France). Nous avons montré que les événements de reproduction des foraminifères sont modulés par des conditions défavorables (hydrodynamisme plus fort en conditions hivernales) par rapport à des conditions favorables (hydrodynamisme plus faible en conditions estivales). Nos résultats suggèrent que les espèces de foraminifères se nourrissent préférentiellement des espèces de diatomées en fonction de leur forme, de leur taille et de leur mode de vie. Nous avons également comparé avec des méthodes à haute résolution spatiale les conditions géochimiques de deux mois contrastés, ce qui a permis de clarifier le comportement des espèces redox et des nutriments. De plus, les micro-distributions des foraminifères indiquent l'état d'instabilité versus stabilité des sédiments. Enfin, cette recherche doctorale ouvre de nouvelles perspectives dans l’utilisation des hautes résolutions spatiales en 2D/3D pour résoudre des problèmes d'écologie benthique complexes

Trophic strategies of intertidal foraminifera explored with single-cell microbiome metabarcoding and morphological methods: What is on the menu?

In mudflats, interactions and transfers of nutrients and secondary metabolites may drive ecosystems and biodiversity. Foraminifera have complex trophic strategies as they often rely on bacteria and eukaryotes or on potential symbionts for carbon and nitrogen resources. The capacity of these protists to use a wide range of adaptive mechanisms requires clarifying the relationships between them and their microbial associates. Here, we investigate the interactions of three foraminiferal species with nearby organisms in situ, by coupling molecular (cloning/Sanger and high-throughput sequencing) and direct counting and morphological identification with microscopy. This coupling allows the identification of the organisms found in or around three foraminiferal species through molecular tools combined with a direct counting of foraminifera and diatoms present in situ through microscopy methods. Depending on foraminiferal species, and in addition to diatom biomass, diatom frustule shape, size and species are key factors driving the abundance and diversity of foraminifera in mudflat habitats. Three different trophic strategies were deduced for the foraminifera investigated in this study: Ammonia sp. T6 has an opportunistic strategy and is feeding on bacteria, nematoda, fungi, and diatoms when abundant; Elphidium oceanense is feeding mainly on diatoms, mixed with other preys when they are less abundant; and Haynesina germanica is feeding almost solely on medium-large pennate diatoms. Although there are limitations due to the lack of species coverage in DNA sequence databases and to the difficulty to compare morphological and molecular data, this study highlights the relevance of combining molecular with morphological tools to study trophic interactions and microbiome communities of protists at the single-cell scale

Trophic strategies of intertidal foraminifera explored with single-cell microbiome metabarcoding and morphological methods: What is on the menu?

International audienceIn mudflats, interactions and transfers of nutrients and secondary metabolites may drive ecosystems and biodiversity. Foraminifera have complex trophic strategies as they often rely on bacteria and eukaryotes or on potential symbionts for carbon and nitrogen resources. The capacity of these protists to use a wide range of adaptive mechanisms requires clarifying the relationships between them and their microbial associates. Here, we investigate the interactions of three foraminiferal species with nearby organisms in situ, by coupling molecular (cloning/Sanger and high-throughput sequencing) and direct counting and morphological identification with microscopy. This coupling allows the identification of the organisms found in or around three foraminiferal species through molecular tools combined with a direct counting of foraminifera and diatoms present in situ through microscopy methods. Depending on foraminiferal species, and in addition to diatom biomass, diatom frustule shape, size and species are key factors driving the abundance and diversity of foraminifera in mudflat habitats. Three different trophic strategies were deduced for the foraminifera investigated in this study: Ammonia sp. T6 has an opportunistic strategy and is feeding on bacteria, nematoda, fungi, and diatoms when abundant; Elphidium oceanense is feeding mainly on diatoms, mixed with other preys when they are less abundant; and Haynesina germanica is feeding almost solely on medium-large pennate diatoms. Although there are limitations due to the lack of species coverage in DNA sequence databases and to the difficulty to compare morphological and molecular data, this study highlights the relevance of combining molecular with morphological tools to study trophic interactions and microbiome communities of protists at the single-cell scal

Trophic strategies of intertidal foraminifera explored with single-cell microbiome metabarcoding and morphological methods : What is on the menu?

In mudflats, interactions and transfers of nutrients and secondary metabolites may drive ecosystems and biodiversity. Foraminifera have complex trophic strategies as they often rely on bacteria and eukaryotes or on potential symbionts for carbon and nitrogen resources. The capacity of these protists to use a wide range of adaptive mechanisms requires clarifying the relationships between them and their microbial associates. Here, we investigate the interactions of three foraminiferal species with nearby organisms in situ, by coupling molecular (cloning/Sanger and high-throughput sequencing) and direct counting and morphological identification with microscopy. This coupling allows the identification of the organisms found in or around three foraminiferal species through molecular tools combined with a direct counting of foraminifera and diatoms present in situ through microscopy methods. Depending on foraminiferal species, and in addition to diatom biomass, diatom frustule shape, size and species are key factors driving the abundance and diversity of foraminifera in mudflat habitats. Three different trophic strategies were deduced for the foraminifera investigated in this study: Ammonia sp. T6 has an opportunistic strategy and is feeding on bacteria, nematoda, fungi, and diatoms when abundant; Elphidium oceanense is feeding mainly on diatoms, mixed with other preys when they are less abundant; and Haynesina germanica is feeding almost solely on medium-large pennate diatoms. Although there are limitations due to the lack of species coverage in DNA sequence databases and to the difficulty to compare morphological and molecular data, this study highlights the relevance of combining molecular with morphological tools to study trophic interactions and microbiome communities of protists at the single-cell scale

Trophic strategies of intertidal foraminifera explored with single-cell microbiome metabarcoding and morphological methods: What is on the menu?

