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11 results on '"Dipankar Bachar"'

1. Region-specific microRNA alterations in marmosets carrying SLC6A4 polymorphisms are associated with anxiety-like behavior

Author

Natalia Popa, Dipankar Bachar, Angela C. Roberts, Andrea M. Santangelo, Eduardo Gascon, Institut de Neurosciences de la Timone (INT), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK, Aix Marseille Université (AMU), University of Cambridge [UK] (CAM), ANR-18-CE37-0017,Marmobrain,Un nouveau modèle primate non-humain pour la recherche translationnelle sur le cerveau(2018), Gascon, Eduardo [0000-0002-2625-5509], and Apollo - University of Cambridge Repository

Subjects
[SDV]Life Sciences [q-bio], Ventromedial prefrontal cortex, Context (language use), 03 medical and health sciences, 0302 clinical medicine, Region specific, biology.animal, microRNA, medicine, Animals, Humans, Gene, DCC, 030304 developmental biology, Serotonin Plasma Membrane Transport Proteins, marmoset, 0303 health sciences, Polymorphism, Genetic, biology, Marmoset, Callithrix, anxiety, 3. Good health, MicroRNAs, medicine.anatomical_structure, depression, Anxiety, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], non-human primates, medicine.symptom, ventro-medial prefrontal cortex, Neuroscience, 030217 neurology & neurosurgery, Psychopathology
Abstract

BACKGROUND: Psychiatric diseases such as depression and anxiety are multifactorial conditions, highly prevalent in western societies. Human studies have identified a number of high-risk genetic variants for these diseases. Among them, polymorphisms in the promoter region of the serotonin transporter gene (SLC6A4) have attracted much attention. However, due to the paucity of experimental models, molecular alterations induced by these genetic variants and how they correlate to behavioral deficits have not been examined. In this regard, marmosets have emerged as a powerful model in translational neuroscience to investigate molecular underpinnings of complex behaviors. METHODS: Here, we took advantage of naturally occurring genetic polymorphisms in marmoset SLC6A4 gene that have been linked to anxiety-like behaviors. Using FACS-sorting, we profiled microRNA contents in different brain regions of genotyped and behaviorally-phenotyped marmosets. FINDINGS: We revealed that marmosets bearing different SLC6A4 variants exhibit distinct microRNAs signatures in a region of the prefrontal cortex whose activity has been consistently altered in patients with depression/anxiety. We also identified Deleted in Colorectal Cancer (DCC), a gene previously linked to these diseases, as a downstream target of the differently expressed microRNAs. Significantly, we showed that levels of both microRNAs and DCC in this region were highly correlated to anxiety-like behaviors. INTERPRETATION: Our findings establish links between genetic variants, molecular modifications in specific cortical regions and complex behavioral responses, providing new insights into gene-behavior relationships underlying human psychopathology. FUNDING: This work was supported by France National Agency, NRJ Foundation, Celphedia and Fondation de France as well as the Wellcome Trust.

Published
2021

2. Patho-Genes.org: a website dedicated to gene sequences of potential bioterror bacteria and PCR primers used to amplify them

Author

Olivier Croce, Richard Christen, Dipankar Bachar, and Julien Gardès

Subjects
Genetics, 0303 health sciences, Melting temperature, 030302 biochemistry & molecular biology, Bioengineering, Biology, MOLECULAR BIOLOGY METHODS, biology.organism_classification, Applied Microbiology and Biotechnology, Biochemistry, 3. Good health, law.invention, 03 medical and health sciences, Functional annotation, law, Target gene, Primer (molecular biology), Gene, Polymerase chain reaction, Bacteria, 030304 developmental biology, Biotechnology
Abstract

Pathogenic agents can be very hard to detect, and usually they do not cause illness for several hours or days. To improve the speed and the accuracy of detection tests and satisfy the needs of early diagnosis, molecular biology methods such as PCR are now used. However, selecting a proper target gene and designing good primers is often not easy. We present a dedicated website, http://patho-genes.org, where we provide every sequence, functional annotation, published primer and relevant article for every annotated gene of major pathogenic bacterial species listed as key agents to be used for a bioterrorism attack. Each published primer was analysed to determine its melting temperature, its specificity and its coverage (i.e. its sensitivity against every allele of its target gene). Data generated have been organized in the form of data sheet for each gene, which are available through multiple browser panels and query systems.

