Biocontrol Characteristics and Whole-Genome Analysis of Pantoea vagans YC2472, an Antagonistic Strain against Phytophthora nicotianae

doi:10.16409/j.cnki.2095-039x.2026.02.060

Abstract

Abstract: Tobacco black shank, caused by Phytophthora nicotianae, is a severe soil-borne disease. To explore novel biological control resources, this study isolated and screened antagonistic bacteria from the tobacco rhizosphere, followed by characterization of their taxonomic status, plant growth-promoting traits, and genomic features. An antagonistic strain, YC2472, which exhibited an inhibition rate of 51.33% against Phytophthora nicotianae in a dual-culture assay, was selected from 114 bacterial isolates. Based on morphological characteristics, physiological and biochemical properties, and multilocus sequence analysis (16S rRNA, atpD, infB), strain YC2472 was identified as Pantoea vagans. This strain demonstrated nitrogen-fixing and potassium-solubilizing capacities, as well as the ability to utilize a variety of carbon sources. As a potential biological control agent, strain YC2472 harbors a wealth of metabolic genes in its genome. Whole-genome sequencing revealed a genome size of 5004432 bp with a GC content of 56.49%, encoding 4,738 predicted genes. Functional annotations (GO, KEGG, COG) indicated that its genome is enriched in genes related to carbohydrate metabolism, amino acid transport and metabolism, and secondary metabolism. Using antiSMASH, seven secondary metabolite biosynthetic gene clusters (BGCs) were predicted in strain YC2472. Comparative genomic analysis with five reported antagonistic bacteria showed that gene clusters for nonribosomal peptide synthetase (NRPS) and terpene synthesis are commonly present. Pangenome analysis further revealed that these key gene clusters, such as those for NRPS, are widespread across P. vagans, suggesting that its biocontrol capability may be broad at the species level. This study reports the antagonistic potential of P. vagans YC2472 against P. nicotianae and elucidates its biocontrol mechanisms from a genomic perspective, providing new potential microbial resources, key strain information, and a theoretical foundation for the green control of tobacco black shank.

Key words: tobacco black shank, Pantoea vagans, biological control, pangenome analysis, nonribosomal peptide synthetase (NRPS)

CLC Number:

S476

LIU Meng, ZHANG Mingya, REN Quan, LU Ning, SUN Wenxiu, CAO Yi. Biocontrol Characteristics and Whole-Genome Analysis of Pantoea vagans YC2472, an Antagonistic Strain against Phytophthora nicotianae[J]. Chinese Journal of Biological Control, 2026, 42(5): 1264-1278.

