Pan-Genome Analyses of the Genus Cohnella and Proposal of the Novel Species Cohnella silvisoli sp. nov., Isolated from Forest Soil
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strain Isolation and Cultivation
2.2. 16S rRNA Gene Sequence and Phylogenetic Analysis
2.3. Morphological, Physiological, and Biochemical Characteristics
2.4. Chemotaxonomic Properties
2.5. Genome Sequencing, Annotation, and Pan-Genomic Analysis
2.6. OGRI Calculation and Phylogenomic Analysis
3. Results
3.1. Phylogenetic Analysis Based on 16S rRNA Genes and Genomic Sequences
3.2. Physiological Characterization
3.3. Chemotaxonomic Analysis
3.4. Genomic Characteristics and OGRI Values
3.5. Pan-Genome Analysis of the Genus Cohnella
4. Discussion
5. Description of Cohnella silvisoli sp. nov.
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
GDMCC | Guangdong Microbial Culture Collection Center |
JCM | Japan Collection of Microorganism |
LMG | Belgian Co-ordinated Collections of Micro-organisms |
NRRL | Agricultural Research Service Culture Collection |
ANI | Average Nucleotide Identity |
dDDH | the Digital DNA-DNA Hybridization |
UBCG | Up-to-date Bacterial Core Gene set |
DPG | diphosphatidylglycerol |
PE | phosphatidylethanolamine |
PG | phosphatidylglycerol |
APL | unidentified aminophospholipid |
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Characteristics | NL03-T5T | NL03-T5-1 | C. abietis HS21T [32] | C. lupini LMG 27416T | C. arctica NRRL B-59459T |
---|---|---|---|---|---|
Isolation source | soil | soil | soil | root nodules of Lupinus albus | soil |
Colony colour | white-cream | white-cream | white | orange | white-cream |
Oxidase | − | − | + | + | + |
Catalase | − | − | − | + | + |
Growth at 37 °C | w | + | − | − | − |
Temperature range | 10–37 | 10–37 | 4–30 | 10–35 | 10–35 |
pH range | 5.0–8.5 | 5.0–8.5 | 6–8 | 5.5–8.5 | 5.0–9.0 |
Growth on media: | |||||
Reasoner’s 2A | + | + | + | − | + |
NA | − | − | + | + | − |
Hydrolysis of: | |||||
Gelatin | + | + | − | + | + |
Tweens 20 | + | + | ND | − | − |
Assimilation of: | |||||
Mannitol | + | + | + | − | + |
N-Acetyl-D-glucosamine | + | + | + | − | + |
Gluconate | + | + | − | − | + |
Capric acid | − | + | − | − | + |
Enzyme activities: | |||||
Esterase (C8) | + | + | ND | − | + |
β-Glucosidase | + | − | ND | + | + |
α-Mannosidase | + | + | ND | − | − |
GC content (mol%) | 49.2 | 49.2 | 44.8 | 50.7 | 50.3 |
Fatty Acid | 1 | 2 | 3 | 4 |
---|---|---|---|---|
anteiso-C13:0 | 1.6 | 4.3 | - | 2.1 |
iso-C14:0 | 3.7 | 2.7 | 1.1 | 2.6 |
C14:0 | 1.3 | 1.6 | 2.3 | 3.3 |
iso-C15:0 | 5.5 | 6.0 | 2.1 | 2.1 |
anteiso-C15:0 | 50.7 | 50.9 | 42.2 | 44.7 |
C16:0 | 7.2 | 9.9 | 22.0 | 14.5 |
alcohol-C16:1 ω7c | - | - | 6.5 | - |
C16:1 ω11c | - | - | 7.0 | - |
iso-C16:0 | 21.2 | 13.7 | 6.9 | 18.0 |
iso-C17:0 | 1.9 | 2.4 | 1.2 | - |
anteiso-C17:0 | 4.0 | 3.2 | 5.2 | 4.1 |
C17:0 | - | - | - | 2.1 |
C18:0 | - | - | - | 1.4 |
Summed feature 8 | - | - | - | 1.4 |
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Wang, C.; Mao, L.; Bao, G.; Zhu, H. Pan-Genome Analyses of the Genus Cohnella and Proposal of the Novel Species Cohnella silvisoli sp. nov., Isolated from Forest Soil. Microorganisms 2023, 11, 2726. https://doi.org/10.3390/microorganisms11112726
Wang C, Mao L, Bao G, Zhu H. Pan-Genome Analyses of the Genus Cohnella and Proposal of the Novel Species Cohnella silvisoli sp. nov., Isolated from Forest Soil. Microorganisms. 2023; 11(11):2726. https://doi.org/10.3390/microorganisms11112726
Chicago/Turabian StyleWang, Chunling, Lutian Mao, Gegen Bao, and Honghui Zhu. 2023. "Pan-Genome Analyses of the Genus Cohnella and Proposal of the Novel Species Cohnella silvisoli sp. nov., Isolated from Forest Soil" Microorganisms 11, no. 11: 2726. https://doi.org/10.3390/microorganisms11112726