Integrated Analysis of Metatranscriptome and Amplicon Sequencing to Reveal Distinctive Rhizospheric Microorganisms of Salt-Tolerant Rice
Salt stress poses a significant constraint on rice production, so further exploration is imperative to elucidate the intricate molecular mechanisms governing salt tolerance in rice. By manipulating the rhizosphere microbial communities or targeting specific microbial functions, it is possible to enh...
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2024-12-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/14/1/36 |
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| author | Wenna Meng Zhenling Zhou Mingpu Tan Anqi Liu Shuai Liu Jiaxue Wang Zhiguang Sun Yiluo Tan Yan Liu Baoxiang Wang Yanming Deng |
| author_facet | Wenna Meng Zhenling Zhou Mingpu Tan Anqi Liu Shuai Liu Jiaxue Wang Zhiguang Sun Yiluo Tan Yan Liu Baoxiang Wang Yanming Deng |
| author_sort | Wenna Meng |
| collection | DOAJ |
| description | Salt stress poses a significant constraint on rice production, so further exploration is imperative to elucidate the intricate molecular mechanisms governing salt tolerance in rice. By manipulating the rhizosphere microbial communities or targeting specific microbial functions, it is possible to enhance salt tolerance in crops, improving crop yields and food security in saline environments. In this study, we conducted rice rhizospheric microbial amplicon sequencing and metatranscriptome analysis, revealing substantial microbiomic differences between the salt-tolerant rice cultivar TLJIAN and the salt-sensitive HUAJING. Fungal taxa including <i>Hormiactis</i>, <i>Emericellopsis</i>, <i>Ceriosporopsis</i>, <i>Dirkmeia</i>, and <i>Moesziomyces</i> predominated in the rhizosphere of salt-tolerant rice, while bacterial genera such as <i>Desulfoprunum</i> and <i>Hydrogenophaga</i> exhibited notable differences. Metatranscriptomic analysis identified 7192 differentially expressed genes (DEGs) in the two rice varieties, with 3934 genes being upregulated and 3258 genes being downregulated. Enrichment analyses in KEGG and GO pathways highlighted the majority of DEGs were associated with the “two-component system”, “sulfur metabolism”, and “microbial metabolism in diverse environments”. The interaction network of DEGs and microbial taxa revealed upregulation of transporters, transcriptional factors, and chaperones, such as ABC transporters and chaperonin GroEL, in the rhizosphere microbiomes of salt-tolerant varieties. Our multi-omics network analysis unveiled that fungi like <i>Ceriosporopsis</i> and <i>Dirkmeria</i>, along with bacteria such as <i>Desulfoprunum</i>, <i>Rippkaea</i>, and <i>Bellilinea</i>, showed a positive correlation with flavonoid synthesis in salt-tolerant rice. This study provides an in-depth exploration of the distinctive microbial communities associated with the rhizosphere of salt-tolerant rice varieties, shedding light on the complex interactions between these microbial consortia and their host plants under stress conditions. |
| format | Article |
| id | doaj-art-cc25c5a8a96349e89b1696c95f8eaafc |
| institution | Kabale University |
| issn | 2223-7747 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj-art-cc25c5a8a96349e89b1696c95f8eaafc2025-01-10T13:19:33ZengMDPI AGPlants2223-77472024-12-011413610.3390/plants14010036Integrated Analysis of Metatranscriptome and Amplicon Sequencing to Reveal Distinctive Rhizospheric Microorganisms of Salt-Tolerant RiceWenna Meng0Zhenling Zhou1Mingpu Tan2Anqi Liu3Shuai Liu4Jiaxue Wang5Zhiguang Sun6Yiluo Tan7Yan Liu8Baoxiang Wang9Yanming Deng10College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, ChinaLianyungang Academy of Agricultural Sciences, Lianyungang 222000, ChinaCollege of Life Sciences, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Life Sciences, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Life Sciences, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Life Sciences, Nanjing Agricultural University, Nanjing 