Chemical dialogues in the rhizosphere: Metabolomics perspectives on plant defence and microbial interactions

Nompumelelo R. Sibanyoni; Kamogelo Mmotla; Manamele D. Mashabela; Lizelle A. Piater; Pavel Kerchev; Msizi I. Mhlongo

doi:10.1007/s11104-025-08010-4

journal article Open Access Dec 10, 2025

Chemical dialogues in the rhizosphere: Metabolomics perspectives on plant defence and microbial interactions

Nompumelelo R. Sibanyoni Kamogelo Mmotla Manamele D. Mashabela Lizelle A. Piater

Pavel Kerchev Msizi I. Mhlongo

Plant and Soil Vol. 518 No. 1 pp. 577-603 · Springer Science and Business Media LLC

View at Publisher Save 10.1007/s11104-025-08010-4

Topics

No keywords indexed for this article. Browse by subject →

References

187

[1]

Abramovitch RB, Martin GB (2004) Strategies used by bacterial pathogens to suppress plant defenses. Curr Opin Plant Biol 7:356–364. https://doi.org/10.1016/j.pbi.2004.05.002 10.1016/j.pbi.2004.05.002

[2]

Adeniji AA, Babalola OO, Loots DT (2020) Metabolomic applications for understanding complex tripartite plant-microbes interactions: strategies and perspectives. Biotechnol Rep 25:e00425. https://doi.org/10.1016/j.btre.2020.e00425 10.1016/j.btre.2020.e00425

[3]

Afridi MS, Fakhar A, Kumar A et al (2022) Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering. Microbiol Res 265:127199. https://doi.org/10.1016/j.micres.2022.127199 10.1016/j.micres.2022.127199

[4]

Ahmed E, Holmström SJM (2014) Siderophores in environmental research: roles and applications. Microb Biotechnol 7:196–208. https://doi.org/10.1111/1751-7915.12117 10.1111/1751-7915.12117

[5]

Ai G, Peng H, Pan W et al (2024) A catalogue of virulence strategies mediated by phytopathogenic effectors. Fundamental Research 5:663–673. https://doi.org/10.1016/j.fmre.2023.10.026 10.1016/j.fmre.2023.10.026

[6]

Akter S, Huang J, Waszczak C et al (2015) Cysteines under ROS attack in plants: a proteomics view. J Exp Bot 66:2935–2944. https://doi.org/10.1093/jxb/erv044 10.1093/jxb/erv044

[7]

Albert T, Braun PG, Saffaf J, Wiacek C (2021) Physical methods for the decontamination of meat surfaces. Curr Clin Microbiol Rep 8:9–20. https://doi.org/10.1007/s40588-021-00156-w 10.1007/s40588-021-00156-w

[8]

Alotaibi M (2023) Climate change, its impact on crop production, challenges, and possible solutions. Not Bot Horti Agrobot Cluj-Napoca 51(1):13020. https://doi.org/10.15835/nbha51113020 10.15835/nbha51113020

[9]

Alseekh S, Fernie AR (2018) Metabolomics 20 years on: what have we learned and what hurdles remain? Plant J 94(6):933–942. https://doi.org/10.1111/tpj.2018.94.issue-6 10.1111/tpj.2018.94.issue-6

[10]

Armitage SA, Genersch E, McMahon DP et al (2022) Tripartite interactions: how immunity, microbiota and pathogens interact and affect pathogen virulence evolution. Curr Opin Insect Sci. https://doi.org/10.1016/j.cois.2021.12.011 10.1016/j.cois.2021.12.011

[11]

Arora NK, Khare E (2008) Biocontrol of soil-borne phytopathogens by fluorescent pseudomonads, as a sustainable alternative to agrochemicals. Potential microorganisms for sustainable agriculture: a techno-commercial perspective. IK International Publ. P Ltd, New Delhi, pp 99–114

[12]

Aznar A, Dellagi A (2015) New insights into the role of siderophores as triggers of plant immunity: what can we learn from animals? J Exp Bot 66:3001–3010. https://doi.org/10.1093/jxb/erv155 10.1093/jxb/erv155

[13]

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 2018 10.3389/fpls.2018.01473

[14]

Bailly A, Weisskopf L (2012) The modulating effect of bacterial volatiles on plant growth. Plant Signal Behav 7:79–85. https://doi.org/10.4161/psb.7.1.18418 10.4161/psb.7.1.18418

[15]

Bais HP, Park S-W, Weir TL et al (2004) How plants communicate using the underground information superhighway. Trends Plant Sci 9:26–32. https://doi.org/10.1016/j.tplants.2003.11.008 10.1016/j.tplants.2003.11.008

[16]

Balloux F, van Dorp L (2017) Q&A: What are pathogens, and what have they done to and for us? BMC Biology 15:433–439. https://doi.org/10.1186/s12915-017-0433-z 10.1186/s12915-017-0433-z

[17]

