Functional adaptations of the rhizosphere microbiome for drought-tolerance promotion in common bean

Ana Vitória Reina da Silva; Izadora de Cássia Mesquita Cunha; Thierry Alexandre Pellegrinetti; Eduardo Henrique Marcandalli Boleta; Luis Felipe Guandalin Zagatto; Solange dos Santos Silva Zagatto; Caroline Sayuri Nishisaka; Teresa Maria Lorizolla Mafra; Camila Maistro Patreze; Gordon F. Custer; Francisco Dini-Andreote; Rodrigo Mendes; Siu Mui Tsai; Lucas William Mendes

doi:10.1016/j.stress.2025.100860

Functional adaptations of the rhizosphere microbiome for drought-tolerance promotion in common bean

Ana Vitória Reina da Silva, Izadora de Cássia Mesquita Cunha, Thierry Alexandre Pellegrinetti, Eduardo Henrique Marcandalli Boleta, Luis Felipe Guandalin Zagatto, Solange dos Santos Silva Zagatto, Caroline Sayuri Nishisaka, Teresa Maria Lorizolla Mafra, Camila Maistro Patreze, Gordon F. Custer, Francisco Dini-Andreote, Rodrigo Mendes, Siu Mui Tsai, Lucas William Mendes^* (Corresponding author)

^*Corresponding author for this work

NIOO - Terrestrial Ecology (TE)

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

2 Citations (Scopus)

Abstract

Drought stress threatens global food security, highlighting the need for resilient crops. Harnessing rhizosphere microorganisms can improve plant performance in harsh conditions. Here, we investigated the rhizosphere microbiomes of drought-tolerant (BAT477, SEA5) and susceptible (IAC Milênio, IAC-Carioca 80SH) common bean cultivars (Phaseolus vulgaris L.) under contrasting water regimes in mesocosm experiments to assess microbiome functional modulation under drought. Analysis of plant growth, physiological responses, nutrient dynamics, and rhizosphere microbial functional diversity revealed that drought-tolerant cultivars exhibited greater water management, minimal growth reductions, and enrichment of beneficial microbial functions, including genes linked to drought tolerance. Notably, drought stress triggered differential abundance in 1864 microbial genes, highlighting a robust functional shift. Specifically, drought-tolerant cultivars showed an enrichment of genes related to osmotic response, photosynthetic efficiency (82–87 % reduction in photosynthesis in susceptible cultivars), oxidative stress mitigation, and osmoprotectant production, whereas susceptible cultivars relied more on genes associated with DNA repair and antioxidant defense, indicating a reactive rather than proactive stress response. Additionally, the rhizosphere microbiomes of drought-tolerant cultivars were enriched in functions related to biofilm formation, dormancy survival, and oxidative stress resistance. These cultivars also maintained higher photosynthetic activity and transpiration rates with more stable stomatal conductance. Upon rehydration, they partially restored physiological functions (e.g., 48–57 % recovery in photosynthesis), further demonstrating microbiome-conferred resilience. These findings underscore the potential of plant-microbiome interactions in adapting to water stress, suggesting that microbiome selection could be a promising strategy for developing drought-resilient crops and advancing sustainable agricultural practices.

Original language	English
Article number	100860
Journal	Plant Stress
Volume	16
DOIs	https://doi.org/10.1016/j.stress.2025.100860
Publication status	Published - Jun 2025

Keywords

Abiotic stress
Metagenomics
Plant-microbe interaction
Water stress

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10.1016/j.stress.2025.100860Licence: CC BY-NC

Cite this

Silva, A. V. R. D., Cunha, I. D. C. M., Pellegrinetti, T. A., Boleta, E. H. M., Zagatto, L. F. G., Zagatto, S. D. S. S., Nishisaka, C. S., Mafra, T. M. L., Patreze, C. M., Custer, G. F., Dini-Andreote, F., Mendes, R., Tsai, S. M., & Mendes, L. W. (2025). Functional adaptations of the rhizosphere microbiome for drought-tolerance promotion in common bean. Plant Stress, 16, Article 100860. https://doi.org/10.1016/j.stress.2025.100860

