番茄根际放线菌GNLJ-7菌株的生物功能及全基因组分析

doi:10.13560/j.cnki.biotech.bull.1985.2025-1174

摘要/Abstract

摘要：

目的从番茄根际分离出菌株GNLJ-7，通过全基因组测序技术解析其功能，为开发绿色促生生防菌剂提供优良菌种与理论支撑。方法通过皿内种子萌发及盆栽实验验证GNLJ-7对番茄生长及杂草分枝列当寄生的影响；检测平板测定其溶磷、固氮和产铁载体能力；采用16S rRNA和全基因组学测序，明确菌株GNLJ-7的分类学地位，利用PacBio和Illumina双平台测序技术完成全基因组测序，并通过COG、KEGG、GO等数据库进行基因功能注释与次级代谢产物合成基因簇和主要代谢通路的预测。结果经鉴定菌株GNLJ-7为海鞘戈登氏菌（Gordonia didemni）。盆栽实验表明，该菌株能显著促进番茄根系发育，使根长和根重分别增加26%和47%，并有效抑制分枝列当种子的萌发与寄生，在菌剂浓度为1.0×10² CFU/mL时，对列当种子萌发的抑制率达到86.47%。功能验证显示其具有固氮、溶磷和产铁载体的能力。基因组中鉴定到与吲哚-3-乙酸（IAA）合成（trpA/B/C/D/E/F/S）、溶磷（phoA、phoD）、铁载体合成（pksD/E/F）及固氮（nifH、nifA）相关的关键基因，并预测到10个次级代谢产物生物合成基因簇和与促生生防功能相关的代谢通路。结论菌株G. didemni GNLJ-7能够显著促进番茄根系生长并抑制分枝列当寄生。其基因组中存在的固氮（nifH、nifA）、溶磷（phoA、phoD）、铁载体合成（pksD/E/F）及IAA合成（trpA/B/C/D/E/F/S）相关基因，共同构成了其发挥促生和生物防治作用的分子基础。

关键词: Gordonia didemni, 全基因组测序, 分枝列当, 生物防治, 促生机制, 根际促生菌, 功能基因

Abstract:

Objective Strain GNLJ-7 was isolated from tomato rhizosphere. Its functional mechanisms were elucidated through whole-genome sequencing, aiming to provide an excellent microbial strain and theoretical support for developing green plant-growth-promoting and biocontrol agents. Method The effects of GNLJ-7 on tomato growth and Phelipanche aegyptiaca parasitism were evaluated via in-plate seed germination and pot experiments. Its phosphate-solubilizing, nitrogen-fixing, and siderophore-producing abilities were assessed using plate-based assays. Taxonomic identification of strain GNLJ-7 was performed by 16S rRNA and whole-genome sequencing. The genome was sequenced using both PacBio and Illumina platforms, followed by functional annotation via COG, KEGG, and GO databases. Secondary metabolite biosynthetic gene clusters and key metabolic pathways were predicted. Result Strain GNLJ‑7 was identified as Gordonia didemni. Pot experiments showed that the strain significantly promoted tomato root development, increasing root length and root weight by 26% and 47%, respectively, and effectively inhibited the germination and parasitism of P. aegyptiaca seeds. At a concentration of 1.0×10² CFU/mL, the inhibition rate on Orobanche seed germination reached 86.47%. Functional tests confirmed its abilities in nitrogen fixation, phosphate solubilization, and siderophore production. Key genes involved in indole‑3‑acetic acid (IAA) biosynthesis (trpA/B/C/D/E/F/S), phosphate solubilization (phoA, phoD), siderophore synthesis (pksD/E/F), and nitrogen fixation (nifH/A) were identified in the genome. Ten secondary metabolite biosynthetic gene clusters and metabolic pathways associated with plant‑growth‑promoting and biocontrol functions were predicted. Conclusion The strain Gordonia didemni GNLJ-7 significantly promotes tomato root growth and inhibits the parasitism of Phelipanche aegyptiaca. Genes associated with nitrogen fixation (nifH, nifA), phosphorus solubilization (phoA, phoD), siderophore synthesis (pksD/E/F), and IAA biosynthesis (trpA/B/C/D/E/F/S) identified in its genome collectively form the molecular basis for its plant growth-promoting and biocontrol activities.

Key words: Gordonia didemni, whole-genome sequencing, Phelipanche aegyptiaca, biocontrol, growth-promoting mechanism, plant growth-promoting rhizobacteria, functional genes

迪丽拜尔·吐尔逊, 祖丽胡玛尔·亚库普, 包慧芳, 詹发强, 杨蓉, 史应武, 杨红梅, 楚敏, 房世杰, 王宁. 番茄根际放线菌GNLJ-7菌株的生物功能及全基因组分析[J]. 生物技术通报, 2026, 42(8): 276-286.

