Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Culture Conditions
2.2. DNA Extraction, Genome Sequencing, Assembly and Annotation
2.3. Physiological Characterization
2.4. Evaluation of Heavy Metals Tolerance
2.5. Comparative Genomics Analyses
3. Results
3.1. General Properties of the NOV2-1 and OV2-1 Genomes
3.2. Phylogenetic Characterization
3.3. Physiological Characteristics of NOV2-1 and OV2-1
3.4. Tolerance to Heavy Metals
3.5. Genomic Analysis of HMR Gene Clusters
3.5.1. ars Cluster
3.5.2. czc Cluster
3.5.3. cop Cluster I
3.5.4. sil and cop Cluster 2
3.5.5. cup Cluster
3.5.6. mmf Cluster
3.5.7. mer Cluster
4. Discussion
5. Major Implications and Future Perspectives
6. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Feature | NOV2-1 | OV2-1 |
---|---|---|
Genome size (bp) | 5,687,442 | 5,647,760 |
CDS | 5024 | 5011 |
rRNA | 12 | 12 |
tRNA | 59 | 59 |
GC content (%) | 67.53 | 67.58 |
Contigs number | 2 | 2 |
Chromosomes number | 2 | 2 |
Hypothetical proteins | 1186 | 1186 |
Proteins with functional assignments | 4095 | 4064 |
Characteristics | C. necator | C. metalidurans | C. taiwanensis | C. gilardii | ||
---|---|---|---|---|---|---|
LMG8453 | CH34 | LMG19424 | CCUG 38401 | NOV2-1 | OV2-1 | |
Range for growth: | ||||||
Temperature (°C) | 30–37 | 30–35 | 30–37 | 30–48 | ||
pH | 5.0–9.0 | 7.0–9.0 | 7.0–9.9 | 5.5–9.0 | ||
NaCl (% w/v) | >1 | <1 | ||||
Heavy metal tolerance (mM): | ||||||
Cd | 1.5 | 5 | 0.75 | 1.5 | 5 | 0.75 |
Co | 0.5 | 0.8 | 0.8 | 0.7 | 0.7 | 0.7 |
Cu | 3 | 3 | 1.5 | 3 | 1 | 3 |
Pb | 8.5 | 9 | 8.5 | 9 | 8.5 | 8.5 |
Ni | 3 | 7 | 3 | 7 | 3 | 3 |
Zn | 2 | 7.5 | 7.5 | 7.5 | 7.5 | 1.5 |
Assimilation of: | ||||||
L-Lactate | + | − | + | − | + | + |
Sodium citrate | + | + | + | − | − | + |
L-Malate | - | + | - | - | + | + |
Enzymatic activities: | ||||||
L-Proline Arylamidase | + | + | + | − | − | − |
L-Pyrrolydonyl-Arylamidase | + | + | + | − | − | − |
Gamma-Glutamyl-Transferase | + | − | + | − | − | − |
Urease | − | + | + | − | − | − |
Alpha-Glucosidase | − | − | − | − | − | − |
Glutamyl Arylamidase pNA | + | − | − | + | − | + |
Other tests: | ||||||
ELLMAN | + | + | + | + | − | − |
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González-Sánchez, A.; Lozano-Aguirre, L.; Jiménez-Flores, G.; López-Sámano, M.; García-de Los Santos, A.; Cevallos, M.A.; Le Borgne, S. Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico). Microorganisms 2025, 13, 809. https://doi.org/10.3390/microorganisms13040809
González-Sánchez A, Lozano-Aguirre L, Jiménez-Flores G, López-Sámano M, García-de Los Santos A, Cevallos MA, Le Borgne S. Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico). Microorganisms. 2025; 13(4):809. https://doi.org/10.3390/microorganisms13040809
Chicago/Turabian StyleGonzález-Sánchez, Antonio, Luis Lozano-Aguirre, Guadalupe Jiménez-Flores, Mariana López-Sámano, Alejandro García-de Los Santos, Miguel A. Cevallos, and Sylvie Le Borgne. 2025. "Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico)" Microorganisms 13, no. 4: 809. https://doi.org/10.3390/microorganisms13040809
APA StyleGonzález-Sánchez, A., Lozano-Aguirre, L., Jiménez-Flores, G., López-Sámano, M., García-de Los Santos, A., Cevallos, M. A., & Le Borgne, S. (2025). Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico). Microorganisms, 13(4), 809. https://doi.org/10.3390/microorganisms13040809