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Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus

Bacteriophages are viral agents that infect and replicate within bacterial cells. Despite the increasing importance of phage ecology, environmental phages—particularly those targeting phyllosphere-associated bacteria—remain underexplored, and current genomic databases lack high-quality phage genome...

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Autores principales: Riber, Leise, Carstens, Alexander Byth, Dougherty, Peter Erdmann, Roy, Chayan, Willenbücher, Katharina, Hille, Frank, Franz, Charles M. A. P., Hansen, Lars Hestbjerg
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10385605/
https://www.ncbi.nlm.nih.gov/pubmed/37513003
http://dx.doi.org/10.3390/microorganisms11071831
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author Riber, Leise
Carstens, Alexander Byth
Dougherty, Peter Erdmann
Roy, Chayan
Willenbücher, Katharina
Hille, Frank
Franz, Charles M. A. P.
Hansen, Lars Hestbjerg
author_facet Riber, Leise
Carstens, Alexander Byth
Dougherty, Peter Erdmann
Roy, Chayan
Willenbücher, Katharina
Hille, Frank
Franz, Charles M. A. P.
Hansen, Lars Hestbjerg
author_sort Riber, Leise
collection PubMed
description Bacteriophages are viral agents that infect and replicate within bacterial cells. Despite the increasing importance of phage ecology, environmental phages—particularly those targeting phyllosphere-associated bacteria—remain underexplored, and current genomic databases lack high-quality phage genome sequences linked to specific environmentally important bacteria, such as the ubiquitous sphingomonads. Here, we isolated three novel phages from a Danish wastewater treatment facility. Notably, these phages are among the first discovered to target and regulate a Sphingomonas genus within the wheat phyllosphere microbiome. Two of the phages displayed a non-prolate Siphovirus morphotype and demonstrated a narrow host range when tested against additional Sphingomonas strains. Intergenomic studies revealed limited nucleotide sequence similarity within the isolated phage genomes and to publicly available metagenome data of their closest relatives. Particularly intriguing was the limited homology observed between the DNA polymerase encoding genes of the isolated phages and their closest relatives. Based on these findings, we propose three newly identified genera of viruses: Longusvirus carli, Vexovirus birtae, and Molestusvirus kimi, following the latest ICTV binomial nomenclature for virus species. These results contribute to our current understanding of phage genetic diversity in natural environments and hold promising implications for phage applications in phyllosphere microbiome manipulation strategies.
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spelling pubmed-103856052023-07-30 Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus Riber, Leise Carstens, Alexander Byth Dougherty, Peter Erdmann Roy, Chayan Willenbücher, Katharina Hille, Frank Franz, Charles M. A. P. Hansen, Lars Hestbjerg Microorganisms Article Bacteriophages are viral agents that infect and replicate within bacterial cells. Despite the increasing importance of phage ecology, environmental phages—particularly those targeting phyllosphere-associated bacteria—remain underexplored, and current genomic databases lack high-quality phage genome sequences linked to specific environmentally important bacteria, such as the ubiquitous sphingomonads. Here, we isolated three novel phages from a Danish wastewater treatment facility. Notably, these phages are among the first discovered to target and regulate a Sphingomonas genus within the wheat phyllosphere microbiome. Two of the phages displayed a non-prolate Siphovirus morphotype and demonstrated a narrow host range when tested against additional Sphingomonas strains. Intergenomic studies revealed limited nucleotide sequence similarity within the isolated phage genomes and to publicly available metagenome data of their closest relatives. Particularly intriguing was the limited homology observed between the DNA polymerase encoding genes of the isolated phages and their closest relatives. Based on these findings, we propose three newly identified genera of viruses: Longusvirus carli, Vexovirus birtae, and Molestusvirus kimi, following the latest ICTV binomial nomenclature for virus species. These results contribute to our current understanding of phage genetic diversity in natural environments and hold promising implications for phage applications in phyllosphere microbiome manipulation strategies. MDPI 2023-07-18 /pmc/articles/PMC10385605/ /pubmed/37513003 http://dx.doi.org/10.3390/microorganisms11071831 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Riber, Leise
Carstens, Alexander Byth
Dougherty, Peter Erdmann
Roy, Chayan
Willenbücher, Katharina
Hille, Frank
Franz, Charles M. A. P.
Hansen, Lars Hestbjerg
Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus
title Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus
title_full Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus
title_fullStr Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus
title_full_unstemmed Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus
title_short Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus
title_sort pheno- and genotyping of three novel bacteriophage genera that target a wheat phyllosphere sphingomonas genus
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10385605/
https://www.ncbi.nlm.nih.gov/pubmed/37513003
http://dx.doi.org/10.3390/microorganisms11071831
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