/ Recommend

References

[1] Ji P, Csinos A S, Hickman L L, et al. Efficacy and application methods of oxathiapiprolin for management of black shank on tobacco[J]. Plant Disease, 2014, 98(11):1551-1554.
[2] Speight G. Distribution of Phytophthora parasitica var. nicotianae races and their sensitivity to metalaxyl in Georgia[J]. Plant Disease, 1994, 78(5): 471-474.
[3] 朱贤朝,王彦亭,王智发,等.中国烟草病害[M].北京:中国农业出版社, 2002.
[4] Panabières F, Ali G S, Allagui M B, et al. Phytophthora nicotianae diseases worldwide:new knowledge of a long-recognised pathogen[J]. Phytopathologia Mediterranea, 2016, 55(1):20-40.
[5] Gai X T, Lu C H, Xia Z Y, et al. Crop rotation suppresses tobacco black shank disease incited by Phytophthora nicotianae and influenced the structure of rhizosphere bacterial communities[J]. Journal of Plant Pathology, 2023, 105(3):673-682.
[6] 付堯,耿怀婷,姬瑾,等.烟草黑胫病的发生与综合防治措施[J].安徽农学通报, 2025, 31(14):80-83.
[7] Zhu X, Chen Y, Jia M, et al. Managing tobacco black shank disease using biochar:direct toxicity and indirect ecological mechanisms[J]. Microbiology Spectrum, 2024, 12(10):e00149-24.
[8] Tan J, Li Q, Chen L, et al. Study on the migration of Phytophthora nicotianae zoospores in the soil[J]. International Journal of Agriculture and Biology, 2018, 20(2):397-403.
[9] 刘畅,姚晨虓,李小杰,等.复合生防菌剂对田间烟草根茎类病害的防治效果[J].烟草科技, 2021, 54(11):18-24.
[10] Ma Y, Gu Y, Liu J, et al. Deciphering the rhizosphere bacteriome associated with biological control of tobacco black shank disease[J]. Frontiers in Plant Science, 2023, 14:1152639.
[11] 孙会忠,王洁琼,郝浩浩,等.两株异源生防菌的鉴定及其对烟草根腐病的协防增效[J].河南大学学报(自然科学版), 2023, 53(5):575-583.
[12] Liu Y, Zhang W, Guo L, et al. Development of a chemotactic SynCom bioorganic fertilizer for biocontrol of bacterial wilt in tobacco fields[J]. Applied Microbiology and Biotechnology, 2025, 109(1):168.
[13] 刘天波,赵誉强,滕凯,等.烟草疫霉拮抗细菌B44R-1的筛选及其生防效果[J].中国生物防治学报, 2022, 38(6):1545-1552.
[14] 饶清琳,钱发聪,张廷金,等.哈茨木霉菌LTR-2对烟草黑胫病的田间防治效果[J].昆明学院学报, 2021, 43(3):16-19.
[15] Chen X, Li J, Cortesi P, et al. Antagonisms of two biocontrol Streptomyces strains against tobacco pathogens[J]. Journal of Biotechnology, 2017, 256: S105.
[16] 郝浩浩,张雨薇,唐培培,等.生防菌防治烟草黑胫病的研究进展[J].农学学报,2025,15(5):41-47.
[17] Jia H, Lv X, Sohail M A, et al. Control efficiency of biochar loaded with Bacillus subtilis Tpb55 against tobacco black shank[J]. Processes, 2022, 10(12): 2663.
[18] 王亚月,贾方方,李俊营,等.烟草黑胫病拮抗菌的筛选鉴定与防病促生作用研究[J].中国烟草科学, 2022, 43(6):60-67, 75.
[19] 王典,匡志豪,孙晓伟,等.哈茨木霉对烟草生长/产质量及黑胫病防效的影响[J].贵州农业科学, 2023, 51(3):27-35.
[20] Liu T, Xiao Y, Yin J, et al. Effects of cultured root and soil microbial communities on the disease of Nicotiana tabacum caused by Phytophthora nicotianae[J]. Frontiers in Microbiology, 2020, 11:929.
[21] 王艳,马军,唐荣阳,等.玉米茎基腐病拮抗菌的筛选及系统发育分析[J].安徽农学通报, 2025, 31(11):81-85.
[22] 郑洒洒,李强,魏硕,等.分散泛菌(Pantoea dispersa) S8797对烟草防病促生多功能分析[J].中国土壤与肥料, 2024(11):205-213.
[23] Jiang L, Jeong J C, Lee J S, et al. Potential of Pantoea dispersa as an effective biocontrol agent for black rot in sweet potato[J]. Scientific Reports, 2019, 9(1):16354.
[24] 东秀珠,蔡妙英.常见细菌系统鉴定手册[M].北京:科学出版社, 2001, 353-398.
[25] Weisburg W G, Barns S M, Pelletier D A, et al. 16S ribosomal DNA amplification for phylogenetic study[J]. Journal of Bacteriology, 1991, 173(2): 697-703.
[26] Vinuesa P, Silva C, Lorite M J, et al. Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands[J]. Systematic and Applied Microbiology, 2005, 28(8):702-716.
[27] Brady C, Cleenwerck I, Venter S, et al. Phylogeny and identification of Pantoea species associated with plants, humans and the natural environment based on multilocus sequence analysis (MLSA)[J]. Systematic and Applied Microbiology, 2008, 31(6-8):447-460.
[28] 赵延昌.植物病原细菌鉴定实验指导[M].第三版.北京:中国农业科学技术出版社, 2011, 113-121.
[29] 德吉,周生灵,任建财,等.长鞭红景天(Rhodiola fastigiata)内生细菌的分离及其生理生化特性测定[J].西藏大学学报(自然科学版), 2013, 28(1): 41-45.
[30] 王贵生.亳菊内生菌的分离鉴定及抑菌促生功能研究[D].阜阳:阜阳师范学院, 2018.
[31] 李统华.马铃薯炭疽菌生防细菌的筛选、鉴定及发酵工艺优化[D].兰州:甘肃农业大学, 2022.
[32] Medison R G, Jiang J, Medison M B, et al. Evaluating the potential of Bacillus licheniformis YZCUO202005 isolated from lichens in maize growth promotion and biocontrol[J]. Heliyon, 2023, 9(10):e20204.
