Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Media
2.2. Environmental Samples for Phage Isolation
2.3. Phage Enrichment
2.4. Phage Isolation, Propagation and Purification
2.5. Negative Staining and Transmission Electron Microscopy (TEM)
2.6. Phage Genome Sequencing and Genetic Analysis
2.7. Phage Host Range
2.8. Phage Nomenclature and Nucleotide Sequence Accession Numbers
3. Results
3.1. Strategy to Isolate Xf-Specific Phages
3.2. Genomic Diversity of the Phages Isolated
3.3. Genomic Characterization
3.4. Morphological Characterization
3.5. Phylogenetic Analysis of the Sequenced Phage Genomes
3.6. Host Range Determination
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Strain/Genotype | Abbreviation | Collection Code | NCBI |
---|---|---|---|
Xylella fastidiosa subsp. fastidiosa | Xff | CFBP 7970 | PRJNA417585 |
Xylella fastidiosa subsp. pauca | Xfp | CFBP 8402 | PRJNA383475 |
Xylella fastidiosa subsp. multiplex | Xfm | CFBP 8418 | PRJNA314986 |
Xanthomonas albilineans | Xa | CFBP 2523 | PRJNA338244 |
Xanthomonas arboricola pv. juglandis | Xaj | CFBP 2528 | PRJNA275685 |
Xanthomonas citri pv. citri | Xcci | CFBP 3369 | PRJNA254373 |
Xanthomonas vesicatoria | Xv | CFBP 2537 | PRJNA60019 |
Xanthomonas campestris pv. campestris | Xcc | CFBP 5241 | PRJNA296 |
Xanthomonas translucens pv. cerealis | Xtc | CFBP 2541 | PRJNA268946 |
Phage Name | Full Nomenclature | Accession Number | Raw Sequence ID |
---|---|---|---|
FC03-Usme FC08-Olaya | Xylella phage Usme Xanthomonas phage Olaya | LR743523 MW802488 | ERR5548206 SRX10492030 |
FC12-Bacata FC15-Bolivar FC17-Usaquen | Xylella phage Bacata Xanthomonas phage Bolivar Xanthomonas phage Usaquen | LR743524 MW822535 MW822536 | ERR5548205 SRX10492031 SRX10492032 |
FC23-Cota FC25-Alcala | Xylella phage Cota Xanthomonas phage Alcala | LR778216 MW822537 | ERR5548199 SRX10492033 |
FC28-Sopo | Xanthomonas phage Sopo | LR743529 | ERR5548204 |
FC30-Tabio | Xanthomonas phage Tabio | LR743528 | ERR5548203 |
FC39-Tenjo | Xanthomonas phage Tenjo | LR743531 | ERR5548202 |
FC41-Suba | Xanthomonas phage Suba | LR743530 | ERR5548201 |
FC44-Bosa FC47-Fontebon FC57-Sumapaz | Xanthomonas phage Bosa Xanthomonas phage Fontebon Xanthomonas phage Sumapaz | LR743532 MW822538 MW822539 | ERR5548200 SRX10492034 SRX10492035 |
PCR Groups a | ||||||||
---|---|---|---|---|---|---|---|---|
Source | Conditions | Isolated Phages | Sequenced Phage Genomes | FC03 | FC44 | FC12 | FC23 | Potential New Phages |
Plant extracts | Enrichment on Xff | NA b | - | - | - | - | - | - |
Enrichment on Xfm | NA | - | - | - | - | - | - | |
Enrichment on Xa | NA | - | - | - | - | - | - | |
Insect extracts | Enrichment on Xff | 6 | LR743523 MW802488 | 6 | - | - | - | 0 |
Enrichment on Xfm | 6 | MW822538 MW822539 | 6 | - | - | - | 0 | |
Enrichment on Xa | 12 | MW822535 MW822536 | 11 | 1 | - | - | 0 | |
Sewage watersample | Enrichment on Xff | 6 | LR743524 (x2) c | - | 2 | 4 | - | 0 |
Enrichment on Xfm | 6 | LR778216 MW822537 | 1 | 1 | - | 3 | 1 | |
Direct plaquing on Xa | 12 | LR743531 LR743532 | 4 | 4 | 2 | - | 1 + LR743530 d | |
Runoff waters sample | Enrichment on Xff | NA | - | - | - | - | - | - |
Enrichment on Xfm | NA | - | - | - | - | - | - | |
Direct plaquing on Xa | 8 | LR743529 LR743528 | 4 | - | - | - | 4 |
Phage | Size (bp) | %GC | CDS | BLAST Nearest Organism | Coverage (%) | Identity (%) | E-Value | Order | Family | Genus | Specie |
