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Mergeay M, Van Houdt R. Cupriavidus metallidurans CH34, a historical perspective on its discovery, characterization and metal resistance. FEMS Microbiol Ecol 2021; 97:6019867. [PMID: 33270823 DOI: 10.1093/femsec/fiaa247] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/01/2020] [Indexed: 11/14/2022] Open
Abstract
Cupriavidus metallidurans, and in particular type strain CH34, became a model bacterium to study bacterial resistance to metals. Although nowadays the routine use of a wide variety of omics and molecular techniques allow refining, deepening and expanding our knowledge on adaptation and resistance to metals, these were not available at the onset of C. metallidurans research starting from its isolation in 1976. This minireview describes the early research and legacy tools used to study its metal resistance determinants, characteristic megaplasmids, ecological niches and environmental applications.
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Affiliation(s)
- Max Mergeay
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
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Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance. Appl Environ Microbiol 2020; 86:AEM.02907-19. [PMID: 32111593 DOI: 10.1128/aem.02907-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/15/2020] [Indexed: 12/18/2022] Open
Abstract
Metallothionein (MT) genes are valuable genetic materials for developing metal bioremediation tools. Currently, a limited number of prokaryotic MTs have been experimentally identified, which necessitates the expansion of bacterial MT diversity. In this study, we conducted a metagenomics-guided analysis for the discovery of potential bacterial MT genes from the soil microbiome. More specifically, we combined resistance gene enrichment through diversity loss, metagenomic mining with a dedicated MT database, evolutionary trace analysis, DNA chemical synthesis, and functional genomic validation to identify novel MTs. Results showed that Cu stress induced a compositional change in the soil microbiome, with an enrichment of metal-resistant bacteria in soils with higher Cu concentrations. Shotgun metagenomic sequencing was performed to obtain the gene pool of environmental DNA (eDNA), which was subjected to a local BLAST search against an MT database for detecting putative MT genes. Evolutional trace analysis led to the identification of 27 potential MTs with conserved cysteine/histidine motifs different from those of known prokaryotic MTs. Following chemical synthesis of these 27 potential MT genes and heterologous expression in Escherichia coli, six of them were found to improve the hosts' growth substantially and enhanced the hosts' sorption of Cu, Cd, and Zn, among which MT5 led to a 13.7-fold increase in Cd accumulation. Furthermore, four of them restored Cu and/or Cd resistance in two metal-sensitive E. coli strains.IMPORTANCE The metagenomics-guided procedure developed here bypasses the difficulties encountered in classic PCR-based approaches and led to the discovery of novel MT genes, which may be useful in developing bioremediation tools. The procedure used here expands our knowledge on the diversity of bacterial MTs in the environment and may also be applicable to identify other functional genes from eDNA.
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Mazhar SH, Herzberg M, Ben Fekih I, Zhang C, Bello SK, Li YP, Su J, Xu J, Feng R, Zhou S, Rensing C. Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine. Front Microbiol 2020; 11:47. [PMID: 32117100 PMCID: PMC7019866 DOI: 10.3389/fmicb.2020.00047] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/10/2020] [Indexed: 12/12/2022] Open
Abstract
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.
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Affiliation(s)
- Sohaib H Mazhar
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.,Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Ibtissem Ben Fekih
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chenkang Zhang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Suleiman Kehinde Bello
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Ping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junming Su
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junqiang Xu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Renwei Feng
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.,Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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