Published
2012

3. Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

Author

Mélanie Lelievre, Patrick Wincker, Christophe Mougel, Claudy Jolivet, Sébastien Terrat, Richard Christen, Dipankar Bachar, Pierre-Alain Maron, Pierre Plassart, Antonio Bispo, Philippe Lemanceau, Samuel Dequiedt, Tiffanie Regnier, Lionel Ranjard, and Virginie Nowak

Subjects
2. Zero hunger, 0303 health sciences, biology, 030306 microbiology, Firmicutes, Soil chemistry, Bioengineering, 15. Life on land, biology.organism_classification, complex mixtures, Applied Microbiology and Biotechnology, Biochemistry, Actinobacteria, 03 medical and health sciences, Crenarchaeota, Metagenomics, Soil water, Botany, Pyrosequencing, Soil microbiology, 030304 developmental biology, Biotechnology
Abstract

Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15,000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.

Published
2011

4. Exploration of Deinococcus-Thermus molecular diversity by novel group-specific PCR primers

Author

Richard Christen, Karine Alain, Virginie Chapon, Nicolas Theodorakopoulos, Dipankar Bachar, Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Interactions Protéine Métal (IPM), Laboratoire de Biogéochimie, Biodisponibilité et Transfert des Radionucléides (IRSN/PRP-ENV/SERIS/L2BT), Service de Recherche et d'Expertise sur les Risques environnementaux (IRSN/PRP-ENV/SERIS), Institut de Radioprotection et de Sûreté Nucléaire (IRSN)-Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Symbiose Marine (SM), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), CEA - Toxicology programme, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), IRSN, PRP-ENV, SERIS, L2BT, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)

Subjects
DNA, Bacterial, molecular diversity, Hot Temperature, Tunisia, [SDV]Life Sciences [q-bio], information science, group-specific primers, Microbiology, Polymerase Chain Reaction, Sensitivity and Specificity, law.invention, 03 medical and health sciences, Phylogenetics, law, RNA, Ribosomal, 16S, Deinococcus-Thermus, Extreme environment, Deinococcus, Thermus, Polymerase chain reaction, Phylogeny, 030304 developmental biology, Original Research, DNA Primers, Genetics, 0303 health sciences, biology, 030306 microbiology, Phylum, Genetic Variation, biology.organism_classification, 16S ribosomal RNA, bacteria
Abstract

International audience; The deeply branching Deinococcus-Thermus lineage is recognized as one of the most extremophilic phylum of bacteria. In previous studies, the presence of Deinococcus-related bacteria in the hot arid Tunisian desert of Tataouine was demonstrated through combined molecular and culture-based approaches. Similarly , Thermus-related bacteria have been detected in Tunisian geothermal springs. The present work was conducted to explore the molecular diversity within the Deinococcus-Thermus phylum in these extreme environments. A set of specific primers was designed in silico on the basis of 16S rRNA gene sequences, validated for the specific detection of reference strains, and used for the polymerase chain reaction (PCR) amplification of metagenomic DNA retrieved from the Tataouine desert sand and Tunisian hot spring water samples. These analyses have revealed the presence of previously undescribed Deino-coccus-Thermus bacterial sequences within these extreme environments. The primers designed in this study thus represent a powerful tool for the rapid detection of Deinococcus-Thermus in environmental samples and could also be applicable to clarify the biogeography of the Deinococcus-Thermus phylum.

