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Insight Into Heavy Metal Resistome of Soil Psychrotolerant Bacteria Originating from King George Island (Antarctica)

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Insight Into Heavy Metal Resistome of Soil Psychrotolerant Bacteria Originating from King George Island (Antarctica) Polar Biology https://doi.org/10.1007/s00300-018-2287-4 ORIGINAL PAPER Insight into heavy metal resistome of soil psychrotolerant bacteria originating from King George Island (Antarctica) Krzysztof Romaniuk1 · Anna Ciok1 · Przemyslaw Decewicz1 · Witold Uhrynowski1 · Karol Budzik1 · Marta Nieckarz1 · Julia Pawlowska2 · Marek K. Zdanowski3 · Dariusz Bartosik1 · Lukasz Dziewit1 Received: 8 May 2017 / Revised: 7 February 2018 / Accepted: 19 February 2018 © The Author(s) 2018. This article is an open access publication Abstract The presence of heavy metals in Antarctica is an emerging issue, especially as (bio)weathering of metal-containing minerals occurs and human infuence is more and more visible in this region. Chemical analysis of three soil samples collected from the remote regions of King George Island (Antarctica) revealed the presence of heavy metals (mainly copper, mercury, and zinc) at relatively high concentrations. Physiological characterization of over 200 heavy metal-resistant, psychrotolerant bacterial strains isolated from the Antarctic soil samples was performed. This enabled an insight into the heavy metal resistome of these cultivable bacteria and revealed the prevalence of co-resistance phenotypes. All bacteria identifed in this study were screened for the presence of selected heavy metal-resistance genes, which resulted in identifcation of arsB (25), copA (3), czcA (33), and merA (26) genes in 62 strains. Comparative analysis of their nucleotide sequences provided an insight into the diversity of heavy metal-resistance genes in Antarctic bacteria. Keywords Antarctica · Psychrotolerant bacteria · Heavy metal · Heavy metal resistance · Resistome Introduction have no or limited biological roles and are highly cytotoxic even in trace amounts (Bruins et al. 2000). Metals (and metalloids) play an integral role in metabolic Heavy metal-rich regions are common across our planet. processes, and many of them are required for life; however, This is a consequence of natural processes (e.g., [bio]weath- each metal is known to have unique features and physico- ering of metal-containing minerals, volcanic emissions, chemical properties that are responsible for its specifc toxi- forest fres, deep-sea vents, and geysers) and anthropogenic cological mechanisms of action (Tchounwou et al. 2012). activities (e.g., large-scale burning of fossil fuels, mining, Moreover, some metals (e.g., Ag, Al, Au, Cd, Hg, and Pb) and metal manufacturing) (Adriano 2001). To lessen the toxic efect of heavy metals, many microorganisms have developed efcient resistance mechanisms. To date, three Electronic supplementary material The online version of this main types of such mechanisms have been described: (i) article (https​://doi.org/10.1007/s0030​0-018-2287-4) contains efux of toxic ions from bacterial cells, (ii) enzymatic trans- supplementary material, which is available to authorized users. formations of metals, and (iii) incorporation of heavy met- * Lukasz Dziewit als into complexes by metal-binding proteins, which makes [email protected] them less toxic to the cell (Silver and Phung le 2005; Dziewit and Drewniak 2016). 1 Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Efux systems constitute the largest group of metal- Miecznikowa 1, 02‑096 Warsaw, Poland resistance mechanisms (Amiard-Triquet and Rainbow 2 Department of Molecular Phylogenetics and Evolution, 2011). In general, they involve active transport of toxic Faculty of Biology, Institute of Botany, Biological metals from the cytoplasm, in which three main types of and Chemical Research Center, University of Warsaw, Zwirki proteins are usually involved: (i) resistance–nodulation- i Wigury 101, 02‑089 Warsaw, Poland cell division (RND superfamily) proteins, (ii) cation dif- 3 Department of Antarctic Biology, Institute of Biochemistry fusion facilitators (CDF family), and (iii) P-type ATPases. and Biophysics, Polish Academy of Sciences, Pawińskiego Heavy metal resistance may also involve enzymatic 5a, 02‑106 Warsaw, Poland Vol.:(0123456789)1 3 Polar Biology transformations of toxic ions, involving their oxidation, Materials and methods reduction, methylation, and demethylation. Model exam- ples of enzymatic detoxifcation systems in bacteria are Sample collection and isolation of bacteria mercury- and arsenate-resistance mechanisms. The third heavy metal-resistance mechanism involves intracellular Soil samples were collected in 2012 from three sites sequestration of heavy metals as complexes, by small, located at King George Island (Antarctica) difering in cysteine-rich, metal-binding proteins—metallothioneins