Shifts in the rhizosphere microbiome and exudation profile of avocado (Persea americana Mill.) during infection by Phytophthora cinnamomi and in presence of a biocontrol bacterial strain
Abstract Background Rhizosphere microbiomes are fundamental for plant health, development, and productivity, but can be altered by the incidence of soil-borne pathogens. The dysbiosis (disturbance of the microbiome structure of healthy plants) caused by these pathogens, combined with the recruitment...
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| Format: | Article |
| Language: | English |
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CABI
2023-07-01
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| Series: | CABI Agriculture and Bioscience |
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| Online Access: | https://doi.org/10.1186/s43170-023-00167-1 |
| _version_ | 1826829936490446848 |
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| author | Frédérique Reverchon Mariel García-Meléndez Edgar Guevara-Avendaño Oscar Mora-Chávez Itzel A. Solís-García Wesley Dáttilo José A. Guererro-Analco Alfonso Méndez-Bravo Juan L. Monribot-Villanueva Violeta Patiño-Conde Fernando Pineda-García Eria A. Rebollar |
| author_facet | Frédérique Reverchon Mariel García-Meléndez Edgar Guevara-Avendaño Oscar Mora-Chávez Itzel A. Solís-García Wesley Dáttilo José A. Guererro-Analco Alfonso Méndez-Bravo Juan L. Monribot-Villanueva Violeta Patiño-Conde Fernando Pineda-García Eria A. Rebollar |
| author_sort | Frédérique Reverchon |
| collection | DOAJ |
| description | Abstract Background Rhizosphere microbiomes are fundamental for plant health, development, and productivity, but can be altered by the incidence of soil-borne pathogens. The dysbiosis (disturbance of the microbiome structure of healthy plants) caused by these pathogens, combined with the recruitment of beneficial microorganisms by the diseased plant, may cause shifts in the rhizosphere microbiome during the infection process. These shifts are likely to be associated with changes in the rhizosphere metabolic profile, as the biochemical dialog, or crosstalk, between host plants and their microbiome is mostly mediated by root exudates. Our objective was to elucidate the shifts in the avocado rhizosphere microbiome and associated changes in the rhizosphere metabolome induced by the infection of the oomycete Phytophthora cinnamomi. We also evaluated the effect of inoculating a bacterial biological control agent (BCA) of P. cinnamomi on the avocado rhizosphere microbiome, in the presence and absence of the pathogen, and on morphological and physiological plant variables, to confirm the potential of the BCA to alleviate the stress induced by the disease. Dataset presentation Here, we present a novel dataset collected from a time-course experiment with four treatments: (1) control trees; (2) trees infected with P. cinnamomi; (3) trees inoculated with the BCA; (4) trees infected with P. cinnamomi and inoculated with the BCA. During the infection process, we measured plant morphological and physiological variables and collected rhizosphere soil samples for bacterial and fungal amplicon sequencing, bacterial RNA-seq and metabolomic analyses. Conclusions Collectively, our data elucidate the shifts in the avocado rhizosphere microbiome after infection by P. cinnamomi and when inoculated with a BCA, and help understand how a pathogen or a beneficial bacterium can alter plant-microbiome crosstalk. Understanding the effect of P. cinnamomi or a BCA on the avocado tree physiology and on the avocado rhizosphere microbiome and metabolome will direct our search for disease biomarkers or potential pathogen antagonists, help identify metabolites related to the recruitment of microorganisms, and assist us in developing integrated disease management strategies. |
| first_indexed | 2024-03-13T00:40:35Z |
| format | Article |
| id | doaj.art-5dcb0728f58b44b9a2593c7c5edc3547 |
| institution | Directory Open Access Journal |
| issn | 2662-4044 |
| language | English |
| last_indexed | 2025-02-16T09:23:26Z |
| publishDate | 2023-07-01 |
| publisher | CABI |
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| series | CABI Agriculture and Bioscience |
| spelling | doaj.art-5dcb0728f58b44b9a2593c7c5edc35472025-02-03T04:49:35ZengCABICABI Agriculture and Bioscience2662-40442023-07-01411610.1186/s43170-023-00167-1Shifts in the rhizosphere microbiome and exudation profile of avocado (Persea americana Mill.) during infection by Phytophthora cinnamomi and in presence of a biocontrol bacterial strainFrédérique Reverchon0Mariel García-Meléndez1Edgar Guevara-Avendaño2Oscar Mora-Chávez3Itzel A. Solís-García4Wesley Dáttilo5José A. Guererro-Analco6Alfonso Méndez-Bravo7Juan L. Monribot-Villanueva8Violeta Patiño-Conde9Fernando Pineda-García10Eria A. Rebollar11Red de Diversidad Biológica del Occidente Mexicano, Centro Regional del Bajío, Instituto de Ecología, A.C.Red de Diversidad Biológica del Occidente Mexicano, Centro Regional del Bajío, Instituto de Ecología, A.C.Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C.Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C.Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C.Red de Ecoetología, Instituto de Ecología, A.C.Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C.CONACYT, Laboratorio Nacional de Análisis y Síntesis Ecológica, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de MéxicoRed de Estudios Moleculares Avanzados, Instituto de Ecología, A.C.Laboratorio Nacional de Análisis y Síntesis Ecológica, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de MéxicoLaboratorio Nacional de Análisis y Síntesis Ecológica, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de MéxicoCentro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoAbstract Background Rhizosphere microbiomes are fundamental for plant health, development, and productivity, but can be altered by the incidence of soil-borne pathogens. The dysbiosis (disturbance of the microbiome structure of healthy plants) caused by these pathogens, combined with the recruitment of beneficial microorganisms by the diseased plant, may cause shifts in the rhizosphere microbiome during the infection process. These shifts are likely to be associated with changes in the rhizosphere metabolic profile, as the biochemical dialog, or crosstalk, between host plants and their microbiome is mostly mediated by root exudates. Our objective was to elucidate the shifts in the avocado rhizosphere microbiome and associated changes in the rhizosphere metabolome induced by the infection of the oomycete Phytophthora cinnamomi. We also evaluated the effect of inoculating a bacterial biological control agent (BCA) of P. cinnamomi on the avocado rhizosphere microbiome, in the presence and absence of the pathogen, and on morphological and physiological plant variables, to confirm the potential of the BCA to alleviate the stress induced by the disease. Dataset presentation Here, we present a novel dataset collected from a time-course experiment with four treatments: (1) control trees; (2) trees infected with P. cinnamomi; (3) trees inoculated with the BCA; (4) trees infected with P. cinnamomi and inoculated with the BCA. During the infection process, we measured plant morphological and physiological variables and collected rhizosphere soil samples for bacterial and fungal amplicon sequencing, bacterial RNA-seq and metabolomic analyses. Conclusions Collectively, our data elucidate the shifts in the avocado rhizosphere microbiome after infection by P. cinnamomi and when inoculated with a BCA, and help understand how a pathogen or a beneficial bacterium can alter plant-microbiome crosstalk. Understanding the effect of P. cinnamomi or a BCA on the avocado tree physiology and on the avocado rhizosphere microbiome and metabolome will direct our search for disease biomarkers or potential pathogen antagonists, help identify metabolites related to the recruitment of microorganisms, and assist us in developing integrated disease management strategies.https://doi.org/10.1186/s43170-023-00167-1Bacterial and fungal communitiesBiological controlPathobiomePhytophthora root rotRhizosphere metabolome |
| spellingShingle | Frédérique Reverchon Mariel García-Meléndez Edgar Guevara-Avendaño Oscar Mora-Chávez Itzel A. Solís-García Wesley Dáttilo José A. Guererro-Analco Alfonso Méndez-Bravo Juan L. Monribot-Villanueva Violeta Patiño-Conde Fernando Pineda-García Eria A. Rebollar Shifts in the rhizosphere microbiome and exudation profile of avocado (Persea americana Mill.) during infection by Phytophthora cinnamomi and in presence of a biocontrol bacterial strain CABI Agriculture and Bioscience Bacterial and fungal communities Biological control Pathobiome Phytophthora root rot Rhizosphere metabolome |
| title | Shifts in the rhizosphere microbiome and exudation profile of avocado (Persea americana Mill.) during infection by Phytophthora cinnamomi and in presence of a biocontrol bacterial strain |
| title_full | Shifts in the rhizosphere microbiome and exudation profile of avocado (Persea americana Mill.) during infection by Phytophthora cinnamomi and in presence of a biocontrol bacterial strain |
| title_fullStr | Shifts in the rhizosphere microbiome and exudation profile of avocado (Persea americana Mill.) during infection by Phytophthora cinnamomi and in presence of a biocontrol bacterial strain |
| title_full_unstemmed | Shifts in the rhizosphere microbiome and exudation profile of avocado (Persea americana Mill.) during infection by Phytophthora cinnamomi and in presence of a biocontrol bacterial strain |
| title_short | Shifts in the rhizosphere microbiome and exudation profile of avocado (Persea americana Mill.) during infection by Phytophthora cinnamomi and in presence of a biocontrol bacterial strain |
| title_sort | shifts in the rhizosphere microbiome and exudation profile of avocado persea americana mill during infection by phytophthora cinnamomi and in presence of a biocontrol bacterial strain |
| topic | Bacterial and fungal communities Biological control Pathobiome Phytophthora root rot Rhizosphere metabolome |
| url | https://doi.org/10.1186/s43170-023-00167-1 |
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