A Comparison of Rice Root Microbial Dynamics in Organic and Conventional Paddy Fields
The assembly of plant root microbiomes is a dynamic process. Understanding the roles of root-associated microbiomes in rice development requires dissecting their assembly throughout the rice life cycle under diverse environments and exploring correlations with soil properties and rice physiology. In...
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2024-12-01
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| author | Fangming Zhu Takehiro Kamiya Toru Fujiwara Masayoshi Hashimoto Siyu Gong Jindong Wu Hiromi Nakanishi Masaru Fujimoto |
| author_facet | Fangming Zhu Takehiro Kamiya Toru Fujiwara Masayoshi Hashimoto Siyu Gong Jindong Wu Hiromi Nakanishi Masaru Fujimoto |
| author_sort | Fangming Zhu |
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| description | The assembly of plant root microbiomes is a dynamic process. Understanding the roles of root-associated microbiomes in rice development requires dissecting their assembly throughout the rice life cycle under diverse environments and exploring correlations with soil properties and rice physiology. In this study, we performed amplicon sequencing targeting fungal ITS and the bacterial 16S rRNA gene to characterize and compare bacterial and fungal community dynamics of the rice root endosphere and soil in organic and conventional paddy fields. Our analysis revealed that root microbial diversity and composition was significantly influenced by agricultural practices and rice developmental stages (<i>p</i> < 0.05). The root microbiome in the organic paddy field showed greater temporal variability, with typical methane-oxidizing bacteria accumulating during the tillering stage and the amount of symbiotic nitrogen-fixing bacteria increasing dramatically at the early ripening stage. Redundancy analysis identified ammonium nitrogen, iron, and soil organic matter as key drivers of microbial composition. Furthermore, correlation analysis between developmental stage-enriched bacterial biomarkers in rice roots and leaf mineral nutrients showed that highly mobile macronutrient concentrations positively correlated with early-stage biomarkers and negatively correlated with later-stage biomarkers in both paddy fields. Notably, later-stage biomarkers in the conventional paddy field tended to show stronger correlations with low-mobility nutrients. These findings suggest potential strategies for optimizing microbiome management to enhance productivity and sustainability. |
| format | Article |
| id | doaj-art-891edd4d9e024ca0830b93bb79c29c2b |
| institution | Kabale University |
| issn | 2076-2607 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
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| series | Microorganisms |
| spelling | doaj-art-891edd4d9e024ca0830b93bb79c29c2b2025-01-24T13:42:24ZengMDPI AGMicroorganisms2076-26072024-12-011314110.3390/microorganisms13010041A Comparison of Rice Root Microbial Dynamics in Organic and Conventional Paddy FieldsFangming Zhu0Takehiro Kamiya1Toru Fujiwara2Masayoshi Hashimoto3Siyu Gong4Jindong Wu5Hiromi Nakanishi6Masaru Fujimoto7Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, JapanDepartment of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, JapanDepartment of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, JapanDepartment of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, JapanDepartment of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, JapanDepartment of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, JapanDepartment of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, JapanDepartment of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, JapanThe assembly of plant root microbiomes is a dynamic process. Understanding the roles of root-associated microbiomes in rice development requires dissecting their assembly throughout the rice life cycle under diverse environments and exploring correlations with soil properties and rice physiology. In this study, we performed amplicon sequencing targeting fungal ITS and the bacterial 16S rRNA gene to characterize and compare bacterial and fungal community dynamics of the rice root endosphere and soil in organic and conventional paddy fields. Our analysis revealed that root microbial diversity and composition was significantly influenced by agricultural practices and rice developmental stages (<i>p</i> < 0.05). The root microbiome in the organic paddy field showed greater temporal variability, with typical methane-oxidizing bacteria accumulating during the tillering stage and the amount of symbiotic nitrogen-fixing bacteria increasing dramatically at the early ripening stage. Redundancy analysis identified ammonium nitrogen, iron, and soil organic matter as key drivers of microbial composition. Furthermore, correlation analysis between developmental stage-enriched bacterial biomarkers in rice roots and leaf mineral nutrients showed that highly mobile macronutrient concentrations positively correlated with early-stage biomarkers and negatively correlated with later-stage biomarkers in both paddy fields. Notably, later-stage biomarkers in the conventional paddy field tended to show stronger correlations with low-mobility nutrients. These findings suggest potential strategies for optimizing microbiome management to enhance productivity and sustainability.https://www.mdpi.com/2076-2607/13/1/41riceroot-associated microbiomedevelopmental stageorganic and conventional paddiesamplicon sequencingdiversity analysis |
| spellingShingle | Fangming Zhu Takehiro Kamiya Toru Fujiwara Masayoshi Hashimoto Siyu Gong Jindong Wu Hiromi Nakanishi Masaru Fujimoto A Comparison of Rice Root Microbial Dynamics in Organic and Conventional Paddy Fields Microorganisms rice root-associated microbiome developmental stage organic and conventional paddies amplicon sequencing diversity analysis |
| title | A Comparison of Rice Root Microbial Dynamics in Organic and Conventional Paddy Fields |
| title_full | A Comparison of Rice Root Microbial Dynamics in Organic and Conventional Paddy Fields |
| title_fullStr | A Comparison of Rice Root Microbial Dynamics in Organic and Conventional Paddy Fields |
| title_full_unstemmed | A Comparison of Rice Root Microbial Dynamics in Organic and Conventional Paddy Fields |
| title_short | A Comparison of Rice Root Microbial Dynamics in Organic and Conventional Paddy Fields |
| title_sort | comparison of rice root microbial dynamics in organic and conventional paddy fields |
| topic | rice root-associated microbiome developmental stage organic and conventional paddies amplicon sequencing diversity analysis |
| url | https://www.mdpi.com/2076-2607/13/1/41 |
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