Biological Function and Whole-genome Analysis of Actinobacteria Strain GNLJ-7 Isolated from Tomato Rhizosphere

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

Abstract

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

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.

Figures/Tables 10

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

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

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)

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

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

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

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

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

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

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

References 32

[1]	中华人民共和国农业农村部. 中华人民共和国农业农村部公告第351号 [EB/OL]. (2020-11-04) [2026-03-22]. .
	Ministry of Agriculture and Rural Affairs of the People’s Republic of China. Announcement No. 351 of the Ministry of Agriculture and Rural Affairs of the People’s Republic of China [EB/OL]. (2020-11-04) [2026-03-23]. .
[2]	Zhao NN, Zhong MN, Grey TL, et al. Further investigations on the occurrence patterns of multiple broomrape species in Xinjiang China [J]. Crop Prot, 2025, 197: 107287.
[3]	Mutuku JM, Cui SK, Yoshida S, et al. Orobanchaceae parasite-host interactions [J]. New Phytol, 2021, 230(1): 46-59.
[4]	Jamil M, Kountche BA, Al-Babili S. Current progress in Striga management [J]. Plant Physiol, 2021, 185(4): 1339-1352.
[5]	Pongpamorn P, Zwart M, Bouwmeester HJ. The role of soil microbiota in the control of parasitic weeds [J]. Plant Cell Physiol, 2025: pcaf125.
[6]	Lenard G M, Williams O A, Rasche F. Tripartite interaction between Striga spp., cereals, and plant root-associated microorganisms: a review [J]. CABI Rev, 2020: PAVSNNR202015005.
[7]	Yu K, Pieterse CMJ, Bakker PAHM, et al. Beneficial microbes going underground of root immunity [J]. Plant Cell Environ, 2019, 42(10): 2860-2870.
[8]	Du JF, Li Y, Yin ZY, et al. High-throughput customization of plant microbiomes for sustainable agriculture [J]. Front Plant Sci, 2020, 11: 569742.
[9]	Osman NY, Hamdani MS, Oslan SN, et al. Biological control strategies of purple witchweed, Striga hermonthica: a review [J]. Pertanika J Trop Agric Sci, 2022, 46(1): 177-195.
[10]	陈杰, 马永清, 薛泉宏. 利用微生物防除根寄生杂草列当 [J]. 中国生态农业学报, 2018, 26(1): 49-56.
	Chen J, Ma YQ, Xue QH. Use of microorganisms in controlling parasitic root weed Orobanche spp. [J]. Chin J Eco Agric, 2018, 26(1): 49-56.
[11]	Goudjal Y, Toumatia O, Sabaou N, et al. Endophytic actinomycetes from spontaneous plants of Algerian Sahara: indole-3-acetic acid production and tomato plants growth promoting activity [J]. World J Microbiol Biotechnol, 2013, 29(10): 1821-1829.
[12]	Salwan R, Sharma V. Molecular and biotechnological aspects of secondary metabolites in Actinobacteria [J]. Microbiol Res, 2020, 231: 126374.
[13]	Vesuna AP, Nerurkar AS. Biocontrol impact of AHL degrading Actinobacteria on quorum sensing regulated virulence of phytopathogen Pectobacterium carotovorum subsp. carotovorum BR1 [J]. Plant Soil, 2020, 453(1/2): 371-388.
[14]	Bouwmeester HJ, Roux C, Lopez-Raez JA, et al. Rhizosphere communication of plants, parasitic plants and AM fungi [J]. Trends Plant Sci, 2007, 12(5): 224-230.
[15]	李福艳, 刘晓玉, 颜静婷, 等. 三株产吲哚乙酸根际促生芽孢杆菌的筛选鉴定及其促生作用 [J]. 浙江农业学报, 2021, 33(5): 873-884.