210095, ChinaLianyungang Academy of Agricultural Sciences, Lianyungang 222000, ChinaLianyungang Academy of Agricultural Sciences, Lianyungang 222000, ChinaLianyungang Academy of Agricultural Sciences, Lianyungang 222000, ChinaLianyungang Academy of Agricultural Sciences, Lianyungang 222000, ChinaCollege of Life Sciences, Nanjing Agricultural University, Nanjing 210095, ChinaSalt stress poses a significant constraint on rice production, so further exploration is imperative to elucidate the intricate molecular mechanisms governing salt tolerance in rice. By manipulating the rhizosphere microbial communities or targeting specific microbial functions, it is possible to enhance salt tolerance in crops, improving crop yields and food security in saline environments. In this study, we conducted rice rhizospheric microbial amplicon sequencing and metatranscriptome analysis, revealing substantial microbiomic differences between the salt-tolerant rice cultivar TLJIAN and the salt-sensitive HUAJING. Fungal taxa including <i>Hormiactis</i>, <i>Emericellopsis</i>, <i>Ceriosporopsis</i>, <i>Dirkmeia</i>, and <i>Moesziomyces</i> predominated in the rhizosphere of salt-tolerant rice, while bacterial genera such as <i>Desulfoprunum</i> and <i>Hydrogenophaga</i> exhibited notable differences. Metatranscriptomic analysis identified 7192 differentially expressed genes (DEGs) in the two rice varieties, with 3934 genes being upregulated and 3258 genes being downregulated. Enrichment analyses in KEGG and GO pathways highlighted the majority of DEGs were associated with the “two-component system”, “sulfur metabolism”, and “microbial metabolism in diverse environments”. The interaction network of DEGs and microbial taxa revealed upregulation of transporters, transcriptional factors, and chaperones, such as ABC transporters and chaperonin GroEL, in the rhizosphere microbiomes of salt-tolerant varieties. Our multi-omics network analysis unveiled that fungi like <i>Ceriosporopsis</i> and <i>Dirkmeria</i>, along with bacteria such as <i>Desulfoprunum</i>, <i>Rippkaea</i>, and <i>Bellilinea</i>, showed a positive correlation with flavonoid synthesis in salt-tolerant rice. This study provides an in-depth exploration of the distinctive microbial communities associated with the rhizosphere of salt-tolerant rice varieties, shedding light on the complex interactions between these microbial consortia and their host plants under stress conditions.https://www.mdpi.com/2223-7747/14/1/36metatranscriptomeplant–microbe interactionsalt tolerancerice |
| spellingShingle | Wenna Meng Zhenling Zhou Mingpu Tan Anqi Liu Shuai Liu Jiaxue Wang Zhiguang Sun Yiluo Tan Yan Liu Baoxiang Wang Yanming Deng Integrated Analysis of Metatranscriptome and Amplicon Sequencing to Reveal Distinctive Rhizospheric Microorganisms of Salt-Tolerant Rice Plants metatranscriptome plant–microbe interaction salt tolerance rice |
| title | Integrated Analysis of Metatranscriptome and Amplicon Sequencing to Reveal Distinctive Rhizospheric Microorganisms of Salt-Tolerant Rice |
| title_full | Integrated Analysis of Metatranscriptome and Amplicon Sequencing to Reveal Distinctive Rhizospheric Microorganisms of Salt-Tolerant Rice |
| title_fullStr | Integrated Analysis of Metatranscriptome and Amplicon Sequencing to Reveal Distinctive Rhizospheric Microorganisms of Salt-Tolerant Rice |
| title_full_unstemmed | Integrated Analysis of Metatranscriptome and Amplicon Sequencing to Reveal Distinctive Rhizospheric Microorganisms of Salt-Tolerant Rice |
| title_short | Integrated Analysis of Metatranscriptome and Amplicon Sequencing to Reveal Distinctive Rhizospheric Microorganisms of Salt-Tolerant Rice |
| title_sort | integrated analysis of metatranscriptome and amplicon sequencing to reveal distinctive rhizospheric microorganisms of salt tolerant rice |
| topic | metatranscriptome plant–microbe interaction salt tolerance rice |
| url | https://www.mdpi.com/2223-7747/14/1/36 |
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