Plant development influences dynamic shifts in the root compartment microbiomes of wild and domesticated finger millet cultivars
Abstract Background Plant-microbe interactions in the rhizosphere and endosphere are crucial for maintaining plant health and ecosystem dynamics. These interactions are shaped by several factors, including the plant’s developmental stage, domestication, and specific root compartments. Different plan...
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2025-04-01
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| Online Access: | https://doi.org/10.1186/s12866-025-03976-8 |
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| author | Fantaye Ayele Dadi Saraladevi Muthusamy Samrat Ghosh Diriba Muleta Kassahun Tesfaye Fassil Assefa Jie Xu Farideh Ghadamgahi Rodomiro Ortiz Ramesh Raju Vetukuri |
| author_facet | Fantaye Ayele Dadi Saraladevi Muthusamy Samrat Ghosh Diriba Muleta Kassahun Tesfaye Fassil Assefa Jie Xu Farideh Ghadamgahi Rodomiro Ortiz Ramesh Raju Vetukuri |
| author_sort | Fantaye Ayele Dadi |
| collection | DOAJ |
| description | Abstract Background Plant-microbe interactions in the rhizosphere and endosphere are crucial for maintaining plant health and ecosystem dynamics. These interactions are shaped by several factors, including the plant’s developmental stage, domestication, and specific root compartments. Different plant cultivars influence unique microbial communities by secreting root exudates that either support beneficial symbionts or inhibit pathogens. This study examined the microbial community structures in the endosphere and rhizosphere of wild-type finger millet and five domesticated cultivars at two developmental stages. Results Our results revealed that the plant developmental stage, root compartment, and domestication significantly influence the root-associated microbiomes. Interestingly, only about 8% of the core microbiota was consistently shared between the soil and plants, indicating that 92% shifted dynamically depending on plant type and developmental stage. Pseudomonadota, Actinomycedota, and Bacteroidota were the dominant bacterial phyla, while Ascomycota and Basidiomycota were the primary fungal phyla across all samples, displaying distinct abundance patterns. Notably, an increase in Actinomycedota in the endosphere correlated with a reduction in Pseudomonadota. The most significant shifts in microbial community composition occurred in the rhizosphere during the flowering stage, primarily driven by the genus Pseudomonas. These findings demonstrate that plant developmental stages and domestication influence the recruitment of specific microbial taxa to meet the plant’s needs, particularly in various root compartments. This selective recruitment highlights the active role of plants in shaping their microbiomes, providing insights into the potential for manipulating these communities to enhance crop productivity sustainably. Conclusion Our results indicate that both the host developmental stage and domestication significantly influence the assembly and structure of the plant microbiome. Plant root compartments can selectively recruit specific taxa from associated core microbial communities to meet their needs, depending on the plant’s developmental stage and the particular root compartment involved. These findings demonstrate that the deterministic selection pressures exerted by plants during their growth and development greatly affect their microbial communities. This has important implications for developing sustainable farming practices, reducing reliance on chemical fertilizers and pesticides, and enhancing future crop productivity. |
| format | Article |
| id | doaj-art-a8f42c2cb9d94705a5fff5432cdcee96 |
| institution | DOAJ |
| issn | 1471-2180 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
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| series | BMC Microbiology |
