Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks
The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequenc...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-02-01
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| Series: | Virus Research |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0168170224002181 |
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| author | Peter Erdmann Dougherty Maja Schmidt Pedersen Laura Milena Forero-Junco Alexander Byth Carstens Jos M. Raaijmakers Leise Riber Lars Hestbjerg Hansen |
| author_facet | Peter Erdmann Dougherty Maja Schmidt Pedersen Laura Milena Forero-Junco Alexander Byth Carstens Jos M. Raaijmakers Leise Riber Lars Hestbjerg Hansen |
| author_sort | Peter Erdmann Dougherty |
| collection | DOAJ |
| description | The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be. |
| format | Article |
| id | doaj-art-3c18e1bba58a4ff89544a4eff6bb6dc5 |
| institution | Kabale University |
| issn | 1872-7492 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Virus Research |
| spelling | doaj-art-3c18e1bba58a4ff89544a4eff6bb6dc52025-01-29T04:59:54ZengElsevierVirus Research1872-74922025-02-01352199524Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaksPeter Erdmann Dougherty0Maja Schmidt Pedersen1Laura Milena Forero-Junco2Alexander Byth Carstens3Jos M. Raaijmakers4Leise Riber5Lars Hestbjerg Hansen6Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, DenmarkDepartment of Plant and Environmental Science, University of Copenhagen, Frederiksberg, DenmarkDepartment of Plant and Environmental Science, University of Copenhagen, Frederiksberg, DenmarkDepartment of Plant and Environmental Science, University of Copenhagen, Frederiksberg, DenmarkDepartment of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the NetherlandsDepartment of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark; Corresponding authors.Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark; Corresponding authors.The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.http://www.sciencedirect.com/science/article/pii/S0168170224002181BacteriophagesGenomicsDNA modificationsPhyllosphere |
| spellingShingle | Peter Erdmann Dougherty Maja Schmidt Pedersen Laura Milena Forero-Junco Alexander Byth Carstens Jos M. Raaijmakers Leise Riber Lars Hestbjerg Hansen Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks Virus Research Bacteriophages Genomics DNA modifications Phyllosphere |
| title | Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks |
| title_full | Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks |
| title_fullStr | Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks |
| title_full_unstemmed | Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks |
| title_short | Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks |
| title_sort | novel bacteriophages targeting wheat phyllosphere bacteria carry dna modifications and single strand breaks |
| topic | Bacteriophages Genomics DNA modifications Phyllosphere |
| url | http://www.sciencedirect.com/science/article/pii/S0168170224002181 |
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