Genomic Insights into Denitrifying Methane-Oxidizing Bacteria Gemmobacter fulva sp. Nov., Isolated from an Anabaena Culture
Abstract
:1. Introduction
2. Material and Methods
2.1. Isolation and Culture Conditions of the Strains
2.2. Morphological, Physiological, and Chemotaxonomic Characteristics
2.3. Phylogenetic and Genomic Analyses
3. Results and Discussion
3.1. Physiological Tests
3.2. Phylogenetic and Genomic Analysis: The Taxonomic Status
3.3. Genome Properties
3.4. Genome Analyses for Denitrification and Methane Oxidation
4. Conclusions
5. Nucleotide Sequence Accession Numbers
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Characteristics | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Isolation source | Anabaena culture | Anabaena culture | snow sample | forest pond | tidal flat | freshwater |
Colony color | yellow | yellow | yellowish brown | colorless | cream | creamy white |
NaCl tolerance range (w/v%) | 0–2.0 | 0 | 0–4.0 | 0–2.0 | 0–7.0 | 0–1.0 |
Indole production | − | − | − | + | − | − |
Gelatin hydrolysis | + | + | − | − | + | − |
Carbon utilization: | ||||||
N-Acetyl-glucosamine | + | + | + | − | + | − |
Adipate | − | − | − | − | − | − |
l-Arabinose | − | − | + | − | + | − |
Caprate | − | − | − | − | − | − |
Citrate | − | − | − | − | + | − |
Gluconate | − | − | + | − | − | − |
d-Glucose | + | + | + | − | + | + |
Malate | + | + | + | − | + | − |
Maltose | + | + | + | − | + | − |
d-Mannitol | + | + | + | − | + | + |
d-Mannose | + | + | + | − | + | − |
Phenyl acetate | − | − | − | − | + | − |
Enzyme activity: | ||||||
N-Acetyl-β-glucosaminidase | − | − | − | − | − | + |
Acid phosphatase | − | − | + | + | + | + |
Alkaline phosphatase | − | − | + | + | + | + |
Cystine arylamidase | − | − | − | + | − | + |
β-Galactosidase | − | − | − | + | + | + |
β-Glucosidase | − | − | − | + | − | + |
Lipase (C14) | − | − | − | + | − | + |
Valine arylamidase | − | − | − | + | − | + |
Major polar lipids | PG, PE, PC, GL | PG, PE, PC, GL | PG, PE, PC, GL, AL | PG, PE, PC, PL | PG, PE, PC, L | PG, PE, PC, AL |
DNA G + C content (mol%) | 64.1 | 64.1 | 69.1 | 65.1 | 65.6 | 61.5 |
No. | Strains | 1. con5T (%) | 2. con4 (%) | ||||
---|---|---|---|---|---|---|---|
16S rDNA | ANI | dDDH | 16S rDNA | ANI | dDDH | ||
1 | Gemmobacter sp. con5T (CP076361-CP076367) | – | – | – | – | – | – |
2 | Gemmobacter sp. con4 (JAHHWR000000000) | 100 | 99.99 | 98.29 | – | – | – |
3 | Gemmobacter aestuarii CC-PW-75T (SSND00000000) | 94.9 | 75.85 | 22.62 | 94.9 | 75.85 | 22.67 |
4 | Gemmobacter aquaticus A1-9T (VOAK00000000) | 96.4 | 76.46 | 21.81 | 96.4 | 76.45 | 21.86 |
5 | Gemmobacter aquatilis DSM 3857T (FOCE00000000) | 97.9 | 80.49 | 19.03 | 97.9 | 80.61 | 19.07 |
6 | Gemmobacter caeni CGMCC 1.7745T (VLLH00000000) | 96.4 | 78.22 | 20.76 | 96.4 | 78.16 | 20.89 |
7 | Gemmobacter caeruleus N8T (VKKX00000000) | 96.0 | 78.59 | 20.61 | 96.0 | 78.62 | 20.64 |
8 | Gemmobacter changlensis JA139T (PZKG00000000) | 97.7 | 75.84 | 21.99 | 97.7 | 75.79 | 22.07 |
9 | Gemmobacter lanyuensis KCTC 23714T (BMYQ00000000) | 96.2 | 77.76 | 21.35 | 96.2 | 77.69 | 21.39 |
10 | Gemmobacter lutimaris YJ-T1-11T (QXXQ00000000) | 97.4 | 78.57 | 20.54 | 97.4 | 78.42 | 20.68 |
11 | Gemmobacter megaterium DSM 26375T (FTOT00000000) | 95.6 | 73.82 | 22.49 | 95.6 | 73.76 | 22.59 |
12 | Gemmobacter nanjingensis KCTC 23298T (BMYI00000000) | 95.8 | 78.16 | 20.68 | 95.8 | 78.31 | 20.74 |
13 | Gemmobacter nectariphilus DSM 15620T (AUCM00000000) | 95.3 | 74.69 | 22.11 | 95.3 | 74.82 | 22.17 |
14 | Gemmobacter serpentinus HB-1T (WCHR00000000) | 96.6 | 77.38 | 21.15 | 96.6 | 77.42 | 21.22 |
15 | Gemmobacter straminiformis CAM-8T (JACLQD000000000) | 95.9 | 75.20 | 22.16 | 95.9 | 75.12 | 22.24 |