Barea JM, Gryndler M, Philippe Lemanceau et al (2002) The rhizosphere of mycorrhizal plants. Birkhäuser Basel eBooks 1–18. https://doi.org/10.1007/978-3-0348-8117-3_1 10.1007/978-3-0348-8117-3_1

[18]

Beecher C, Tarcea G (2015) Visualizing and analyzing metabolomic data using MetScape plugin for Cytoscape. In: Academia.edu. https://www.academia.edu/17173273/Visualizing_and_Analyzing_Metabolomic_Data_Using_MetScape_plugin_for_Cytoscape?auto=download. Accessed 11 Oct 2024

[19]

Berendsen RL, Vismans G, Yu K et al (2018) Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J 12:1496–1507. https://doi.org/10.1038/s41396-018-0093-1 10.1038/s41396-018-0093-1

[20]

Bielach A, Hrtyan M, Tognetti VB (2017) Plants under stress: involvement of auxin and cytokinin. Int J Mol Sci 18:1427. https://doi.org/10.3390/ijms18071427 10.3390/ijms18071427

[21]

Biondi S, Antognoni F, Marincich L, Lianza M, Tejos R, Ruiz KB (2022) The polyamine “multiverse” and stress mitigation in crops: a case study with seed priming in quinoa. Scientia Horticulturae 304:111292. https://doi.org/10.1016/j.scienta.2022.111292 10.1016/j.scienta.2022.111292

[22]

Braga RM, Dourado MN, Araújo WL (2016) Microbial interactions: ecology in a molecular perspective. Braz J Microbiol 47:86–98. https://doi.org/10.1016/j.bjm.2016.10.005 10.1016/j.bjm.2016.10.005

[23]

Buhian WP, Bensmihen S (2018) Mini-review: nod factor regulation of phytohormone signaling and homeostasis during rhizobia-legume symbiosis. Front Plant Sci 9:1247. https://doi.org/10.3389/fpls.2018.01247 10.3389/fpls.2018.01247

[24]

Buxdorf K, Yaffe H, Barda O, Levy M (2013) The effects of glucosinolates and their breakdown products on necrotrophic fungi. PLoS ONE 8:e70771. https://doi.org/10.1371/journal.pone.0070771 10.1371/journal.pone.0070771

[25]

Canchola A, Tran LN, Woo W, Tian L, Lin Y-H, Chou W-C (2025) Advancing non-target analysis of emerging environmental contaminants with machine learning: current status and future implications. Environ Int 198:109404. https://doi.org/10.1016/j.envint.2025.109404 10.1016/j.envint.2025.109404

[26]

Castro-Moretti FR, Gentzel IN, Mackey D, Alonso AP (2020) Metabolomics as an emerging tool for the study of plant–pathogen interactions. Metabolites 10:52. https://doi.org/10.3390/metabo10020052 10.3390/metabo10020052

[27]

Plant Growth-Promoting Rhizobacteria as a Green Alternative for Sustainable Agriculture

Hema Chandran, Mukesh Meena, Prashant Swapnil

Sustainability 2021 10.3390/su131910986

[28]

Chen Q, Song Y, An Y et al (2024) Soil microorganisms: their role in enhancing crop nutrition and health. Diversity 16:734–734. https://doi.org/10.3390/d16120734 10.3390/d16120734

[29]

Cordovez V, Dini-Andreote F, Carrión VJ, Raaijmakers JM (2019) Ecology and evolution of plant microbiomes. Annu Rev Microbiol 73(1):69–88. https://doi.org/10.1146/micro.2019.73.issue-1 10.1146/micro.2019.73.issue-1

[30]

Crouzet J, Arguelles-Arias A, Dhondt-Cordelier S et al (2020) Biosurfactants in plant protection against diseases: Rhamnolipids and lipopeptides case study. Front Bioeng Biotechnol. https://doi.org/10.3389/fbioe.2020.01014 10.3389/fbioe.2020.01014

[31]

Debona D, Rodrigues FÁ, Rios JA, Juliane K (2012) Biochemical changes in the leaves of wheat plants onfected by Pyricularia oryzae. Phytopathology 102:1121–1129. https://doi.org/10.1094/phyto-06-12-0125-r 10.1094/phyto-06-12-0125-r

[32]

Dinesh R, Anandaraj M, Kumar A et al (2015) Isolation, characterization, and evaluation of multi-trait plant growth promoting rhizobacteria for their growth promoting and disease suppressing effects on ginger. Microbiol Res 173:34–43. https://doi.org/10.1016/j.micres.2015.01.014 10.1016/j.micres.2015.01.014

[33]

do Vale A, Cabanes D, Sousa S (2016) Bacterial toxins as pathogen weapons against phagocytes. Front Microbiol 7. https://doi.org/10.3389/fmicb.2016.00042 10.3389/fmicb.2016.00042

[34]

Dodds PN, Rathjen JP (2010) Plant immunity: towards an integrated view of plant–pathogen interactions. Nat Rev Genet 11:539–548. https://doi.org/10.1038/nrg2812 10.1038/nrg2812

[35]