International audienceIn mudflats, interactions and transfers of nutrients and secondary metabolites may drive ecosystems and biodiversity. Foraminifera have complex trophic strategies as they often rely on bacteria and eukaryotes or on potential symbionts for carbon and nitrogen resources. The capacity of these protists to use a wide range of adaptive mechanisms requires clarifying the relationships between them and their microbial associates. Here, we investigate the interactions of three foraminiferal species with nearby organisms in situ, by coupling molecular (cloning/Sanger and high-throughput sequencing) and direct counting and morphological identification with microscopy. This coupling allows the identification of the organisms found in or around three foraminiferal species through molecular tools combined with a direct counting of foraminifera and diatoms present in situ through microscopy methods. Depending on foraminiferal species, and in addition to diatom biomass, diatom frustule shape, size and species are key factors driving the abundance and diversity of foraminifera in mudflat habitats. Three different trophic strategies were deduced for the foraminifera investigated in this study: Ammonia sp. T6 has an opportunistic strategy and is feeding on bacteria, nematoda, fungi, and diatoms when abundant; Elphidium oceanense is feeding mainly on diatoms, mixed with other preys when they are less abundant; and Haynesina germanica is feeding almost solely on medium-large pennate diatoms. Although there are limitations due to the lack of species coverage in DNA sequence databases and to the difficulty to compare morphological and molecular data, this study highlights the relevance of combining molecular with morphological tools to study trophic interactions and microbiome communities of protists at the single-cell scal

Comparison of Four Foraminiferal Biotic Indices Assessing the Environmental Quality of Coastal Mediterranean Soft Bottoms

International audienceCoastal environments are exposed to numerous pressures that potentially affect marine soft bottom faunas. Among these pressures, organic matter enrichment is very frequent. Several indices based on living (Rose Bengal-stained) foraminiferal communities have recently been developed to assess the induced impact and determine the environmental quality of these environments. Here, we use an open waters Mediterranean Sea data set to test the benefits and drawbacks of four foraminiferal indices: (1) the effective number of species (exp(H’bc)), (2) the Tolerant Species Index for the Mediterranean (TSI-Med), (3) the Foraminifera AMBI (Foram-AMBI), and (4) the Foram Stress Index (FSI). These indices all intend to measure the response of the foraminiferal communities to organic matter enrichment, and therefore, their results should be very similar. We found that the diversity-based index, exp(H’bc), was not suitable to evaluate the environmental quality of our Mediterranean coastal settings, as it had a non-monotonic relationship with the organic matter enrichment gradient. The three indices based on groups of indicator species (TSI-Med, Foram-AMBI, and FSI) yielded fairly similar results. For Foram-AMBI, using only assigned species to calculate proportions of indicator species partly avoided to misinterpret the results. In TSI-Med, a correction based on sediment grain size is applied to distinguish between natural and anthropogenic organic enrichment. Such a correction could also be added to Foram-AMBI and FSI. The limits between the Ecological Quality Status (EQS) classes used for macrofauna were not adapted for Foram-AMBI. Here, we propose new EQS class limits for the Foram-AMBI as follows: very good: 0 ≤ x < 1.4; good: 1.4 ≤ x < 2.4; moderate: 2.4 ≤ x < 3.4; poor: 3.4 ≤ x < 4.4; bad: 4.4 ≤ x ≤ 6. These limits could evolve in the future as new data become available, especially with a poor and bad environmental quality

Living (RB-stained) benthic foraminiferal fauna sampled along the French Mediterranean coast in 2015

The stations were sampled along the French Mediterranean coast in spring (March-April) 2015 onboard the RV Europe. Bottom sediment at 28 stations (11 to 64 m water depth) was sampled using a Reineck box-corer. Three replicates (“a”, “b”, “c”; different box-corer launches) were done at each station. Each box-corer was sub-cored with a 7.4 cm diameter tube. Only the first top centimetre was preserved in 96% ethanol and stained with 2 g/L Rose Bengal. At the laboratory, after minimum two weeks each sample was washed through four sieves of 63, 125, 150, and 500 µm mesh sizes. Living (stained) benthic foraminifera from the 125-150 µm and 150-500 µm were collected under stereomicroscope and preserved in micropaleontological slides. Taxonomical recognition was done to the species level. The presented data in the table indicate the raw densities of foraminifera sorted per sample. The exact volume of sampled sediment was measured for each sample. Some samples were treated with Sodium Polytungstate (SPT) to separate benthic foraminifera from the sediment. The SPT density is indicated for each treated sample

Denitrification by benthic foraminifera and their contribution to N-loss from a fjord environment

Oxygen availability impacts the marine nitrogen cycle at a range of spatial and temporal scales. Invasive organisms have shown to sustainably affect sediment geochemistry and benthic ecology. Nonionella sp. T1 was recently described as an invasive benthic foraminifer in the North Sea region. Here, we demonstrate the impact of this denitrifying species on the foraminifera fauna and the nitrogen cycle of the Gullmar Fjord (Sweden). The foraminifera contribution to benthic denitrification was estimated by coupling living foraminifera micro-distribution, denitrification rate measurement and sedimentary nitrate 2D distribution. Nonionella sp. T1 dominated the foraminifera fauna and could denitrify up to 50–100 % of nitrate porewater in oxygenated bottom waters of the fjord. Contrastingly, at the deepest hypoxic low-nitrate station, denitrifying foraminifera species were scarce and did not contribute to nitrogen removal (~ 5 %). Our study showed that benthic foraminifera can be a major contributor of nitrogen mitigation in oxic coastal ecosystems and should be included in ecological and diagenetic models aiming at understanding biogeochemical cycles coupled to nitrogen