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Archaeal diversity: temporal variation in the arsenic-rich creek sediments of Carnoulès Mine, France

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Abstract

The Carnoulès mine is an extreme environment located in the South of France. It is an unusual ecosystem due to its acidic pH (2–3), high concentration of heavy metals, iron, and sulfate, but mainly due to its very high concentration of arsenic (up to 10 g L−1 in the tailing stock pore water, and 100–350 mg L−1 in Reigous Creek, which collects the acid mine drainage). Here, we present a survey of the archaeal community in the sediment and its temporal variation using a culture-independent approach by cloning of 16S rRNA encoding genes. The taxonomic affiliation of Archaea showed a low degree of biodiversity with two different phyla: Euryarchaeota and Thaumarchaeota. The archaeal community varied in composition and richness throughout the sampling campaigns. Many sequences were phylogenetically related to the order Thermoplasmatales represented by aerobic or facultatively anaerobic, thermoacidophilic autotrophic or heterotrophic organisms like the organotrophic genus Thermogymnomonas. Some members of Thermoplasmatales can also derive energy from sulfur/iron oxidation or reduction. We also found microorganisms affiliated with methanogenic Archaea (Methanomassiliicoccus luminyensis), which are involved in the carbon cycle. Some sequences affiliated with ammonia oxidizers, involved in the first and rate-limiting step in nitrification, a key process in the nitrogen cycle were also observed, including Candidatus Nitrososphaera viennensis and Candidatus nitrosopumilus sp. These results suggest that Archaea may be important players in the Reigous sediments through their participation in the biochemical cycles of elements, including those of carbon and nitrogen.

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Acknowledgments

The French CRG is gratefully acknowledged for provision of beamtime on the FAME BM30B beamline. This work was supported by EC2CO CNRS/INSU program, by ACI/FNS Grant #3033 and by SESAME IdF Grant #1775. Part of the field chemical data was acquired through the OSU OREME.

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Authors and Affiliations

  1. Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Place E. Bataillon, CC MSE, 34095, Montpellier, France

    A. Volant, A. Desoeuvre, C. Casiot, S. Delpoux, J. C. Personné, M. Héry, F. Elbaz-Poulichet & O. Bruneel

  2. Equipe Environnement et Microbiologie, EEM, UMR 5254 (IPREM, CNRS), Université de Pau et des Pays de l’Adour, BP 1155, 64013, Pau, France

    B. Lauga

  3. Institut de Minéralogie et de Physique des Milieux Condensés, IMPMC, UMR 7590 (CNRS, Université Pierre et marie curie/Paris 6), 4 place Jussieu, 75252, Paris, France

    G. Morin

  4. Laboratoire de Génétique Moléculaire, Génomique, Microbiologie, GMGM, UMR 7156 (Université de Strasbourg, CNRS), Département Microorganismes, Génomes, Environnement, 28 Rue Goethe, 67083, Strasbourg, France

    P. N. Bertin

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  1. A. Volant
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Correspondence to O. Bruneel.

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Communicated by F. Robb.

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Mineralogical and As speciation data obtained from XANES, EXAFS, and XRD analyses of the solid samples studied are provided as Supporting Information in Figures S1, S2 and S3, respectively.

792_2012_466_MOESM1_ESM.tiff

Figure S1 Results of As K-edge XANES data fit using linear combination of two model compound spectra representative of arsenate and arsenite. These model compounds are amorphous As(V)- and As(III)-Fe(III) oxyhydroxide phases (referred to as cppAs(V) and cppAs(III), respectively) and characterized in detail in Morin et al. (2003). Accuracy of individual components is estimated to ± 5% and components lower than 10% are not significant. A minor component of arsenopyrite was suspected in sample COWG Jan09, while being close to the limit of detection (TIFF 1062 kb)

792_2012_466_MOESM2_ESM.pdf

Figure S2 Results of As K-edge EXAFS data fit using linear combination of three model compound spectra representative of arsenate and arsenite species in the samples studied. These model compounds include biogenic amorphous As(V)-Fe(III) oxyhydroxysulfate synthesized using Thiomonas sp. strain B2, abiotic amorphous As(V)-Fe(III) oxyhydroxysulfate with As/Fe = 0.8 mol/mol (Maillot et al., 2011), and biogenic As(III) rich schwertmannite synthesized using Acidithiobacillus ferrooxidans strain CC1. Accuracy of individual components is estimated to ± 20% and components lower than 15% are not significant (PDF 52 kb)

792_2012_466_MOESM3_ESM.tiff

Figure S3 XRD powder data of the solid COWG samples studied. Qz: quartz, Fk: K-feldspar, Mu: muscovite; Ja: jarosite; Py: pyrite (TIFF 1062 kb)

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Volant, A., Desoeuvre, A., Casiot, C. et al. Archaeal diversity: temporal variation in the arsenic-rich creek sediments of Carnoulès Mine, France. Extremophiles 16, 645–657 (2012). https://doi.org/10.1007/s00792-012-0466-8

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