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Schweizer M, Jauffrais T, Choquel C, Méléder V, Quinchard S, Geslin E. Trophic strategies of intertidal foraminifera explored with single‐cell microbiome metabarcoding and morphological methods: What is on the menu? Ecol Evol 2022; 12:e9437. [PMCID: PMC9666909 DOI: 10.1002/ece3.9437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Magali Schweizer
- UMR 6112 LPG, Laboratoire de Planétologie et Géosciences, Univ Angers, Nantes Université, Le Mans Université CNRS Angers France
| | - Thierry Jauffrais
- UMR 6112 LPG, Laboratoire de Planétologie et Géosciences, Univ Angers, Nantes Université, Le Mans Université CNRS Angers France
- UMR 9220 ENTROPIE, Ifremer, IRD, Univ Nouvelle‐Calédonie, Univ La Réunion CNRS Noumea New Caledonia
| | - Constance Choquel
- UMR 6112 LPG, Laboratoire de Planétologie et Géosciences, Univ Angers, Nantes Université, Le Mans Université CNRS Angers France
- Department of Geology Lund University Lund Sweden
| | - Vona Méléder
- UR 2160, ISOMer, Institut des Substances et Organismes de la Mer Nantes Université Nantes France
| | - Sophie Quinchard
- UMR 6112 LPG, Laboratoire de Planétologie et Géosciences, Univ Angers, Nantes Université, Le Mans Université CNRS Angers France
| | - Emmanuelle Geslin
- UMR 6112 LPG, Laboratoire de Planétologie et Géosciences, Univ Angers, Nantes Université, Le Mans Université CNRS Angers France
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2
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Yun HY, Larsen T, Choi B, Won E, Shin K. Amino acid nitrogen and carbon isotope data: Potential and implications for ecological studies. Ecol Evol 2022; 12:e8929. [PMID: 35784034 PMCID: PMC9163675 DOI: 10.1002/ece3.8929] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/18/2022] [Accepted: 04/25/2022] [Indexed: 12/17/2022] Open
Abstract
Explaining food web dynamics, stability, and functioning depend substantially on understanding of feeding relations within a community. Bulk stable isotope ratios (SIRs) in natural abundance are well‐established tools to express direct and indirect feeding relations as continuous variables across time and space. Along with bulk SIRs, the SIRs of individual amino acids (AAs) are now emerging as a promising and complementary method to characterize the flow and transformation of resources across a diversity of organisms, from microbial domains to macroscopic consumers. This significant AA‐SIR capacity is based on empirical evidence that a consumer's SIR, specific to an individual AA, reflects its diet SIR coupled with a certain degree of isotopic differences between the consumer and its diet. However, many empirical ecologists are still unfamiliar with the scope of applicability and the interpretative power of AA‐SIR. To fill these knowledge gaps, we here describe a comprehensive approach to both carbon and nitrogen AA‐SIR assessment focusing on two key topics: pattern in AA‐isotope composition across spatial and temporal scales, and a certain variability of AA‐specific isotope differences between the diet and the consumer. On this basis we review the versatile applicability of AA‐SIR to improve our understanding of physiological processes as well as food web functioning, allowing us to reconstruct dominant basal dietary sources and trace their trophic transfers at the specimen and community levels. Given the insightful and opportunities of AA‐SIR, we suggest future applications for the dual use of carbon and nitrogen AA‐SIR to study more realistic food web structures and robust consumer niches, which are often very difficult to explain in nature.
