1
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Ishitani Y, Ciacci C, Ujiié Y, Tame A, Tiboni M, Tanifuji G, Inagaki Y, Frontalini F. Fascinating strategies of marine benthic organisms to cope with emerging pollutant: Titanium dioxide nanoparticles. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 330:121538. [PMID: 37011780 DOI: 10.1016/j.envpol.2023.121538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/20/2023] [Accepted: 03/29/2023] [Indexed: 05/20/2023]
Abstract
Titanium dioxide nanoparticles (NPs) have numerous applications, and their demands have increased as an alternative for banned sunscreen filters. However, the underlying mechanisms of their toxicity, remain largely unknown. Here, we investigate the mechanism of TiO2 NP cytotoxicity and detoxification through time-course experiments (1, 6, and 24 h) based on cellular observations and single-cell transcriptome analyses in a marine benthic foraminifer strain, derived from a common unicellular eukaryotic organism worldwide. After exposure for 1 h, cells enhanced the production of reactive oxygen species (ROS) in acidic endosomes containing TiO2 NPs as well as in mitochondria. In acidic endosomes, ROS were produced through the Fenton reaction on the surface of charged TiO2 NPs. In mitochondria, ROS were associated with porphyrin synthesis that chelated metal ions. Glutathione peroxide and neutral lipids acted as a sink for free radicals, whereas lipid peroxides were excreted to prevent further radical chain reactions. By 24 h, aggregated TiO2 NPs were encapsulated in organic compounds, possibly ceramide, and excreted as mucus, thereby preventing their further uptake. Thus, we reveal that foraminifers can tolerate the toxicity of TiO2 NPs and even prevent their further phagocytosis and uptake by trapping TiO2 NPs inside mucus. This previously unknown strategy could be applied in bioremediation to sequester NPs from the marine environment and can guide management of TiO2 pollution.
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Affiliation(s)
- Yoshiyuki Ishitani
- Institute for Extra-Cutting-Edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Caterina Ciacci
- Department of Biomolecular Science, Universita Degli Studi di Urbino, Urbino, Italy
| | - Yurika Ujiié
- Center for Advanced Marine Core Research, Kochi University, Kochi, Japan
| | - Akihiro Tame
- Department of Marine and Earth Sciences, Marine Works Japan Ltd, Yokosuka, Japan
| | - Mattia Tiboni
- Department of Biomolecular Science, Universita Degli Studi di Urbino, Urbino, Italy
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Tsukuba, Japan
| | - Yuji Inagaki
- Center for Computational Sciences and Institute of Biological Sciences, University of Tsukuba, Tsukuba, Japan
| | - Fabrizio Frontalini
- Department of Pure and Applied Science, Universita Degli Studi di Urbino, Urbino, Italy
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2
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Kleptoplast distribution, photosynthetic efficiency and sequestration mechanisms in intertidal benthic foraminifera. THE ISME JOURNAL 2022; 16:822-832. [PMID: 34635793 PMCID: PMC8857221 DOI: 10.1038/s41396-021-01128-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 11/19/2022]
Abstract
Foraminifera are ubiquitously distributed in marine habitats, playing a major role in marine sediment carbon sequestration and the nitrogen cycle. They exhibit a wide diversity of feeding and behavioural strategies (heterotrophy, autotrophy and mixotrophy), including species with the ability of sequestering intact functional chloroplasts from their microalgal food source (kleptoplastidy), resulting in a mixotrophic lifestyle. The mechanisms by which kleptoplasts are integrated and kept functional inside foraminiferal cytosol are poorly known. In our study, we investigated relationships between feeding strategies, kleptoplast spatial distribution and photosynthetic functionality in two shallow-water benthic foraminifera (Haynesina germanica and Elphidium williamsoni), both species feeding on benthic diatoms. We used a combination of observations of foraminiferal feeding behaviour, test morphology, cytological TEM-based observations and HPLC pigment analysis, with non-destructive, single-cell level imaging of kleptoplast spatial distribution and PSII quantum efficiency. The two species showed different feeding strategies, with H. germanica removing diatom content at the foraminifer's apertural region and E. williamsoni on the dorsal site. All E. williamsoni parameters showed that this species has higher autotrophic capacity albeit both feeding on benthic diatoms. This might represent two different stages in the evolutionary process of establishing a permanent symbiotic relationship, or may reflect different trophic strategies.
