Molecular Characterization and Taxonomic Assignment of Three Phage Isolates from a Collection Infecting Pseudomonas syringae pv. actinidiae and P. syringae pv. phaseolicola from Northern Italy
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Isolation
2.2. Sample Preparation, Phage Isolation, Amplification and Purification
2.3. Transmission Electron Microscopy
2.4. Host Range Assay
2.5. Influence of pH, Temperature, and UV Radiation to Phage Viability
2.6. Phage Genome Sequencing, Assembly, and Annotation
2.7. Phylogenetic Analysis
3. Results
3.1. Bacterial Isolation
3.2. Phage Isolation and Morphology
3.3. Phage Sequencing and Annotation
3.3.1. Genomic Characteristics of pphageB1
3.3.2. Genomic Characteristics of psageB1
3.3.3. Genomic Characteristics of psageA1
3.3.4. Genomic Characteristics of psageB2 and psageK9
3.3.5. Genomic Characteristics of psageK4
3.4. Phage Host Ranges
3.5. Phage Resistance to Abiotic Stresses
3.6. Phylogenetic Analysis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Identification | Origin | Geographical Origin | Source | Bacterial Strains | Year | pphageB1 | pphageB21 | pphageBV72 | pphage T12 | pphage T21 | psage A1 | psage K4 | psage K4e | psage B1 | psage B2 | MR8 | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | Agrion | K7#1 | 2019 | - | - | - | - | - | EOP | |||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | Agrion | K7#8 | 2019 | - | - | - | - | - | <0.01 | |||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | Agrion | K4#3 | 2018 | - | - | - | - | - | 0.01–0.1 | |||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | Agrion | K4#6 | 2018 | - | - | - | - | - | - | - | 0.1–1 | |||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | Agrion | K4#7 | 2018 | - | - | - | - | - | 1 | |||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | Agrion | K4#9 | 2018 | - | - | - | - | - | - | 1–10 | ||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | Agrion | K4#10 | 2018 | - | - | - | - | - | - | - | 10–100 | |||||
P.s. pv. actinidiae | Actinidia chinensis * | Veneto | PIS $ | #5712.19 | 2019 | - | - | - | - | - | >100 | |||||||
P.s. pv. actinidiae | Actinidia chinensis * | Veneto | PIS $ | #5726.19 | 2019 | - | - | - | - | - | - | - | ||||||
P.s. pv. actinidiae | Actinidia chinensis * | Veneto | PIS $ | #5747.19 | 2019 | - | - | - | - | - | ||||||||
P.s. pv. actinidiae | Actinidia chinensis * | Veneto | PIS $ | #5846.19 | 2019 | - | - | - | - | - | - | - | ||||||
P.s. pv. actinidiae | Actinidia chinensis * | Veneto | PIS $ | #5847.19 | 2019 | - | - | - | - | - | ||||||||
P.s. pv. actinidiae | Actinidia chinensis * | Veneto | PIS $ | #5850.19 | 2019 | - | - | - | - | - | ||||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | PIS $ | #298a | 2019 | - | - | - | - | - | - | - | ||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | PIS $ | #391a | 2018 | - | - | - | - | - | ||||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | PIS $ | #392a | 2018 | - | - | - | - | - | - | |||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | PIS $ | #453d | 2016 | - | - | - | - | - | - | - | ||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | PIS $ | #453e | 2016 | - | - | - | - | - | - | |||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | PIS $ | #454d | 2018 | - | - | - | - | - | - | - | ||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | PIS $ | #454e | 2018 | - | - | - | - | - | - | - | ||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | PIS $ | #509c | 2018 | - | - | - | - | - | ||||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | PIS $ | #509d | 2018 | - | - | - | - | - | ||||||||