TUERXUN Di-li-bai-er, YAKUPU Zu-li-hu-ma-er, BAO Hui-fang, ZHAN Fa-qiang, YANG Rong, SHI Ying-wu, YANG Hong-mei, CHU Min, FANG Shi-jie, WANG Ning. Biological Function and Whole-genome Analysis of Actinobacteria Strain GNLJ-7 Isolated from Tomato Rhizosphere[J]. Biotechnology Bulletin, 2026, 42(8): 276-286.

图/表 10

图1 菌株GNLJ-7菌落形态（A）和系统进化树（B）

Fig. 1 Colony morphology (A) and phylogenetic tree (B) of the strain GNLJ-7

图2 菌株GNLJ-7的促生功能定性测定A：固氮能力；B：解磷能力；C：产铁载体能力

Fig. 2 Qualitative determination of the growth-promoting function of strain GNLJ-7A: Nitrogen fixation ability. B: Phosphate solubilization ability. C: Siderophore production ability

图3 菌株GNLJ-7对番茄的促生和生防效应及综合能力评价A：列当种子抑制率及萌发率；B：不同处理下的番茄根部形态；C：根长；D：根重；E：茎粗；F：株高；G：列当数；H：列当重量；NB为营养肉汤对照组，GNLJ-7为供试菌株，DNKAS为对照菌株。不同字母表示差异显著（P<0.05）

Fig. 3 Evaluation of growth-promoting, biocontrol effects and comprehensive capabilities of strain GNLJ-7 on tomatoA: Orobanche seed inhibition rate and germination rate. B: Tomato root morphology under different treatments. C: Root length. D: Root weight. E: Stem diameter. F: Plant height. G: Orobanche quantity. H: Orobanche weight. NB represents the nutrient broth control group, GNLJ-7 represents the tested strain, and DNKAS represents the control strain. Different letters indicate significant differences (P<0.05)

表1 菌株GNLJ-7的基因组信息

Table 1 Genome characteristics of strain GNLJ-7

菌株GNLJ-7特征 Characteristics of strain GNLJ-7	数值 Value
Genome size （bp）	4 073 730
GC content （%）	46.44
Chromosome	1
Plasmid	1
tRNA	86
rRNA （5S， 16S， 23S）	27 （9， 9， 9）
Protein-coding genes （CDS）	3 971
Genomic islands （GIs）	10
Secondary metabolite gene clusters	10
Genes assigned to NR	3 962
Genes assigned to COGs	3 148
Genes assigned to KEGG	2 894
Genes assigned to GO	2 626
Genes assigned to Pfam	3 459
Genes assigned to Swiss-Prot	3 597

图4 菌株GNLJ-7基因组图谱（A）及COG功能注释（B）

Fig. 4 Genomic mapping (A) and COG functional annotation (B) of strain GNLJ-7

图5 菌株GNLJ-7基因组功能注释及通路注释A：KEGG通路注释；B：基因组GO功能注释

Fig. 5 Genome functional and pathway annotation of strain GNLJ-7A： KEGG pathway annotation. B： Genomic GO functional annotation

表2 预测GNLJ-7基因组中与PGP相关的基因

Table 2 Predicted genes associated with PGP in GNLJ-7 genome

促生特性 PGP traits	基因 Gene
吲哚-3-乙酸 Indole-3-acetic acid （IAA）	trpA， trpB， trpC， trpD， trpE， trpF，trpS
铁载体 Siderophore	pksD， pksE， pksF
解磷 Phosphate solubilization	phoD， phoA， pyk， gltA， gltB， gltC，gltX， gltP
固氮 Nitrogen fixation	nifA， nifH

图6 GNLJ-7基因组中19个预测蛋白与已报道的植物促生菌相关蛋白之间的进化关系

Fig. 6 The evolutionary relationship between 19 predicted proteins in the Gordonia didemni GNLJ-7 genome and the reported proteins from PGPRs

表3 菌株GNLJ-7中与抑草活性相关的次级代谢产物合成基因簇

Table 3 Secondary metabolite synthesis gene clusters related to grass inhibition activity in strain GNLJ-7

基因簇 Gene cluster	基因组位置 Genomic location	合成类型 Composite type	相似度 Similarity （%）
Cluster1	314 582‒379 637	Surfactin	82
Cluster5	1 438 110‒1 525 944	transAT-PKS macrolactin	100
Cluster6	1 748 067‒1 843 852	transAT-PKS bacillaene	100
Cluster7	1 922 536‒2 057 216	NRPS fengycin	100

图7 GNLJ-7表面活性素合成基因簇图谱

Fig. 7 Mapping of surfactin gene clusters in the GNLJ-7 genome

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