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3
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Gomaa F, Utter DR, Powers C, Beaudoin DJ, Edgcomb VP, Filipsson HL, Hansel CM, Wankel SD, Zhang Y, Bernhard JM. Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments. SCIENCE ADVANCES 2021; 7:7/22/eabf1586. [PMID: 34039603 PMCID: PMC8153729 DOI: 10.1126/sciadv.abf1586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/05/2021] [Indexed: 05/14/2023]
Abstract
Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a diatom's plastid genome in one foraminiferal species suggests kleptoplasty or sequestration of functional plastids, conferring a metabolic advantage despite the host living far below the euphotic zone. Through a unique integration of functions largely unrecognized among "typical" eukaryotes, benthic foraminifera represent winning microeukaryotes in the face of ongoing oceanic deoxygenation.
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Affiliation(s)
- Fatma Gomaa
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Daniel R Utter
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher Powers
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - David J Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | | | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Joan M Bernhard
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
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4
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Nomaki H, Chen C, Oda K, Tsuchiya M, Tame A, Uematsu K, Isobe N. Abundant Chitinous Structures in Chilostomella (Foraminifera, Rhizaria) and Their Potential Functions. J Eukaryot Microbiol 2021; 68:e12828. [PMID: 33128276 PMCID: PMC7894498 DOI: 10.1111/jeu.12828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/28/2020] [Accepted: 10/20/2020] [Indexed: 12/01/2022]
Abstract
Benthic foraminifera, members of Rhizaria, inhabit a broad range of marine environments and are particularly common in hypoxic sediments. The biology of benthic foraminifera is key to understanding benthic ecosystems and relevant biogeochemical cycles, especially in hypoxic environments. Chilostomella is a foraminiferal genus commonly found in hypoxic deep-sea sediments and has poorly understood ecological characteristics. For example, the carbon isotopic compositions of their lipids are substantially different from other co-occurring genera, probably reflecting unique features of its metabolism. Here, we investigated the cytoplasmic and ultrastructural features of Chilostomella ovoidea from bathyal sediments of Sagami Bay, Japan, based on serial semi-thin sections examined using an optical microscope followed by a three-dimensional reconstruction, combined with TEM observations of ultra-thin sections. Observations by TEM revealed the presence of abundant electron-dense structures dividing the cytoplasm. Based on histochemical staining, these structures are shown to be composed of chitin. Our 3D reconstruction revealed chitinous structures in the final seven chambers. These exhibited a plate-like morphology in the final chambers but became rolled up in earlier chambers (toward the proloculus). These chitinous, plate-like structures may function to partition the cytoplasm in a chamber to increase the surface/volume ratio and/or act as a reactive site for some metabolic functions.
