Insights into the Potential Role of Gordonia alkanivorans Strains in Biotechnologies †
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Cultivation Conditions
2.2. Genome Sequencing and Analysis
3. Results
3.1. Identifying the Strains
3.2. Physiological and Biochemical Characteristics of Strains
3.3. Osmoprotectant Metabolism
3.4. Pangenome Analysis
3.5. Features of the Genetic Organization of G. alkanivorans
3.5.1. Hydrocarbon Degradation Ability
3.5.2. Plasmids
3.5.3. Biosynthesis of Secondary Metabolites
- Terpene (SF2575 biosynthetic gene cluster: polyketide type II; carotenoid);
- Streptozotocin;
- Type I polyketide synthase;
- NRPS (non-ribosomal peptide synthetase);
- Non-alpha poly-amino acids (ε-Poly-L-lysine);
- Ectoine;
- Redox cofactor;
- NRPS-independent, IucA/IucC-like siderophores;
- Arylpolyene (primycin like most similar known cluster is found in all strains except for 134, 142, and 144, which do not exhibit similarity to this group).
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Strain | Collection Number | Isolation Source | Previously Identified As |
---|---|---|---|
96 | IEGM 96 | crude oil-contaminated soil, Ukraine | G. rubripertincta |
129 | IEGM 129 | crude oil-contaminated soil, Ivano-Frankovsk, Ukraine | G. rubripertincta |
132 | IEGM 132 | crude oil-contaminated soil, Ivano-Frankovsk, Ukraine | G. rubripertincta |
133 | IEGM 133 | crude oil-contaminated soil, Ivano-Frankovsk, Ukraine | G. rubripertincta |
134 | IEGM 134 | crude oil-contaminated soil, oilfield, Lvov, Ukraine | G. rubripertincta |
142 | IEGM 142 | crude oil-contaminated soil, Ukraine | G. rubripertincta |
144 | IEGM 144 | crude oil-contaminated soil, Lvov, Ukraine | G. terrae |
12 | - | oil-polluted soil, Moscow, Russia | G. alkanivorans |
152 | - | oil-polluted soil, Moscow, Russia | G. alkanivorans |
Strain | Read Pairs before Filtration | Read Pairs after Filtration | Read Pairs after Filtration (%) |
---|---|---|---|
96 | 2,962,813 | 2,835,521 | 95.70 |
129 | 3,147,953 | 3,003,848 | 95.42 |
132 | 4,354,967 | 4,162,088 | 95.57 |
133 | 5,192,473 | 5,019,737 | 96.67 |
134 | 5,815,565 | 5,558,107 | 95.57 |
142 | 3,330,918 | 3,171,608 | 95.22 |
144 | 5,382,881 | 5,150,561 | 95.68 |
12 | 9,985,963 | 8,692,673 | 87.05 |
152 | 6,985,286 | 4,928,247 | 70.55 |
Strain | ANI Value with the Type Strain of G. rubripertincta, % | DDH Value with the Type Strain of G. rubripertincta, % | ANI Value with the Type Strain of G. alkanivorans, % | DDH Value with the Type Strain of G. alkanivorans, % | Taxonomic Position of the Strain |
---|---|---|---|---|---|
96 | 92.58 | 76.20 | 98.45 | 89.70 | G. alkanivorans |
129 | 92.45 | 76.00 | 98.42 | 88.60 | G. alkanivorans |
132 | 92.40 | 76.30 | 98.42 | 88.60 | G. alkanivorans |
133 | 92.40 | 76.10 | 98.37 | 88.50 | G. alkanivorans |
