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Bacterial and archaeal communities in the acid pit lake sediments of a chalcopyrite mine

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Abstract

Bacterial and archaeal community structures and diversity of three different sedimentary environments (BH1A, BH2A and BH3A) in the acid pit lake of a chalcopyrite mine at Touro (Spain) were determined by 16S rRNA gene PCR-DGGE and sequencing of clone libraries. DGGE of bacterial and archaeal amplicons showed that the sediments harbor different communities. Bacterial 16S rRNA gene sequences were assigned to Acidobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, Proteobacteria, Chloroflexi and uncultured bacteria, after clustering into 42 operational taxonomic units (OTUs). OTU 2 represented approximately 37, 42 and 37 % of all sequences from sediments BH1A, BH2A and BH3A, respectively, and was phylogenetically related to uncultured Chloroflexi. Remaining OTUs were phylogenetically related to heterotrophic bacteria, including representatives of Ferrithrix and Acidobacterium genera. Archaeal 16S rRNA gene sequences were clustered into 54 OTUs. Most of the sequences from the BH1A sediment were assigned to Euryarchaeota, whereas those from BH2A sediment were assigned to Crenarchaeota. The majority of the sequences from BH3A sediment were assigned to unclassified Archaea, and showed similarities to uncultured and unclassified environmental clones. No sequences related to Acidithiobacillus and Leptospirillum, commonly associated with acid mine drainage, were detected in this study.

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  1. Departamento de Ciência do Solo, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Av. Pádua Dias, 11, Caixa Postal 9, CEP13418-900, Piracicaba, São Paulo, Brazil

    A. R. Lucheta & M. R. Lambais

  2. Departamento de Edafoloxía e Química Agrícola, Facultade de Bioloxía, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain

    X. L. Otero & F. Macías

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  1. A. R. Lucheta
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  2. X. L. Otero
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  3. F. Macías
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Communicated by M. da Costa.

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792_2013_576_MOESM1_ESM.jpg

Online Resource 1 Details of the pit lake of the Touro mine collecting the AMD and sediment characteristics. Samples: BH1A. BH2A. BH3A (jpg 995 kb)

792_2013_576_MOESM2_ESM.tif

Online Resource 2 Rarefaction curves representing the estimated number of bacterial (a) and archaeal (b) OTUs as a function of the sequence effort, considering a cut-off evolutionary distance of 0.03. Bars represent 95 % confidence intervals (TIFF 17820 kb)

792_2013_576_MOESM3_ESM.pdf

Online Resource 3 List of sequences comprising each bacterial and archaeal OTU from sediments BH1A, BH2A and BH3A. A cut-off evolutionary distance of 0.03 was used to define OTU (PDF 407 kb)

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Lucheta, A.R., Otero, X.L., Macías, F. et al. Bacterial and archaeal communities in the acid pit lake sediments of a chalcopyrite mine. Extremophiles 17, 941–951 (2013). https://doi.org/10.1007/s00792-013-0576-y

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