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Affiliation(s)
- Hidetaka Nomaki
- SUGAR, X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)2‐15 Natsushima‐choYokosukaKanagawa237‐0061Japan
| | - Chong Chen
- SUGAR, X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)2‐15 Natsushima‐choYokosukaKanagawa237‐0061Japan
| | - Kaya Oda
- SUGAR, X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)2‐15 Natsushima‐choYokosukaKanagawa237‐0061Japan
| | - Masashi Tsuchiya
- Research Institute for Global Change (RIGC)Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaKanagawa
237‐0061Japan
| | - Akihiro Tame
- Marine Works Japan Ltd.3‐54‐1 Oppamahigashi‐choYokosukaKanagawa237‐0063Japan
| | - Katsuyuki Uematsu
- Marine Works Japan Ltd.3‐54‐1 Oppamahigashi‐choYokosukaKanagawa237‐0063Japan
| | - Noriyuki Isobe
- Research Institute for Marine Resources Utilization (MRU)Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaKanagawa237‐0061Japan
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5
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Bird C, LeKieffre C, Jauffrais T, Meibom A, Geslin E, Filipsson HL, Maire O, Russell AD, Fehrenbacher JS. Heterotrophic Foraminifera Capable of Inorganic Nitrogen Assimilation. Front Microbiol 2020; 11:604979. [PMID: 33343548 PMCID: PMC7744380 DOI: 10.3389/fmicb.2020.604979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/11/2020] [Indexed: 11/17/2022] Open
Abstract
Nitrogen availability often limits biological productivity in marine systems, where inorganic nitrogen, such as ammonium is assimilated into the food web by bacteria and photoautotrophic eukaryotes. Recently, ammonium assimilation was observed in kleptoplast-containing protists of the phylum foraminifera, possibly via the glutamine synthetase/glutamate synthase (GS/GOGAT) assimilation pathway imported with the kleptoplasts. However, it is not known if the ubiquitous and diverse heterotrophic protists have an innate ability for ammonium assimilation. Using stable isotope incubations (15N-ammonium and 13C-bicarbonate) and combining transmission electron microscopy (TEM) with quantitative nanoscale secondary ion mass spectrometry (NanoSIMS) imaging, we investigated the uptake and assimilation of dissolved inorganic ammonium by two heterotrophic foraminifera; a non-kleptoplastic benthic species, Ammonia sp., and a planktonic species, Globigerina bulloides. These species are heterotrophic and not capable of photosynthesis. Accordingly, they did not assimilate 13C-bicarbonate. However, both species assimilated dissolved 15N-ammonium and incorporated it into organelles of direct importance for ontogenetic growth and development of the cell. These observations demonstrate that at least some heterotrophic protists have an innate cellular mechanism for inorganic ammonium assimilation, highlighting a newly discovered pathway for dissolved inorganic nitrogen (DIN) assimilation within the marine microbial loop.
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Affiliation(s)
- Clare Bird
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom.,School of GeoSciences, Grant Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Charlotte LeKieffre
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,UMR CNRS 6112 LPG, Bio-Indicateurs Actuels et Fossiles, Université d'Angers, Angers, France
| | - Thierry Jauffrais
- Ifremer, IRD, Univ Nouvelle-Calédonie, Univ La Réunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Centre for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Emmanuelle Geslin
- UMR CNRS 6112 LPG, Bio-Indicateurs Actuels et Fossiles, Université d'Angers, Angers, France
| | | | - Olivier Maire
- Université de Bordeaux, EPOC, UMR 5805, Talence, France.,CNRS, EPOC, UMR 5805, Talence, France
| | - Ann D Russell
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, CA, United States
| | - Jennifer S Fehrenbacher
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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6
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Jauffrais T, LeKieffre C, Schweizer M, Jesus B, Metzger E, Geslin E. Response of a kleptoplastidic foraminifer to heterotrophic starvation: photosynthesis and lipid droplet biogenesis. FEMS Microbiol Ecol 2020; 95:5427914. [PMID: 30947330 DOI: 10.1093/femsec/fiz046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/02/2019] [Indexed: 01/21/2023] Open
Abstract
The aim of this work is to document the complex nutritional strategy developed by kleptoplastic intertidal foraminifera. We study the mixotrophic ability of a common intertidal foraminifer, Elphidium williamsoni, by (i) investigating the phylogenetic identity of the foraminiferal kleptoplasts, (ii) following their oxygenic photosynthetic capacity and (iii) observing the modification in cellular ultrastructural features in response to photoautotrophic conditions. This was achieved by coupling molecular phylogenetic analyses and TEM observations with non-destructive measurements of kleptoplast O2 production over a 15-day experimental study. Results show that the studied E. williamsoni actively selected kleptoplasts mainly from pennate diatoms and had the ability to produce oxygen, up to 13.4 nmol O2 cell-1 d-1, from low to relatively high irradiance over at least 15 days. Ultrastructural features and photophysiological data showed significant differences over time, the number of lipid droplets, residual bodies and the dark respiration increased; whereas, the number of kleptoplasts decreased accompanied by a minor decrease of the photosynthetic rate. These observations suggest that in E. williamsoni kleptoplasts might provide extra carbon storage through lipid droplets synthesis and highlight the complexity of E. williamsoni feeding strategy and the necessity of further dedicated studies regarding mechanisms developed by kleptoplastidic foraminifera for carbon partitioning and storage.
