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Isolation, characterization, and comparative genomic analysis of vB_PlaM_Pd22F, a new bacteriophage of the family Myoviridae

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Abstract

The use of phage and phage-based products for the prevention and treatment of bee disease is one of the promising natural alternatives to chemical or antibiotic treatments in beekeeping. A novel lysogenic bacteriophage, phage Pd22F (vB_PlaM_Pd22F), was isolated from Paenibacillus dendritiformis by the prophage induction method. This phage, which is capable of infecting Paenibacillus larvae and P. dendritiformis strains, was characterized by microbiological and comparative genomic analysis. Transmission electron microscopy images showed that phage Pd22F had the morphology of a myovirus. Whole-genome sequencing results showed that vB_Pla M_Pd22F has an 86,388-bp linear dsDNA genome with a GC content of 50.68%. This genome has 124 coding sequences (CDSs), 53% of which encode functionally unknown proteins and 57 of which encode proteins that show similarity to known proteins. In addition, one tRNA gene was found. The phage Pd22F genome does not contain any antimicrobial resistance genes. The similarity between the genome sequence of phage Pd22F and the whole genome sequences of other Paenibacillus phages available in the NCBI Virus Database was found to be below 50% (42%), indicating that phage Pd22F differs greatly from previously characterized phages at the DNA level. The results of comparative genomics and phylogenetic analysis revealed that Pd22F is a new phage belonging to the family Myoviridae, order Caudovirales. This is the first report of genomic and morphological characterization of a Paenibacillus dendritiformis prophage.

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Acknowledgments

Sincere thanks to Bayram Toraman of Karadeniz Technical University for providing advice on bioinformatics application. Thanks to Dr. Cantekin Dursun of Recep Tayyip Erdoğan University for providing help on the phylogenetic tree of phages. We thank Elif Sevim and Müberra Pinarbaş for their technical comments and assistance in the study.

Funding

This study was financially supported by the RTEU Scientific Research Projects (RTEU-FBA-2017-807).

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Authors and Affiliations

  1. Biology Department, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Turkey

    Arif Bozdeveci, Merve Karali & Şengül Alpay Karaoğlu

  2. Veterinary Control Institute, Bee Diseases, Samsun, Turkey

    Rahşan Akpinar

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  1. Arif Bozdeveci
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  2. Merve Karali
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  3. Rahşan Akpinar
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Contributions

All authors contributed to the study's conception and design. Material preparation, experimental studies, data collection, evaluation of results, and interpretation of bioinformatic analysis were performed by Arif Bozdeveci and Şengül Alpay Karaoğlu. The main draft of the article was written by Arif Bozdeveci and Şengül Alpay Karaoğlu, and all authors contributed to and commented on the main draft of the article. All authors read and approved the final version of the manuscript.

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Correspondence to Şengül Alpay Karaoğlu.

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Bozdeveci, A., Karali, M., Akpinar, R. et al. Isolation, characterization, and comparative genomic analysis of vB_PlaM_Pd22F, a new bacteriophage of the family Myoviridae. Arch Virol 167, 1269–1284 (2022). https://doi.org/10.1007/s00705-022-05429-3

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