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

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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.

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Abbreviations

B-C:

Bray-Curtis dissimilarity coefficient

bp:

base pair

Chao 1, Chao 1 index (species richness estimator):

CzcA, heavy metal efflux pump (cobalt-zinc-cadmium resistance)

D:

dominance

H’:

Shanon-Wiener diversity index

I:

numbers of reads

J’:

equitability

nccA:

heavy-metal-resistance determinant (nickel-cobalt-cadmium resistance)

PAHs:

polycyclic aromatic hydrocarbons

PCBs:

polychlorinated biphenyls

R:

species richness

S:

Simpson’s index

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Authors and Affiliations

  1. Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551, Bratislava, Slovakia

    Matej Remenár, Jana Harichová, Marcel Zámocký & Peter Ferianc

  2. Division of Biochemistry, Department of Chemistry, BOKU — University of Natural Resources and Life Sciences, A-1190, Vienna, Austria

    Marcel Zámocký

  3. Laboratory of Environmental and Food Microbiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551, Bratislava, Slovakia

    Domenico Pangallo

  4. Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynská dolina, Ilkovičova 6, SK-84215, Bratislava, Slovakia

    Tomáš Szemes & Katarína Soltys

  5. Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina, SK-84248, Bratislava, Slovakia

    Jaroslav Budiš

  6. Comenius University Science Park, Comenius University in Bratislava, Ilkovičova 8, SK-84104, Bratislava, Slovakia

    Katarína Soltys

Authors
  1. Matej Remenár
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  2. Jana Harichová
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  8. Peter Ferianc
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Correspondence to Peter Ferianc.

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Remenár, M., Harichová, J., Zámocký, M. et al. Metagenomics of a nickel-resistant bacterial community in an anthropogenic nickel-contaminated soil in southwest Slovakia. Biologia 72, 971–981 (2017). https://doi.org/10.1515/biolog-2017-0117

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  • DOI: https://doi.org/10.1515/biolog-2017-0117

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