	Li FY, Liu XY, Yan JT, et al. Isolation and identification of three indole-3-acetic acid producing plant-growth-promoting rhizosphere Bacillus sp. and their growth-promoting effects [J]. Acta Agric Zhejiangensis, 2021, 33(5): 873-884.
[16]	de Andrade LA, Santos CHB, Frezarin ET, et al. Plant growth-promoting rhizobacteria for sustainable agricultural production [J]. Microorganisms, 2023, 11(4): 1088.
[17]	Conrath U, Beckers GJM, Flors V, et al. Priming: getting ready for battle [J]. Mol Plant Microbe Interact, 2006, 19(10): 1062-1071.
[18]	Shayanowako AIT, Shimelis H, Laing MD, et al. Striga resistance and compatibility of maize genotypes to a biocontrol agent, Fusarium oxysporum f. sp. strigea [J]. J Crop Improv, 2020, 34(4): 437-454.
[19]	Nzioki HS, Oyosi F, Morris CE, et al. Striga biocontrol on a toothpick: a readily deployable and inexpensive method for smallholder farmers [J]. Front Plant Sci, 2016, 7: 1121.
[20]	Baker CS, Sands DC, Nzioki HS. The Toothpick Project: commercialization of a virulence-selected fungal bioherbicide for Striga hermonthica (witchweed) biocontrol in Kenya [J]. Pest Manag Sci, 2024, 80(1): 65-71.
[21]	Sánchez-Suárez J, Díaz L, Coy-Barrera E, et al. Specialized metabolism of Gordonia genus: an integrated survey on chemodiversity combined with a comparative genomics-based analysis [J]. BioTech, 2022, 11(4): 53.
[22]	Liu HW, Brettell LE, Qiu ZG, et al. Microbiome-mediated stress resistance in plants [J]. Trends Plant Sci, 2020, 25(8): 733-743.
[23]	Alori ET, Dare MO, Babalola OO. Microbial inoculants for soil quality and plant health [M]//Lichtfouse E. Sustainable Agriculture Reviews. Cham: Springer International Publishing, 2017: 281-307.
[24]	Nair KP. Phosphate solubilizing microorganisms and their role in sustainable agriculture [M]//Intelligent Soil Management for Sustainable Agriculture: The Nutrient Buffer Power Concept. Cham: Springer International Publishing, 2019: 245-266.
[25]	Saha M, Sarkar S, Sarkar B, et al. Microbial siderophores and their potential applications: a review [J]. Environ Sci Pollut Res, 2016, 23(5): 3984-3999.
[26]	Dheeman S, Maheshwari DK. Ecology of nitrogen-fixing bacteria for sustainable development of non-legume crops [M]//Maheshwari DK, Dobhal R, Dheeman S. Nitrogen Fixing Bacteria: Sustainable Growth of Non-legumes. Singapore: Springer Nature Singapore, 2022: 301-315.
[27]	Pérez-García LA, Sáenz-Mata J, Fortis-Hernández M, et al. Plant-growth-promoting rhizobacteria improve germination and bioactive compounds in cucumber seedlings [J]. Agronomy, 2023, 13(2): 315.
[28]	Polli EG, Alves GS, Gizotti de Moraes J, et al. Influence of surfactant-humectant adjuvants on physical properties, droplet size, and efficacy of glufosinate formulations [J]. Agrosystems Geosci & Env, 2022, 5: e20230.
[29]	Mirgorodskaya АB, Kushnazarova RА, Lukashenko SS, et al. Carbamate-bearing surfactants as effective adjuvants promoted the penetration of the herbicide into the plant [J]. Colloids Surf A Physicochem Eng Aspects, 2020, 586: 124252.
[30]	Fazle Rabbee M, Baek KH. Antimicrobial activities of lipopeptides and polyketides of Bacillus velezensis for agricultural applications [J]. Molecules, 2020, 25(21): 4973.
[31]	Golovatskaya IF, Boyko EV. Melatonin and the transmission of light and auxin signals in plants [M]//Baluška F, Mukherjee S, Ramakrishna A. Neurotransmitters in Plant Signaling and Communication. Cham: Springer International Publishing, 2020: 189-211.
[32]	Moormann J, Heinemann B, Hildebrandt TM. News about amino acid metabolism in plant-microbe interactions [J]. Trends Biochem Sci, 2022, 47(10): 839-850.