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Affiliation(s)
- Thierry Jauffrais
- UMR CNRS 6112 LPG-BIAF, Bio-Indicateurs Actuels et Fossiles, Université d'Angers, 2 Boulevard Lavoisier, 49045 Angers CEDEX 1, France.,Ifremer, RBE/LEAD, 101 Promenade Roger Laroque, 98897 Nouméa, New Caledonia, France
| | - Charlotte LeKieffre
- UMR CNRS 6112 LPG-BIAF, Bio-Indicateurs Actuels et Fossiles, Université d'Angers, 2 Boulevard Lavoisier, 49045 Angers CEDEX 1, France
| | - Magali Schweizer
- UMR CNRS 6112 LPG-BIAF, Bio-Indicateurs Actuels et Fossiles, Université d'Angers, 2 Boulevard Lavoisier, 49045 Angers CEDEX 1, France
| | - Bruno Jesus
- EA2160, Laboratoir Mer Molécules Santé, 2 rue de la Houssinière, Université de Nantes, 4433 Nantes Cedex 1, France
| | - Edouard Metzger
- UMR CNRS 6112 LPG-BIAF, Bio-Indicateurs Actuels et Fossiles, Université d'Angers, 2 Boulevard Lavoisier, 49045 Angers CEDEX 1, France
| | - Emmanuelle Geslin
- UMR CNRS 6112 LPG-BIAF, Bio-Indicateurs Actuels et Fossiles, Université d'Angers, 2 Boulevard Lavoisier, 49045 Angers CEDEX 1, France
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7
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Enrichment of intracellular sulphur cycle -associated bacteria in intertidal benthic foraminifera revealed by 16S and aprA gene analysis. Sci Rep 2019; 9:11692. [PMID: 31406214 PMCID: PMC6690927 DOI: 10.1038/s41598-019-48166-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 07/30/2019] [Indexed: 12/21/2022] Open
Abstract
Benthic foraminifera are known to play an important role in marine carbon and nitrogen cycles. Here, we report an enrichment of sulphur cycle -associated bacteria inside intertidal benthic foraminifera (Ammonia sp. (T6), Haynesina sp. (S16) and Elphidium sp. (S5)), using a metabarcoding approach targeting the 16S rRNA and aprA -genes. The most abundant intracellular bacterial groups included the genus Sulfurovum and the order Desulfobacterales. The bacterial 16S OTUs are likely to originate from the sediment bacterial communities, as the taxa found inside the foraminifera were also present in the sediment. The fact that 16S rRNA and aprA -gene derived intracellular bacterial OTUs were species-specific and significantly different from the ambient sediment community implies that bacterivory is an unlikely scenario, as benthic foraminifera are known to digest bacteria only randomly. Furthermore, these foraminiferal species are known to prefer other food sources than bacteria. The detection of sulphur-cycle related bacterial genes in this study suggests a putative role for these bacteria in the metabolism of the foraminiferal host. Future investigation into environmental conditions under which transcription of S-cycle genes are activated would enable assessment of their role and the potential foraminiferal/endobiont contribution to the sulphur-cycle.