Du Y, Wang Y, Cui T et al (2023) Efficient production of biosurfactant surfactin by a newly isolated Bacillus subtilis (sp.) 50499 strain from oil-contaminated soil. Food Bioprod Process 142:40–49. https://doi.org/10.1016/j.fbp.2023.09.002 10.1016/j.fbp.2023.09.002

[36]

Dudenhöffer J, Scheu S, Jousset A (2016) Systemic enrichment of antifungal traits in the rhizosphere microbiome after pathogen attack. J Ecol 104:1566–1575. https://doi.org/10.1111/1365-2745.12626 10.1111/1365-2745.12626

[37]

Eitas TK, Dangl JL (2010) NB-lrr proteins: pairs, pieces, perception, partners, and pathways. Curr Opin Plant Biol 13:472–477. https://doi.org/10.1016/j.pbi.2010.04.007 10.1016/j.pbi.2010.04.007

[38]

Elsharkawy MM, Khedr AA, Mehiar F et al (2023) Rhizobacterial colonization and management of bacterial speck pathogen in tomato by Pseudomonas spp. Microorganisms 11:1103–1103. https://doi.org/10.3390/microorganisms11051103 10.3390/microorganisms11051103

[39]

Erickson J, Weckwerth P, Romeis T, Lee J (2022) What’s new in protein kinase/phosphatase signalling in the control of plant immunity? Essays Biochem 66:621–634. https://doi.org/10.1042/ebc20210088 10.1042/ebc20210088

[40]

Etesami H, Glick BR (2024) Bacterial indole-3-acetic acid: a key regulator for plant growth, plant-microbe interactions, and agricultural adaptive resilience. Microbiol Res 281:127602. https://doi.org/10.1016/j.micres.2024.127602 10.1016/j.micres.2024.127602

[41]

Etesami H, Maheshwari DK (2018) Use of plant growth promoting rhizobacteria (PGPRs) with multiple plant growth promoting traits in stress agriculture: action mechanisms and future prospects. Ecotoxicol Environ Saf 156:225–246. https://doi.org/10.1016/j.ecoenv.2018.03.013 10.1016/j.ecoenv.2018.03.013

[42]

Farooqi ZUR, Ayub MA, Zia ur Rehman M et al (2020) Regulation of drought stress in plants. In: Tripathi DK, Singh VP, Chauchan D et al (eds) Plant life under changing environment. Academic Press, New York, pp 77–104 10.1016/b978-0-12-818204-8.00004-7

[43]

Fróna D, Szenderák J, Harangi-Rákos M (2019) The challenge of feeding the world. Sustainability 11:5816. https://doi.org/10.3390/su11205816 10.3390/su11205816

[44]

Gao J, Tarcea VG, Karnovsky A et al (2010) Metscape: a cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. Bioinformatics 26:971–973. https://doi.org/10.1093/bioinformatics/btq048 10.1093/bioinformatics/btq048

[45]

Gong F, Yang L, Tai F et al (2014) “Omics” of maize stress response for sustainable food production: Opportunities and challenges. OMICS 18:714–732. https://doi.org/10.1089/omi.2014.0125 10.1089/omi.2014.0125

[46]

Grady EN, MacDonald J, Liu L et al (2016) Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact. https://doi.org/10.1186/s12934-016-0603-7 10.1186/s12934-016-0603-7

[47]

Gupta A, Nair S (2020) Dynamics of insect–microbiome interaction influence host and microbial symbiont. Front Microbiol 11:01357. https://doi.org/10.3389/fmicb.2020.01357 10.3389/fmicb.2020.01357

[48]

Gupta G, Parihar SS, Singh V et al (2015) Plant growth promoting rhizobacteria (PGPR): Current and future prospects for development of sustainable agriculture. J Microb Biochem Technol 07. https://doi.org/10.4172/1948-5948.1000188 10.4172/1948-5948.1000188

[49]

Gupta S, Schillaci M, Roessner U (2022) Metabolomics as an emerging tool to study plant–microbe interactions. Emerg Top Life Sci 6:175–183. https://doi.org/10.1042/etls20210262 10.1042/etls20210262

[50]

Biological control of soil-borne pathogens by fluorescent pseudomonads

Dieter Haas, Geneviève Défago

Nature Reviews Microbiology 2005 10.1038/nrmicro1129

Showing 50 of 187 references

Metrics

1

Citations

187

References

Details

Published: Dec 10, 2025
Vol/Issue: 518(1)
Pages: 577-603
License: View

Authors

N

Nompumelelo R. Sibanyoni

K

Kamogelo Mmotla

M

Manamele D. Mashabela

Cite This Article

Nompumelelo R. Sibanyoni, Kamogelo Mmotla, Manamele D. Mashabela, et al. (2025). Chemical dialogues in the rhizosphere: Metabolomics perspectives on plant defence and microbial interactions. Plant and Soil, 518(1), 577-603. https://doi.org/10.1007/s11104-025-08010-4

Chemical dialogues in the rhizosphere: Metabolomics perspectives on plant defence and microbial interactions

You May Also Like