Characterization of Halomonassp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA

Abstract

BackgroundHalomonas sp. ZM3 was isolated from Zelazny Most post-flotation mineral waste repository (Poland), which is highly contaminated with heavy metals and various organic compounds. Mobile DNA of the strain (i.e. plasmids and transposons) were analyzed in order to identify genetic information enabling adaptation of the bacterium to the harsh environmental conditions.ResultsThe analysis revealed that ZM3 carries plasmid pZM3H1 (31,370 bp), whose replication system may be considered as an archetype of a novel subgroup of IncU-like replicons. pZM3H1 is a narrow host range, mobilizable plasmid (encodes a relaxase of the MOBV family) containing mercury resistance operon (mer) and czcD genes (mediate resistance to zinc and cobalt), which are part of a large truncated Tn3 family transposon. Further analysis demonstrated that the phenotypes determined by the pZM3H1 resistance cassette are highly dependent on the host strain. In another strand of the study, the trap plasmid pMAT1 was employed to identify functional transposable elements of Halomonas sp. ZM3. Using the sacB positive selection strategy two insertion sequences were identified: ISHsp1 - representing IS5 group of IS5 family and ISHsp2 - a distinct member of the IS630 family.ConclusionsThis study provides the first detailed description of mobile DNA in a member of the family Halomonadaceae. The identified IncU plasmid pZM3H1 confers resistance phenotypes enabling adaptation of the host strain to the Zelazny Most environment. The extended comparative analysis has shed light on the distribution of related IncU plasmids among bacteria, which, in many cases, reflects the frequency and direction of horizontal gene transfer events. Our results also identify plasmid-encoded modules, which may form the basis of novel shuttle vectors, specific for this group of halophilic bacteria.

High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite

“…The affiliation of Halomonas (1 %) to Biom is consistent with findings in gold mines [ 23 ] and in contaminated heavy metals wastes [ 24 ], as both environments are rich in chemicals. Halomonas metabolize cyanide [ 25 ] and some are reported to carry plasmid pZM3H which confers resistance to different chemicals [ 24 ] , leading to their application in soil remediation [ 25 , 26 ]. The fact that these bacteria are predominant, it would be worthwhile to study their roles in the dumpsite, and examining if they contain plasmids that confer resistance to different chemicals.…”

Genome Structure of the Opportunistic Pathogen Paracoccus yeei (Alphaproteobacteria) and Identification of Putative Virulence Factors

“…The temperature, pH and salinity tolerance of P. yeei CCUG 32053 were analyzed by monitoring changes in the optical density (OD) of cultures (in comparison with non-inoculated controls) according to previously described procedures ( Dziewit et al, 2013 ). Motility was tested on soft LB agar plates containing 0.3, 0.35, or 0.4% (w/v) agar.…”

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

“…The temperature, pH and salinity tolerance of bacteria were analyzed by monitoring changes in the optical density of cultures (in comparison with non-inoculated controls) according to the procedures described previously (Dziewit et al, 2013 ). For the motility assay LB soft agar plates containing 0.3, 0.35, or 0.4% (w/v) agar were inoculated with the bacteria using a sterile toothpick and incubated at 30°C for 48 h.…”

“…The minimum inhibitory concentrations (MICs) of selected heavy metal ions were established. For this purpose, analytical grade salts (3CdSO 4 × 8H 2 0; CoSO 4 × 7H 2 0; CuSO 4 ; HgCl 2 ; K 2 Cr 2 O 7 ; NaAsO 2 ; Na 2 HAsO 4 × 7H 2 O; NiCl 2 × 6H 2 0; NaO 3 V; ZnSO 4 × 7H 2 0) were used in an assay procedure described previously (Dziewit et al, 2013 ). Isolates that grew in the presence of at least the following metal ion concentrations were considered resistant: (i) 20 mM V 5+ , (ii) 10 mM As 5+ , (iii) 1 mM As 3+ , Cd 2+ , Co 2+ , Cu 2+ , Ni 2+ , Zn 2+ , or Cr 6+ , and (iv) 0.1 mM Hg 2+ (Nieto et al, 1987 ; Abou-Shanab et al, 2007 ).…”