Draft Genome of Nocardia canadensis sp. nov. Isolated from Petroleum-Hydrocarbon-Contaminated Soil
Abstract
:1. Introduction
2. Materials and Methods
2.1. Isolation and Media Culture of Bacteria
2.2. DNA Extraction and Whole-Genome Shot Gun Sequencing
2.3. Bioinformatics Pipeline and Processing of Data
2.4. Description of Nocardia canadensis sp. nov.
3. Results and Discussion
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Traits | Assays | Activity |
---|---|---|
Hydrocarbon degradation potential b | Naphthalene | ++ |
Phenanthrene | +++ | |
Pyrene | ++ | |
Dodecane | ++ | |
Hexadecane | +++ | |
Catabolic genes c | Alkane monooxygenase (alkB) | + |
Cytochrome P450 hydroxylase (CYP153) | − | |
Naphthalene dioxygenase (nah1) | + | |
Cell growth measurement at 600 nm b | 1% diesel | ++++ |
1% hexadecane | ++++ | |
2% hexadecane | ++++ | |
3% hexadecane | ++++ | |
Plant-growth-promoting traits | 1-Aminocyclopropane-1-carboxylate deaminase (ACCD) | − |
Phosphate solubilization | − | |
Siderophore production | + (8.2%) | |
Nitrogen fixation | − | |
Indole-3-acetic (IAA) production | + (1.46 μg mL−1) | |
Ammonia production | + (2.9 μmol mL−1) | |
Root elongation assay (cm) d | 0% | 13.4 |
1% | 12.2 | |
2% | 10.1 | |
3% | 8.6 |
Analysis | Value | Comments |
---|---|---|
In silico DNA–DNA hybridization (DDH) | 63.4% | Below the threshold level of 70% |
Type (Strain) Genome Server (TYGS) | No match | Tagged as novel species |
Average nucleotide identity (ANI) | 88.63% | Below the species boundary cut-off of 95–96% |
16S rRNA gene sequence (RDP) | 98.8% | High similarity to Nocardia asteroides |
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Alotaibi, F.; Lee, S.-J.; Lahrach, Z.; St-Arnaud, M.; Hijri, M. Draft Genome of Nocardia canadensis sp. nov. Isolated from Petroleum-Hydrocarbon-Contaminated Soil. Microorganisms 2023, 11, 2972. https://doi.org/10.3390/microorganisms11122972
Alotaibi F, Lee S-J, Lahrach Z, St-Arnaud M, Hijri M. Draft Genome of Nocardia canadensis sp. nov. Isolated from Petroleum-Hydrocarbon-Contaminated Soil. Microorganisms. 2023; 11(12):2972. https://doi.org/10.3390/microorganisms11122972
Chicago/Turabian StyleAlotaibi, Fahad, Soon-Jae Lee, Zakaria Lahrach, Marc St-Arnaud, and Mohamed Hijri. 2023. "Draft Genome of Nocardia canadensis sp. nov. Isolated from Petroleum-Hydrocarbon-Contaminated Soil" Microorganisms 11, no. 12: 2972. https://doi.org/10.3390/microorganisms11122972
APA StyleAlotaibi, F., Lee, S. -J., Lahrach, Z., St-Arnaud, M., & Hijri, M. (2023). Draft Genome of Nocardia canadensis sp. nov. Isolated from Petroleum-Hydrocarbon-Contaminated Soil. Microorganisms, 11(12), 2972. https://doi.org/10.3390/microorganisms11122972