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Characterization of the Active Bacterial Community Involved in Natural Attenuation Processes in Arsenic-Rich Creek Sediments

  • Environmental Microbiology
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Abstract

Acid mine drainage of the Carnoulès mine (France) is characterized by acid waters containing high concentrations of arsenic and iron. In the first 30 m along the Reigous, a small creek draining the site, more than 38% of the dissolved arsenic was removed by co-precipitation with Fe(III), in agreement with previous studies, which suggest a role of microbial activities in the co-precipitation of As(III) and As(V) with Fe(III) and sulfate. To investigate how this particular ecosystem functions, the bacterial community was characterized in water and sediments by 16S rRNA encoding gene library analysis. Based on the results obtained using a metaproteomic approach on sediments combined with high-sensitivity HPLC-chip spectrometry, several GroEL orthologs expressed by the community were characterized, and the active members of the prokaryotic community inhabiting the creek sediments were identified. Many of these bacteria are β-proteobacteria such as Gallionella and Thiomonas, but γ-proteobacteria such as Acidithiobacillus ferrooxidans and α-proteobacteria such as Acidiphilium, Actinobacteria, and Firmicutes were also detected.

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Acknowledgements

The study was financed by the EC2CO program (“Institut National des Sciences de l’Univers,” CNRS), the “Observatoire de Recherche Méditerranéen en Environnement” (OSU-OREME), and by the ANR 07-BLANC-0118 project (“Agence Nationale de la Recherche”). Sébastien Gallien and Aurélie Volant were supported by a grant from the French Ministry of Education and Research. This work was performed in the framework of the “Groupement de recherche: Métabolisme de l’Arsenic chez les Microorganismes” (GDR2909-CNRS).

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Authors and Affiliations

  1. Laboratoire HydroSciences Montpellier, UMR5569 (CNRS-IRD-Universités Montpellier I et II), Université Montpellier II, CC MSE, Place Eugène Bataillon, 34095, Montpellier Cedex 05, France

    Odile Bruneel, Aurélie Volant, Corinne Casiot, Amélie Bardil, Christian J. Personné & Françoise Elbaz-Poulichet

  2. Génétique Moléculaire, Génomique Microbiologie, UMR7156, Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France

    Bertrand Chaumande, Philippe N. Bertin & Florence Arsène-Ploetze

  3. Laboratoire de Spectrométrie de Masse Bio-organique, Institut Pluridisciplinaire Hubert Curien, UMR7178 (CNRS-Université de Strasbourg), 25 rue Becquerel, 67087, Strasbourg, France

    Sébastien Gallien, Christine Carapito, Christine Schaeffer & Alain Van Dorsselaer

  4. Institut de Minéralogie et de Physique des Milieux Condensés (IMPMC), UMR7590 (CNRS - Universités Paris 6&7 - IPGP), 140, rue de Lourmel, 75015, Paris, France

    Guillaume Morin

  5. Surface and Aqueous Geochemistry Group, Department of Geological and Environmental Sciences, Stanford University, Stanford, CA, 94305-2115, USA

    Gordon E. Brown Jr

  6. Stanford Synchrotron Radiation Laboratory, SLAC, 2575 23 Sand Hill Road, MS 69, Menlo Park, CA, 94025, USA

    Gordon E. Brown Jr

  7. Génomique Métabolique, UMR8030, CNRS, 2 rue Gaston Crémieux, 91057, Evry Cedex, France

    Denis Le Paslier

  8. Commissariat à l’Energie Atomique (CEA), Direction des Sciences du Vivant, Institut de Génomique, Genoscope, Laboratoire de Génomique Comparative, 2 rue Gaston Crémieux, 91057, Evry Cedex, France

    Denis Le Paslier

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  1. Odile Bruneel
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  2. Aurélie Volant
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Correspondence to Odile Bruneel.

Electronic supplementary material

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ESM 1

(DOCX 32.2 kb)

Supplementary Table 1

MS/MS identification of the proteins extracted from the Carnoulès microbial community and separated by 2-D PAGE. (XLS 194 kb)

Supplementary Figure 1

2DE metaproteomic map of the main cytosolic proteins expressed by the bacterial community inhabiting the Reigous creek sediments. Spots analyzed with nanoLC-MS/MS are circled and numbered. The size of protein markers (BenchMark™ Protein Ladder, Invitrogen) and the pI gradient are schematized from 10 to 220 kDa on the left and from 4 to 7 at the top, respectively. (PDF 63.6 kb)

Supplementary Figure 2

Phylogenetic tree based on GroEL amino acid sequences. A total number of 530 GroEL bacterial sequences were retrieved from the RefSeq database: these sequences were 500–550 amino acids in length. From these sequences, only one representative of each genus was kept for the comparisons, which involved 259 sequences. These GroEL sequences were aligned using ClustalW2 (http://www.ebi.ac.uk/Tools/clustalw2/index.html) [55]. Accession numbers: see supplementary data. In red: GroEL sequences identified using the metaproteomic approach; in black: GroEL sequences detected in the Uniprot database. (PDF 1.78 mb)

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Bruneel, O., Volant, A., Gallien, S. et al. Characterization of the Active Bacterial Community Involved in Natural Attenuation Processes in Arsenic-Rich Creek Sediments. Microb Ecol 61, 793–810 (2011). https://doi.org/10.1007/s00248-011-9808-9

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