134 | 92.25 | 76.80 | 98.23 | 87.60 | G. alkanivorans |
142 | 92.54 | 76.30 | 98.23 | 91.00 | G. alkanivorans |
144 | 92.42 | 66.80 | 98.63 | 78.10 | G. alkanivorans |
12 | 92.38 | 76.20 | 98.40 | 90.10 | G. alkanivorans |
152 | 92.48 | 76.60 | 98.34 | 88.00 | G. alkanivorans |
Strain | Alkanes C10–C16 | Alkanes C18–C20 | Benzoate | Phenol | Naphthalene | Catechol | DBT |
---|---|---|---|---|---|---|---|
96 | ++ | + | + | - | - | - | ± |
129 | + | + | + | - | - | - | - |
132 | + | + | + | - | - | - | ± |
133 | + | + | + | - | - | - | - |
134 | ++ | ++ | + | - | - | - | - |
142 | + | + | + | - | - | - | - |
144 | + | + | + | - | - | - | - |
12 | ++ | + | + | - | - | - | ± |
152 | ++ | + | + | - | - | - | - |
135 | ++ | ++ | + | - | - | - | + |
Strain | betA/codA | betB | betT | opuA | opuBD | opuC |
---|---|---|---|---|---|---|
96 | 1 | 4 | 1 | 1 | 2 | 2 |
129 | - | 5 | 1 | 1 | 3 | 2 |
132 | 1 | 3 | 1 | 1 | 2 | 2 |
133 | 1 | 3 | 1 | 1 | 2 | 2 |
134 | 1 | 3 | 1 | 1 | 2 | 2 |
142 | 1 | 4 | 1 | 1 | 2 | 2 |
144 | 1 | 3 | 1 | 1 | 2 | 2 |
12 | 1 | 4 | 1 | 1 | 2 | 2 |
152 | 1 | 3 | 1 | 1 | 2 | 2 |
Strain | Concentration of NaCl | |||
---|---|---|---|---|
1% | 3% | 7% | 10% | |
96 | + | + | + | + |
129 | + | ± | ± | - |
132 | + | + | - | - |
133 | + | + | ± | ± |
134 | + | + | - | - |
142 | + | + | - | - |
144 | + | ± | ± | - |
12 | + | + | - | - |
152 | + | + | ± | - |
Strain | Proteins | Clusters | Singletons |
---|---|---|---|
96 | 4446 | 4318 | 61 |
129 | 4380 | 4252 | 22 |
132 | 4521 | 4404 | 1 |
133 | 4520 | 4399 | 4 |
134 | 4587 | 4312 | 60 |
142 | 4530 | 4329 | 63 |
144 | 5390 | 4506 | 315 |
12 | 4480 | 4522 | 25 |
152 | 4421 | 4183 | 88 |
NBRC 16433 | 4445 | 4155 | 109 |
Strain | CYP153 |
---|---|
96 | 2 |
129 | 1 |
132 | 3 |
133 | 3 |
134 | 2 |
142 | 2 |
144 | 3 |
12 | 2 |
152 | 2 |
Strain | Most Similar Known Cluster | Similarity |
---|---|---|
96 | sarpeptin | 25% |
129 | ulbactin echoside | 28% 11% |
144 | cahuitamycin | 12% |
12 | leucomycin | 3% |
152 | icosalide | 100% |
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Frantsuzova, E.; Bogun, A.; Shishkina, L.; Vetrova, A.; Solyanikova, I.; Delegan, Y. Insights into the Potential Role of Gordonia alkanivorans Strains in Biotechnologies. Processes 2023, 11, 3184. https://doi.org/10.3390/pr11113184
Frantsuzova E, Bogun A, Shishkina L, Vetrova A, Solyanikova I, Delegan Y. Insights into the Potential Role of Gordonia alkanivorans Strains in Biotechnologies. Processes. 2023; 11(11):3184. https://doi.org/10.3390/pr11113184
Chicago/Turabian StyleFrantsuzova, Ekaterina, Alexander Bogun, Lidiya Shishkina, Anna Vetrova, Inna Solyanikova, and Yanina Delegan. 2023. "Insights into the Potential Role of Gordonia alkanivorans Strains in Biotechnologies" Processes 11, no. 11: 3184. https://doi.org/10.3390/pr11113184