Matej Remenár, Jana Harichová, Marcel Zámocký, Domenico Pangallo, Tomáš Szemes, Jaroslav Budiš, Katarína Soltys, Peter Ferianc. Metagenomics of a nickel-resistant bacterial community in an anthropogenic nickel-contaminated soil in southwest Slovakia. Biologia, 72(9):971-981. 2017.
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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.