Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interactions

Carmen Escudero-Martinez; Eithne Y. Browne; Henning Schwalm; Michael Santangeli; Molly Brown; Lawrie Brown; David M. Roberts; Aoife M. Duff; Jenny Morris; Peter E. Hedley; Peter Thorpe; James Abbott; Fiona P Brennan; Davide Bulgarelli; Tim S. George; Eva Oburger

doi:10.1111/nph.71174

Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interactions

Carmen Escudero-Martinez (Lead / Corresponding author)
, Eithne Y. Browne
, Henning Schwalm
, Michael Santangeli
, Molly Brown
, Lawrie Brown
, David M. Roberts
, Aoife M. Duff
, Jenny Morris
, Peter E. Hedley
, Peter Thorpe
, James Abbott
, Fiona P Brennan
, Davide Bulgarelli
, Tim S. George
, Eva Oburger (Lead / Corresponding author)

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

20 Downloads (Pure)

Abstract

Summary

• Deciphering the root exudate-driven interplay between plants and the rhizosphere microbiota is essential for understanding plant adaptation to the environment and future-proofing crop production. However, sampling root exudates and rhizosphere soil remains challenging due to the low throughput and destructive nature of the process.

• We used the staple crop barley [Hordeum vulgare] as a model to benchmark different sampling approaches for simultaneous exudation and microbiota profiling of soil-grown plants.

• Exudate profiles and total dissolved organic carbon exudation rates were consistent across different sampling approaches, whereas root biomass, root morphology measurements, and organic nitrogen exudation varied.

• High-throughput amplicon sequencing and quantitative PCR (qPCR) of phylogenetic markers and nitrogen cycle-selected genes revealed a protocol-specific footprint in the composition and abundance of rhizosphere bacterial and fungal microbiota. Yet, on average, 75% of microbes enriched in, and differentiating between, barley rhizosphere and unplanted soil controls were recovered across all the sampling approaches evaluated.

• Our results demonstrated that, under the tested conditions, different sampling approaches produced comparable microbiota and exudation patterns, enabling the integrated study of root exudation and microbial profiles from the same plant. The observed differences across sampling approaches must be considered according to the experimental scope.

Original language	English
Pages (from-to)	4077-4092
Number of pages	16
Journal	New Phytologist
Volume	250
Issue number	6
Early online date	19 Apr 2026
DOIs	https://doi.org/10.1111/nph.71174
Publication status	Published - Jun 2026

Keywords

below ground interactions
methods
root exudates
rhizosphere microbiota
root traits
rhizosphere processes
soil-grown plants
sustainable agriculture

ASJC Scopus subject areas

Physiology
Plant Science

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10.1111/nph.71174Licence: CC BY-NC

Final Published VersionFinal published version, 1.3 MBLicence: CC BY-NC

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Escudero-Martinez, C., Browne, E. Y., Schwalm, H., Santangeli, M., Brown, M., Brown, L., Roberts, D. M., Duff, A. M., Morris, J., Hedley, P. E., Thorpe, P., Abbott, J., Brennan, F. P., Bulgarelli, D., George, T. S., & Oburger, E. (2026). Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interactions. New Phytologist, 250(6), 4077-4092. https://doi.org/10.1111/nph.71174

@article{8663eddd4f7b426bbf78c8b3beaeccb2,

title = "Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interactions",

abstract = "Summary • Deciphering the root exudate-driven interplay between plants and the rhizosphere microbiota is essential for understanding plant adaptation to the environment and future-proofing crop production. However, sampling root exudates and rhizosphere soil remains challenging due to the low throughput and destructive nature of the process. • We used the staple crop barley [Hordeum vulgare] as a model to benchmark different sampling approaches for simultaneous exudation and microbiota profiling of soil-grown plants. • Exudate profiles and total dissolved organic carbon exudation rates were consistent across different sampling approaches, whereas root biomass, root morphology measurements, and organic nitrogen exudation varied. • High-throughput amplicon sequencing and quantitative PCR (qPCR) of phylogenetic markers and nitrogen cycle-selected genes revealed a protocol-specific footprint in the composition and abundance of rhizosphere bacterial and fungal microbiota. Yet, on average, 75\% of microbes enriched in, and differentiating between, barley rhizosphere and unplanted soil controls were recovered across all the sampling approaches evaluated. • Our results demonstrated that, under the tested conditions, different sampling approaches produced comparable microbiota and exudation patterns, enabling the integrated study of root exudation and microbial profiles from the same plant. The observed differences across sampling approaches must be considered according to the experimental scope.",

keywords = "below ground interactions, methods, root exudates, rhizosphere microbiota, root traits, rhizosphere processes, soil-grown plants, sustainable agriculture",

