Dataset Information

Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter kameinonensis and Mucilaginibacter rubeus Isolated from a Gold/Copper Mine.

ABSTRACT: Heavy metals (HMs) are compounds that can be hazardous and impair growth of living organisms. Bacteria have evolved the capability not only to cope with heavy metals but also to detoxify polluted environments. Three heavy metal-resistant strains of Mucilaginibacer rubeus and one of Mucilaginibacter kameinonensis were isolated from the gold/copper Zijin mining site, Longyan, Fujian, China. These strains were shown to exhibit high resistance to heavy metals with minimal inhibitory concentration reaching up to 3.5 mM Cu(II), 21 mM Zn(II), 1.2 mM Cd(II), and 10.0 mM As(III). Genomes of the four strains were sequenced by Illumina. Sequence analyses revealed the presence of a high abundance of heavy metal resistance (HMR) determinants. One of the strain, M. rubeus P2, carried genes encoding 6 putative PIB-1-ATPase, 5 putative PIB-3-ATPase, 4 putative Zn(II)/Cd(II) PIB-4 type ATPase, and 16 putative resistance-nodulation-division (RND)-type metal transporter systems. Moreover, the four genomes contained a high abundance of genes coding for putative metal binding chaperones. Analysis of the close vicinity of these HMR determinants uncovered the presence of clusters of genes potentially associated with mobile genetic elements. These loci included genes coding for tyrosine recombinases (integrases) and subunits of mating pore (type 4 secretion system), respectively allowing integration/excision and conjugative transfer of numerous genomic islands. Further in silico analyses revealed that their genetic organization and gene products resemble the Bacteroides integrative and conjugative element CTnDOT. These results highlight the pivotal role of genomic islands in the acquisition and dissemination of adaptive traits, allowing for rapid adaption of bacteria and colonization of hostile environments.

SUBMITTER: Li YP

PROVIDER: S-EPMC6316836 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter kameinonensis and Mucilaginibacter rubeus Isolated from a Gold/Copper Mine.

Li Yuan Ping YP Carraro Nicolas N Yang Nan N Liu Bixiu B Xia Xian X Feng Renwei R Saquib Quaiser Q Al-Wathnani Hend A HA van der Meer Jan Roelof JR Rensing Christopher C

Genes 20181123 12

Heavy metals (HMs) are compounds that can be hazardous and impair growth of living organisms. Bacteria have evolved the capability not only to cope with heavy metals but also to detoxify polluted environments. Three heavy metal-resistant strains of Mucilaginibacer rubeus and one of Mucilaginibacter kameinonensis were isolated from the gold/copper Zijin mining site, Longyan, Fujian, China. These strains were shown to exhibit high resistance to heavy metals with minimal inhibitory co ...[more]

PMID: 30477188

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Project description:The highly heavy metal resistant strain Cupriavidus metallidurans BS1 was isolated from the Zijin gold-copper mine in China. This was of particular interest since the extensively studied, closely related strain, C. metallidurans CH34 was shown to not be only highly heavy metal resistant but also able to reduce metal complexes and biomineralizing them into metallic nanoparticles including gold nanoparticles. After isolation, C. metallidurans BS1 was characterized and complete genome sequenced using PacBio and compared to CH34. Many heavy metal resistance determinants were identified and shown to have wide-ranging similarities to those of CH34. However, both BS1 and CH34 displayed extensive genome plasticity, probably responsible for significant differences between those strains. BS1 was shown to contain three prophages, not present in CH34, that appear intact and might be responsible for shifting major heavy metal resistance determinants from plasmid to chromid (CHR2) in C. metallidurans BS1. Surprisingly, the single plasmid - pBS1 (364.4 kbp) of BS1 contains only a single heavy metal resistance determinant, the czc determinant representing RND-type efflux system conferring resistance to cobalt, zinc and cadmium, shown here to be highly similar to that determinant located on pMOL30 in C. metallidurans CH34. However, in BS1 another homologous czc determinant was identified on the chromid, most similar to the czc determinant from pMOL30 in CH34. Other heavy metal resistance determinants such as cnr and chr determinants, located on megaplasmid pMOL28 in CH34, were shown to be adjacent to the czc determinant on chromid (CHR2) in BS1. Additionally, other heavy metal resistance determinants such as pbr, cop, sil, and ars were located on the chromid (CHR2) and not on pBS1 in BS1. A diverse range of genomic rearrangements occurred in this strain, isolated from a habitat of constant exposure to high concentrations of copper, gold and other heavy metals. In contrast, the megaplasmid in BS1 contains mostly genes encoding unknown functions, thus might be more of an evolutionary playground where useful genes could be acquired by horizontal gene transfer and possibly reshuffled to help C. metallidurans BS1 withstand the intense pressure of extreme concentrations of heavy metals in its environment.

Project description:Understanding the level of heavy metal contamination coupled with the assessment of environmental and human risks associated with mine waste dumpsites is an important step to initiating efficient measures for mine wasteland restoration, stabilization, and bioremediation. In the present study, concentration of the heavy metals; Copper (Cu), Cobalt (Co), Iron (Fe), Lead (Pb), Manganese (Mn), and Zinc (Zn) in soil from mine waste dumpsites around Kitwe (Sites: TD25 and TD26) and Mufulira (Site: TD10), Zambia, was assessed to determine the level of contamination, ecological risks, and progress made in reclamation. The mine waste dumpsites in the two towns are located in the vicinity of residential areas. Therefore, there is need to provide information for optimization of protocols for post-mining landscape in Zambia and elsewhere to limit soil, river, and groundwater contamination and to accelerate the restoration process . Mean values for soil pH, electrical conductivity, and organic matter varied between 5.9-8.4, 2534.8-538.6 μS/cm, and 0.90-2.75%, respectively. The mean concentrations of heavy metals of TD25, TD26, and TD10 decreased in order of Fe > Cu > Co > Mn > Pb > Zn across all sites. However, the order of overall degree of heavy metal contamination computed using control soil as a baseline in TD25, TD26, and TD10 was Cu > Co > Fe > Pb > Mn > Zn. The pollution load index was 0.355 at TD25, 0.329 at TD26, and 0.189 at TD10, indicating high soil pollution at TD25 and TD26. The Potential Ecological Risk Index for all heavy metals tested at TD25, TD26, and TD10 showed low ecological risk in the vicinity of the studied dumpsites. Furthermore, the present study also showed that the polluted soils around smelter sites and mine waste dumpsites are susceptible to dispersion by wind and water. Additionally, results from TD10 revealed that the initiated remediation of the tailings dam was somewhat successful. Finally, this study provided an updated status regarding the accumulation of heavy metals in mine waste dumpsites of Kitwe and Mufulira, Zambia and baseline information necessary to enhance post-mining landscape reclamation.

Dataset Information

Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter kameinonensis and Mucilaginibacter rubeus Isolated from a Gold/Copper Mine.

Publications

Genomic Islands Confer Heavy Metal Resistance in <i>Mucilaginibacter kameinonensis</i> and <i>Mucilaginibacter rubeus</i> Isolated from a Gold/Copper Mine.

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