P.s. pv. actinidiae | Actinidia chinensis * | Piedmont | PIS $ | #509e | 2018 | - | - | - | - | - | ||||||||
P.s. pv. phaseolicola | Phaseolus vulgaris | Piedmont | PIS $ | Pph PSS | 2015 | - | - | - | - | |||||||||
P.s. pv. phaseolicola | Phaseolus vulgaris | China | Private company | Pph #9 | 2015 | - | ||||||||||||
P.s. pv. phaseolicola | Phaseolus vulgaris | China | Private company | Pph #13 | 2015 | - | - | |||||||||||
P.s. pv. phaseolicola | Phaseolus vulgaris | China | Private company | Pph #14 | 2015 | - | - | |||||||||||
P.s. pv. phaseolicola | Phaseolus vulgaris | Piedmont | IPSP | Pph Cuneo | 2016 | - | - | - | ||||||||||
P.s. pv. phaseolicola | Phaseolus vulgaris | Piedmont | Agrion | Pph Cuneo #6_17 | 2017 | - | - | - | ||||||||||
P.s. pv. phaseolicola | Phaseolus vulgaris | Piedmont | Agrion | Pph Cuneo #6_18 | 2018 | - | - | |||||||||||
P.s. pv. phaseolicola | Phaseolus vulgaris | Piedmont | Agrion | Pph Cuneo #7 | 2018 | - | - | |||||||||||
P.s. pv. phaseolicola | Phaseolus vulgaris | Piedmont | Agrion | Pph Cuneo #13 | 2017 | - | - | - | ||||||||||
P. syringae | Water | France | INRAe | UB197 | 2010 | - | - | - | - | - | - | - | - | - | - | - | ||
P. syringae | Water | France | INRAe | UB210 | 2010 | - | - | - | - | - | - | - | - | - | - | |||
P. syringae | Water | France | INRAe | UB246 | 2010 | - | - | - | - | - | - | - | - | - | - | |||
P. syringae | Water | United States | INRAe | USA052 | 2010 | - | - | - | - | - | - | - | - | - | - | |||
P. syringae | Water | France | INRAe | CC1504 | 2010 | - | - | - | - | - | - | - | - | - | - | - | ||
P. syringae | Water | France | INRAe | SZ030 | 2010 | - | - | - | - | - | - | - | - | - | - | - | ||
P. syringae | Water | France | INRAe | SZ122 | 2010 | - | - | - | - | - | - | - | - | - | - | - | ||
P. syringae | Water | France | INRAe | SZ131 | 2010 | - | - | - | - | - | - | - | - | - | - | |||
P.s. pv. syringae | Prunus armeniaca | Lombardia | UNIMI | Pss ML#1 | 2018 | - | - | - | - | - | - | - | - | - | - | - |
Phage Name | Source | Origin a | Field Species and Cultivar | Source | Region | Year | Plaque Morphology (LBLS 0.6%) b | Classification c |
---|---|---|---|---|---|---|---|---|
psageK4 | Soil | Manta (CN) | Actinidia chinensis var. deliciosa | Agrion | Piedmont | 2018 | Clear, 1 mm | Myoviridae |
psageK4e | Soil | Manta (CN) | Actinidia chinensis var. deliciosa | Agrion | Piedmont | 2019 | Clear, 1 mm | Myoviridae |
psageK9 | Soil | Borgo d’Ale (VC) | Actinidia chinensis var. deliciosa | IPSP | Piedmont | 2019 | clear or turbid 2 mm | Siphoviridae |
psageA1 | Soil | Manta (CN) | Actinidia chinensis var. deliciosa | Agrion | Piedmont | 2018 | Clear, 1–2 mm | Myoviridae |
psageA2 | Soil | Manta (CN) | Actinidia chinensis var. deliciosa | Agrion | Piedmont | 2018 | Clear, 1–2 mm | Myoviridae |
psageB1 | Soil | Manta (CN) | Actinidia chinensis var. deliciosa | Agrion | Piedmont | 2018 | Clear, 2 mm | Siphoviridae |
psageB2 | Soil | Manta (CN) | Actinidia chinensis var. deliciosa | Agrion | Piedmont | 2018 | Clear or turbid, 2 mm | Siphoviridae |
pphageB1 | Soil | Boves (CN) | Phaseolus vulgaris cv. Billò | Agrion | Piedmont | 2018 | Clear, 5 mm | Autographiviridae |
pphageB12 | Soil | Boves (CN) | Phaseolus vulgaris cv. Billò | Agrion | Piedmont | 2019 | Clear, 5 mm | Autographiviridae |
pphageB13 | Soil | Boves (CN) | Phaseolus vulgaris cv. Billò | Agrion | Piedmont | 2020 | Clear, 5 mm | Autographiviridae |
pphageB21 | Soil | Boves (CN) | Phaseolus vulgaris cv. Billò | Agrion | Piedmont | 2018 | Clear, 5 mm | Autographiviridae |
