Identification and whole-genome sequence analysis of antagonistic bacterium XL-09 against Sclerotinia sclerotiorum in broccoli

doi:10.3969/j.issn.1004-1524.20250661

Acta Agriculturae Zhejiangensis ›› 2026, Vol. 38 ›› Issue (8): 1628-1635.DOI: 10.3969/j.issn.1004-1524.20250661

• Plant Protection • Previous Articles Next Articles

Identification and whole-genome sequence analysis of antagonistic bacterium XL-09 against Sclerotinia sclerotiorum in broccoli

WEI Haizhong¹(), PAN Liqin¹, ZHAO Wenxuan², LI Yanan², ZHANG Huijuan², JIANG Ming²^,^*()

¹ College of Agriculture and Bioengineering, Taizhou Vocational College of Science and Technology, Taizhou 318020, Zhejiang, China
² School of Life Sciences, Taizhou University, Taizhou 318000, Zhejiang, China

Received:2025-10-20 Online:2026-08-25 Published:2026-09-14

Abstract

Abstract:

Sclerotinia sclerotiorum is an important pathogenic fungus causing Sclerotinia disease, which poses serious threats to the production of broccoli (Brassica oleracea var. italica). In this study, an endophytic bacterial strain XL-09 previously isolated from broccoli leaves was used as material. Its taxonomic status was determined through morphological observation, physiological and biochemical characterization, and molecular identification. The antagonistic effect of this bacterium against Sclerotinia disease was evaluated using plate confrontation and detached leaf inoculation methods. Furthermore, based on genome assembly, the composition of secondary metabolite gene clusters was analyzed. The results showed that strain XL09 formed creamy white colonies on LB solid medium, was Grampositive, and could utilize D-xylose, sucrose, and L-arabinose as carbon sources. It was positive for catalase, nitrate reduction, and Voges-Proskauer reaction. Phylogenetic analysis based on gyrA gene sequences revealed that XL09 clustered with Bacillus subtilis. Combining morphological, physiological, biochemical, and molecular identification results, the strain was identified as Bacillus subtilis. XL09 exhibited significant antagonistic activity against the growth of Sclerotinia sclerotiorum, with colony diameter significantly smaller than that of the control and the number of sclerotia markedly reduced. Moreover, broccoli leaves treated with XL09 developed significantly smaller lesions after inoculation with S. sclerotiorum compared to the control. Genome assembly revealed that the complete genome of XL09 is 4.28 Mb in length, containing 4 525 genes, of which 4 308 are protein-coding genes. A total of nine secondary metabolite gene clusters were detected, involved in the synthesis of sporulation lethal factor, surfactin, and bacillocin, among others. The identification and whole genome sequence analysis of antagonistic bacterium XL09 lay a foundation for future studies on disease resistance mechanisms and biocontrol applications.

Key words: Sclerotinia sclerotiorum, Bacillus subtilis, broccoli, antagonism, genome

CLC Number:

S436.35

WEI Haizhong, PAN Liqin, ZHAO Wenxuan, LI Yanan, ZHANG Huijuan, JIANG Ming. Identification and whole-genome sequence analysis of antagonistic bacterium XL-09 against Sclerotinia sclerotiorum in broccoli[J]. Acta Agriculturae Zhejiangensis, 2026, 38(8): 1628-1635.

Figures/Tables 6

References 32

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序号 Number	试验名称 Test name	结果 Result	序号 Number	试验名称 Test name	结果 Result
1	D-木糖D-Xylose	+	9	蔗糖Sucrose	+
2	L-阿拉伯糖L-Arabinose	+	10	柠檬酸盐Citrate	+
3	半乳糖Galactose	-	11	接触酶Catalase	+
4	淀粉Starch	+	12	硝酸盐还原Nitrate reduction	+
5	D-甘露醇D-Mannitol	+	13	明胶液化Gelatin liquefaction	+
6	果糖Fructose	+	14	酪氨酸水解Tyrosine hydrolysis	-
7	乳糖Lactose	-	15	V-P测定Voges-Proskauer test	+
8	D-葡萄糖D-Glucose	+	16	苯丙氨酸脱氨酶Phenylalanine deaminase	-