Published
2013

5. Stimulation of different functional groups of bacteria by various plant residues as a driver of soil priming effect

Author

Séverine Boiry, Lionel Ranjard, Christophe Mougel, Sébastien Terrat, Noémie Pascault, Pierre-Alain Maron, Jean Lévêque, Richard Christen, Michel Pean, Aurore Kaisermann, Olivier Mathieu, Dipankar Bachar, Catherine Hénault, Sébastien Fontaine, Philippe Lemanceau, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institut de signalisation, biologie du développement et cancer (ISBDC), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Groupe de Recherches Appliquées en Phytotechnologie (GRAP), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de recherche sur l'Ecosystème Prairial (UREP), Institut National de la Recherche Agronomique (INRA), Study financially supported by the Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME) and the Burgundy region., European Project: 264465,EC:FP7:ENV,FP7-ENV-2010,ECOFINDERS(2011), Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UR 0874 Unité de recherche sur l'Ecosystème Prairial, Institut National de la Recherche Agronomique (INRA)-Unité de recherche sur l'Ecosystème Prairial (UREP)-Ecologie des Forêts, Prairies et milieux Aquatiques (EFPA), Université Côte d'Azur (UCA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)

Subjects
Firmicutes, [SDE.MCG]Environmental Sciences/Global Changes, Stable-isotope probing, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Decomposer, soil, 03 medical and health sciences, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, soil organic matter, Botany, carbon cycle, Environmental Chemistry, Gemmatimonadetes, Organic matter, stable isotope probing, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, chemistry.chemical_classification, 0303 health sciences, Ecology, biology, Soil organic matter, Verrucomicrobia, bacterial diversity, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, pyrosequencing, Agronomy, chemistry, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Acidobacteria
Abstract

13 pages; International audience; The turnover of organic matter in soil depends on the activity of microbial decomposers. However, little is known about how modifications of the diversity of soil microbial communities induced by fresh organic matter (FOM) inputs can regulate carbon cycling. Here, we investigated the decomposition of two 13C labeled crop residues (wheat and alfalfa) and the dynamics of the genetic structure and taxonomic composition of the soil bacterial communities decomposing 13C labeled FOM and native unlabeled soil organic matter (SOM), respectively. It was achieved by combining the stable isotope probing method with molecular tools (DNA genotyping and pyrosequencing of 16S rDNA). Although a priming effect (PE) was always induced by residue addition, its intensity increased with the degradability of the plant residue. The input of both wheat and alfalfa residues induced a rapid dynamics of FOM-degrading communities, corresponding to the stimulation of bacterial phyla which have been previously described as copiotrophic organisms. However, the dynamics and the identity of the bacterial groups stimulated depended on the residue added, with Firmicutes dominating in the wheat treatment and Proteobacteria dominating in the alfalfa treatment after 3 days of incubation. In both treatments, SOMdegrading communities were dominated by Acidobacteria, Verrucomicrobia, and Gemmatimonadetes phyla which have been previously described as oligotrophic organisms. An early stimulation of SOM-degrading populations mainly belonging to Firmicutes and Bacteroidetes groups was observed in the alfalfa treatment whereas no change occurred in the wheat treatment. Our findings support the hypothesis that the succession of bacterial taxonomic groups occurring in SOM- and FOMdegrading communities during the degradation process may be an important driver of the PE, and consequently of carbon dynamics in soil.