the extents of anthropogenic and zoogenic infuence: (i) (Silver and Misra 1988; Silver et al. 1989; Nies 2003; Sil- petroleum-contaminated soil found near the petroleum ver and Phung le 2005; Haferburg and Kothe 2007; Blin- pumping and storage warehouse at the Henryk Arctowski dauer 2011; Dziewit and Drewniak 2016). Polish Antarctic Station—a site under constant anthropo- The occurrence of heavy metals at high concentrations pression (GPS coordinates: 62°09.601′ S, 58°28.464′ may signifcantly infuence the taxonomic and functional W), (ii) organic matter-rich soil from the Adélie pen- diversities of soil microbial communities (Kandeler et al. guin breeding colony (soil mixed with birds feces)—a 1996, 2000). Studies of extreme, polar environments char- region under strong zoogenic infuence (62°09.778′ S, acterized by a still limited anthropogenic infuence (e.g., 58°27.711′ W) and (iii) a soil sample from the Jardine High Arctic or Antarctica) are of great importance, as they Peak—a region with no visible vegetation and no vis- may reveal novel genes encoding heavy metal-resistance ible signs of human and animal activities (62°09.997′ S, and metabolism mechanisms, and show the role of naturally 58°29.505′ W) (Fig. 1). Soil samples were taken from a occurring microorganisms in biogeochemical cycles. The depth of 15–20 cm, after gentle removal of the surface soil results of several studies revealed that bacteria isolated from layer, and stored at − 20 °C for further study in laboratory various Arctic and Antarctic environments show resistances (in Poland). to various toxic, antimicrobial agents, such as antibiotics For isolation of bacteria, 1 g of each soil sample was and heavy metals (De Souza et al. 2006, 2007; Lo Giudice taken and homogenized in 10 ml of 0.85% NaCl (pH 7.0) et al. 2013; Mangano et al. 2014; Moller et al. 2014; Tomova in sterile, trace metal-free, plastic (50 ml) falcon by mix- et al. 2014; Perron et al. 2015; Rahman et al. 2015; Tomova ing vigorously (120 rpm for 2 h at 15 °C). After waiting et al. 2015; González-Aravena et al. 2016; Rodriguez-Rojas for 20 min to allow larger particles to settle, a series of et al. 2016). However, overall knowledge on the resistome supernatant dilutions were prepared in saline. Aliquots of of polar bacteria is still rather limited, and the lack of a sys- 100 µl of the respective dilutions were plated on R2A and tematic approach, combining chemical, microbiological, and lysogeny broth (LB) media solidifed by the addition of molecular analyses, is apparent. 1.5% (w/v) agar (Sambrook and Russell 2001) and incu- The presence of heavy metals in Antarctica is an emerg- bated at 15 °C. All operations were carried out aseptically. ing issue, given both local and remote anthropogenic activi- The inoculated plates were incubated at 15 °C for ties likely contributing to their presence in this region (Plan- 2 weeks. After 14 days of incubation, 100 colonies from chon et al. 2002; Jerez et al. 2011). However, it is worth each sample were selected for taxonomical identifcation noting, that the presence of heavy metals in Antarctic soils is (based on 16S rDNA sequencing) and further characteriza- (in most cases) primarily a consequence of naturally occur- tion. The selection of the samples was based on apparent ring (bio)geochemical weathering of terrigenous sources, diferences in size, color, shape, and other colony charac- i.e., metal-rich minerals (Santos et al. 2005; Dold et al. teristics. If two or more strains had an identical 16S rDNA 2013). All together, it has fostered interest in heavy metal- sequence and characteristics (the methodology described resistant bacteria as their collective metabolic activity may below), they were considered as the same strain, and only cause the biotransformation of toxic ions. one of them was further analyzed. Ultimately, for further The aim of this study was to analyze heavy metal content, analyses, 216 strains were chosen, including (i) 90 from as well as the diversity of heavy metal-resistant bacteria and the petroleum-contaminated soil near the Arctowski sta- heavy metal-resistance genes in various Antarctic soils from tion, (ii) 68 from the penguin colony, and (iii) 58 from regions difering in anthropogenic and zoogenic infuence. the Jardine Peak (the strains were presented in Online For those purposes, samples of soil collected at King George Resource 1). Island (Antarctica) were analyzed for the presence of heavy metals, and bacteria showing resistance to these elements. Characterization of over 200 heavy metal-resistant, psychro- Chemical analyses of the soil samples tolerant bacterial strains revealed the prevalence of co-resist- ance phenotypes and provided insight into the diversity of Quantitative analysis of chemical elements (Ag, Al, As, the heavy metal-resistance genes among bacteria inhabiting Ba, Ca, Cd, Co, Cr, Cu, Fe, K,
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