Characterization of Immunity-Inducing Rhizobacteria Highlights Diversity in Plant–Microbe Interactions

Mackenzie Eli William Loranger; Winfield Yim; Matthew Toffoli; Marie-Christine Groleau; Arvin Nickzad; Nadia Morales-Lizcano; Thomas Berleth; Wolfgang Moeder; Eric Déziel; Keiko Yoshioka

doi:10.1094/pbiomes-01-25-0004-r

journal article Nov 01, 2025

Characterization of Immunity-Inducing Rhizobacteria Highlights Diversity in Plant–Microbe Interactions

Mackenzie Eli William Loranger

Winfield Yim Matthew Toffoli Marie-Christine Groleau Arvin Nickzad Nadia Morales-Lizcano Thomas Berleth Wolfgang Moeder

Eric Déziel

Keiko Yoshioka

Phytobiomes Journal Vol. 9 No. 4 pp. 499-511 · Scientific Societies

View at Publisher Save 10.1094/pbiomes-01-25-0004-r

Abstract

The narrow region of soil surrounding roots (rhizosphere) contains an astonishing diversity of microorganisms. Some rhizosphere bacteria can improve plant health and immunity, via direct competition with pathogens or by establishing heightened immunity in aboveground tissues, a phenomenon known as induced systemic resistance (ISR). To identify novel immunity-activating bacterial strains, we established a screening method from a library of agricultural soil-derived culturable bacteria, using Solanum lycopersicum (tomato) and the fungal pathogen Botrytis cinerea, the causal agent of gray mold disease. Here, we report the establishment of a screening method and the identification of 13 immunity-inducing strains in tomato plants, including a strain of Chitinophaga arvensicola. A detailed characterization of a subset of five strains, belonging to the species Bacillus velezensis, Paenibacillus peoriae, and Pseudomonas parafulva, revealed that only two of them triggered canonical ISR in Arabidopsis, indicating plant host specificity, alternative modes of action, or both. Furthermore, some of the strains displayed direct anti-microbial activity, and two strains became endophytic. We also found the requirement of the lipid-binding protein DIR1, which is an important factor for systemic acquired resistance, for ISR establishment in Arabidopsis, indicating a possible convergence of systemic acquired resistance and ISR signaling. Finally, we found that P. parafulva TP18m promoted root development as well as enhanced immunity. Taken together, we have established a screening system for immunity-inducing bacteria and identified taxonomically diverse bacterial strains that may be useful for agricultural application. Our characterization revealed diverse features for each strain, which highlights the complexity of the bacteria–host interactions in the rhizosphere.
[Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Topics

No keywords indexed for this article. Browse by subject →

References

89

[1]

10.1007/s10526-005-4362-3

[2]

Plant beneficial endophytic bacteria: Mechanisms, diversity, host range and genetic determinants

Imran Afzal, Zabta Khan Shinwari, Shomaila Sikandar et al.

Microbiological Research 10.1016/j.micres.2019.02.001

[3]

10.1126/science.284.5423.2148

[4]

10.3389/fpls.2019.00102

[5]

Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture

Rachel Backer, J. Stefan Rokem, Gayathri Ilangumaran et al.

Frontiers in Plant Science 10.3389/fpls.2018.01473

[6]

10.5423/ppj.si.07.2012.0111

[7]

The rhizosphere microbiome and plant health

Roeland L. Berendsen, Corné M.J. Pieterse, Peter A.H.M. Bakker

Trends in Plant Science 10.1016/j.tplants.2012.04.001

[8]

10.1186/s12864-015-1632-z

[9]

10.1094/mpmi-08-20-0225-cr

[10]

10.1038/ncomms8658

[11]

10.4161/psb.1.4.3221

[12]

10.1094/mpmi-19-1062

[13]

Molecular mechanisms of early plant pattern-triggered immune signaling

Thomas A. DeFalco, Cyril Zipfel

Molecular Cell 10.1016/j.molcel.2021.07.029

[14]

10.1105/tpc.16.00953

[15]

