A New Thioalkalivibrio sp. Strain Isolated from Petroleum-Contaminated Brackish Estuary Sediments: A New Candidate for Bio-Based Application for Sulfide Oxidation in Halo-Alkaline Conditions
Abstract
:1. Introduction
2. Materials and Methods
2.1. Total Petroleum Hydrocarbon Quantification in Sediments
2.2. Isolation of Thioalkalivibrio sp. 10fs10
2.3. Thioalkalivibrio sp. 10fs10 Genome Sequencing
2.4. Taxonomic Characterisation of the Thioalkalivibrio sp. 10fs10
2.5. Maximum Likelihood Tree Based on Multi-Locus Sequence (MLS) Analysis
2.6. Classification of Thioalkalivibrio sp. 10fs10 by ANI-BBH, dDDH, and Genome Taxonomy Database
2.7. Thioalkalivibrio sp. 10fs10 Growth in Halo-Alkaline Conditions
2.8. Thioalkalivibrio sp. 10fs10 Hydrogen Sulfide Oxidation Kinetics
3. Results
3.1. Thioalkalivibrio sp. 10fs10 Strain Isolation and Phylogenetic Characterisation
3.2. Genome Properties
3.3. Halo-Alkaline Condition of Growth
3.4. Thioalkalivibrio sp. 10fs10 Capacity of Hydrogen Sulfide Oxidation in Halo-Alkaline Growth Conditions
3.5. Thioalkalivibrio sp. 10fs10 Genome Sequencing and Annotation
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Genomes | ANI-BBH | dDDH | |||||
---|---|---|---|---|---|---|---|
Reference genome | ANI 1->2 | ANI 2->1 | AF 1->2 | AF 2->1 | Estimated DDH value (%) | PdDDH>70% | PdDDH>79% |
Tv. sulfidiphilus HL-EbGR7 | 95.52 | 95.52 | 78.39 | 80.31 | 56.8–62.4 | 51.07% | 12.52% |
Tv. sulfidiphilus ALJ17 | 94.33 | 94.33 | 82.68 | 73.67 | 49.1–54.4 | 24.30% | 5.08% |
Genome Properties | Value |
---|---|
Total scaffolds | 17 |
Length | 3.42 Mbp |
G + C content | 64.95% |
Total DNA coding region | 3243 |
Protein coding region | 3175 |
rRNA genes | 3 (5S rRNA, 16S rRNA, 23s rRNA) |
tRNA | 52 |
tmRNA | 1 |
Protein coding region with Pfam | 2966 |
Protein coding region with COG | 2241 |
Protein coding region with KEGG | 1656 |
Transmembrane protein coding gene | 781 |
CRISPR repeats | 2 |
Air Flow | 0.25 NL/min | 0.09 NL/min |
---|---|---|
Vmax (mmol/mg-N/h) | 2.648 | 0.745 |
KM (mM) | 2.438 | 4.547 |
Ki (mM) | 4.053 | 3.491 |
Parameters | Low Air Flow (0.018 NL/min) | High Air Flow (0.25 NL/min) |
---|---|---|
(HS-) initial (mM) | 5.21 | 6 |
Vox spec (mmol/(mg-N·h)) | 0.057 | 0.318 |
Biomass (mg-N/L) | 7.31 | 6.51 |
ΔpH | Negligible | −0.1 |
Elemental sulfur | Yes | no |
Gene | 10fs10 | HL-EbGr7 | ALJ17 |
---|---|---|---|
soxA | 3 | 4 | 4 |
soxX | 3 | 4 | 4 |
soxY | 2 | 1 | not found |
soxZ | 2 | 1 | 1 |
soxB | 1 | 1 | 1 |
soxC | 0 | 0 | 0 |
soxD | 0 | 0 | 0 |
fccA | 1 | 3 | 2 |
fccB | 1 | 3 | 2 |
dsrA | 1 | 1 | 1 |
dsrB | 1 | 1 | 1 |
dsrC | 1 | 1 | 1 |
aprA | 1 | 1 | 1 |
aprB | 1 | 1 | 1 |
sat | 2 | 1 | 1 |
hdrA | 1 | 1 | 1 |
hdrB | 2 | 1 | 1 |
hdrC | 2 | 1 | 1 |
sorA | 1 | 1 | 1 |
sor B | 1 | 1 | 1 |
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Becarelli, S.; La China, S.; Lapidus, A.; Prijibelski, A.; Polev, D.; Petroni, G.; Di Gregorio, S. A New Thioalkalivibrio sp. Strain Isolated from Petroleum-Contaminated Brackish Estuary Sediments: A New Candidate for Bio-Based Application for Sulfide Oxidation in Halo-Alkaline Conditions. Water 2020, 12, 1385. https://doi.org/10.3390/w12051385
Becarelli S, La China S, Lapidus A, Prijibelski A, Polev D, Petroni G, Di Gregorio S. A New Thioalkalivibrio sp. Strain Isolated from Petroleum-Contaminated Brackish Estuary Sediments: A New Candidate for Bio-Based Application for Sulfide Oxidation in Halo-Alkaline Conditions. Water. 2020; 12(5):1385. https://doi.org/10.3390/w12051385
Chicago/Turabian StyleBecarelli, Simone, Salvatore La China, Alla Lapidus, Andrey Prijibelski, Dmitrii Polev, Giulio Petroni, and Simona Di Gregorio. 2020. "A New Thioalkalivibrio sp. Strain Isolated from Petroleum-Contaminated Brackish Estuary Sediments: A New Candidate for Bio-Based Application for Sulfide Oxidation in Halo-Alkaline Conditions" Water 12, no. 5: 1385. https://doi.org/10.3390/w12051385