@article{2a68ffb73990473aba8b7bd82e4ecfbf,

title = "Functional adaptations of the rhizosphere microbiome for drought-tolerance promotion in common bean",

abstract = "Drought stress threatens global food security, highlighting the need for resilient crops. Harnessing rhizosphere microorganisms can improve plant performance in harsh conditions. Here, we investigated the rhizosphere microbiomes of drought-tolerant (BAT477, SEA5) and susceptible (IAC Mil{\^e}nio, IAC-Carioca 80SH) common bean cultivars (Phaseolus vulgaris L.) under contrasting water regimes in mesocosm experiments to assess microbiome functional modulation under drought. Analysis of plant growth, physiological responses, nutrient dynamics, and rhizosphere microbial functional diversity revealed that drought-tolerant cultivars exhibited greater water management, minimal growth reductions, and enrichment of beneficial microbial functions, including genes linked to drought tolerance. Notably, drought stress triggered differential abundance in 1864 microbial genes, highlighting a robust functional shift. Specifically, drought-tolerant cultivars showed an enrichment of genes related to osmotic response, photosynthetic efficiency (82–87 % reduction in photosynthesis in susceptible cultivars), oxidative stress mitigation, and osmoprotectant production, whereas susceptible cultivars relied more on genes associated with DNA repair and antioxidant defense, indicating a reactive rather than proactive stress response. Additionally, the rhizosphere microbiomes of drought-tolerant cultivars were enriched in functions related to biofilm formation, dormancy survival, and oxidative stress resistance. These cultivars also maintained higher photosynthetic activity and transpiration rates with more stable stomatal conductance. Upon rehydration, they partially restored physiological functions (e.g., 48–57 % recovery in photosynthesis), further demonstrating microbiome-conferred resilience. These findings underscore the potential of plant-microbiome interactions in adapting to water stress, suggesting that microbiome selection could be a promising strategy for developing drought-resilient crops and advancing sustainable agricultural practices.",

keywords = "Abiotic stress, Metagenomics, Plant-microbe interaction, Water stress",

author = "Silva, {Ana Vit{\'o}ria Reina da} and Cunha, {Izadora de C{\'a}ssia Mesquita} and Pellegrinetti, {Thierry Alexandre} and Boleta, {Eduardo Henrique Marcandalli} and Zagatto, {Luis Felipe Guandalin} and Zagatto, {Solange dos Santos Silva} and Nishisaka, {Caroline Sayuri} and Mafra, {Teresa Maria Lorizolla} and Patreze, {Camila Maistro} and Custer, {Gordon F.} and Francisco Dini-Andreote and Rodrigo Mendes and Tsai, {Siu Mui} and Mendes, {Lucas William}",

note = "Data archiving: no NIOO data",

year = "2025",

month = jun,

doi = "10.1016/j.stress.2025.100860",

language = "English",

volume = "16",

journal = "Plant Stress",

issn = "2667-064X",

publisher = "Elsevier B.V.",

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Silva, AVRD, Cunha, IDCM, Pellegrinetti, TA, Boleta, EHM, Zagatto, LFG, Zagatto, SDSS, Nishisaka, CS, Mafra, TML, Patreze, CM, Custer, GF, Dini-Andreote, F, Mendes, R, Tsai, SM & Mendes, LW 2025, 'Functional adaptations of the rhizosphere microbiome for drought-tolerance promotion in common bean', Plant Stress, vol. 16, 100860. https://doi.org/10.1016/j.stress.2025.100860

TY - JOUR

T1 - Functional adaptations of the rhizosphere microbiome for drought-tolerance promotion in common bean

AU - Silva, Ana Vitória Reina da

AU - Cunha, Izadora de Cássia Mesquita

AU - Pellegrinetti, Thierry Alexandre

AU - Boleta, Eduardo Henrique Marcandalli

AU - Zagatto, Luis Felipe Guandalin

AU - Zagatto, Solange dos Santos Silva

AU - Nishisaka, Caroline Sayuri

AU - Mafra, Teresa Maria Lorizolla

AU - Patreze, Camila Maistro

AU - Custer, Gordon F.

