Genome Analysis of Endobacterium cerealis, a Novel Genus and Species Isolated from Zea mays Roots in North Spain
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strain Isolation
2.2. 16S rRNA Gene Phylogenetic Analysis
2.3. Genome Sequencing, Assembling, Annotation and Analysis
2.4. Fatty Acid Analysis and Phenotypic Characterization
3. Results
3.1. 16S rRNA Gene Phylogenetic Analysis
3.2. Genome Analyses
3.2.1. Genome Properties
3.2.2. Genome Mining
3.2.3. Genetic Relatedness and Pangenome Analysis
3.3. Fatty Acid Analysis and Phenotypic Characterization
4. Discussion
5. Conclusions
6. Description of Endobacterium gen. nov.
7. Description of Endobacterium cerealis sp. nov.
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Attributes | E. cerealis RZME27T | P. pelagicum RI-200B4T | N. galegae HAMBI 540T | R. leguminosarum USDA 2370T |
---|---|---|---|---|
Sequence size (bp) | 6,114,623 | 5,134,606 | 6,455,027 | 7,851,935 |
Number of contigs | 51 | 62 | 2 | 108 |
GC content (%) | 58.8 | 62.8 | 61.3 | 60.6 |
Longest contig size | 649,048 | 392,382 | 4,647,962 | 1,820,721 |
Shortest contig size | 285 | 4118 | 1,807,065 | 502 |
N50 value | 345,671 | 184,300 | 4,647,962 | 413,138 |
L50 value | 7 | 11 | 1 | 5 |
Total number of genes | 5893 | 4509 | 6248 | 7753 |
Total CDSs | 5836 | 4458 | 6,181 | 7699 |
Number of coding sequences/CDSs (with protein) | 5705 | 4417 | 6014 | 7312 |
Pseudogenes | 131 | 41 | 167 | 387 |
Number of RNAs (tRNAs, rRNAs, ncRNAs) | 57 (49, 4, 4) | 51 (47, 3, 1) | 67 (51, 9, 7) | 54 (46, 4, 4) |
Species | RZME27T | HAMBI 540T | R1-200B4T | USDA 2370T | WS11T | DSM 29853T | DSM 25528T | DSM 18401T | Casida AT | ORS 992T | LMG 140T | H152T |
---|---|---|---|---|---|---|---|---|---|---|---|---|
RZME17T | 100 | |||||||||||
HAMBI 540T | 75.61 | 100 | ||||||||||
R1-200B4T | 75.09 | 75.40 | 100 | |||||||||
USDA 2370T | 73.34 | 74.49 | 73.03 | 100 | ||||||||
WS11T | 70.91 | 70.23 | 70.69 | 70.24 | 100 | |||||||
DSM 29853T | 72.78 | 72.34 | 73.02 | 72.56 | 70.75 | 100 | ||||||
DSM 25528T | 73.82 | 73.47 | 74.19 | 73.15 | 70.87 | 73.33 | 100 | |||||
DSM 18401T | 73.14 | 73.53 | 73.40 | 73.92 | 71.08 | 73.55 | 73.70 | 100 | ||||
Casida AT | 72.75 | 73.20 | 73.03 | 73.64 | 70.87 | 72.82 | 73.04 | 76.03 | 100 | |||
ORS 992T | 72.97 | 72.70 | 72.65 | 72.81 | 69.94 | 72.50 | 73.27 | 72.75 | 72.23 | 100 | ||
DSM 30147T | 74.30 | 73.77 | 73.39 | 73.29 | 70.10 | 72.26 | 73.11 | 73.20 | 72.63 | 72.76 | 100 | |
H152T | 72.90 | 73.17 | 72.73 | 74.57 | 70.70 | 72.57 | 72.97 | 75.43 | 75.74 | 71.96 | 72.52 | 100 |
Fatty Acid * | E. cerealis RZME27T | N. galegae HAMBI 540T | P. pelagicum R1-200B4T | R. leguminosarum USDA 2370T |
---|---|---|---|---|
C16:0 | 8.86 | 11.58 | 7.69 | 7.18 |
C17:0 | 0.10 | 1.91 | nd | nd |
C18:0 | 2.08 | 2.28 | 2.26 | 12.71 |
C16:0 3OH | 2.14 | 2.54 | nd | nd |
C18:0 3OH | 1.30 | 1.60 | 1.49 | 0.99 |
C18:1ω7c 11-methyl | 0.38 | 0.55 | 3.04 | 7.06 |
C19:0 cyclo ω8c | nd | 10.76 | 4.37 | 3.74 |
Summed feature 2 1 | 5.18 | 4.63 | 4.41 | 3.59 |
Summed feature 3 2 | 1.78 | 0.63 | 1.49 | 1.19 |
Summed feature 8 3 | 77.70 | 61.14 | 73.84 | 62.77 |
Characteristics | E. cerealis RZME27T | N. galegae HAMBI 540T | P. pelagicum R1-200B4T | R. leguminosarum USDA 2370T |
---|---|---|---|---|
Colony colour (on YMA) | white | white-pink | white | white-cream |
Nitrate reduction | + | − | + | − |
Growth in 1% NaCl | + | + | + | − |
Growth in 4% NaCl | + | − | + | − |
Growth in 7% NaCl | − | − | + | − |
Growth at 37 °C | w | + | + | − |
Assimilation of (API 20NE): | ||||
Malate | + | + | − | w |
Assimilation of (API 32GN): | ||||
l-rhamnose | + | − | + | + |
d-ribose | w | + | − | + |
Inositol | + | + | − | + |
Melibiose | + | + | − | + |
5-keto-gluconate | + | + | + | − |
2-keto-gluconate | − | − | w | − |
Propionate | + | − | − | − |
3-hydroxybutyrate | − | − | − | + |
l-histidine | + | + | − | + |
l-alanine | w | + | w | − |
l-serine | − | − | + | − |
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Menéndez, E.; Flores-Félix, J.D.; Ramírez-Bahena, M.H.; Igual, J.M.; García-Fraile, P.; Peix, A.; Velázquez, E. Genome Analysis of Endobacterium cerealis, a Novel Genus and Species Isolated from Zea mays Roots in North Spain. Microorganisms 2020, 8, 939. https://doi.org/10.3390/microorganisms8060939
Menéndez E, Flores-Félix JD, Ramírez-Bahena MH, Igual JM, García-Fraile P, Peix A, Velázquez E. Genome Analysis of Endobacterium cerealis, a Novel Genus and Species Isolated from Zea mays Roots in North Spain. Microorganisms. 2020; 8(6):939. https://doi.org/10.3390/microorganisms8060939
Chicago/Turabian StyleMenéndez, Esther, Jose David Flores-Félix, Martha Helena Ramírez-Bahena, Jose M. Igual, Paula García-Fraile, Alvaro Peix, and Encarna Velázquez. 2020. "Genome Analysis of Endobacterium cerealis, a Novel Genus and Species Isolated from Zea mays Roots in North Spain" Microorganisms 8, no. 6: 939. https://doi.org/10.3390/microorganisms8060939