---|---|---|---|---|---|---|---|---|---|---|---|
FC03-Usme a | 43721 | 66.6 | 58 | X. axonopodis phage CP2 | 83 | 92.11% | 0.0 | Caudovirales | Podovirus | Unclassified Podovirus | Usmevirus |
FC12-Bacata | 56232 | 62.9 | 73 | X. fastidiosa phage Salvo | 89 | 96.29% | 0.0 | Caudovirales | Siphovirus | Sanovirus | Bacatavirus |
FC23-Cota | 42307 | 58.8 | 52 | none | NA | NA | NA | NA | NA | NA | Tejovirus |
FC28-Sopo | 43861 | 66.9 | 58 | X. axonopodis phage CP2 | 82 | 93.96% | 0.0 | Caudovirales | Podovirus | Unclassified Podovirus | Bacatavirus |
FC30-Tabio | 43458 | 66.9 | 58 | X. axonopodis phage CP2 | 83 | 95.39% | 0.0 | Caudovirales | Podovirus | Unclassified Podovirus | Bacatavirus |
FC39-Tenjo | 43850 | 67.2 | 58 | X. axonopodis phage CP2 | 83 | 94.70% | 0.0 | Caudovirales | Podovirus | Unclassified Podovirus | Bacatavirus |
FC41-Suba | 45510 | 52.3 | 71 | none | NA | NA | NA | NA | NA | NA | Subavirus |
FC44-Bosa | 63828 | 64.8 | 81 | Stenotrophomonas phage DLP4 | 99% | 97.40 % | 0.0 | Caudovirales | Siphovirus | Unclassified Siphovirus | Bosavirus |
Phage | Head Shape & Diameter (nm) | Tail Shape & Length (nm) | Morphotype a | |
---|---|---|---|---|
FC03-Usme (n = 15) | Isometric, 61.7 ± 2 | *NA | Podovirus | C1 |
FC12-Bacata (n = 14) | Isometric, 66.5 ± 2 | Long, Flexible, 220.5 ± 5 | Siphovirus | B1 |
FC23-Cota (n = 14) | Isometric, 64.1 ± 1 | *NA | Podovirus | C1 |
FC24-Teja (n = 15) | Isometric, 65.3 ± 2 | *NA | Podovirus | C1 |
FC28-Sopo (n = 6) | Isometric, 65.4 ± 2 | *NA | Podovirus | C1 |
FC30-Tabio (n = 6) | Isometric, 63.6 ± 2 | *NA | Podovirus | C1 |
FC34-Cajica (n = 15) | Isometric, 64.4 ± 2 | *NA | Podovirus | C1 |
FC39-Tenjo (n = 6) | Isometric, 60.6 ± 2 | *NA | Podovirus | C1 |
FC41-Suba (n = 15) | Isometric, 61.2 ± 2 | Long, Flexible, 199.5 ± 4 | Siphovirus | B1 |
FC44-Bosa (n = 12) | Heterometric, 60.1 ± 1 × 88.8 ± 2 | Long, Flexible, 140.5 ± 7 | Siphovirus | B3 |
CFBP | Strain | FC03-Usme | FC12-Bacata | FC23-Cota | FC24-Teja | FC32-Tabio | FC34-Tenjo | FC41-Suba | FC44-Bosa |
---|---|---|---|---|---|---|---|---|---|
7970 | X. fastidiosa subsp. fastidiosa | ||||||||
8402 | X. fastidiosa subsp. pauca | ||||||||
8418 | X. fastidiosa subsp. multiplex | ||||||||
2523 | X. albilineans | ||||||||
2528 | X. arboricola pv. juglandis | ||||||||
3369 | X. citri pv. citri | ||||||||
2537 | X. vesicatoria | ||||||||
5241 | X. campestris pv. campestris | ||||||||
2541 | X. translucens pv. cerealis |
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Clavijo-Coppens, F.; Ginet, N.; Cesbron, S.; Briand, M.; Jacques, M.-A.; Ansaldi, M. Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans. Viruses 2021, 13, 725. https://doi.org/10.3390/v13050725
Clavijo-Coppens F, Ginet N, Cesbron S, Briand M, Jacques M-A, Ansaldi M. Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans. Viruses. 2021; 13(5):725. https://doi.org/10.3390/v13050725
Chicago/Turabian StyleClavijo-Coppens, Fernando, Nicolas Ginet, Sophie Cesbron, Martial Briand, Marie-Agnès Jacques, and Mireille Ansaldi. 2021. "Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans" Viruses 13, no. 5: 725. https://doi.org/10.3390/v13050725
APA StyleClavijo-Coppens, F., Ginet, N., Cesbron, S., Briand, M., Jacques, M.-A., & Ansaldi, M. (2021). Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans. Viruses, 13(5), 725. https://doi.org/10.3390/v13050725