预测与植物相关的细菌中的根球竞争相关的代谢基因集群与根球SMASH
Yuze Li1,2,3,4, Mingxue Sun1,2,3,4, Jos M Raaijmakers4,5
1State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China.
Nature communications
|September 25, 2025
概括
科学家们开发了RhizoSMASH,这是一个新的计算工具,用于识别植物根排泄物的微生物通路. 这有助于理解植物微生物相互作用,并通过微生物组辅助育种促进可持续农业.
科学领域:
- 微生物学 微生物学
- 植物科学 植物科学
- 生物信息学是一种生物信息学.
背景情况:
- 植物将碳化合物 (根排泄物) 释放到土壤中,影响根微生物群.
- 了解微生物如何代谢根排泄物是植物微生物相互作用的关键,但缺乏专门的计算工具.
研究的目的:
- 开发一种用于识别细菌基因和参与根排泄物代谢的途径的计算方法.
- 分析这些通路在细菌种群中的分布,并评估它们在根球能力中的作用.
主要方法:
- 整合了关于细菌催化基因的已公布数据.
- 开发了基因组合成基因组相关的可变基因集群 (rCGCs) 的基因组合成基因注释的rhizoSMASH算法.
- 应用机器学习根据rCGC的存在来预测根球能力.
主要成果:
- 通过使用58个检测规则, rhizoSMASH成功地在细菌中注释了rCGCs.
- 在细菌种群中和细菌种群内观察到rCGC患病率的显著异质性,这表明了利基专业化.
- 在机器学习模型中,rCGCs的存在或不存在是根球能力的强有力的预测指标.
结论:
- 树根SMASH为研究树根球中的细菌代谢提供了一个新的框架.
- 这些发现突出了根球细菌之间基于代谢能力的广泛的利基专业化.
- 这项工作支持微生物组辅助育种的发展,以实现可持续农业.
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