No abstract

Heavy metals are a significant source of pollution in soils that have been demonstrated to exert significant toxic effect on soil microbial assemblages. Here we investigate the occurrence and metabolic characteristics of actinobacteria, which form a predominated component of farmland bacterial community near the town of Sereď in southwest Slovakia, contaminated by close nickel ore facility. Actinobacteria occurred in this environment with high concentrations of nickel (2.109 mg/kg), slightly above the natural occurrence of cobalt (355 mg/kg) and zinc (177 mg/kg), even too low concentration of iron (35.75 mg/kg) for a normal soil and not a toxic amount of copper (32.2 mg/kg) and cadmium (<0.25 mg/kg). The phylogeny was reconstructed using partial sequences of 16S rDNA genes of both, actinobacterial isolates and clones. A total of 105 actinobacterial representatives were divided into 66 species belonging to one order, 7 genera and 5 uncategorized groups. The selected 14 morphologically distinct isolates were able to produce drop collapsing, haemolytic and lipase activities. Whereas only 4 isolates produced dark brown melanin pigment and only 5 of them produced decolourization of the azo dye, all isolates tested were capable of assimilating all 11 sugars tested. All these actinobacterial isolates were resistant to nickel, cobalt, zinc, cadmium, copper, but the level of resistance differed between the individual isolates, and the resistance profiles of antibiotics (gentamycin, ampicillin, ciprofloxacin, chloramphenicol, erythromycin, rifampicin, penicillin-G) varied among them to a certain extent. Our results suggested that actinobacteria in soil contaminated by nickel present a relatively divergent group inside of microbial assemblage.

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.