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8
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Jauffrais T, LeKieffre C, Schweizer M, Geslin E, Metzger E, Bernhard JM, Jesus B, Filipsson HL, Maire O, Meibom A. Kleptoplastidic benthic foraminifera from aphotic habitats: insights into assimilation of inorganic C, N and S studied with sub-cellular resolution. Environ Microbiol 2018; 21:125-141. [PMID: 30277305 DOI: 10.1111/1462-2920.14433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/31/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022]
Abstract
The assimilation of inorganic compounds in foraminiferal metabolism compared to predation or organic matter assimilation is unknown. Here, we investigate possible inorganic-compound assimilation in Nonionellina labradorica, a common kleptoplastidic benthic foraminifer from Arctic and North Atlantic sublittoral regions. The objectives were to identify the source of the foraminiferal kleptoplasts, assess their photosynthetic functionality in light and darkness and investigate inorganic nitrogen and sulfate assimilation. We used DNA barcoding of a ~ 830 bp fragment from the SSU rDNA to identify the kleptoplasts and correlated transmission electron microscopy and nanometre-scale secondary ion mass spectrometry (TEM-NanoSIMS) isotopic imaging to study 13 C-bicarbonate, 15 N-ammonium and 34 S-sulfate uptake. In addition, respiration rate measurements were determined to assess the response of N. labradorica to light. The DNA sequences established that over 80% of the kleptoplasts belonged to Thalassiosira (with 96%-99% identity), a cosmopolitan planktonic diatom. TEM-NanoSIMS imaging revealed degraded cytoplasm and an absence of 13 C assimilation in foraminifera exposed to light. Oxygen measurements showed higher respiration rates under light than dark conditions, and no O2 production was detected. These results indicate that the photosynthetic pathways in N. labradorica are not functional. Furthermore, N. labradorica assimilated both 15 N-ammonium and 34 S-sulfate into its cytoplasm, which suggests that foraminifera might have several ammonium or sulfate assimilation pathways, involving either the kleptoplasts or bona fide foraminiferal pathway(s) not yet identified.
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Affiliation(s)
- Thierry Jauffrais
- UMR CNRS 6112 LPG-BIAF, Université d'Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 1, France.,Ifremer, RBE/LEAD, 101 Promenade Roger Laroque, 98897, Nouméa, New Caledonia
| | - Charlotte LeKieffre
- UMR CNRS 6112 LPG-BIAF, Université d'Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 1, France.,Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Magali Schweizer
- UMR CNRS 6112 LPG-BIAF, Université d'Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 1, France
| | - Emmanuelle Geslin
- UMR CNRS 6112 LPG-BIAF, Université d'Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 1, France
| | - Edouard Metzger
- UMR CNRS 6112 LPG-BIAF, Université d'Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 1, France
| | - Joan M Bernhard
- Woods Hole Oceanographic Institution, Geology & Geophysics Department, Woods Hole, MA, USA
| | - Bruno Jesus
- EA2160, Laboratoire Mer Molécules Santé, Université de Nantes, Nantes, France.,BioISI - Biosystems & Integrative Sciences Institute, Campo Grande University of Lisboa, Faculty of Sciences, Lisbon, Portugal
| | - Helena L Filipsson
- Department of Geology, Lund University, Sölvegatan 12, 223 62, Lund, Sweden
| | - Olivier Maire
- Univ. Bordeaux, EPOC, UMR 5805, 33400, Talence, France.,CNRS, EPOC, UMR 5805, 33400, Talence, France
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, 1015, Lausanne, Switzerland
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9
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Bernhard JM, Panieri G. Keystone Arctic paleoceanographic proxy association with putative methanotrophic bacteria. Sci Rep 2018; 8:10610. [PMID: 30006509 PMCID: PMC6045607 DOI: 10.1038/s41598-018-28871-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/29/2018] [Indexed: 11/09/2022] Open
Abstract
Foraminifera in sediments exposed to gas-hydrate dissociation are not expected to have cellular adaptations that facilitate inhabitation of chemosynthesis-based ecosystems because, to date, there are no known endemic seep foraminifera. To establish if foraminifera inhabit sediments impacted by gas-hydrate dissociation, we examined the cellular ultrastructure of Melonis barleeanus (Williamson, 1858) from the Vestnesa gas hydrate province (Arctic Ocean, west of Svalbard at ~79 °N; ~1200-m depth; n = 4). From sediments with gas hydrate indicators, living M. barleeanus had unusual pore plugs composed of a thick, fibrous meshwork; mitochondria were concentrated at the cell periphery, under pore plugs. While there was no evidence of endosymbioses with prokaryotes, most M. barleeanus specimens were associated with what appear to be Type I methanotrophic bacteria. One foraminifer had a particularly large bolus of these microbes concentrated near its aperture. This is the first documented instance of bona fide living M. barleeanus in gas-hydrate sediments and first documentation of a foraminifer living in close association with putative methanotrophs. Our observations have implications to paleoclimate records utilizing this foundational foraminiferal species.