Published
2013

6. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Author

Christophe Boutte, Raphael Morard, Gaëtan Burgaud, Micah Dunthorn, Pascal Zimmermann, David Bass, Noan Le Bescot, Laure Guillou, Fabrice Not, Bente Edvardsen, Enrique Lara, Dipankar Bachar, Colomban de Vargas, Thorsten Stoeck, Anne Laure Sauvadet, Marina Montresor, Jan Pawlowski, Cédric Berney, Daniel Vaulot, Maria Holzmann, Lucie Bittner, Ramon Massana, Johan Decelle, Javier del Campo, Wiebe H. C. F. Kooistra, Ramiro Logares, Richard Christen, Stéphane Audic, Frédéric Mahé, John R. Dolan, Raffaele Siano, Ian Probert, Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Department of life sciences, The Natural History Museum [London] (NHM), Groupe Plancton Océanique, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Instituto de Ciencia de Materiales de Aragón [Saragoza, España] (ICMA-CSIC), University of Zaragoza - Universidad de Zaragoza [Zaragoza], Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of Kaiserslautern [Kaiserslautern], Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Department of Evolutionary Genetics, Stazione Zoologica Anton Dohrn (SZN), Laboratory of Soil Biodiversity, Université de Neuchâtel (UNINE), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Department of genetics and evolution, University of Geneva [Switzerland], Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of ecology, Universität Kaiserslautern, Point Compétence Informatique, European Union [2008-6530, 287589], ANR (France), ANR Paralex (French), BIOMARKS, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], Computational biology, medicine.disease_cause, Ribosome, DNA, Ribosomal, DNA sequencing, 03 medical and health sciences, Genetics, medicine, DNA Barcoding, Taxonomic, Gene, 030304 developmental biology, Ribosome Subunits, Small, Eukaryotic, 0303 health sciences, Internet, biology, 030306 microbiology, fungi, Intron, Protist, Eukaryota, High-Throughput Nucleotide Sequencing, Genes, rRNA, Articles, Ribosomal RNA, biology.organism_classification, Molecular biology, RNA, Ribosomal, [SDE]Environmental Sciences, Eukaryote, Databases, Nucleic Acid, Cercozoa
Abstract

Laure Guillou ... et al. -- 8 pages, 1 figure, 1 table, The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists, The European Union’s Seventh Framework Programmes (FP7) BIOMARKS (2008-6530, ERA-net Biodiversa) and MicroB3 [287589] and the following ANR (France) projects: AQUAPARADOX, PARALEX and GIME. Funding for open access charge: ANR Paralex (French) and BIOMARKS (FP7)

Published
2013

7. Microbacterium lemovicicum sp. nov., a bacterium isolated from a natural uranium-rich soil

Author

Virginie Chapon, Dipankar Bachar, Laure Mondani, Richard Christen, Laurie Piette, Catherine Berthomieu, Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Interactions Protéine Métal (IPM), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Symbiose Marine (SM), Evolution Paris Seine, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, type strain, Sequence analysis, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Peptidoglycan, Biology, medicine.disease_cause, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Soil, RNA, Ribosomal, 16S, Actinomycetales, medicine, Ecology, Evolution, Behavior and Systematics, Phospholipids, Phylogeny, Soil Microbiology, 030304 developmental biology, 0303 health sciences, Base Composition, Strain (chemistry), 030306 microbiology, Fatty Acids, Nucleic Acid Hybridization, Vitamin K 2, General Medicine, Sequence Analysis, DNA, Microbacterium lemovicicum, Ribosomal RNA, biology.organism_classification, 16S ribosomal RNA, Bacterial Typing Techniques, chemistry, Uranium, Microbacterium binotii, France, Soil microbiology, Bacteria
Abstract

An actinobacterial strain, designated ViU22T, was isolated from a natural uranium-rich soil and was studied using a polyphasic approach. Cells formed orange-pigmented colonies, were rod-shaped, Gram-positive (non-staining method), non-motile and non-spore-forming. This organism grew in 0–4.5 % (w/v) NaCl and at 15–37 °C, with optimal growth occurring in 0.5 % (w/v) NaCl and at 30 °C. Comparative 16S rRNA gene sequence analysis revealed that the strain ViU22T belonged to the genus Microbacterium . It exhibited highest 16S rRNA gene sequence similarity with the type strains of Microbacterium testaceum (98.14 %) and Microbacterium binotii (98.02 %). The DNA–DNA relatedness of strains ViU22T with the most closely related type strains Microbacterium testaceum and Microbacterium binotii DSM 19164T was 20.10 % (±0.70) and 28.05 % (±0.35), respectively. Strain ViU22T possessed a type B2β peptidoglycan with partial substitution of glutamic acid by 3-hydroxy glutamic acid. The major menaquinones were MK-11 and MK-12. Major polar lipids detected in the strain ViU22T were diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and unknown glycolipids. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, a pattern reported for other Microbacterium species. The major cell-wall sugars were galactose, xylose and mannose and the DNA G+C content was 71 mol%. Together, the DNA–DNA hybridization results and the differentiating phenotypic characteristics, showed that strain ViU22T should be classified as the type strain of a novel species within the genus Microbacterium , for which the name Microbacterium lemovicicum sp. nov. is proposed. The type strain is ViU22T ( = ATCC BAA-2396T = CCUG 62198T = DSM 25044T).