10.1105/tpc.111.083394

[16]

10.1093/pcp/pcx014

[17]

10.3389/fmicb.2018.02491

[18]

10.1007/978-3-319-23371-0

[19]

10.1111/1751-7915.12028

[20]

10.1046/j.1365-313x.1999.00451.x

[21]

10.3389/fmicb.2019.01506

[22]

10.1146/annurev-phyto-080516-035623

[23]

10.1111/mec.14400

[24]

10.1016/j.tim.2008.07.008

[25]

10.1007/s11104-008-9814-y

[26]

10.1038/s41467-018-05122-7

[27]

10.1111/nph.19981

[28]

10.1016/j.biocontrol.2019.04.006

[29]

10.1385/1-59745-003-0:263

[30]

10.3389/fpls.2021.766095

[31]

10.3390/microorganisms10030596

[32]

10.1094/phyto-86-149

[33]

10.1111/nph.18199

[34]

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

Hongwei Liu, Lilia C. Carvalhais, Mark Crawford et al.

Frontiers in Microbiology 10.3389/fmicb.2017.02552

[35]

10.1186/s13007-024-01193-4

[36]

10.1038/s41477-021-00920-2

[37]

10.1016/j.tplants.2021.08.004

[38]

10.1038/nature00962

[39]

10.1016/s0167-7012(99)00028-7

[40]

10.1105/tpc.109.069658

[41]

10.3390/plants9050626

[42]

10.1111/j.1574-6968.1999.tb13383.x

[43]

A Review on the Biotechnological Applications of the Operational Group Bacillus amyloliquefaciens

Mohamad Syazwan Ngalimat, Radin Shafierul Radin Yahaya, Mohamad Malik Al-adil Baharudin et al.

Microorganisms 10.3390/microorganisms9030614

[44]

10.1016/j.tplants.2021.08.012

[45]

10.3389/fpls.2017.00238

[46]

10.1094/mpmi-09-10-0213

[47]

10.3390/applmicrobiol3030076

[48]

10.1371/journal.ppat.1009472

[49]

10.1371/journal.pgen.1003953

[50]

Pseudomonas simiae WCS417: star track of a model beneficial rhizobacterium

Corné M. J. Pieterse, Roeland L. Berendsen, Ronnie de Jonge et al.

Plant and Soil 10.1007/s11104-020-04786-9

Showing 50 of 89 references

Metrics

1

Citations

89

References

Details

Published: Nov 01, 2025
Vol/Issue: 9(4)
Pages: 499-511

Authors

M

Mackenzie Eli William Loranger

University of Toronto, Cell and Systems Biology, Toronto, ON, Canada

W

Winfield Yim

University of Toronto, Cell and Systems Biology, Toronto, ON, Canada

M

Matthew Toffoli

University of Toronto, Cell and Systems Biology, Toronto, ON, Canada

M

Marie-Christine Groleau

Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Canada

A

Arvin Nickzad

Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Canada

N

Nadia Morales-Lizcano

University of Toronto, Cell and Systems Biology, Toronto, ON, Canada

T

Thomas Berleth

University of Toronto, Cell and Systems Biology, Toronto, ON, Canada

W

Wolfgang Moeder

University of Toronto, Cell and Systems Biology, Toronto, ON, Canada

E

Eric Déziel

Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Canada

K

Keiko Yoshioka

University of Toronto, Cell and Systems Biology, Toronto, ON, Canada

Funding

Natural Sciences and Engineering Research Council of Canada

Ontario Graduate Scholarship

Cite This Article

Mackenzie Eli William Loranger, Winfield Yim, Matthew Toffoli, et al. (2025). Characterization of Immunity-Inducing Rhizobacteria Highlights Diversity in Plant–Microbe Interactions. Phytobiomes Journal, 9(4), 499-511. https://doi.org/10.1094/pbiomes-01-25-0004-r

Characterization of Immunity-Inducing Rhizobacteria Highlights Diversity in Plant–Microbe Interactions

You May Also Like