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Affiliation(s)
- Joan M Bernhard
- Woods Hole Oceanographic Institution, Department of Geology & Geophysics, MS #52, Woods Hole, MA, 02543, USA.
| | - Giuliana Panieri
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT the Arctic University in Norway, Dramsveien 201, N-9037, Tromsø, Norway
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10
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Inorganic carbon and nitrogen assimilation in cellular compartments of a benthic kleptoplastic foraminifer. Sci Rep 2018; 8:10140. [PMID: 29973634 PMCID: PMC6031614 DOI: 10.1038/s41598-018-28455-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/20/2018] [Indexed: 11/08/2022] Open
Abstract
Haynesina germanica, an ubiquitous benthic foraminifer in intertidal mudflats, has the remarkable ability to isolate, sequester, and use chloroplasts from microalgae. The photosynthetic functionality of these kleptoplasts has been demonstrated by measuring photosystem II quantum efficiency and O2 production rates, but the precise role of the kleptoplasts in foraminiferal metabolism is poorly understood. Thus, the mechanism and dynamics of C and N assimilation and translocation from the kleptoplasts to the foraminiferal host requires study. The objective of this study was to investigate, using correlated TEM and NanoSIMS imaging, the assimilation of inorganic C and N (here ammonium, NH4+) in individuals of a kleptoplastic benthic foraminiferal species. H. germanica specimens were incubated for 20 h in artificial seawater enriched with H13CO3- and 15NH4+ during a light/dark cycle. All specimens (n = 12) incorporated 13C into their endoplasm stored primarily in the form of lipid droplets. A control incubation in darkness resulted in no 13C-uptake, strongly suggesting that photosynthesis is the process dominating inorganic C assimilation. Ammonium assimilation was observed both with and without light, with diffuse 15N-enrichment throughout the cytoplasm and distinct 15N-hotspots in fibrillar vesicles, electron-opaque bodies, tubulin paracrystals, bacterial associates, and, rarely and at moderate levels, in kleptoplasts. The latter observation might indicate that the kleptoplasts are involved in N assimilation. However, the higher N assimilation observed in the foraminiferal endoplasm incubated without light suggests that another cytoplasmic pathway is dominant, at least in darkness. This study clearly shows the advantage provided by the kleptoplasts as an additional source of carbon and provides observations of ammonium uptake by the foraminiferal cell.