AU - Dini-Andreote, Francisco

AU - Mendes, Rodrigo

AU - Tsai, Siu Mui

AU - Mendes, Lucas William

N1 - Data archiving: no NIOO data

PY - 2025/6

Y1 - 2025/6

N2 - Drought stress threatens global food security, highlighting the need for resilient crops. Harnessing rhizosphere microorganisms can improve plant performance in harsh conditions. Here, we investigated the rhizosphere microbiomes of drought-tolerant (BAT477, SEA5) and susceptible (IAC Milênio, IAC-Carioca 80SH) common bean cultivars (Phaseolus vulgaris L.) under contrasting water regimes in mesocosm experiments to assess microbiome functional modulation under drought. Analysis of plant growth, physiological responses, nutrient dynamics, and rhizosphere microbial functional diversity revealed that drought-tolerant cultivars exhibited greater water management, minimal growth reductions, and enrichment of beneficial microbial functions, including genes linked to drought tolerance. Notably, drought stress triggered differential abundance in 1864 microbial genes, highlighting a robust functional shift. Specifically, drought-tolerant cultivars showed an enrichment of genes related to osmotic response, photosynthetic efficiency (82–87 % reduction in photosynthesis in susceptible cultivars), oxidative stress mitigation, and osmoprotectant production, whereas susceptible cultivars relied more on genes associated with DNA repair and antioxidant defense, indicating a reactive rather than proactive stress response. Additionally, the rhizosphere microbiomes of drought-tolerant cultivars were enriched in functions related to biofilm formation, dormancy survival, and oxidative stress resistance. These cultivars also maintained higher photosynthetic activity and transpiration rates with more stable stomatal conductance. Upon rehydration, they partially restored physiological functions (e.g., 48–57 % recovery in photosynthesis), further demonstrating microbiome-conferred resilience. These findings underscore the potential of plant-microbiome interactions in adapting to water stress, suggesting that microbiome selection could be a promising strategy for developing drought-resilient crops and advancing sustainable agricultural practices.

AB - Drought stress threatens global food security, highlighting the need for resilient crops. Harnessing rhizosphere microorganisms can improve plant performance in harsh conditions. Here, we investigated the rhizosphere microbiomes of drought-tolerant (BAT477, SEA5) and susceptible (IAC Milênio, IAC-Carioca 80SH) common bean cultivars (Phaseolus vulgaris L.) under contrasting water regimes in mesocosm experiments to assess microbiome functional modulation under drought. Analysis of plant growth, physiological responses, nutrient dynamics, and rhizosphere microbial functional diversity revealed that drought-tolerant cultivars exhibited greater water management, minimal growth reductions, and enrichment of beneficial microbial functions, including genes linked to drought tolerance. Notably, drought stress triggered differential abundance in 1864 microbial genes, highlighting a robust functional shift. Specifically, drought-tolerant cultivars showed an enrichment of genes related to osmotic response, photosynthetic efficiency (82–87 % reduction in photosynthesis in susceptible cultivars), oxidative stress mitigation, and osmoprotectant production, whereas susceptible cultivars relied more on genes associated with DNA repair and antioxidant defense, indicating a reactive rather than proactive stress response. Additionally, the rhizosphere microbiomes of drought-tolerant cultivars were enriched in functions related to biofilm formation, dormancy survival, and oxidative stress resistance. These cultivars also maintained higher photosynthetic activity and transpiration rates with more stable stomatal conductance. Upon rehydration, they partially restored physiological functions (e.g., 48–57 % recovery in photosynthesis), further demonstrating microbiome-conferred resilience. These findings underscore the potential of plant-microbiome interactions in adapting to water stress, suggesting that microbiome selection could be a promising strategy for developing drought-resilient crops and advancing sustainable agricultural practices.

KW - Abiotic stress

KW - Metagenomics

KW - Plant-microbe interaction

KW - Water stress

U2 - 10.1016/j.stress.2025.100860

DO - 10.1016/j.stress.2025.100860

M3 - Article

AN - SCOPUS:105003493153

SN - 2667-064X

VL - 16

JO - Plant Stress

JF - Plant Stress

M1 - 100860

ER -