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Natural variation of the holobiont for sustainable agroecosystems
Journal article   Peer reviewed

Natural variation of the holobiont for sustainable agroecosystems

Wolfram Weckwerth, Palak Chaturvedi, Arindam Ghatak, Melina Kerou, Vanika Garg, Abhishek Bohra, Guntur V. Subbarao, Lisa Stein, Christa Schleper, Rajeev K. Varshney, …
Trends in plant science, Vol.30(9), pp.972-979
09/01/2025
DOI: https://doi.org/10.1016/j.tplants.2025.05.006
PMID: 40579258
url
https://doi.org/10.1016/j.tplants.2025.05.006View
Published (Version of record) Open

Abstract

biological nitrification inhibition (BNI) food security genome-wide association studies (GWAS) holobiont nature-based solutions (NbS) plant–microbiome association rhizosphere microbiome root exudates sustainable agriculture
Increasing nitrogen use efficiency (NUE) in plants and introducing biological nitrification inhibition (BNI) are essential developments towards sustainable agroecosystems. One effective strategy involves analyzing root exudates and their interactions with the soil microbiome.Root exudates release metabolites into the rhizosphere with inhibitory effects on the nitrification process in soil and control of the recruitment of beneficial microbiota enhancing growth and NUE.Systematic molecular analysis of plant–soil microbiome interactions provides essential insights towards a new sustainable green revolution by implementing the holobiont concept into breeding programs.Employing an intersectional panome-wide association study (PWAS) approach, combined with metabolome, microbiome, and phenotypic GWAS, can identify gene candidates in host plants that control root exudates, soil microbiome composition, and BNI activity. Plant evolution is largely driven by plant–microbe interactions, yet the ecology of the plant holobiont is not well understood at a molecular level. However, these relationships hold diverse benefits for sustainable agriculture as nature-based solutions (NbS). We propose a workflow to enhance understanding of natural variation in the plant–soil microbiome holobiont, addressing key challenges like growth promotion, stress resilience, nitrogen use efficiency (NUE), biological nitrification inhibition (BNI), healthy soils, and improving fertilization practices towards a more natural agroecosystem. We discuss a panome-wide association study (PWAS) approach to discover and incorporate novel genetic diversity from exotic germplasm into breeding populations. Ultimately, understanding natural variation of the holobiont in agroecosystems will contribute to the development of novel climate-resilient crop varieties for food security. Plant evolution is largely driven by plant–microbe interactions, yet the ecology of the plant holobiont is not well understood at a molecular level. However, these relationships hold diverse benefits for sustainable agriculture as nature-based solutions (NbS). We propose a workflow to enhance understanding of natural variation in the plant–soil microbiome holobiont, addressing key challenges like growth promotion, stress resilience, nitrogen use efficiency (NUE), biological nitrification inhibition (BNI), healthy soils, and improving fertilization practices towards a more natural agroecosystem. We discuss a panome-wide association study (PWAS) approach to discover and incorporate novel genetic diversity from exotic germplasm into breeding populations. Ultimately, understanding natural variation of the holobiont in agroecosystems will contribute to the development of novel climate-resilient crop varieties for food security.

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