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11
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Wukovits J, Bukenberger P, Enge AJ, Gerg M, Wanek W, Watzka M, Heinz P. Food supply and size class depending variations in phytodetritus intake in the benthic foraminifer Ammonia tepida. Biol Open 2018. [PMID: 29540430 PMCID: PMC5936058 DOI: 10.1242/bio.030056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ammonia tepida is a common and abundant benthic foraminifer in intertidal mudflats. Benthic foraminifera are primary consumers and detritivores and act as key players in sediment nutrient fluxes. In this study, laboratory feeding experiments using isotope-labeled phytodetritus were carried out with A. tepida collected at the German Wadden Sea, to investigate the response of A. tepida to varying food supply. Feeding mode (single pulse, constant feeding; different incubation temperatures) caused strong variations in cytoplasmic carbon and nitrogen cycling, suggesting generalistic adaptations to variations in food availability. To study the influence of intraspecific size to foraminiferal carbon and nitrogen cycling, three size fractions (125-250 µm, 250-355 µm, >355 µm) of A. tepida specimens were separated. Small individuals showed higher weight specific intake for phytodetritus, especially for phytodetrital nitrogen, highlighting that size distribution within foraminiferal populations is relevant to interpret foraminiferal carbon and nitrogen cycling. These results were used to extrapolate the data to natural populations of living A. tepida in sediment cores, demonstrating the impact of high abundances of small individuals on phytodetritus processing and nutrient cycling. It is estimated that at high abundances of individuals in the 125-250 µm size fraction, Ammonia populations can account for more than 11% of phytodetritus processing in intertidal benthic communities.
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Affiliation(s)
- Julia Wukovits
- Department of Palaeontology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Patrick Bukenberger
- Department of Palaeontology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Annekatrin Julie Enge
- Department of Palaeontology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Maximillian Gerg
- Department of Palaeontology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Wolfgang Wanek
- Department of Microbiology and Ecosystem Science, Terrestrial Ecosystem Research, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Margarete Watzka
- Department of Microbiology and Ecosystem Science, Terrestrial Ecosystem Research, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Petra Heinz
- Department of Palaeontology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer). PLoS One 2018; 13:e0191653. [PMID: 29377905 PMCID: PMC5788372 DOI: 10.1371/journal.pone.0191653] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/09/2018] [Indexed: 02/01/2023] Open
Abstract
Uncovering the complexities of trophic and metabolic interactions among microorganisms is essential for the understanding of marine biogeochemical cycling and modelling climate-driven ecosystem shifts. High-throughput DNA sequencing methods provide valuable tools for examining these complex interactions, although this remains challenging, as many microorganisms are difficult to isolate, identify and culture. We use two species of planktonic foraminifera from the climatically susceptible, palaeoceanographically important genus Neogloboquadrina, as ideal test microorganisms for the application of 16S rRNA gene metabarcoding. Neogloboquadrina dutertrei and Neogloboquadrina incompta were collected from the California Current and subjected to either 16S rRNA gene metabarcoding, fluorescence microscopy, or transmission electron microscopy (TEM) to investigate their species-specific trophic interactions and potential symbiotic associations. 53–99% of 16S rRNA gene sequences recovered from two specimens of N. dutertrei were assigned to a single operational taxonomic unit (OTU) from a chloroplast of the phylum Stramenopile. TEM observations confirmed the presence of numerous intact coccoid algae within the host cell, consistent with algal symbionts. Based on sequence data and observed ultrastructure, we taxonomically assign the putative algal symbionts to Pelagophyceae and not Chrysophyceae, as previously reported in this species. In addition, our data shows that N. dutertrei feeds on protists within particulate organic matter (POM), but not on bacteria as a major food source. In total contrast, of OTUs recovered from three N. incompta specimens, 83–95% were assigned to bacterial classes Alteromonadales and Vibrionales of the order Gammaproteobacteria. TEM demonstrates that these bacteria are a food source, not putative symbionts. Contrary to the current view that non-spinose foraminifera are predominantly herbivorous, neither N. dutertrei nor N. incompta contained significant numbers of phytoplankton OTUs. We present an alternative view of their trophic interactions and discuss these results within the context of modelling global planktonic foraminiferal abundances in response to high-latitude climate change.
