Resistance breeding of common bean shapes the physiology of the rhizosphere microbiome

Lucas William Mendes; Miriam Gonçalves De Chaves; Mariley de Cássia da Fonseca; Rodrigo Mendes; Jos M Raaijmakers; Siu Mui Tsai

doi:10.3389/fmicb.2019.02252

Resistance breeding of common bean shapes the physiology of the rhizosphere microbiome

Lucas William Mendes (Corresponding author), Miriam Gonçalves De Chaves, Mariley de Cássia da Fonseca, Rodrigo Mendes, Jos M Raaijmakers, Siu Mui Tsai

NIOO - Microbial Ecology (ME)

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

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Abstract

The taxonomically diverse rhizosphere microbiome contributes to plant nutrition, growth and health, including protection against soil-borne pathogens. We previously showed that breeding for Fusarium-resistance in common bean changed the rhizosphere microbiome composition and functioning. Here, we assessed the impact of Fusarium-resistance breeding in common bean on microbiome physiology. Combined with metatranscriptome data, community-level physiological profiling by Biolog EcoPlate analyses revealed that the rhizosphere microbiome of the Fusarium-resistant accession was distinctly different from that of the Fusarium-susceptible accession, with higher consumption of amino acids and amines, higher metabolism of xylanase and sialidase, and higher expression of genes associated with nitrogen, phosphorus and iron metabolism. The resistome analysis indicates higher expression of soxR, which is involved in protecting bacteria against oxidative stress induced by a pathogen invasion. These results further support our hypothesis that breeding for resistance has unintentionally shaped the assembly and activity of the rhizobacterial community towards a higher abundance of specific rhizosphere competent bacterial taxa that can provide complementary protection against fungal root infections.

Original language	English
Article number	2019.02252
Journal	Frontiers in Microbiology
Volume	10
Early online date	2019
DOIs	https://doi.org/10.3389/fmicb.2019.02252
Publication status	Published - 2019

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international
Plan_S-Compliant_OA

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10.3389/fmicb.2019.02252Licence: CC BY

6821_MendesFinal published version, 1.75 MBLicence: CC BY

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title = "Resistance breeding of common bean shapes the physiology of the rhizosphere microbiome",

abstract = "The taxonomically diverse rhizosphere microbiome contributes to plant nutrition, growth and health, including protection against soil-borne pathogens. We previously showed that breeding for Fusarium-resistance in common bean changed the rhizosphere microbiome composition and functioning. Here, we assessed the impact of Fusarium-resistance breeding in common bean on microbiome physiology. Combined with metatranscriptome data, community-level physiological profiling by Biolog EcoPlate analyses revealed that the rhizosphere microbiome of the Fusarium-resistant accession was distinctly different from that of the Fusarium-susceptible accession, with higher consumption of amino acids and amines, higher metabolism of xylanase and sialidase, and higher expression of genes associated with nitrogen, phosphorus and iron metabolism. The resistome analysis indicates higher expression of soxR, which is involved in protecting bacteria against oxidative stress induced by a pathogen invasion. These results further support our hypothesis that breeding for resistance has unintentionally shaped the assembly and activity of the rhizobacterial community towards a higher abundance of specific rhizosphere competent bacterial taxa that can provide complementary protection against fungal root infections.",

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author = "Mendes, {Lucas William} and {Gon{\c c}alves De Chaves}, Miriam and {da Fonseca}, {Mariley de C{\'a}ssia} and Rodrigo Mendes and Raaijmakers, {Jos M} and Tsai, {Siu Mui}",

note = "6821, ME; Data Archiving: Data archived at MG-RAST The metatranscriptome data used in this study are available in MG-RAST server under the project {\textquoteleft}Common Bean Rhizosphere Metatranscriptome{\textquoteright} (mgp20659). Not NIOO data",

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AU - Mendes, Lucas William

AU - Gonçalves De Chaves, Miriam

AU - da Fonseca, Mariley de Cássia

AU - Mendes, Rodrigo

AU - Raaijmakers, Jos M

AU - Tsai, Siu Mui

N1 - 6821, ME; Data Archiving: Data archived at MG-RAST The metatranscriptome data used in this study are available in MG-RAST server under the project ‘Common Bean Rhizosphere Metatranscriptome’ (mgp20659). Not NIOO data

PY - 2019

Y1 - 2019

N2 - The taxonomically diverse rhizosphere microbiome contributes to plant nutrition, growth and health, including protection against soil-borne pathogens. We previously showed that breeding for Fusarium-resistance in common bean changed the rhizosphere microbiome composition and functioning. Here, we assessed the impact of Fusarium-resistance breeding in common bean on microbiome physiology. Combined with metatranscriptome data, community-level physiological profiling by Biolog EcoPlate analyses revealed that the rhizosphere microbiome of the Fusarium-resistant accession was distinctly different from that of the Fusarium-susceptible accession, with higher consumption of amino acids and amines, higher metabolism of xylanase and sialidase, and higher expression of genes associated with nitrogen, phosphorus and iron metabolism. The resistome analysis indicates higher expression of soxR, which is involved in protecting bacteria against oxidative stress induced by a pathogen invasion. These results further support our hypothesis that breeding for resistance has unintentionally shaped the assembly and activity of the rhizobacterial community towards a higher abundance of specific rhizosphere competent bacterial taxa that can provide complementary protection against fungal root infections.

AB - The taxonomically diverse rhizosphere microbiome contributes to plant nutrition, growth and health, including protection against soil-borne pathogens. We previously showed that breeding for Fusarium-resistance in common bean changed the rhizosphere microbiome composition and functioning. Here, we assessed the impact of Fusarium-resistance breeding in common bean on microbiome physiology. Combined with metatranscriptome data, community-level physiological profiling by Biolog EcoPlate analyses revealed that the rhizosphere microbiome of the Fusarium-resistant accession was distinctly different from that of the Fusarium-susceptible accession, with higher consumption of amino acids and amines, higher metabolism of xylanase and sialidase, and higher expression of genes associated with nitrogen, phosphorus and iron metabolism. The resistome analysis indicates higher expression of soxR, which is involved in protecting bacteria against oxidative stress induced by a pathogen invasion. These results further support our hypothesis that breeding for resistance has unintentionally shaped the assembly and activity of the rhizobacterial community towards a higher abundance of specific rhizosphere competent bacterial taxa that can provide complementary protection against fungal root infections.

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KW - Plan_S-Compliant_OA

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DO - 10.3389/fmicb.2019.02252

M3 - Article

SN - 1664-302X

VL - 10

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

M1 - 2019.02252

ER -

Resistance breeding of common bean shapes the physiology of the rhizosphere microbiome

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