Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals.

Lukasz Dziewit,Adam Pyzik,Sebastian Mielnicki,Daniel Wibberg,Renata Matlakowska,Magdalena Szuplewska,Alfred Pã¼Hler,Dariusz Bartosik,Andreas Schlã¼Ter

doi:10.3389/fmicb.2015.00152

Lukasz Dziewit, Adam Pyzik + Show 7 more

Open Access

https://doi.org/10.3389/fmicb.2015.00152

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Abstract

The Lubin underground mine, is one of three mining divisions in the Lubin-Glogow Copper District in Lower Silesia province (Poland). It is the source of polymetallic ore that is rich in copper, silver and several heavy metals. Black shale is also significantly enriched in fossil organic matter in the form of long-chain hydrocarbons, polycyclic aromatic hydrocarbons, organic acids, esters, thiophenes and metalloporphyrins. Biological analyses have revealed that this environment is inhabited by extremophilic bacteria and fungi. Kupfershiefer black shale and samples of water, bottom and mineral sediments from the underground (below 600 m) Lubin mine were taken and 20 bacterial strains were isolated and characterized. All exhibited multi-resistant and hypertolerant phenotypes to heavy metals. We analyzed the plasmidome of these strains in order to evaluate the diversity and role of mobile DNA in adaptation to the harsh conditions of the mine environment. Experimental and bioinformatic analyses of 11 extrachromosomal replicons were performed. Three plasmids, including a broad-host-range replicon containing a Tn3 family transposon, carried genes conferring resistance to arsenic, cadmium, cobalt, mercury and zinc. Functional analysis revealed that the resistance modules exhibit host specificity, i.e., they may increase or decrease tolerance to toxic ions depending on the host strain. The other identified replicons showed diverse features. Among them we identified a catabolic plasmid encoding enzymes involved in the utilization of histidine and vanillate, a putative plasmid-like prophage carrying genes responsible for NAD biosynthesis, and two repABC-type plasmids containing virulence-associated genes. These findings provide an unique molecular insight into the pool of extrachromosomal replicons and highlight their role in the biology and adaptation of extremophilic bacteria inhabiting terrestrial deep subsurface.

Highlights

Bacterial plasmids, as extrachromosomal mobile genetic elements, are components of many microbial genomes
In this study we analyzed 20 bacterial strains isolated from various samples collected from the terrestrial deep subsurface environment, namely Lubin copper mine: (i) black shale; (ii) water (LM10, LM12, LM24); (iii) mineral sediment (LM11, LM14, LM21) and (iv) bottom sediment (LM15, LM16, LM19, LM22)
We demonstrated the diversity of the plasmids and defined their adaptive value, focusing on heavy metal resistance, since these toxic elements are major contaminants of the Lubin copper mine environment influencing indigenous microoganisms

Summary

Introduction

As extrachromosomal mobile genetic elements, are components of many microbial genomes. Many plasmids carry accessory genes determining various phenotypes, e.g., antibiotics resistance and utilization of toxic compounds Such genetic information is not crucial for host viability, but it may play an important role in the adaptation of bacteria to various environments, including terrestrial deep subsurface habitats (Sobecky and Coombs, 2009; Heuer and Smalla, 2012; Nojiri, 2013). Metal resistance genes are often co-localized on plasmids together with antibiotic resistance genes, and they are frequently present within transposable and integrative mobile elements (Rahube et al, 2014) Such plasmidencoded heavy metal resistance systems are usually related to chromosomally-encoded determinants found in other bacteria, which exemplifies the naturally occurring gene flow (Silver, 1996)

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