Published
2013

8. Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

Author

Charles G Howes, David VanInsberghe, Rolf Henrik Nilsson, Richard Christen, William W. Mohn, Martin Hartmann, Steven J. Hallam, Dipankar Bachar, Hang Yu, Symbiose Marine (SM), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Genome British Columbia, Canadian Institute for Advanced Research, Tula Foundation, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
DNA, Bacterial, Genetic Markers, massively parallel pyrosequencing, Sustainable forest management, organic matter removal, Biodiversity, Biology, Microbiology, Trees, soil compaction, 03 medical and health sciences, Forest ecology, Soil ecology, Cluster Analysis, DNA, Fungal, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, geography, 0303 health sciences, geography.geographical_feature_category, Bacteria, British Columbia, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Logging, Fungi, Forestry, bacteria and fungi, Sequence Analysis, DNA, 04 agricultural and veterinary sciences, 15. Life on land, Old-growth forest, Tracheophyta, 13. Climate action, microbial community structure, Soil compaction, Multivariate Analysis, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Original Article, timber harvesting, Corrigendum, Soil microbiology
Abstract

International audience; Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting. The ISME Journal (2012) 6, 2199-2218; doi:10.1038/ismej.2012.84; published online 2 August 2012

Published
2012

9. Midgut microbiota of the malaria mosquito vector Anopheles gambiae and interactions with Plasmodium falciparum infection

Author

Anne Boissière, Majoline T. Tchioffo, Alexandra Marie, Parfait Awono-Ambene, Richard Christen, Luc Abate, Isabelle Morlais, Sandrine E. Nsango, Hamid Reza Shahbazkia, Dipankar Bachar, Elena A. Levashina, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale (OCEAC), Modèles Insectes de l'Immunité Innée (M3I), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Symbiose Marine (SM), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Developpement (IRD), French Agence Nationale pour la Recherche [ANR-11-BSV7-009-01], European Community [242095, 223601], Laboratoire de Recherche sur le Paludisme, Organization de Coordination pour la lutte contre les Endémies en Afrique Centrale (OCEAC), Organization de Coordination pour la lutte contre les Endémies en Afrique Centrale, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS)

Subjects
Molecular-forms, Intestinal microbiota, Anopheles gambiae, Plasmodium, Malaria, Falciparum, lcsh:QH301-705.5, 0303 health sciences, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Anopheles, Genomics, 3. Good health, Research Article, lcsh:Immunologic diseases. Allergy, Burkholderia, Immunology, Plasmodium falciparum, Enterobacter, Zoology, Paratransgenesis, Gut microbiota, Environment, Biology, Microbiology, Host-Parasite Interactions, 03 medical and health sciences, Virology, parasitic diseases, medicine, Genetics, Animals, Molecular Biology, 030304 developmental biology, Evolutionary Biology, Population Biology, 030306 microbiology, Diptera, Communities, fungi, Midgut, Sporogonic development, biology.organism_classification, medicine.disease, Insect Vectors, Culicidae, Bacterial diversity, Gene Expression Regulation, lcsh:Biology (General), Vector (epidemiology), Parasitology, lcsh:RC581-607, Digestive System, Malaria
Abstract

