Metagenome-based diversity and functional analysis of culturable microbes in sugarcane
ABSTRACT Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a compreh...
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| Language: | English |
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American Society for Microbiology
2025-01-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01982-24 |
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| author | Haidong Lin Liang Wu Lijun Zhang Quang Kiet Ta Peng Liu Jinkang Song Xiping Yang |
| author_facet | Haidong Lin Liang Wu Lijun Zhang Quang Kiet Ta Peng Liu Jinkang Song Xiping Yang |
| author_sort | Haidong Lin |
| collection | DOAJ |
| description | ABSTRACT Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane’s tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields.IMPORTANCEThis work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields. |
| format | Article |
| id | doaj-art-448db1246a184a3e83dc9482f01d83c9 |
| institution | Kabale University |
| issn | 2165-0497 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj-art-448db1246a184a3e83dc9482f01d83c92025-01-07T14:05:19ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972025-01-0113110.1128/spectrum.01982-24Metagenome-based diversity and functional analysis of culturable microbes in sugarcaneHaidong Lin0Liang Wu1Lijun Zhang2Quang Kiet Ta3Peng Liu4Jinkang Song5Xiping Yang6State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, ChinaABSTRACT Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane’s tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields.IMPORTANCEThis work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.https://journals.asm.org/doi/10.1128/spectrum.01982-24sugarcaneculturable microbesmetagenomediversity analysisfunctional analysis |
| spellingShingle | Haidong Lin Liang Wu Lijun Zhang Quang Kiet Ta Peng Liu Jinkang Song Xiping Yang Metagenome-based diversity and functional analysis of culturable microbes in sugarcane Microbiology Spectrum sugarcane culturable microbes metagenome diversity analysis functional analysis |
| title | Metagenome-based diversity and functional analysis of culturable microbes in sugarcane |
| title_full | Metagenome-based diversity and functional analysis of culturable microbes in sugarcane |
| title_fullStr | Metagenome-based diversity and functional analysis of culturable microbes in sugarcane |
| title_full_unstemmed | Metagenome-based diversity and functional analysis of culturable microbes in sugarcane |
| title_short | Metagenome-based diversity and functional analysis of culturable microbes in sugarcane |
| title_sort | metagenome based diversity and functional analysis of culturable microbes in sugarcane |
| topic | sugarcane culturable microbes metagenome diversity analysis functional analysis |
| url | https://journals.asm.org/doi/10.1128/spectrum.01982-24 |
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