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Affiliation(s)
- Hee Young Yun
- Deparment of Marine Science and Convergent Technology Hanyang University Ansan Korea
| | - Thomas Larsen
- Department of Archaeology Max Planck Institute for the Science of Human History Jena Germany
| | - Bohyung Choi
- Deparment of Marine Science and Convergent Technology Hanyang University Ansan Korea
- Inland Fisheries Research Institute National Institute of Fisheries Science Geumsan‐gun Korea
| | - Eun‐Ji Won
- Deparment of Marine Science and Convergent Technology Hanyang University Ansan Korea
| | - Kyung‐Hoon Shin
- Deparment of Marine Science and Convergent Technology Hanyang University Ansan Korea
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3
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Jesus B, Jauffrais T, Trampe ECL, Goessling JW, Lekieffre C, Meibom A, Kühl M, Geslin E. Kleptoplast distribution, photosynthetic efficiency and sequestration mechanisms in intertidal benthic foraminifera. ISME J 2022; 16:822-32. [PMID: 34635793 DOI: 10.1038/s41396-021-01128-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Salonen IS, Chronopoulou PM, Nomaki H, Langlet D, Tsuchiya M, Koho KA. 16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes in Deep-Sea Benthic Foraminifera. Front Microbiol 2021; 12:694406. [PMID: 34385987 PMCID: PMC8353385 DOI: 10.3389/fmicb.2021.694406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Foraminifera are unicellular eukaryotes that are an integral part of benthic fauna in many marine ecosystems, including the deep sea, with direct impacts on benthic biogeochemical cycles. In these systems, different foraminiferal species are known to have a distinct vertical distribution, i.e., microhabitat preference, which is tightly linked to the physico-chemical zonation of the sediment. Hence, foraminifera are well-adapted to thrive in various conditions, even under anoxia. However, despite the ecological and biogeochemical significance of foraminifera, their ecology remains poorly understood. This is especially true in terms of the composition and diversity of their microbiome, although foraminifera are known to harbor diverse endobionts, which may have a significant meaning to each species' survival strategy. In this study, we used 16S rRNA gene metabarcoding to investigate the microbiomes of five different deep-sea benthic foraminiferal species representing differing microhabitat preferences. The microbiomes of these species were compared intra- and inter-specifically, as well as with the surrounding sediment bacterial community. Our analysis indicated that each species was characterized with a distinct, statistically different microbiome that also differed from the surrounding sediment community in terms of diversity and dominant bacterial groups. We were also able to distinguish specific bacterial groups that seemed to be strongly associated with particular foraminiferal species, such as the family Marinilabiliaceae for Chilostomella ovoidea and the family Hyphomicrobiaceae for Bulimina subornata and Bulimina striata. The presence of bacterial groups that are tightly associated to a certain foraminiferal species implies that there may exist unique, potentially symbiotic relationships between foraminifera and bacteria that have been previously overlooked. Furthermore, the foraminifera contained chloroplast reads originating from different sources, likely reflecting trophic preferences and ecological characteristics of the different species. This study demonstrates the potential of 16S rRNA gene metabarcoding in resolving the microbiome composition and diversity of eukaryotic unicellular organisms, providing unique in situ insights into enigmatic deep-sea ecosystems.
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Affiliation(s)
- Iines S Salonen
- Ecosystems and Environment Research Program, University of Helsinki, Helsinki, Finland.,SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Hidetaka Nomaki
- SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Dewi Langlet
- SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.,UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, Université de Lille - CNRS, Université du Littoral Côte d'Opale, Station Marine de Wimereux, Lille, France.,Evolution, Cell Biology, and Symbiosis Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Masashi Tsuchiya
- Research Institute for Global Change (RIGC), Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Karoliina A Koho
- Ecosystems and Environment Research Program, University of Helsinki, Helsinki, Finland
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5
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Vera-Villalobos H, Pérez V, Contreras F, Alcayaga V, Avalos V, Riquelme C, Silva-Aciares F. Characterization and removal of biofouling from reverse osmosis membranes (ROMs) from a desalination plant in Northern Chile, using Alteromonas sp. Ni1-LEM supernatant. Biofouling 2020; 36:505-515. [PMID: 32545993 DOI: 10.1080/08927014.2020.1776268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/21/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
Biofouling control in reverse osmosis membranes (ROMs) is challenging due to the high cost of treatments, and reduction in the life of ROMs. This study characterizes the biofouling in the ROMs from a desalination plant and reports its effective removal using the supernatant obtained from Alteromonas sp. strain Ni1-LEM. The characterization of the bacterial community revealed that the most abundant taxa in ROMs were the genera Fulvivirga and Pseudoalteromonas, and unclassified species of the families Flavobacteriaceae and Sphingomonadaceae. This bacterial community significantly decreased upon treatment with the supernatant from Alteromonas sp. Ni1-LEM, resulting in the prevalence of the genus Pseudoalteromonas. Furthermore, this bacterial supernatant significantly inhibited cell adhesion of seven benthic microalgae isolated from ROMs as well as promoting cell detachment of the existing microbial biofilms. The study showed that the extracellular supernatant modified the conformation of extracellular polymeric substances (EPS) in the biofouling of ROMs without any biocidal effects.
