Physiological and Genomic Characterization of a Novel Obligately Chemolithoautotrophic, Sulfur-Oxidizing Bacterium of Genus Thiomicrorhabdus Isolated from a Coastal Sediment
Abstract
:1. Introduction
2. Materials and Methods
2.1. Enrichment and Isolation
2.2. DNA Extraction and Genomic Analyses
2.3. 16S rRNA Gene Phylogeny
2.4. Morphology, Physiology, and Chemotaxonomic Analysis
2.5. The Determination of Extracellular Sulfur via Scanning Electron Microscopy and Raman Spectromicroscopy
3. Results and Discussion
3.1. Phylogenetic Analysis Based on 16S rRNA Gene
3.2. Morphology, Physiology, and Chemotaxonomic Analysis
3.3. Genome Features and Central Metabolism among Genus Thiomicrorhabdus
3.4. Characterization of Extracellular Sulfur Produced by Thiomicrorhabdus Species with SEM, XRD, and Raman Spectroscopy
4. Conclusions
Description of Thiomicrorhabdus lithotrophica sp. nov
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Characteristic | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Shape | Rod | Rod | Rod | Rod | Rod |
G+C content (mol%) | 39.1 | 39.6 | 39.6 | 42.5 | 42.2 |
Maximum growth rate (h−1) | 0.15 | 0.40 | 0.45 | 0.20 | 0.14 |
Temperature range (°C) | 4.0–45.0 | 2.0–40.0 | 3.5–39.0 | −2.0–20.8 | −2.0–20.8 |
Optimal temperature (°C) | 30.0 | 30.0 | 25.0–32.0 | 14.6–15.4 | 11.5–13.2 |
Optimal Na+ concentration (mM) | 510 | 270 | 470 | 250 | 250 |
pH range | 5.0–9.0 | 5.0–8.0 | 4.2–8.5 | 6.5–9.0 | 6.5–9.0 |
Optimal pH | 7.0 | 6.0 | 6.5 | 7.5–8.5 | 7.3–8.0 |
Electron donor: | |||||
Thiosulfate | + | + | + | + | + |
Sulfide | + | + | + | + | + |
Elemental sulfur | + | + | + | + | + |
Sulfite | − | − | − | − | − |
Tetrathionate | + | + | + | + | + |
Hydrogen | − | + | − | − | − |
Fatty Acid | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Saturated: | ||||
C9:0 | 0.23 | ND | 1.11 | 2.85 |
C11:0 | 0.06 | ND | ND | 1.01 |
C12:0 | 0.43 | 1.00 | 1.63 | 1.08 |
C14:0 | 1.38 | 0.80 | 3.61 | 2.90 |
C16:0 | 15.97 | 16.90 | 27.03 | 25.65 |
C17:0 | ND | ND | 1.34 | 1.18 |
C18:0 | 5.91 | 1.90 | 33.79 | 29.42 |
C19:0 | 0.17 | ND | ND | 2.24 |
Unsaturated: | ||||
C16:1 | 6.90 | 44.40 | 3.60 | 3.17 |
C17:1 | 0.81 | ND | 4.87 | 3.17 |
C18:1 | 50.14 | 30.40 | 9.21 | 7.47 |
C18:2 | 0.56 | ND | 3.60 | 2.59 |
C18:3 | 0.42 | ND | 1.32 | 1.27 |
Hydroxy: | ||||
C8:0 3OH | 0.25 | ND | 0.68 | 0.57 |
C12:0 3OH | 5.01 | ND | 1.76 | 3.03 |
C18:1 2OH | 0.49 | ND | 4.25 | ND |
Characteristic | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Genome size (Mb) | 2.5 | 2.7 | 2.6 | 2.4 | 2.6 |
GC content (%) | 39.1 | 39.6 | 42.2 | 49.9 | 38.0 |
ANI | − | 71.1 | 70.1 | 70.4 | 71.5 |
Gene count | 2292 | 2526 | 2337 | 2285 | 2382 |
rRNA operons | 9 | 3 | 3 | 2 | 3 |
tRNA count | 47 | 45 | 45 | 43 | 46 |
Sox | ABCDXYZ | ABCDXYZ | ABCDXYZ | ABCDXYZ | ABCDXYZ |
Fcc | + | + | − | + | + |
Sqr | + | + | + | + | + |
TCA Cycle | + | + | + | + | + |
Pentose phosphate pathway | + | + | + | + | + |
Glycolysis/Gluconeogenesis | + | + | + | + | + |
Carboxysome | + | + | + | + | + |
Carbonic anhydrase | 1α-class, 1γ-class | 1α-class, 1γ-class, 1β-class | 1α-class, 1γ-class, 1β-class | 1α-class, 2γ-class | 1α-class, 1γ-class, 1β-class |
Nitrate reductase | − | + | − | − | − |
Nitrite reductase | − | + | − | + | − |
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Gao, Y.; Zhu, H.; Wang, J.; Shao, Z.; Wei, S.; Wang, R.; Cheng, R.; Jiang, L. Physiological and Genomic Characterization of a Novel Obligately Chemolithoautotrophic, Sulfur-Oxidizing Bacterium of Genus Thiomicrorhabdus Isolated from a Coastal Sediment. Microorganisms 2023, 11, 2569. https://doi.org/10.3390/microorganisms11102569
Gao Y, Zhu H, Wang J, Shao Z, Wei S, Wang R, Cheng R, Jiang L. Physiological and Genomic Characterization of a Novel Obligately Chemolithoautotrophic, Sulfur-Oxidizing Bacterium of Genus Thiomicrorhabdus Isolated from a Coastal Sediment. Microorganisms. 2023; 11(10):2569. https://doi.org/10.3390/microorganisms11102569
Chicago/Turabian StyleGao, Yu, Han Zhu, Jun Wang, Zongze Shao, Shiping Wei, Ruicheng Wang, Ruolin Cheng, and Lijing Jiang. 2023. "Physiological and Genomic Characterization of a Novel Obligately Chemolithoautotrophic, Sulfur-Oxidizing Bacterium of Genus Thiomicrorhabdus Isolated from a Coastal Sediment" Microorganisms 11, no. 10: 2569. https://doi.org/10.3390/microorganisms11102569
APA StyleGao, Y., Zhu, H., Wang, J., Shao, Z., Wei, S., Wang, R., Cheng, R., & Jiang, L. (2023). Physiological and Genomic Characterization of a Novel Obligately Chemolithoautotrophic, Sulfur-Oxidizing Bacterium of Genus Thiomicrorhabdus Isolated from a Coastal Sediment. Microorganisms, 11(10), 2569. https://doi.org/10.3390/microorganisms11102569