Genomic and Phylogenetic Characterization of Rhodopseudomonas infernalis sp. nov., Isolated from the Hell Creek Watershed (Nebraska)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Isolation and Cultivation
2.2. DNA Purification
2.3. Next Generation Sequencing
2.4. Whole Genome Comparison
2.5. 16S rDNA Phylogenetic Comparison
3. Results and Discussion
3.1. Morphology and Photopigments
3.2. Physiological Characteristics
3.3. Genome Sequence
3.4. Whole Genome-Based Phylogenetic Analysis
3.5. Photosynthetic Gene Cluster
3.6. Growth and Respiration Genes
3.7. Nitrogen Fixation and Hydrogen Production
3.8. Aromatic Compound Degradation
3.9. Antibiotic Resistance
3.10. Description of Rhodopseudomonas infernalis sp. nov.
4. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Characteristic | Strain HC1 | Rps. palustris DSM123 | Rps. julia DSM11549 | Rps. rhenobacensis Rb | |
---|---|---|---|---|---|
cell shape | Rod | Rod | Rod | Rod | |
Cell width (um) | 0.2–0.5 | 0.8–1.2 | 1.0–1.5 | 0.5–0.8 | |
Cell length (um) | 1.2–2.0 | 2.0–3.0 | 2.5 | 1.5–2.0 | |
Motility | + | + | + | + | |
pH optimum | 7–7.5 | 6–9 | 6–6.5 | 5–8 | |
G+C content (mol%) | 65.3 * | 64.1 * | 63.5 | 65.4 | |
Abs. maxima near IR (nm) | 806, 859 | 800, 861–863 | 803, 850 | 805, 878 | |
Organic carbon sources: | |||||
Propionate | - | + | + | - | |
Citrate | - | (+) | - | - | |
Malate | + | + | + | + | |
Tartrate | + | - | - | + | |
D-Gluconate | + | + | nd | + | |
L-Aspartate | + | - | + | nd | |
L-Glutamate | + | - | - | - | |
Casamino acids | + | + | nd | nd | |
L-Arginine | + | - | nd | - | |
Benzoate | - | + | - | - | |
D-Glucose | (+) | (+) | + | - | |
D-Fructose | - | (+) | + | - | |
Fumarate | + | + | + | + | |
Isolation source | Pond water | Lake sediment | Acidic sulfide spring | Eutrophic pond |
Rps rutila DSM 126 | |||||||||||||||||||
97.6 | Rps rutila TIE-1 | ||||||||||||||||||
97.3 | 97.3 | Rps rutila R1T | |||||||||||||||||
88.3 | 88.2 | 88.3 | Rps pantothenatexigens JA575T | ||||||||||||||||
88.3 | 88.2 | 88.2 | 100 | Rps thermotolerans JA576T | |||||||||||||||
88.4 | 88.3 | 88.4 | 89.6 | 89.6 | Rps sp. DX1 | ||||||||||||||
88.1 | 88 | 88.1 | 89.3 | 89.3 | 88 | Rps sp. XCP | |||||||||||||
82 | 82.8 | 82.1 | 82.3 | 82.3 | 82.1 | 82.1 | Rps sp. AAP120 | ||||||||||||
81.6 | 81.5 | 81.6 | 82.1 | 82.1 | 81.8 | 81.6 | 87.1 | Rps sp. ATH 2.1.18 | |||||||||||
81.7 | 81.6 | 81.6 | 82 | 82 | 81.7 | 81.7 | 86.9 | 87.9 | Rps infernalis HC1 | ||||||||||
81.8 | 81.7 | 81.8 | 82.3 | 82.4 | 82.3 | 81.8 | 84 | 83.9 | 83.8 | Rps sp. HaA2 | |||||||||
81.2 | 81.1 | 81.2 | 81.6 | 81.6 | 81.3 | 81.2 | 83.3 | 82.9 | 83.1 | 85.6 | Rps palustris DSM 123T | ||||||||
81.4 | 81.6 | 81.4 | 81.8 | 81.8 | 81.5 | 81.1 | 83.6 | 83 | 83.1 | 85.7 | 98.2 | Rps palustrus BisB5 | |||||||
81 | 81 | 81.1 | 81.5 | 81.5 | 81.1 | 81.3 | 81.9 | 81.6 | 81.3 | 81.1 | 80.5 | 80.4 | Rps sp. B29 | ||||||
78.4 | 78.2 | 78.4 | 78.7 | 78.7 | 78.6 | 78.2 | 78.5 | 78.5 | 78.4 | 79.2 | 79.2 | 79.4 | 77.9 | Rps sp. BisA53 | |||||
77.9 | 77.8 | 77.8 | 78.3 | 78.2 | 78 | 77.7 | 77.8 | 77.8 | 77.3 | 78.3 | 77.9 | 78.2 | 77.5 | 80.9 | Rps faecalis JCM 11668T | ||||
78.6 | 78.8 | 78.7 | 78.9 | 78.9 | 78.6 | 78.6 | 78.9 | 78.9 | 78.6 | 79.6 | 79.4 | 79.5 | 78.5 | 81.2 | 79.3 | Rps. rhenobacensis DSM 12706 | |||
78.2 | 78.1 | 78.2 | 78.5 | 78.5 | 78.4 | 77.9 | 78.3 | 78.4 | 78.1 | 79.2 | 79 | 79.2 | 77.9 | 81.4 | 79.3 | 89.3 | Rps sp. BisB18 | ||
78.6 | 78.5 | 78.6 | 79 | 79 | 78.7 | 78.7 | 79.1 | 78.8 | 78.7 | 80 | 79.4 | 79.7 | 78.2 | 79.5 | 77.8 | 80.5 | 80.7 | Rps sp. BAL398 |
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Humphrey, C.E.; Burnett, N.; Dubey, S.; Kyndt, J.A. Genomic and Phylogenetic Characterization of Rhodopseudomonas infernalis sp. nov., Isolated from the Hell Creek Watershed (Nebraska). Microorganisms 2022, 10, 2024. https://doi.org/10.3390/microorganisms10102024
Humphrey CE, Burnett N, Dubey S, Kyndt JA. Genomic and Phylogenetic Characterization of Rhodopseudomonas infernalis sp. nov., Isolated from the Hell Creek Watershed (Nebraska). Microorganisms. 2022; 10(10):2024. https://doi.org/10.3390/microorganisms10102024
Chicago/Turabian StyleHumphrey, Christine E., Nicole Burnett, Shivangi Dubey, and John A. Kyndt. 2022. "Genomic and Phylogenetic Characterization of Rhodopseudomonas infernalis sp. nov., Isolated from the Hell Creek Watershed (Nebraska)" Microorganisms 10, no. 10: 2024. https://doi.org/10.3390/microorganisms10102024