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Affiliation(s)
- Hernán Vera-Villalobos
- Laboratorio de Ecología Microbiana, Centro de Bioinnovación, Facultad de Ciencias del mar y recursos biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Vilma Pérez
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Francisco Contreras
- Laboratorio de Ecología Microbiana, Centro de Bioinnovación, Facultad de Ciencias del mar y recursos biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Valezka Alcayaga
- Laboratorio de Ecología Microbiana, Centro de Bioinnovación, Facultad de Ciencias del mar y recursos biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Vladimir Avalos
- Laboratorio de Ecología Microbiana, Centro de Bioinnovación, Facultad de Ciencias del mar y recursos biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Carlos Riquelme
- Laboratorio de Ecología Microbiana, Centro de Bioinnovación, Facultad de Ciencias del mar y recursos biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Unidad de Microbiología Aplicada, Centro de Bioinnovación, Facultad de Ciencias del mar y recursos biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Fernando Silva-Aciares
- Unidad de Microbiología Aplicada, Centro de Bioinnovación, Facultad de Ciencias del mar y recursos biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Universidad de Antofagasta, Antofagasta, Chile
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Salonen IS, Chronopoulou P-, Bird C, Reichart G-, Koho KA. 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 DOI: 10.1038/s41598-019-48166-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [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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7
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Chronopoulou PM, Salonen I, Bird C, Reichart GJ, Koho KA. Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera. Front Microbiol 2019; 10:1169. [PMID: 31191490 PMCID: PMC6547873 DOI: 10.3389/fmicb.2019.01169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/07/2019] [Indexed: 12/29/2022] Open
Abstract
Foraminifera are ubiquitous marine protists with an important role in the benthic carbon cycle. However, morphological observations often fail to resolve their exact taxonomic placement and there is a lack of field studies on their particular trophic preferences. Here, we propose the application of metabarcoding as a tool for the elucidation of the in situ feeding behavior of benthic foraminifera, while also allowing the correct taxonomic assignment of the feeder, using the V9 region of the 18S (small subunit; SSU) rRNA gene. Living foraminiferal specimens were collected from two intertidal mudflats of the Wadden Sea and DNA was extracted from foraminiferal individuals and from the surrounding sediments. Molecular analysis allowed us to confirm that our foraminiferal specimens belong to three genetic types: Ammonia sp. T6, Elphidium sp. S5 and Haynesina sp. S16. Foraminiferal intracellular eukaryote communities reflected to an extent those of the surrounding sediments but at different relative abundances. Unlike sediment eukaryote communities, which were largely determined by the sampling site, foraminiferal intracellular eukaryote communities were driven by foraminiferal species, followed by sediment depth. Our data suggests that Ammonia sp. T6 can predate on metazoan classes, whereas Elphidium sp. S5 and Haynesina sp. S16 are more likely to ingest diatoms. These observations, alongside the use of metabarcoding in similar ecological studies, significantly contribute to our overall understanding of the ecological roles of these protists in intertidal benthic environments and their position and function in the benthic food webs.
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Affiliation(s)
- Panagiota-Myrsini Chronopoulou
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Iines Salonen
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Clare Bird
- Biological and Environmental Sciences, University of Stirling, Stirling, United Kingdom
| | - Gert-Jan Reichart
- Department of Ocean Systems, NIOZ-Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, Netherlands
| | - Karoliina A Koho
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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