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Cell. 2025 Mar 10:S0092-8674(25)00198-9. doi: 10.1016/j.cell.2025.02.013 Q145.62024

Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns

作物根部的细菌和病毒基因组揭示了未被发现的物种和微生物组特征 翻译改进

Rui Dai  1, Jingying Zhang  2, Fang Liu  3, Haoran Xu  4, Jing-Mei Qian  4, Shani Cheskis  5, Weidong Liu  4, Binglei Wang  6, Honghui Zhu  7, Lotte J U Pronk  8, Marnix H Medema  8, Ronnie de Jonge  9, Corné M J Pieterse  10, Asaf Levy  5, Klaus Schlaeppi  11, Yang Bai  12

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作者单位

  • 1 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Gene Function and Modulation Research, Peking-Tsinghua-NIBS Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
  • 2 Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Gene Function and Modulation Research, Peking-Tsinghua-NIBS Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
  • 3 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
  • 4 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
  • 5 Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
  • 6 Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Gene Function and Modulation Research, Peking-Tsinghua-NIBS Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China.
  • 7 State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
  • 8 Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, the Netherlands.
  • 9 Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, 3584 CH Utrecht, the Netherlands; AI Technology for Life, Department of Information and Computing Sciences, Science for Life, Utrecht University, 3584 CC Utrecht, the Netherlands.
  • 10 Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, 3584 CH Utrecht, the Netherlands.
  • 11 Department of Environmental Sciences, University of Basel, Basel 4056, Switzerland.
  • 12 Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Gene Function and Modulation Research, Peking-Tsinghua-NIBS Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: ybai@pku.edu.cn.

    • DOI: 10.1016/j.cell.2025.02.013 PMID: 40081368

    摘要 Ai翻译

    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.

    Keywords: bacteria; crop; genome; genomic resources; root microbiome; virus.

    Keywords：Crop root bacterial; viral genomes; unexplored species; microbiome patterns

    关键词：作物根部细菌; 病毒基因组; 未被探索的物种; 微生物群落模式

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    期刊名：Cell

    缩写：CELL

    ISSN：0092-8674

    e-ISSN：1097-4172

    IF/分区：45.6/Q1

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