| spelling | doaj-art-a8f42c2cb9d94705a5fff5432cdcee962025-08-20T02:55:38ZengBMCBMC Microbiology1471-21802025-04-0125111410.1186/s12866-025-03976-8Plant development influences dynamic shifts in the root compartment microbiomes of wild and domesticated finger millet cultivarsFantaye Ayele Dadi0Saraladevi Muthusamy1Samrat Ghosh2Diriba Muleta3Kassahun Tesfaye4Fassil Assefa5Jie Xu6Farideh Ghadamgahi7Rodomiro Ortiz8Ramesh Raju Vetukuri9Department of Plant Breeding, Swedish University of Agricultural SciencesDepartment of Plant Breeding, Swedish University of Agricultural SciencesDepartment of Plant Breeding, Swedish University of Agricultural SciencesInstitute of Biotechnology, Addis Ababa UniversityInstitute of Biotechnology and DMCMB, Addis Ababa UniversityDepartment of Microbial, Cellular and Molecular Biology, Addis Ababa UniversityDepartment of Clinical Sciences, Lund UniversityDepartment of Plant Breeding, Swedish University of Agricultural SciencesDepartment of Plant Breeding, Swedish University of Agricultural SciencesDepartment of Plant Breeding, Swedish University of Agricultural SciencesAbstract Background Plant-microbe interactions in the rhizosphere and endosphere are crucial for maintaining plant health and ecosystem dynamics. These interactions are shaped by several factors, including the plant’s developmental stage, domestication, and specific root compartments. Different plant cultivars influence unique microbial communities by secreting root exudates that either support beneficial symbionts or inhibit pathogens. This study examined the microbial community structures in the endosphere and rhizosphere of wild-type finger millet and five domesticated cultivars at two developmental stages. Results Our results revealed that the plant developmental stage, root compartment, and domestication significantly influence the root-associated microbiomes. Interestingly, only about 8% of the core microbiota was consistently shared between the soil and plants, indicating that 92% shifted dynamically depending on plant type and developmental stage. Pseudomonadota, Actinomycedota, and Bacteroidota were the dominant bacterial phyla, while Ascomycota and Basidiomycota were the primary fungal phyla across all samples, displaying distinct abundance patterns. Notably, an increase in Actinomycedota in the endosphere correlated with a reduction in Pseudomonadota. The most significant shifts in microbial community composition occurred in the rhizosphere during the flowering stage, primarily driven by the genus Pseudomonas. These findings demonstrate that plant developmental stages and domestication influence the recruitment of specific microbial taxa to meet the plant’s needs, particularly in various root compartments. This selective recruitment highlights the active role of plants in shaping their microbiomes, providing insights into the potential for manipulating these communities to enhance crop productivity sustainably. Conclusion Our results indicate that both the host developmental stage and domestication significantly influence the assembly and structure of the plant microbiome. Plant root compartments can selectively recruit specific taxa from associated core microbial communities to meet their needs, depending on the plant’s developmental stage and the particular root compartment involved. These findings demonstrate that the deterministic selection pressures exerted by plants during their growth and development greatly affect their microbial communities. This has important implications for developing sustainable farming practices, reducing reliance on chemical fertilizers and pesticides, and enhancing future crop productivity.https://doi.org/10.1186/s12866-025-03976-8MicrobiomeFinger milletRhizosphereEndosphereSeedling stageFlowering stage |
| spellingShingle | Fantaye Ayele Dadi Saraladevi Muthusamy Samrat Ghosh Diriba Muleta Kassahun Tesfaye Fassil Assefa Jie Xu Farideh Ghadamgahi Rodomiro Ortiz Ramesh Raju Vetukuri Plant development influences dynamic shifts in the root compartment microbiomes of wild and domesticated finger millet cultivars BMC Microbiology Microbiome Finger millet Rhizosphere Endosphere Seedling stage Flowering stage |
| title | Plant development influences dynamic shifts in the root compartment microbiomes of wild and domesticated finger millet cultivars |
| title_full | Plant development influences dynamic shifts in the root compartment microbiomes of wild and domesticated finger millet cultivars |
| title_fullStr | Plant development influences dynamic shifts in the root compartment microbiomes of wild and domesticated finger millet cultivars |
| title_full_unstemmed | Plant development influences dynamic shifts in the root compartment microbiomes of wild and domesticated finger millet cultivars |
| title_short | Plant development influences dynamic shifts in the root compartment microbiomes of wild and domesticated finger millet cultivars |
| title_sort | plant development influences dynamic shifts in the root compartment microbiomes of wild and domesticated finger millet cultivars |
| topic | Microbiome Finger millet Rhizosphere Endosphere Seedling stage Flowering stage |
| url | https://doi.org/10.1186/s12866-025-03976-8 |
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