Section: Microbiology
Topic: Microbiology, Biology of interactions, Plant biology

Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species

Wallner, Adrian1; Klonowska, Agnieszka1 ; Guigard, Ludivine1; King, Eoghan1 ; Rimbault, Isabelle1; Ngonkeu, Eddy2; Nguyen, Phuong3; Béna, Gilles1 ; Moulin, Lionel1  
1 PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
2 Institute of Agronomic Research for Development (IRAD), PO Box 2123, Yaoundé, Cameroon
3 University of Science and Technology of Hanoi (USTH); 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam

Corresponding author(s): Moulin, Lionel (lionel.moulin@ird.fr)

10.24072/pcjournal.252 - Peer Community Journal, Volume 3 (2023), article no. e25.

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Beyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of the Burkholderia and Paraburkholderia genera are frequently found in the rhizosphere of rice. While the latter are often described as plant growth promoting species, Burkholderia are often studied for their human opportunistic traits. Here, we used root exudate stimulation on three Burkholderia and three Paraburkholderia strains isolated from rice roots to characterize their preliminary adaptation to the rice host at the transcriptomic level. Instead of the awaited genus-dependent adaptation, we observed a strongly species-specific response for all tested strains. While all bacteria originate from the rice environment, there are great disparities in their levels of adaptation following the sensing of root exudates. We further report the shared major functions that were differentially regulated in this early step of bacterial adaptation to plant colonization, including amino acids and putrescine metabolism, the Entner-Doudoroff (ED) pathway as well as cyclic diguanylate monophosphate (c-di-GMP) cycling.

Published online:
DOI: 10.24072/pcjournal.252
Type: Research article
Keywords: RNAseq, root exudates, PGPR, rhizobacteria, symbiosis, Oryza sativa
Keywords: RNAseq, root exudates, PGPR, rhizobacteria, symbiosis, Oryza sativa

Wallner, Adrian 1; Klonowska, Agnieszka 1; Guigard, Ludivine 1; King, Eoghan 1; Rimbault, Isabelle 1; Ngonkeu, Eddy 2; Nguyen, Phuong 3; Béna, Gilles 1; Moulin, Lionel 1

1 PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
2 Institute of Agronomic Research for Development (IRAD), PO Box 2123, Yaoundé, Cameroon
3 University of Science and Technology of Hanoi (USTH); 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
@article{10_24072_pcjournal_252,
     author = {Wallner, Adrian and Klonowska, Agnieszka and Guigard, Ludivine and King, Eoghan and Rimbault, Isabelle and Ngonkeu, Eddy and Nguyen, Phuong and B\'ena, Gilles and Moulin, Lionel},
     title = {Comparative genomics and transcriptomic response to root exudates of six rice root-associated {\protect\emph{Burkholderia} sensu lato} species},
     journal = {Peer Community Journal},
     eid = {e25},
     publisher = {Peer Community In},
     volume = {3},
     year = {2023},
     doi = {10.24072/pcjournal.252},
     url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.252/}
}
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AU  - Klonowska, Agnieszka
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%A Klonowska, Agnieszka
%A Guigard, Ludivine
%A King, Eoghan
%A Rimbault, Isabelle
%A Ngonkeu, Eddy
%A Nguyen, Phuong
%A Béna, Gilles
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Wallner, Adrian; Klonowska, Agnieszka; Guigard, Ludivine; King, Eoghan; Rimbault, Isabelle; Ngonkeu, Eddy; Nguyen, Phuong; Béna, Gilles; Moulin, Lionel. Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species. Peer Community Journal, Volume 3 (2023), article  no. e25. doi : 10.24072/pcjournal.252. https://peercommunityjournal.org/articles/10.24072/pcjournal.252/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.microbiol.100002

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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