pphageB51 | Soil | Boves (CN) | Phaseolus vulgaris cv. Billò | Agrion | Piedmont | 2018 | Clear, 5 mm | Autographiviridae |
pphageB101 | Soil | Boves (CN) | Phaseolus vulgaris cv. Billò | Agrion | Piedmont | 2018 | Clear, 5 mm | Autographiviridae |
pphageT11 | Soil | Tetti Pesio (CN) | Phaseolus vulgaris cv. Borlotto nano | Agrion | Piedmont | 2018 | Clear, 5 mm | Autographiviridae |
pphageT12 | Soil | Tetti Pesio (CN) | Phaseolus vulgaris cv. Borlotto nano | Agrion | Piedmont | 2019 | Clear, 5 mm | Autographiviridae |
pphageT13 | Soil | Tetti Pesio (CN) | Phaseolus vulgaris cv. Borlotto nano | Agrion | Piedmont | 2020 | Clear, 5 mm | Autographiviridae |
pphageT21 | Soil | Tetti Pesio (CN) | Phaseolus vulgaris cv. Borlotto nano | Agrion | Piedmont | 2018 | Clear, 5 mm | Autographiviridae |
pphageT22 | Soil | Tetti Pesio (CN) | Phaseolus vulgaris cv. Borlotto nano | Agrion | Piedmont | 2018 | Clear, 5 mm | Autographiviridae |
pphageT23 | Soil | Tetti Pesio (CN) | Phaseolus vulgaris cv. Borlotto nano | Agrion | Piedmont | 2018 | Clear, 5 mm | Autographiviridae |
pphageBV2 | Soil | Verona (VR) | Phaseolus vulgaris cv. Spagnolet (Lamon) | Phytosanitary Inspection Service | Veneto | 2019 | Clear, 5 mm | Autographiviridae |
pphageBV4 | Soil | Verona (VR) | Phaseolus vulgaris cv. Spagnolet (Lamon) | Phytosanitary Inspection Service | Veneto | 2019 | Clear, 5 mm | Autographiviridae |
pphageBV71 | Soil | Verona (VR) | Phaseolus vulgaris cv. Canalino (Lamon) | Phytosanitary Inspection Service | Veneto | 2019 | Clear, 5 mm | Autographiviridae |
pphageBV72 | Soil | Verona (VR) | Phaseolus vulgaris cv. Canalino (Lamon) | Phytosanitary Inspection Service | Veneto | 2019 | Clear, 5 mm | Autographiviridae |
Phage Name | Accession Number | Bacterial Host | Genome Length | GC Content (%) | ORFs | Hypothetical Proteins | Proteins with Predicted Function | ORFans | tRNAs |
---|---|---|---|---|---|---|---|---|---|
psageA1 | MT740307 | Psa K7 #8 | 98,780 bp | 48.79% | 176 | 76 | 51 | 49 | 14 |
psageB1 | MT354569 | Psa K7 #8 | 112,269 bp | 56.47% | 161 | 105 | 40 | 16 | 4 |
pphageB1 | MT354570 | Pph Cuneo #6_18 | 41,714 bp | 56.63% | 52 | 23 | 25 | 4 | 0 |
psageK4 | MZ348426 | Psa K7 #8 | 98,440 bp | 60.44% | 179 | 112 | 51 | 16 | 18 |
psageB2 | MZ348425 | Psa K7 #8 | 50,739 bp | 58.51% | 77 | 47 | 26 | 4 | 0 |
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Martino, G.; Holtappels, D.; Vallino, M.; Chiapello, M.; Turina, M.; Lavigne, R.; Wagemans, J.; Ciuffo, M. Molecular Characterization and Taxonomic Assignment of Three Phage Isolates from a Collection Infecting Pseudomonas syringae pv. actinidiae and P. syringae pv. phaseolicola from Northern Italy. Viruses 2021, 13, 2083. https://doi.org/10.3390/v13102083
Martino G, Holtappels D, Vallino M, Chiapello M, Turina M, Lavigne R, Wagemans J, Ciuffo M. Molecular Characterization and Taxonomic Assignment of Three Phage Isolates from a Collection Infecting Pseudomonas syringae pv. actinidiae and P. syringae pv. phaseolicola from Northern Italy. Viruses. 2021; 13(10):2083. https://doi.org/10.3390/v13102083
Chicago/Turabian StyleMartino, Gabriele, Dominique Holtappels, Marta Vallino, Marco Chiapello, Massimo Turina, Rob Lavigne, Jeroen Wagemans, and Marina Ciuffo. 2021. "Molecular Characterization and Taxonomic Assignment of Three Phage Isolates from a Collection Infecting Pseudomonas syringae pv. actinidiae and P. syringae pv. phaseolicola from Northern Italy" Viruses 13, no. 10: 2083. https://doi.org/10.3390/v13102083