The susceptibility of Anopheles mosquitoes to Plasmodium infections relies on complex interactions between the insect vector and the malaria parasite. A number of studies have shown that the mosquito innate immune responses play an important role in controlling the malaria infection and that the strength of parasite clearance is under genetic control, but little is known about the influence of environmental factors on the transmission success. We present here evidence that the composition of the vector gut microbiota is one of the major components that determine the outcome of mosquito infections. A. gambiae mosquitoes collected in natural breeding sites from Cameroon were experimentally challenged with a wild P. falciparum isolate, and their gut bacterial content was submitted for pyrosequencing analysis. The meta-taxogenomic approach revealed a broader richness of the midgut bacterial flora than previously described. Unexpectedly, the majority of bacterial species were found in only a small proportion of mosquitoes, and only 20 genera were shared by 80% of individuals. We show that observed differences in gut bacterial flora of adult mosquitoes is a result of breeding in distinct sites, suggesting that the native aquatic source where larvae were grown determines the composition of the midgut microbiota. Importantly, the abundance of Enterobacteriaceae in the mosquito midgut correlates significantly with the Plasmodium infection status. This striking relationship highlights the role of natural gut environment in parasite transmission. Deciphering microbe-pathogen interactions offers new perspectives to control disease transmission., Author Summary During their development in the mosquito vector, Plasmodium parasites undergo complex developmental steps and incur severe bottlenecks. The largest parasite losses occur in the mosquito midgut where robust immune responses are activated. Variability in P. falciparum infection levels indicates that parasite transmission is the result of complex interactions between vectors and parasites, which rely on both genetic and environmental factors. However, in contrast to genetically encoded factors, the role of environmental factors in parasite transmission has received little attention. In this study, we characterized the midgut microbiota of mosquitoes derived from diverse breeding sites using pyrosequencing. We show that the composition of the midgut microbiota in adult mosquitoes exhibits great variability, which is likely determined by bacterial richness of the larval habitats. When field mosquitoes were collected at late immature stages in natural breeding sites and the emerging females challenged with Plasmodium falciparum in the laboratory, significant correlation was observed between P. falciparum infection and the presence of Enterobacteriaceae in the mosquito midgut. Greater understanding of these malaria-bacteria interactions may lead to novel malaria control strategies.

Published
2012

10. Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

Author

Linda A. Amaral-Zettler, Richard Christen, Laure Guillou, Jan Pawlowski, Béatrice Lecroq, Dipankar Bachar, Hamid Reza Shahbazkia, Department of genetics and evolution, University of Geneva [Switzerland], Laboratoire de Biologie Virtuelle, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Departamento de Engenharia Electronica e Informatica [Faro], Faculdade de Ciências e Tecnologia [Faro] (FCT), Universidade do Algarve (UAlg)-Universidade do Algarve (UAlg), Brown University, Marine Biological Laboratory (MBL), University of Chicago, Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), and Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
0106 biological sciences, Rare biosphere, Geologic Sediments, Biodiversity, lcsh:Medicine, Cold-seep, Protozoology, 01 natural sciences, 18S ribosomal RNA, ddc:590, Environmental DNA, lcsh:Science, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 0303 health sciences, Diversity, Multidisciplinary, Ecology, Marine Ecology, Eukaryota, High-Throughput Nucleotide Sequencing, Genomics, respiratory system, Arctic-ocean, Research Article, Ecological Metrics, Sequence analysis, Oceans and Seas, Marine Biology, Biology, Microbiology, 010603 evolutionary biology, 03 medical and health sciences, Eastern mediterranean sea, RNA, Ribosomal, 18S, Animals, 14. Life underwater, Gene, 030304 developmental biology, Cercozoa Protozoa, Microbial Eukaryotes, Sequence Analysis, RNA, lcsh:R, Deep-sea, Computational Biology, Dna, Ribosomal RNA, Marine Environments, Hypervariable region, 13. Climate action, Evolutionary biology, lcsh:Q, Metagenomics, Species Richness, Species richness, human activities, Ecological Environments
Abstract