author = "Carmen Escudero-Martinez and Browne, \{Eithne Y.\} and Henning Schwalm and Michael Santangeli and Molly Brown and Lawrie Brown and Roberts, \{David M.\} and Duff, \{Aoife M.\} and Jenny Morris and Hedley, \{Peter E.\} and Peter Thorpe and James Abbott and Brennan, \{Fiona P\} and Davide Bulgarelli and George, \{Tim S.\} and Eva Oburger",

note = "Copyright: {\textcopyright} 2026 The Author(s). New Phytologist {\textcopyright} 2026 New Phytologist Foundation.",

year = "2026",

month = jun,

doi = "10.1111/nph.71174",

language = "English",

volume = "250",

pages = "4077--4092",

journal = "New Phytologist",

issn = "0028-646X",

publisher = "Wiley-Blackwell",

number = "6",

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Escudero-Martinez, C, Browne, EY, Schwalm, H, Santangeli, M, Brown, M, Brown, L, Roberts, DM, Duff, AM, Morris, J, Hedley, PE, Thorpe, P , Abbott, J, Brennan, FP, Bulgarelli, D, George, TS & Oburger, E 2026, 'Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interactions', New Phytologist, vol. 250, no. 6, pp. 4077-4092. https://doi.org/10.1111/nph.71174

TY - JOUR

T1 - Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interactions

AU - Escudero-Martinez, Carmen

AU - Browne, Eithne Y.

AU - Schwalm, Henning

AU - Santangeli, Michael

AU - Brown, Molly

AU - Brown, Lawrie

AU - Roberts, David M.

AU - Duff, Aoife M.

AU - Morris, Jenny

AU - Hedley, Peter E.

AU - Thorpe, Peter

AU - Abbott, James

AU - Brennan, Fiona P

AU - Bulgarelli, Davide

AU - George, Tim S.

AU - Oburger, Eva

PY - 2026/6

Y1 - 2026/6

N2 - Summary • Deciphering the root exudate-driven interplay between plants and the rhizosphere microbiota is essential for understanding plant adaptation to the environment and future-proofing crop production. However, sampling root exudates and rhizosphere soil remains challenging due to the low throughput and destructive nature of the process. • We used the staple crop barley [Hordeum vulgare] as a model to benchmark different sampling approaches for simultaneous exudation and microbiota profiling of soil-grown plants. • Exudate profiles and total dissolved organic carbon exudation rates were consistent across different sampling approaches, whereas root biomass, root morphology measurements, and organic nitrogen exudation varied. • High-throughput amplicon sequencing and quantitative PCR (qPCR) of phylogenetic markers and nitrogen cycle-selected genes revealed a protocol-specific footprint in the composition and abundance of rhizosphere bacterial and fungal microbiota. Yet, on average, 75% of microbes enriched in, and differentiating between, barley rhizosphere and unplanted soil controls were recovered across all the sampling approaches evaluated. • Our results demonstrated that, under the tested conditions, different sampling approaches produced comparable microbiota and exudation patterns, enabling the integrated study of root exudation and microbial profiles from the same plant. The observed differences across sampling approaches must be considered according to the experimental scope.

AB - Summary • Deciphering the root exudate-driven interplay between plants and the rhizosphere microbiota is essential for understanding plant adaptation to the environment and future-proofing crop production. However, sampling root exudates and rhizosphere soil remains challenging due to the low throughput and destructive nature of the process. • We used the staple crop barley [Hordeum vulgare] as a model to benchmark different sampling approaches for simultaneous exudation and microbiota profiling of soil-grown plants. • Exudate profiles and total dissolved organic carbon exudation rates were consistent across different sampling approaches, whereas root biomass, root morphology measurements, and organic nitrogen exudation varied. • High-throughput amplicon sequencing and quantitative PCR (qPCR) of phylogenetic markers and nitrogen cycle-selected genes revealed a protocol-specific footprint in the composition and abundance of rhizosphere bacterial and fungal microbiota. Yet, on average, 75% of microbes enriched in, and differentiating between, barley rhizosphere and unplanted soil controls were recovered across all the sampling approaches evaluated. • Our results demonstrated that, under the tested conditions, different sampling approaches produced comparable microbiota and exudation patterns, enabling the integrated study of root exudation and microbial profiles from the same plant. The observed differences across sampling approaches must be considered according to the experimental scope.

KW - below ground interactions

KW - methods

KW - root exudates

KW - rhizosphere microbiota

KW - root traits

KW - rhizosphere processes

KW - soil-grown plants

KW - sustainable agriculture

UR - https://www.scopus.com/pages/publications/105036114750

U2 - 10.1111/nph.71174

DO - 10.1111/nph.71174

M3 - Article

C2 - 42002837

SN - 0028-646X

VL - 250

SP - 4077

EP - 4092

JO - New Phytologist

JF - New Phytologist

IS - 6

ER -

Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interactions

Abstract

Keywords

ASJC Scopus subject areas

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Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interactions

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