中国科学院西双版纳热带植物园白杨小组报道了作物根部细菌和病毒基因组揭示了未知的物种和微生物模式。2025年3月12日出版的《细胞》发表了这项成果。
通过将高通量细菌培养与宏基因组测序相结合，小组从小麦、水稻、玉米和紫花苜蓿的根部构建了全面的细菌和病毒基因组集合。作物根系细菌基因组收集（CRBC）显著扩大了可公开获得的作物根系细菌基因组的数量和系统发育多样性，共有6699个细菌基因组（68.9%来自分离株）和1817个未定义物种，使作物根系细菌多样性扩大了290.6%。作物根系病毒基因组收集（CRVC）包含9736个非冗余病毒基因组，其中1572个以前未报道的作物根系微生物组中基因组水平的测定器。由此，该课题组确定了在土壤和宿主物种的根微生物组中丰富的保守细菌功能，并揭示了作物根生态系统中以前未被探索的细菌-病毒联系。CRBC和CRVC共同为研究微生物机制和应用提供了宝贵的资源，支持可持续农业。
据介绍，根系微生物的参考基因组对作物根系微生物的宏基因组分析和机制研究至关重要。
附：英文原文
Title: Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns
Author: Rui Dai, Jingying Zhang, Fang Liu, Haoran Xu, Jing-Mei Qian, Shani Cheskis, Weidong Liu, Binglei Wang, Honghui Zhu, Lotte J.U. Pronk, Marnix H. Medema, Ronnie de Jonge, Corné M.J. Pieterse, Asaf Levy, Klaus Schlaeppi, Yang Bai
Issue&Volume: 2025-03-12
Abstract: Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.
DOI: 10.1016/j.cell.2025.02.013
Source: https://www.cell.com/cell/abstract/S0092-8674(25)00198-9