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LeKieffre C, Spangenberg JE, Mabilleau G, Escrig S, Meibom A, Geslin E. Surviving anoxia in marine sediments: The metabolic response of ubiquitous benthic foraminifera (Ammonia tepida). PLoS One 2017; 12:e0177604. [PMID: 28562648 PMCID: PMC5451005 DOI: 10.1371/journal.pone.0177604] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/27/2017] [Indexed: 11/19/2022] Open
Abstract
High input of organic carbon and/or slowly renewing bottom waters frequently create periods with low dissolved oxygen concentrations on continental shelves and in coastal areas; such events can have strong impacts on benthic ecosystems. Among the meiofauna living in these environments, benthic foraminifera are often the most tolerant to low oxygen levels. Indeed, some species are able to survive complete anoxia for weeks to months. One known mechanism for this, observed in several species, is denitrification. For other species, a state of highly reduced metabolism, essentially a state of dormancy, has been proposed but never demonstrated. Here, we combined a 4 weeks feeding experiment, using 13C-enriched diatom biofilm, with correlated TEM and NanoSIMS imaging, plus bulk analysis of concentration and stable carbon isotopic composition of total organic matter and individual fatty acids, to study metabolic differences in the intertidal species Ammonia tepida exposed to oxic and anoxic conditions. Strongly contrasting cellular-level dynamics of ingestion and transfer of the ingested biofilm components were observed between the two conditions. Under oxic conditions, within a few days, intact diatoms were ingested, degraded, and their components assimilated, in part for biosynthesis of different cellular components: 13C-labeled lipid droplets formed after a few days and were subsequently lost (partially) through respiration. In contrast, in anoxia, fewer diatoms were initially ingested and these were not assimilated or metabolized further, but remained visible within the foraminiferal cytoplasm even after 4 weeks. Under oxic conditions, compound specific 13C analyses showed substantial de novo synthesis by the foraminifera of specific polyunsaturated fatty acids (PUFAs), such as 20:4(n-6). Very limited PUFA synthesis was observed under anoxia. Together, our results show that anoxia induced a greatly reduced rate of heterotrophic metabolism in Ammonia tepida on a time scale of less than 24 hours, these observations are consistent with a state of dormancy.
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Affiliation(s)
- Charlotte LeKieffre
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- * E-mail: (CL); (AM); (EG)
| | - Jorge E. Spangenberg
- Stable Isotope and Organic Geochemistry Laboratories, Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Lausanne, Switzerland
| | - Guillaume Mabilleau
- Service commun d'imageries et d'analyses microscopiques (SCIAM), Institut de Biologie en Santé, University of Angers, Angers, France
| | - Stéphane Escrig
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
- * E-mail: (CL); (AM); (EG)
| | - Emmanuelle Geslin
- UMR CNRS 6112 - LPG-BIAF, University of Angers, Angers, France
- * E-mail: (CL); (AM); (EG)
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NanoSIMS chemical imaging combined with correlative microscopy for biological sample analysis. Curr Opin Biotechnol 2016; 41:130-135. [PMID: 27506876 DOI: 10.1016/j.copbio.2016.06.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/17/2016] [Accepted: 06/23/2016] [Indexed: 12/18/2022]
Abstract
Nano-scale Secondary Ion Mass Spectrometry (NanoSIMS) is one of the most powerful in situ elemental and isotopic analysis techniques available to biologists. The combination of stable isotope probing with NanoSIMS (nanoSIP) has opened up new avenues for biological studies over the past decade. However, due to limitations inherent with any analytical methodology, additional information from correlative techniques is usually required to address real biological questions. Here we review recent developments in correlative analysis applied to complex biological systems: first, high-resolution tracking of molecules (e.g. peptides, lipids) by correlation with electron microscopy and atomic force microscopy; second, identification of a specific microbial taxon with fluorescence in situ hybridization and quantification of its metabolic capacities; and, third, molecular specific imaging with new probes.
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