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水稻黄单胞菌噬菌体vB_XaS_HDB2的全基因组分析和生物学特性研究

陈惠莹**，何嘉欣**，朱斌，黄士轩，周星佑，伍君权，杨美艳*   

  1. 华南农业大学食品学院 / 广东省食品质量安全重点实验室，广东广州 510642
  • 收稿日期:2024-04-07 修回日期:2025-04-27 接受日期:2025-04-27 网络出版日期:2025-05-16
  • 基金资助:
    本研究由国家自然科学基金项目(32202194), 广东省重点领域研发计划项目(2022B0202110001), 广州市重点研发计划农业和社会发展科技专题项目(SL2022B03J01243)资助。

Whole genome analysis and biological characterization of phage vB_XaS_HDB2 infected with Xanthomonas oryzae pv. oryzae

CHEN Hui-Ying**,HE Jia-Xin**,ZHU Bin,HUANG Shi-Xuan,ZHOU Xing-You,WU Jun-Quan,YANG Mei-Yan*   

  1. College of Food Science, South China Agricultural University / Guangdong Provincial Key Laboratory of Food Quality and Safety, Guangzhou 510642, Guangdong, China
  • Received:2024-04-07 Revised:2025-04-27 Accepted:2025-04-27 Published online:2025-05-16
  • Supported by:
    This study was supported by the National Natural Science Foundation of China (32202194), the Guangdong Key Areas Research and Development Program Project (2022B0202110001), and the Guangzhou Key Research and Development Program Agricultural and Social Development Science and Technology Project (SL2022B03J01243).

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摘要：

水稻白叶枯病是由水稻黄单胞菌(Xanthomonas oryzae pv. oryzae, Xoo)引起的一种常见病害，可导致水稻大面积减产，对粮食安全造成巨大威胁。防治白叶枯病的化学药剂种类少，效果欠佳且对环境危害大，亟需开发安全高效的新型抗菌剂。噬菌体因其裂解细菌的高度特异性而备受关注。本研究从稻虾田水中分离获得一株水稻黄单胞菌噬菌体，命名为vB_XaS_HDB2 (HDB2)。电镜观察显示，噬菌体HDB2为长尾噬菌体，头部直径和尾部长度分别为(48 ± 3) nm、(166 ± 8) nm。全基因组分析结果显示，HDB2序列长43,697 bp，GC含量为54.31%，含有52个开放阅读框(ORFs)。其中30个为已知功能蛋白，按照不同功能分为DNA代谢、裂解、包装、结构这4个模块；该噬菌体含有1个tRNA，不含毒力基因和抗生素耐药基因。ANI、蛋白网络图与系统发育树分析表明，HDB2属于Septimatrevirus属成员，与噬菌体vB_Xar_IVIA-DoCa8相似度最高(97.74%)。HDB2能够裂解52.9% (9/17)的受测黄单胞菌菌株；一步生长曲线显示，HDB2的潜伏期为3 h，裂解期为5 h，裂解量为44 pfu cell?1；HDB2具有较好的温度(4℃~60℃)和pH (4~11)耐受性。体外抑菌结果显示，感染复数大于0.1时，噬菌体HDB2能有效抑制黄单胞菌Xoo 2086的生长。综上所述，我们分离纯化并鉴定了一株水稻黄单胞菌噬菌体，为噬菌体技术应用于作物细菌病害的防治提供了理论依据。

关键词: 水稻黄单胞菌, 水稻白叶枯病, 噬菌体, 全基因组分析, 生物学特性

Abstract:

Bacterial leaf blight (BLB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a widespread and destructive disease that significantly reduces rice yield and threatens global food security. Currently, few chemical agents are available for BLB control, and most are either ineffective or environmentally hazardous. Therefore, there is an urgent need to develop novel, safe, and effective antibacterial alternatives. Bacteriophages, due to their high specificity against bacterial hosts, have emerged as promising biocontrol agents. In this study, we isolated a lytic phage targeting Xanthomonas, designated vB_XaS_HDB2 (HDB2), from rice and shrimp field water. Transmission electron microscopy revealed that HDB2 is a long-tailed phage with a head diameter of 48 ± 3 nm and a tail length of 166 ± 8 nm. Whole-genome sequencing showed that HDB2 has a genome size of 43,697 bp, a GC content of 54.31%, and encodes 52 open reading frames (ORFs), of which 30 were functionally annotated and grouped into four modules: DNA metabolism, lysis, packaging, and structural assembly. Notably, HDB2 carries one tRNA gene but no virulence or antibiotic resistance genes. Comparative analyses, including average nucleotide identity (ANI), protein network mapping, and phylogenetic tree construction, revealed that HDB2 belongs to the genus Septimatrevirus and is most closely related to phage vB_Xar_IVIA-DoCa8 (97.74% similarity). HDB2 was capable of lysing 52.9% (9/17) of tested Xanthomonas strains. One-step growth curve analysis indicated a latent period of 3?h, a lysis period of 5 h, and a burst size of 44 PFU per cell. HDB2 also demonstrated strong stability across a wide temperature range (4–60℃) and pH range (4–11). In vitro experiments showed that HDB2 effectively inhibited the growth of Xoo strain 2086 at multiplicities of infection (MOIs) greater than 0.1. Collectively, these results highlight the potential of HDB2 as a biocontrol agent and provide a theoretical foundation for the application of phage-based strategies in managing bacterial diseases in crops.

Key words: Xanthomonas oryzae pv. oryzae, bacterial leaf blight of rice, phage, whole genome analysis, biological characteristics

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