Rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systems
Abstract The addition of bacteria and arbuscular mycorrhizal fungi (AMF) is a strategy used to protect plants against disease and improve their growth and yield, known as biocontrol and biostimulation, respectively. In viticulture, the plant growth promotion (PGP) potential of bacteria endogenous to...
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Nature Portfolio
2025-07-01
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| Online Access: | https://doi.org/10.1038/s41598-025-12673-5 |
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| author | Romain Darriaut Vincent Lailheugue Jules Wastin Joseph Tran Guilherme Martins Patricia Ballestra Isabelle Masneuf-Pomarède Nathalie Ollat Virginie Lauvergeat |
| author_facet | Romain Darriaut Vincent Lailheugue Jules Wastin Joseph Tran Guilherme Martins Patricia Ballestra Isabelle Masneuf-Pomarède Nathalie Ollat Virginie Lauvergeat |
| author_sort | Romain Darriaut |
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| description | Abstract The addition of bacteria and arbuscular mycorrhizal fungi (AMF) is a strategy used to protect plants against disease and improve their growth and yield, known as biocontrol and biostimulation, respectively. In viticulture, the plant growth promotion (PGP) potential of bacteria endogenous to vineyard soil has been underexplored. Furthermore, most research about microbial biostimulants focuses on the effect on the plant, but little is known on how their application modify the soil and root microbial ecosystem, which may have an impact on plant growth and resistance. The objectives of this work were (1) to identify bacteria present in vineyard soils with functional PGP traits, (2) to test their PGP activity on young grapevines, in combination with AMF, (3) to assess the impact on the microbial communities and their inferred functions in the rhizosphere and plant roots. Two hundred bacteria were isolated from vineyards and characterized for their biochemical PGP activities. The most efficient were tested in vitro, both singly and in combination, on Lepidium sativum and grapevine plantlets. Two Pseudomonas species particularly increased in vitro growth and were selected for further testing, with and without two Glomus species, on grapevines planted in soil experiencing microbial dysbiosis in a greenhouse setting. After five months of growth, the co-application of PGP rhizobacteria and AMF significantly enhanced root biomass and increased the abundance of potentially beneficial bacterial genera in the roots, compared to untreated conditions and single inoculum treatments. Additionally, the prevalence of Botr ytis cinerea, associated with grapevine diseases, decreased in the root endosphere. The combined inoculation of bacteria and AMF resulted in a more complex bacterial network with higher metabolic functionality than single inoculation treatments. This study investigates the effects of adding indigenous rhizobacteria and commercial fungi on the root system microbiota and vine growth in a soil affected by microbial dysbiosis. The results show a remodeling of microbial communities and their functions associated with a beneficial effect on the plant in terms of growth and presence of pathogens. The observed synergistic effect of bacteria and AMF indicates that it is important to consider the combined effects of individuals from synthetic communities applied in the field. |
| format | Article |
| id | doaj-art-31d78c1f0d564a5fa576d3ecb4db99dd |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
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| spelling | doaj-art-31d78c1f0d564a5fa576d3ecb4db99dd2025-08-20T03:45:48ZengNature PortfolioScientific Reports2045-23222025-07-0115111810.1038/s41598-025-12673-5Rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systemsRomain Darriaut0Vincent Lailheugue1Jules Wastin2Joseph Tran3Guilherme Martins4Patricia Ballestra5Isabelle Masneuf-Pomarède6Nathalie Ollat7Virginie Lauvergeat8EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVEGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVUniversité de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR OEnologie 1366, ISVVEGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVUniversité de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR OEnologie 1366, ISVVUniversité de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR OEnologie 1366, ISVVUniversité de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR OEnologie 1366, ISVVEGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVEGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVAbstract The addition of bacteria and arbuscular mycorrhizal fungi (AMF) is a strategy used to protect plants against disease and improve their growth and yield, known as biocontrol and biostimulation, respectively. In viticulture, the plant growth promotion (PGP) potential of bacteria endogenous to vineyard soil has been underexplored. Furthermore, most research about microbial biostimulants focuses on the effect on the plant, but little is known on how their application modify the soil and root microbial ecosystem, which may have an impact on plant growth and resistance. The objectives of this work were (1) to identify bacteria present in vineyard soils with functional PGP traits, (2) to test their PGP activity on young grapevines, in combination with AMF, (3) to assess the impact on the microbial communities and their inferred functions in the rhizosphere and plant roots. Two hundred bacteria were isolated from vineyards and characterized for their biochemical PGP activities. The most efficient were tested in vitro, both singly and in combination, on Lepidium sativum and grapevine plantlets. Two Pseudomonas species particularly increased in vitro growth and were selected for further testing, with and without two Glomus species, on grapevines planted in soil experiencing microbial dysbiosis in a greenhouse setting. After five months of growth, the co-application of PGP rhizobacteria and AMF significantly enhanced root biomass and increased the abundance of potentially beneficial bacterial genera in the roots, compared to untreated conditions and single inoculum treatments. Additionally, the prevalence of Botr ytis cinerea, associated with grapevine diseases, decreased in the root endosphere. The combined inoculation of bacteria and AMF resulted in a more complex bacterial network with higher metabolic functionality than single inoculation treatments. This study investigates the effects of adding indigenous rhizobacteria and commercial fungi on the root system microbiota and vine growth in a soil affected by microbial dysbiosis. The results show a remodeling of microbial communities and their functions associated with a beneficial effect on the plant in terms of growth and presence of pathogens. The observed synergistic effect of bacteria and AMF indicates that it is important to consider the combined effects of individuals from synthetic communities applied in the field.https://doi.org/10.1038/s41598-025-12673-5PGPR screeningMetabarcoding inferenceMicrobiome engineeringGrapevine dysbiosisMicrobial networkMetabolic activities |
| spellingShingle | Romain Darriaut Vincent Lailheugue Jules Wastin Joseph Tran Guilherme Martins Patricia Ballestra Isabelle Masneuf-Pomarède Nathalie Ollat Virginie Lauvergeat Rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systems Scientific Reports PGPR screening Metabarcoding inference Microbiome engineering Grapevine dysbiosis Microbial network Metabolic activities |
| title | Rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systems |
| title_full | Rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systems |
| title_fullStr | Rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systems |
| title_full_unstemmed | Rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systems |
| title_short | Rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systems |
| title_sort | rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systems |
| topic | PGPR screening Metabarcoding inference Microbiome engineering Grapevine dysbiosis Microbial network Metabolic activities |
| url | https://doi.org/10.1038/s41598-025-12673-5 |
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