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Whole Genome Sequence Analysis of Cupriavidus necator C39, a Multiple Heavy Metal(loid) and Antibiotic Resistant Bacterium Isolated from a Gold/Copper Mine

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Xie, Zhenchen, Wang, Dan, Ben Fekih, Ibtissem, Yu, Yanshuang, Li, Yuanping, Alwathnani, Hend, Herzberg, Martin, Rensing, Christopher·2023·Microorganisms
DOI 10.3390/microorganisms11061518PMC PMC10304115
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Abstract

Here a multiple heavy metal and antibiotic resistant bacterium Cupriavidus necator C39 (C. necator C39) was isolated from a Gold-Copper mine in Zijin, Fujian, China. C. necator C39 was able to tolerate intermediate concentrations of heavy metal(loid)s in Tris Minimal (TMM) Medium (Cu(II) 2 mM, Zn(II) 2 mM, Ni(II) 0.2 mM, Au(III) 70 μM and As(III) 2.5 mM). In addition, high resistance to multiple antibiotics was experimentally observed. Moreover, strain C39 was able to grow on TMM medium containing aromatic compounds such as benzoate, phenol, indole, p-hydroxybenzoic acid or phloroglucinol anhydrous as the sole carbon sources. The complete genome of this strain revealed 2 circular chromosomes and 1 plasmid, and showed the closest type strain is C. necator N-1T based on Genome BLAST Distance Phylogeny. The arsenic-resistance (ars) cluster GST-arsR-arsICBR-yciI and a scattered gene encoding the putative arsenite efflux pump ArsB were identified on the genome of strain C39, which thereby may provide the bacterium a robust capability for arsenic resistance. Genes encoding multidrug resistance efflux pump may confer high antibiotic resistance to strain C39. Key genes encoding functions in degradation pathways of benzene compounds, including benzoate, phenol, benzamide, catechol, 3- or 4-fluorobenzoate, 3- or 4-hydroxybenzoate and 3,4-dihydroxybenzoate, indicated its potential for degrading those benzene compounds.

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  • Cupriavidus necator exhibits significant resistance to heavy metals and demonstrates enhanced growth in the presence of Cu.

    “An example is Cupriavidus necator, which exhibits significant resistance to heavy metals and demonstrates enhanced growth in the presence of Cu [382].”

    From Harnessing bacterial consortia for effective bioremediation: targeted removal of heavy metals, hydrocarbons, and persistent pollutants (2025) · cites this paper as [382]

    Section 3.1 reports that C. necator strain C39 tolerates several heavy metals, including Cu(II) at 2 mM, though it is less tolerant than the comparison strains. The paper does not report enhanced growth in the presence of Cu: its copper experiments measure tolerance, not improved growth relative to a copper-free condition (Sections 2.3 and 3.1). (LLM, conf=0.88)

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Cited by

Sorted by citations

Authors
Xie, Z., Wang, D., Ben Fekih, I., Yu, Y., Li, Y., Alwathnani, H., Herzberg, M., & Rensing, C.
Affiliations
  • Fujian Agriculture and Forestry University (CN)
  • Shenzhen University (CN)
  • Institute of Environmental Microbiology, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
  • King Saud University (SA)
  • Martin Luther University Halle-Wittenberg (DE)
Corresponding author
Rensing, Christopher
ORCID
Venue
Microorganisms
Publisher
MDPI AG
Published
2023-06-07
Volume
11
Issue
6
Pages
1518
ISSN
2076-2607 (ISSN-L)
DOI
10.3390/microorganisms11061518
PMC
PMC10304115
OpenAlex
W4380051606
Cited by
11
References
0
Citations by year
2026: 4 · 2025: 4 · 2024: 2 · 2023: 1
FWCI
0.95
Type
journal article
Language
en
Open access
Licence
Locations
  • Microorganisms (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Open Repository and Bibliography (University of Liège) (submittedVersion, other-oa)
  • Digitalen Hochschulbibliothek Sachsen-Anhalt (Universitäts- und Landesbibliothek Sachsen-Anhalt) (cc-by)
Funders
  • NSFC (31770123, 2018J01668, RSP-2023/205)
  • Natural Science Foundation of Fujian province (31770123, 2018J01668, RSP-2023/205)
  • King Saud University (31770123, 2018J01668, RSP-2023/205)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Engineering › Biomedical Engineering › Metal Extraction and Bioleaching
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords
heavy metal resistance, antibiotic resistance, arsenic resistance, multidrug efflux pumps, aromatic compound degradation, benzoate degradation, bacterial genomes, plasmids

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