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Article

Genomic Basis of Lifestyle Divergence in Rice-Associated Burkholderia: From Pathogenesis to Plant Growth Promotion

by
Andrews Danso Danso Ofori
1,2,†,
Zohreh Nasimi
1,2,†,
Frank Kwekucher Kwekucher Ackah
3,
Muhammad Irfan Irfan Ahmed
1,2,
Yaoting Yan
1,2,
Wang Li
1,2,
Abdul Ghani Ghani Kandro
1,2,
Kazunori Okada
4,
Keiichi Mochida
5,6,7,8,
Yoshiteru Noutoshi
9 and
Aiping Zheng
1,2,*
1
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
2
Department of Plant Pathology, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
3
Department of Crop Science, School of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast 00233, Ghana
4
Agro-Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
5
Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
6
Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, Saitama 351-0198, Japan
7
Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
8
School of Information and Data Sciences, Nagasaki University, Nagasaki 852-8521, Japan
9
Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2026, 27(11), 4730; https://doi.org/10.3390/ijms27114730 (registering DOI)
Submission received: 23 April 2026 / Revised: 14 May 2026 / Accepted: 20 May 2026 / Published: 24 May 2026
(This article belongs to the Special Issue Recent Advances in Plant–Microbe Interactions)
Versions Notes

Abstract

The genus Burkholderia encompasses both plant pathogenic and beneficial species, yet the genomic determinants underlying this lifestyle divergence remain poorly understood. Using 16S rRNA sequencing of 100 rice cultivars, our companion study demonstrated that resistant varieties are enriched in beneficial Burkholderiaceae, leading to the isolation of three phenotypically contrasting strains. Here, we present comparative genomic analyses of non-pathogenic biocontrol strain Burkholderia vietnamiensis J14EpLeaf2 and pathogenic strains Burkholderia gladioli A1EpSeed5 and Burkholderia cepacia J14Eple. Pathogenic strains possess significantly larger genomes (8.36–8.46 Mb) enriched in mobile genetic elements compared to the streamlined 6.95 Mb genome of B. vietnamiensis. CAZyme analysis revealed broader repertoires of glycoside hydrolases and polysaccharide lyases in pathogens, consistent with enhanced plant cell wall degradation. B. gladioli possesses a complete T3SS and expanded T6SS with 301 predicted effectors, while B. cepacia lacks structural T3SS genes but harbors 271 candidate effectors predicted to be secreted via alternative secretion pathways, compared to 180 in B. vietnamiensis. Notably, B. cepacia harbors cystic fibrosis-associated markers (cable pili, ZmpA/ZmpB), raising significant biosafety concerns that preclude its agricultural application. LC-MS validated IAA, ornibactin, and AHL production in B. vietnamiensis, supporting its plant growth-promoting and biocontrol functions. Computational PPI networks predicted distinct interaction landscapes requiring experimental validation. This study provides a genomic framework for distinguishing pathogenic from beneficial Burkholderia and supports B. vietnamiensis as a safe biocontrol agent while cautioning against B. cepacia J14Eple.
Keywords: Burkholderia; comparative genomics; virulence factors; secretion systems; CAZymes; plant-microbe interactions; biocontrol; pathogenicity; protein–protein interaction networks; rice sheath blight Burkholderia; comparative genomics; virulence factors; secretion systems; CAZymes; plant-microbe interactions; biocontrol; pathogenicity; protein–protein interaction networks; rice sheath blight

Share and Cite

MDPI and ACS Style

Ofori, A.D.D.; Nasimi, Z.; Ackah, F.K.K.; Ahmed, M.I.I.; Yan, Y.; Li, W.; Kandro, A.G.G.; Okada, K.; Mochida, K.; Noutoshi, Y.; et al. Genomic Basis of Lifestyle Divergence in Rice-Associated Burkholderia: From Pathogenesis to Plant Growth Promotion. Int. J. Mol. Sci. 2026, 27, 4730. https://doi.org/10.3390/ijms27114730

AMA Style

Ofori ADD, Nasimi Z, Ackah FKK, Ahmed MII, Yan Y, Li W, Kandro AGG, Okada K, Mochida K, Noutoshi Y, et al. Genomic Basis of Lifestyle Divergence in Rice-Associated Burkholderia: From Pathogenesis to Plant Growth Promotion. International Journal of Molecular Sciences. 2026; 27(11):4730. https://doi.org/10.3390/ijms27114730

Chicago/Turabian Style

Ofori, Andrews Danso Danso, Zohreh Nasimi, Frank Kwekucher Kwekucher Ackah, Muhammad Irfan Irfan Ahmed, Yaoting Yan, Wang Li, Abdul Ghani Ghani Kandro, Kazunori Okada, Keiichi Mochida, Yoshiteru Noutoshi, and et al. 2026. "Genomic Basis of Lifestyle Divergence in Rice-Associated Burkholderia: From Pathogenesis to Plant Growth Promotion" International Journal of Molecular Sciences 27, no. 11: 4730. https://doi.org/10.3390/ijms27114730

APA Style

Ofori, A. D. D., Nasimi, Z., Ackah, F. K. K., Ahmed, M. I. I., Yan, Y., Li, W., Kandro, A. G. G., Okada, K., Mochida, K., Noutoshi, Y., & Zheng, A. (2026). Genomic Basis of Lifestyle Divergence in Rice-Associated Burkholderia: From Pathogenesis to Plant Growth Promotion. International Journal of Molecular Sciences, 27(11), 4730. https://doi.org/10.3390/ijms27114730

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