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Biologia

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Volume 72, Issue 9

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Metagenomics of a nickel-resistant bacterial community in an anthropogenic nickel-contaminated soil in southwest Slovakia

Matej Remenár
  • Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
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/ Jana Harichová
  • Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
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/ Marcel Zámocký
  • Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
  • Division of Biochemistry, Department of Chemistry, BOKU – University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
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/ Domenico Pangallo
  • Laboratory of Environmental and Food Microbiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
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/ Tomáš Szemes
  • Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynská dolina, Ilkovićova 6, SK-84215 Bratislava, Slovakia
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/ Jaroslav Budiš
  • Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina, SK-84248 Bratislava, Slovakia
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/ Katarína Soltys
  • Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynská dolina, Ilkovićova 6, SK-84215 Bratislava, Slovakia
  • Comenius University Science Park, Comenius University in Bratislava, Ilkovićova 8, SK-84104 Bratislava, Slovakia
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/ Peter Ferianc
  • Corresponding author
  • Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
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Published Online: 2017-09-30 | DOI: https://doi.org/10.1515/biolog-2017-0117

Abstract

The sampling sites situated in southwest Slovakia are according to environmental monitoring of Slovakia a part of strongly disturbed environment by heavy metals, mainly by high nickel concentrations. The aim of the present study was to characterise a complete microbial assemblage from a dump containing heavy-metal-contaminated waste as well as from farmland situated nearby this dump by using shotgun sequencing of 16S rDNA amplicons. It was found that nickel influenced both species richness and diversity and that microbiota of both samples differed significantly (Bray-Curtis dissimilarity 0.73) at genus level mainly by abundances of sequences from particular genera and occurrences of the unique genera in individual bacterial communities. In spite of these differences between microbial assemblages, both samples shared many bacterial genera that might constitute the specific nickel-resistant bacterial niche, and it was possible to delineate the core microbiome of our two samples at species level. The core set of 30 species, represented by the phyla Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Cyanobacteria, suggest that these species might form a “core microbiome” of the specific nickel-resistant bacterial niche.

Key words: 16S rRNA (16S rDNA); overall microbial assemblage structure and diversity; nickel-contaminated soil and waste; shotgun sequencing (metagenomics); core microbiome

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About the article

Received: 2017-02-16

Accepted: 2017-09-15

Published Online: 2017-09-30

Published in Print: 2017-09-26


Citation Information: Biologia, Volume 72, Issue 9, Pages 971–981, ISSN (Online) 1336-9563, ISSN (Print) 0006-3088, DOI: https://doi.org/10.1515/biolog-2017-0117.

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