序号 Number	试验名称 Test name	结果 Result	序号 Number	试验名称 Test name	结果 Result
1	D-木糖D-Xylose	+	9	蔗糖Sucrose	+
2	L-阿拉伯糖L-Arabinose	+	10	柠檬酸盐Citrate	+
3	半乳糖Galactose	-	11	接触酶Catalase	+
4	淀粉Starch	+	12	硝酸盐还原Nitrate reduction	+
5	D-甘露醇D-Mannitol	+	13	明胶液化Gelatin liquefaction	+
6	果糖Fructose	+	14	酪氨酸水解Tyrosine hydrolysis	-
7	乳糖Lactose	-	15	V-P测定Voges-Proskauer test	+
8	D-葡萄糖D-Glucose	+	16	苯丙氨酸脱氨酶Phenylalanine deaminase	-

次生代谢产物 Secondary metabolite	基因名称 Gene name	基因簇大小/kb Gene cluster size/kb
产孢致死因子 Sporulation lethal factor	skfA、skfB、skfC、ybdM	22.1
表面活性素 Surfactin	nasC、nasB、yciC、yckB、srfAA、srfAB、srfAC、srfAD、gabR_1、sfp、tcyA、bsdB、pip_2	63.4
芽孢杆菌素 Bacillocin	pbpX、tdh、miaB、pksB、pksC、pksD、pksE、acpK、pksF、pksG、pksH、pksI、pksJ、pksL、pksM_1、pksM_ 2、pksN、pksR、pksS_1、aprX	105.4
芬荠素 Fengycin	gtaB_1、accD5、crt、yngG、cfiB、fadD3、bcd、ppsE、ppsD、ppsC、ppsB、ppsA、ggt、adhT	77.0
枯草三十七肽 Sublancin	sunS、lagD、sunA、speG	20.2
杆菌素Corynebactin	pncA、yueD、mbtH、dhbF、dhbB、dhbE、dhbC、dhbA、besA、yumC	47.1
枯草杆菌肽A Subtilosin A	narG、sboA、albA、albE、albF	21.6
芽孢菌溶素 Bacilysin	bacG、bacF_2、bacD、bacC_1、rocC_2、rocA、rfbC、rmlD、rfbB、rmlA、murG_2、arnB	41.4
泰乐菌素 Tylosin	gntZ、ahpC_2、ahpF、yydH、moaA_2、fdhA	21.7

次生代谢产物 Secondary metabolite	基因名称 Gene name	基因簇大小/kb Gene cluster size/kb
产孢致死因子 Sporulation lethal factor	skfA、skfB、skfC、ybdM	22.1
表面活性素 Surfactin	nasC、nasB、yciC、yckB、srfAA、srfAB、srfAC、srfAD、gabR_1、sfp、tcyA、bsdB、pip_2	63.4
芽孢杆菌素 Bacillocin	pbpX、tdh、miaB、pksB、pksC、pksD、pksE、acpK、pksF、pksG、pksH、pksI、pksJ、pksL、pksM_1、pksM_ 2、pksN、pksR、pksS_1、aprX	105.4
芬荠素 Fengycin	gtaB_1、accD5、crt、yngG、cfiB、fadD3、bcd、ppsE、ppsD、ppsC、ppsB、ppsA、ggt、adhT	77.0
枯草三十七肽 Sublancin	sunS、lagD、sunA、speG	20.2
杆菌素Corynebactin	pncA、yueD、mbtH、dhbF、dhbB、dhbE、dhbC、dhbA、besA、yumC	47.1
枯草杆菌肽A Subtilosin A	narG、sboA、albA、albE、albF	21.6
芽孢菌溶素 Bacilysin	bacG、bacF_2、bacD、bacC_1、rocC_2、rocA、rfbC、rmlD、rfbB、rmlA、murG_2、arnB	41.4
泰乐菌素 Tylosin	gntZ、ahpC_2、ahpF、yydH、moaA_2、fdhA	21.7

Identification and whole-genome sequence analysis of antagonistic bacterium XL-09 against Sclerotinia sclerotiorum in broccoli

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