The Bacterial and Viral Communities Associated with Onion Bacterial Bulb Rot
Microbes occur in complex communities within plants as endophytes and establish a network of interactions that can influence plant health positively or negatively. Positive interactions may be synergistic and confer abiotic and biotic stress tolerance. The aim of this study was to identify bacteria...
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The American Phytopathological Society
2025-03-01
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| Series: | Phytobiomes Journal |
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| Online Access: | https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-11-23-0121-R |
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| author | Christopher Liakos Verushka Ibanez Pedro H. Lebre Mike L. Derie Jacquie van der Waals Lindsey du Toit Bhabesh Dutta Brian Kvitko Don A. Cowan Teresa A. Coutinho |
| author_facet | Christopher Liakos Verushka Ibanez Pedro H. Lebre Mike L. Derie Jacquie van der Waals Lindsey du Toit Bhabesh Dutta Brian Kvitko Don A. Cowan Teresa A. Coutinho |
| author_sort | Christopher Liakos |
| collection | DOAJ |
| description | Microbes occur in complex communities within plants as endophytes and establish a network of interactions that can influence plant health positively or negatively. Positive interactions may be synergistic and confer abiotic and biotic stress tolerance. The aim of this study was to identify bacteria and viruses present in storage onion bulbs that were symptomatic and asymptomatic for bacterial bulb rot from crops grown in Georgia and Washington states, and to assess their potential role in the bulbs based on the functions of bacterial and viral genes detected. DNA was extracted from nine asymptomatic bulbs and nine bulbs displaying symptoms of bacterial bulb rot and subjected to 16S rRNA amplicon sequencing and metagenome-assembled genome analysis. The Illumina platform was used to sequence the hypervariable region (V3-V4) of the 16S rRNA gene. The 16S rRNA amplicon profiling revealed the presence of numerous bacteria, including potential onion pathogens in the genera Pantoea and Burkholderia. Metagenome-assembled genome assembly identified P. agglomerans, B. gladioli, and B. cepacia, known bulb rot pathogens, including genes linked to fitness and those involved in both type II and III secretion systems. Eighty-nine unique viral genomes were identified, of which 67 could be classified taxonomically. The bacterial and viral genomes differed significantly in asymptomatic versus symptomatic bulbs. Viral genomes showed evidence of auxiliary metabolic genes, including genes involved in fitness and pathogenicity to bacterial hosts. The onion bulbs hosted endophytic bacteria and viruses, some of which were potentially beneficial and others potentially pathogenic to onion or as hosts to bacteriophages. [Figure: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license. |
| format | Article |
| id | doaj-art-e0e2aceaa6ed4c13b36e78ebdc34c926 |
| institution | DOAJ |
| issn | 2471-2906 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | The American Phytopathological Society |
| record_format | Article |
| series | Phytobiomes Journal |
| spelling | doaj-art-e0e2aceaa6ed4c13b36e78ebdc34c9262025-08-20T02:48:35ZengThe American Phytopathological SocietyPhytobiomes Journal2471-29062025-03-019110912210.1094/PBIOMES-11-23-0121-RThe Bacterial and Viral Communities Associated with Onion Bacterial Bulb RotChristopher Liakos0Verushka Ibanez1Pedro H. Lebre2Mike L. Derie3Jacquie van der Waals4Lindsey du Toit5Bhabesh Dutta6Brian Kvitko7Don A. Cowan8Teresa A. Coutinho9Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South AfricaDepartment of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South AfricaDepartment of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South AfricaDepartment of Plant Pathology, Washington State University, Mount Vernon, WA 98273, U.S.A.Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria 0002, South AfricaDepartment of Plant Pathology, Washington State University, Mount Vernon, WA 98273, U.S.A.Department of Plant Pathology, University of Georgia, Tifton, GA 31793, U.S.A.Department of Plant Pathology, University of Georgia, Tifton, GA 31793, U.S.A.Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South AfricaDepartment of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South AfricaMicrobes occur in complex communities within plants as endophytes and establish a network of interactions that can influence plant health positively or negatively. Positive interactions may be synergistic and confer abiotic and biotic stress tolerance. The aim of this study was to identify bacteria and viruses present in storage onion bulbs that were symptomatic and asymptomatic for bacterial bulb rot from crops grown in Georgia and Washington states, and to assess their potential role in the bulbs based on the functions of bacterial and viral genes detected. DNA was extracted from nine asymptomatic bulbs and nine bulbs displaying symptoms of bacterial bulb rot and subjected to 16S rRNA amplicon sequencing and metagenome-assembled genome analysis. The Illumina platform was used to sequence the hypervariable region (V3-V4) of the 16S rRNA gene. The 16S rRNA amplicon profiling revealed the presence of numerous bacteria, including potential onion pathogens in the genera Pantoea and Burkholderia. Metagenome-assembled genome assembly identified P. agglomerans, B. gladioli, and B. cepacia, known bulb rot pathogens, including genes linked to fitness and those involved in both type II and III secretion systems. Eighty-nine unique viral genomes were identified, of which 67 could be classified taxonomically. The bacterial and viral genomes differed significantly in asymptomatic versus symptomatic bulbs. Viral genomes showed evidence of auxiliary metabolic genes, including genes involved in fitness and pathogenicity to bacterial hosts. The onion bulbs hosted endophytic bacteria and viruses, some of which were potentially beneficial and others potentially pathogenic to onion or as hosts to bacteriophages. [Figure: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-11-23-0121-Ramplicon sequencingmetagenome assembled genomes (MAGs)onion bulb rot |
| spellingShingle | Christopher Liakos Verushka Ibanez Pedro H. Lebre Mike L. Derie Jacquie van der Waals Lindsey du Toit Bhabesh Dutta Brian Kvitko Don A. Cowan Teresa A. Coutinho The Bacterial and Viral Communities Associated with Onion Bacterial Bulb Rot Phytobiomes Journal amplicon sequencing metagenome assembled genomes (MAGs) onion bulb rot |
| title | The Bacterial and Viral Communities Associated with Onion Bacterial Bulb Rot |
| title_full | The Bacterial and Viral Communities Associated with Onion Bacterial Bulb Rot |
| title_fullStr | The Bacterial and Viral Communities Associated with Onion Bacterial Bulb Rot |
| title_full_unstemmed | The Bacterial and Viral Communities Associated with Onion Bacterial Bulb Rot |
| title_short | The Bacterial and Viral Communities Associated with Onion Bacterial Bulb Rot |
| title_sort | bacterial and viral communities associated with onion bacterial bulb rot |
| topic | amplicon sequencing metagenome assembled genomes (MAGs) onion bulb rot |
| url | https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-11-23-0121-R |
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