16 | Gemmobacter tilapiae KCTC 23310T (BMYJ00000000) | 97.3 | 73.41 | 23.00 | 97.3 | 73.63 | 23.15 |
Genus Name | Gemmobacter |
---|---|
Species name | Gemmobacter fulva |
Species epithet | fulva |
Species status | sp. nov. |
Species etymology | ful′va. L. fem. adj. fulva tawny, yellowish brown, the color of the colonies |
Description of the new taxon and diagnostic traits | Gram- negative, non-motile, aerobic, and rod-shaped. The colonies appeared yellow, convex, circular, and smooth, with entire edges, after being grown for two days at 30 °C on R2A agar. The temperatures range for growth is 4 to 37 °C, with an optimum 30 °C; the pH range for growth is pH 5–10, with an optimum at pH 7. Oxidase and catalase activities are present. In the API 20 NE test, it is positive for the urease, hydrolysis of aesculin, and gelatin and the assimilation of N-acetyl-glucosamine, d-glucose, d-mannitol, d-mannose, malate and maltose but negative for the rest. In the API ZYM test, it is positive for the esterase (C4), esterase lipase (C8), α-glucosidase, leucine arylamidase, and naphthol-AS-BI-phosphohydrolase but negative for the rest. NaCl concentration range for growth is 0–2%, with an optimum at 0%. The cells were found to be susceptible to amikacin (30 µg mL−1), ampicillin/sulbactam (1:1; µg mL−1), chloramphenicol (30 µg mL−1), erythromycin (30 µg mL−1), gentamicin (30 µg mL−1), kanamycin (30 µg mL−1), nalidixic acid (30 µg mL−1), rifampicin (30 µg mL−1), spectinomycin (25 µg mL−1), streptomycin (25 µg mL−1), teicoplanin (30 µg mL−1), tetracycline (30 µg mL−1), and vancomycin (30 µg mL−1) but resistant to lincomycin (15 µg mL−1).Major fatty acids are summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). The major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, two unidentified glycolipids (GL1, GL2), and an unidentified aminophospholipid. The major respiratory quinone is Q-10. |
Country of origin | South Korea |
Region of origin | Sangju |
Source of isolation | Anabaena culture |
Sampling date (dd/mm/yyyy) | 03/2020 |
Latitude (xx◦xx xx N/S) | – |
Longitude (xx◦xx xx E/W) | – |
16S rRNA gene accession nr. | MZ317889 (con5T) and MZ317888 (con4) |
Genome accession number [RefSeq; EMBL;] | con5T, CP076361–CP076367; con4, JAHHWR000000000 |
Genome status | Complete for type strain, but incomplete for non-type strain |
Genome size | 4,677,627 (con5T), 4,576,129 (con4) |
GC mol% | 64.1% (con5T), 64.1% (con4) |
Number of strains in study | 2 |
Source of isolation of non-type strains | Anabaena culture |
Designation of the Type strain | con5T |
Strain collection numbers | KCTC 82247T = JCM 34791T |
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Jin, L.; Jin, C.-Z.; Lee, H.-G.; Lee, C.S. Genomic Insights into Denitrifying Methane-Oxidizing Bacteria Gemmobacter fulva sp. Nov., Isolated from an Anabaena Culture. Microorganisms 2021, 9, 2423. https://doi.org/10.3390/microorganisms9122423
Jin L, Jin C-Z, Lee H-G, Lee CS. Genomic Insights into Denitrifying Methane-Oxidizing Bacteria Gemmobacter fulva sp. Nov., Isolated from an Anabaena Culture. Microorganisms. 2021; 9(12):2423. https://doi.org/10.3390/microorganisms9122423
Chicago/Turabian StyleJin, Long, Chun-Zhi Jin, Hyung-Gwan Lee, and Chang Soo Lee. 2021. "Genomic Insights into Denitrifying Methane-Oxidizing Bacteria Gemmobacter fulva sp. Nov., Isolated from an Anabaena Culture" Microorganisms 9, no. 12: 2423. https://doi.org/10.3390/microorganisms9122423
APA StyleJin, L., Jin, C.-Z., Lee, H.-G., & Lee, C. S. (2021). Genomic Insights into Denitrifying Methane-Oxidizing Bacteria Gemmobacter fulva sp. Nov., Isolated from an Anabaena Culture. Microorganisms, 9(12), 2423. https://doi.org/10.3390/microorganisms9122423