Background: The deep sea floor is considered one of the most diverse ecosystems on Earth. Recent environmental DNA surveys based on clone libraries of rRNA genes confirm this observation and reveal a high diversity of eukaryotes present in deep-sea sediment samples. However, environmental clone-library surveys yield only a modest number of sequences with which to evaluate the diversity of abyssal eukaryotes. Methodology/Principal Findings: Here, we examined the richness of eukaryotic DNA in deep Arctic and Southern Ocean samples using massively parallel sequencing of the 18S ribosomal RNA (rRNA) V9 hypervariable region. In very small volumes of sediments, ranging from 0.35 to 0.7 g, we recovered up to 7,499 unique sequences per sample. By clustering sequences having up to 3 differences, we observed from 942 to 1756 Operational Taxonomic Units (OTUs) per sample. Taxonomic analyses of these OTUs showed that DNA of all major groups of eukaryotes is represented at the deep-sea floor. The dinoflagellates, cercozoans, ciliates, and euglenozoans predominate, contributing to 17%, 16%, 10%, and 8% of all assigned OTUs, respectively. Interestingly, many sequences represent photosynthetic taxa or are similar to those reported from the environmental surveys of surface waters. Moreover, each sample contained from 31 to 71 different metazoan OTUs despite the small sample volume collected. This indicates that a significant faction of the eukaryotic DNA sequences likely do not belong to living organisms, but represent either free, extracellular DNA or remains and resting stages of planktonic species. Conclusions/Significance: In view of our study, the deep-sea floor appears as a global DNA repository, which preserves genetic information about organisms living in the sediment, as well as in the water column above it. This information can be used for future monitoring of past and present environmental changes. French ANR Aquaparadox; ANR DeepOases; Swiss National Science Foundation [31003A-125372]; WM Keck foundation SNSF /Project funding info:eu-repo/semantics/publishedVersion

Published
2011

11. Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments

Author

Magne Osteras, Laurent Farinelli, Jan Pawlowski, Loïc Baerlocher, Richard Christen, Philippe Esling, Franck Lejzerowicz, Dipankar Bachar, Béatrice Lecroq, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Department of Genetics and Evolution [Genève], University of Geneva [Switzerland], Institut de signalisation, biologie du développement et cancer (ISBDC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Fasteris SA, Sciences et Technologies de la Musique et du Son (STMS), Institut de Recherche et Coordination Acoustique/Musique (IRCAM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), and Fasteris SA [Plan-les-Ouates, Switzerland]

Subjects
0106 biological sciences, Geologic Sediments, Oceans and Seas, Meiobenthos, Biodiversity, Foraminifera, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 01 natural sciences, Deep sea, 03 medical and health sciences, DNA Barcoding, Taxonomic, 14. Life underwater, Phylogeny, Illumina dye sequencing, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Base Sequence, Geography, biology, Ecology, 010604 marine biology & hydrobiology, High-Throughput Nucleotide Sequencing, Biological Sciences, biology.organism_classification, Taxon, Benthic zone, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Deep-sea floors represent one of the largest and most complex ecosystems on Earth but remain essentially unexplored. The vastness and remoteness of this ecosystem make deep-sea sampling difficult, hampering traditional taxonomic observations and diversity assessment. This problem is particularly true in the case of the deep-sea meiofauna, which largely comprises small-sized, fragile , and difficult-to-identify metazoans and protists. Here, we introduce an ultra-deep sequencing-based metagenetic approach to examine the richness of benthic foraminifera, a principal component of deep-sea meiofauna. We used Illumina sequencing technology to assess foraminiferal richness in 31 unsieved deep-sea sediment samples from five distinct oceanic regions. We sequenced an extremely short fragment (36 bases) of the small subunit ribo-somal DNA hypervariable region 37f, which has been shown to accurately distinguish foraminiferal species. In total, we obtained 495,978 unique sequences that were grouped into 1,643 operational taxonomic units, of which about half (841) could be reliably assigned to foraminifera. The vast majority of the operational tax-onomic units (nearly 90%) were either assigned to early (ancient) lineages of soft-walled, single-chambered (monothalamous) fora-minifera or remained undetermined and yet possibly belong to unknown early lineages. Contrasting with the classical view of multichambered taxa dominating foraminiferal assemblages, our work reflects an unexpected diversity of monothalamous lineages that are as yet unknown using conventional micropaleontological observations. Although we can only speculate about their morphology , the immense richness of deep-sea phylotypes revealed by this study suggests that ultra-deep sequencing can improve understanding of deep-sea benthic diversity considered until now as unknowable based on a traditional taxonomic approach.

Published
2011

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