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; Sieglinde Snapp

doi:10.1016/j.tplants.2025.05.006

Natural variation of the holobiont for sustainable agroecosystems

Wolfram Weckwerth (Corresponding author)
, Palak Chaturvedi
, Arindam Ghatak
, Melina Kerou
, Vanika Garg
, Abhishek Bohra
, Guntur V Subbarao
, Lisa Stein
, Christa Schleper
, Rajeev K Varshney
, Sieglinde Snapp

Publications: Contribution to journal › Review › Peer Reviewed

Abstract

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.

Original language	English
Pages (from-to)	972-979
Number of pages	8
Journal	Trends in Plant Science
Volume	30
Issue number	9
Early online date	27 Jun 2025
DOIs	https://doi.org/10.1016/j.tplants.2025.05.006
Publication status	Published - Sept 2025

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 2 Zero Hunger

Austrian Fields of Science 2012

106022 Microbiology
106030 Plant ecology

Keywords

nature-based solutions (NbS)
biological nitrification inhibition (BNI)
holobiont
food security
rhizosphere microbiome
root exudates
genome-wide association studies (GWAS)
sustainable agriculture
plant–microbiome association

Access to Document

10.1016/j.tplants.2025.05.006Licence: CC BY 4.0

https://phaidra.univie.ac.at/o:2346676Licence: CC BY 4.0

Cite this

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title = "Natural variation of the holobiont for sustainable agroecosystems",

abstract = "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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author = "Wolfram Weckwerth and Palak Chaturvedi and Arindam Ghatak and Melina Kerou and Vanika Garg and Abhishek Bohra and Subbarao, \{Guntur V\} and Lisa Stein and Christa Schleper and Varshney, \{Rajeev K\} and Sieglinde Snapp",

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year = "2025",

month = sep,

doi = "10.1016/j.tplants.2025.05.006",

language = "English",

volume = "30",

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T1 - Natural variation of the holobiont for sustainable agroecosystems

AU - Weckwerth, Wolfram

AU - Chaturvedi, Palak

AU - Ghatak, Arindam

AU - Kerou, Melina

AU - Garg, Vanika

AU - Bohra, Abhishek

AU - Subbarao, Guntur V

AU - Stein, Lisa

AU - Schleper, Christa

AU - Varshney, Rajeev K

AU - Snapp, Sieglinde

PY - 2025/9

Y1 - 2025/9

N2 - 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.

AB - 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.

KW - nature-based solutions (NbS)

KW - biological nitrification inhibition (BNI)

KW - holobiont

KW - food security

KW - rhizosphere microbiome

KW - root exudates

KW - genome-wide association studies (GWAS)

KW - sustainable agriculture

KW - plant–microbiome association

UR - https://www.scopus.com/pages/publications/105009319771

U2 - 10.1016/j.tplants.2025.05.006

DO - 10.1016/j.tplants.2025.05.006

M3 - Review

C2 - 40579258

SN - 1360-1385

VL - 30

SP - 972

EP - 979

JO - Trends in Plant Science

JF - Trends in Plant Science

IS - 9

ER -

Natural variation of the holobiont for sustainable agroecosystems

Abstract

UN SDGs

Austrian Fields of Science 2012

Keywords

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The Holobiont Revolution: How wheat is becoming more climate-resilient through nature-based plant breeding and machine learning

Cite this

Natural variation of the holobiont for sustainable agroecosystems

Abstract

UN SDGs

Austrian Fields of Science 2012

Keywords

Access to Document

Other files and links

Fingerprint

Press/Media

The Holobiont Revolution: How wheat is becoming more climate-resilient through nature-based plant breeding and machine learning

Cite this