[33] 翟祎笑,朱朝华,李欣荣,等.黄芪(Astragalus membranaceus (Fisch.) Bge.)种子内生细菌群落结构和功能[J].生态学杂志, 2025, 44(11): 3578-3587.
[34] Wu L, Huang Z, Li X, et al. Stomatal closure and SA-, JA/ET-signaling pathways are essential for Bacillus amyloliquefaciens FZB42 to restrict leaf disease caused by Phytophthora nicotianae in Nicotiana benthamiana[J]. Frontiers in Microbiology, 2018, 9:847.
[35] Rajaofera M J N, Jin P F, Fan Y M, et al. Antifungal activity of the bioactive substance from Bacillus atrophaeus strain HAB-5 and its toxicity assessment on Danio rerio[J]. Pesticide Biochemistry and Physiology, 2018, 147(SⅠ):153-161.
[36] Ding H, Mo W, Yu S, et al. Whole genome sequence of Bacillus velezensis strain GUMT319:a potential biocontrol agent against tobacco black shank disease[J]. Frontiers in Microbiology, 2021, 12:658113.
[37] Xu G, Wu W, Zhu L, et al. Whole genome sequencing and biocontrol potential of Streptomyces luteireticuli ASG80 against Phytophthora diseases[J]. Microorganisms, 2024, 12(11):2255.
[38] Lindh E, Kjaeldgaard P, Frederiksen W, et al. Phenotypical properties of Enterobacter agglomerans (Pantoea agglomerans) from human, animal and plant sources[J]. APMIS, 1991, 99(4):347-352.
[39] 沈德龙,冯永君,宋未.内生成团泛菌YS19对水稻乳熟期光合产物在旗叶、穗分配中的影响[J].自然科学进展, 2002, 8:81-83.
[40] Castagno L N, Estrella M J, Sannazzaro A I, et al. Phosphate-solubilization mechanism and in vitro plant growth promotion activity mediated by Pantoea eucalypti isolated from Lotus tenuis rhizosphere in the Salado River Basin (Argentina)[J]. Journal of Applied Microbiology, 2011, 110(5):1151-1165.
[41] Tian S, Xu Y, Zhong Y, et al. Exploring the organic acid secretion pathway and potassium solubilization ability of Pantoea vagans ZHS-1 for enhanced rice growth[J]. Plants, 2024, 13(14):1945.
[42] Saadani O, Fatnassi I C, Chiboub M, et al. In situ phytostabilisation capacity of three legumes and their associated plant growth promoting bacteria (PGPBs) in mine tailings of northern Tunisia[J]. Ecotoxicology and Environmental Safety, 2016, 130:263-269.
[43] Zheng J, Liu Q, Xia Y F, et al. Pantoea agglomerans YS19 poly (A) polymerase I gene possesses the indole-sensing sequence in the promoter region[J]. FEMS Microbiology Letters, 2019, 366(14):fnz166.
[44] 徐霞.烟草野火病拮抗菌的筛选、叶际微生物群落多样性及碳源代谢研究[D].贵州:贵州医科大学, 2024.
[45] 周江鸿,夏菲,仲丽,等.黄栌枯萎病拮抗细菌CCBC3-3-1的全基因组测序及比较基因组分析[J].生物技术通报, 2024, 40(7):235-246.
[46] Stockwell V O., Johnson K B, Sugar D, et al. Control of fire blight by Pseudomonas fluorescens A506 and Pantoea vagans C9-1 applied as single strains and mixed inocula[J]. Phytopathology, 2010, 100(12):1330-1339.
[47] 毕婉玲.姜黄素和Pantoea vagans菌防治猕猴桃青霉病的作用研究[D].合肥:合肥工业大学, 2021.
[48] Klein J M, Loper J E, Stockwell V O. Influence of endogenous plasmids on phenotypes of Pantoea vagans strain C9-1 associated with epiphytic fitness[J]. Journal of Plant Pathology, 2017, 99(SI):81-89.
[49] Smits T H M, Rezzonico F, Kamber T, et al. Genome sequence of the biocontrol agent Pantoea vagans strain C9-1[J]. Journal of Bacteriology, 2010, 192(24):6486-6487.
[50] 宋忠文.松树促生菌泛菌FBS135的比较基因组学分析及其促生相关基因的功能研究[D].南京:南京林业大学, 2020.
[51] Smits T H M, Rezzonico F, Kamber T, et al. Metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist Pantoea vagans C9-1[J]. Public Library of Science ONE, 2011, 6(7):e22247.
[52] Kamber T, Lansdell T A, Stockwell V O, et al. Characterization of the antibacterial peptide herbicolin I biosythetic operon in Pantoea vagans biocontrol strain C9-1, prevalence among Pantoea species, and pathogen resistance[J]. Applied and Environmental Microbiology, 2012, 78:4412-4419.
[53] Ji J, Ma W, An J, et al. Nerol as a novel antifungal agent:In vitro inhibitory effects on Fusarium oxysporum, Pestalotiopsis neglecta, and Valsa mali and its potential mechanisms against F. oxysporum[J]. Journal of Fungi, 2024, 10(10):699.
[54] Hilgers F, Habash S S, Loeschcke A, et al. Heterologous production of β-caryophyllene and evaluation of its activity against plant pathogenic fungi[J]. Microorganisms, 2021, 9(1):168.
[55] Yang W, Yin W, Liu H, et al. The antifungal activity and mechanism of action of limonene against tobacco-isolated Fusarium oxysporum causing tobacco root rot[J]. Frontiers in Plant Science, 2026, 17:1897693.