Identifying plant genes shaping microbiota composition in the barley rhizosphere

Carmen Escudero-Martinez; Max Coulter; Rodrigo Alegria Terrazas; Alexandre Foito; Rumana Kapadia; Laura Pietrangelo; Mauro Maver; Rajiv Sharma; Alessio Aprile; Jenny Morris; Pete E Hedley; Andreas Maurer; Klaus Pillen; Gino Naclerio; Tanja Mimmo; Geoffrey J Barton; Robbie Waugh; James Abbott; Davide Bulgarelli

doi:10.1038/s41467-022-31022-y

Identifying plant genes shaping microbiota composition in the barley rhizosphere

Carmen Escudero-Martinez, Max Coulter, Rodrigo Alegria Terrazas, Alexandre Foito, Rumana Kapadia, Laura Pietrangelo, Mauro Maver, Rajiv Sharma, Alessio Aprile, Jenny Morris, Pete E Hedley, Andreas Maurer, Klaus Pillen, Gino Naclerio, Tanja Mimmo, Geoffrey J Barton, Robbie Waugh, James Abbott, Davide Bulgarelli^*

^*Corresponding author for this work

Principal’s Research Group

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

54 Citations (Scopus)

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Abstract

A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant's capacity of shaping rhizosphere microbes.

Original language	English
Article number	3443
Pages (from-to)	3443
Journal	Nature Communications
Volume	13
Issue number	1
Early online date	16 Jun 2022
DOIs	https://doi.org/10.1038/s41467-022-31022-y
Publication status	First published - 16 Jun 2022

Bibliographical note

Keywords

Bacteria/genetics
Genes, Plant/genetics
Hordeum/genetics
Microbiota/genetics
Plant Roots/genetics
Rhizosphere
Soil/chemistry
Soil Microbiology

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s41467-022-31022-yFinal published version, 1.84 MBLicence: CC BY

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Escudero-Martinez, C., Coulter, M., Alegria Terrazas, R., Foito, A., Kapadia, R., Pietrangelo, L., Maver, M., Sharma, R., Aprile, A., Morris, J., Hedley, P. E., Maurer, A., Pillen, K., Naclerio, G., Mimmo, T., Barton, G. J., Waugh, R., Abbott, J., & Bulgarelli, D. (2022). Identifying plant genes shaping microbiota composition in the barley rhizosphere. Nature Communications, 13(1), 3443. Article 3443. Advance online publication. https://doi.org/10.1038/s41467-022-31022-y

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abstract = "A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant's capacity of shaping rhizosphere microbes.",

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Escudero-Martinez, C, Coulter, M, Alegria Terrazas, R, Foito, A, Kapadia, R, Pietrangelo, L, Maver, M, Sharma, R, Aprile, A, Morris, J, Hedley, PE, Maurer, A, Pillen, K, Naclerio, G, Mimmo, T, Barton, GJ, Waugh, R, Abbott, J & Bulgarelli, D 2022, 'Identifying plant genes shaping microbiota composition in the barley rhizosphere', Nature Communications, vol. 13, no. 1, 3443, pp. 3443. https://doi.org/10.1038/s41467-022-31022-y

TY - JOUR

T1 - Identifying plant genes shaping microbiota composition in the barley rhizosphere

AU - Escudero-Martinez, Carmen

AU - Coulter, Max

AU - Alegria Terrazas, Rodrigo

AU - Foito, Alexandre

AU - Kapadia, Rumana

AU - Pietrangelo, Laura

AU - Maver, Mauro

AU - Sharma, Rajiv

AU - Aprile, Alessio

AU - Morris, Jenny

AU - Hedley, Pete E

AU - Maurer, Andreas

AU - Pillen, Klaus

AU - Naclerio, Gino

AU - Mimmo, Tanja

AU - Barton, Geoffrey J

AU - Waugh, Robbie

AU - Abbott, James

AU - Bulgarelli, Davide

PY - 2022/6/16

Y1 - 2022/6/16

N2 - A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant's capacity of shaping rhizosphere microbes.

AB - A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant's capacity of shaping rhizosphere microbes.

KW - Bacteria/genetics

KW - Genes, Plant/genetics

KW - Hordeum/genetics

KW - Microbiota/genetics

KW - Plant Roots/genetics

KW - Rhizosphere

KW - Soil/chemistry

KW - Soil Microbiology

UR - https://github.com/BulgarelliD-Lab/Microbiota_mapping

UR - https://ics.hutton.ac.uk/barleyrtd/bart_v2_18.html

UR - http://www.scopus.com/inward/record.url?scp=85132069806&partnerID=8YFLogxK

U2 - 10.1038/s41467-022-31022-y

DO - 10.1038/s41467-022-31022-y

M3 - Article

C2 - 35710760

SN - 2041-1723

VL - 13

SP - 3443

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 3443

ER -

Identifying plant genes shaping microbiota composition in the barley rhizosphere

Abstract

Bibliographical note

Keywords

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