Rhizobacteria promote plant growth via secretion of N-(3-oxooctanoyl)-L-homoserine lactone

Abstract

Plant growth-promoting rhizobacteria (PGPR) interact with host plants through chemical signals. However, the specific signals in citrus–PGPR interactions remain unclear. Here, we show that a predominant and growth-promoting Burkholderia strain (Burk_2H3) isolated from citrus rhizosphere promotes plant growth by secreting N-(3-oxo-octanoyl)-L-homoserine lactone (PGPHL). Metabolomic analysis revealed that PGPHL abundance in Burk_2H3 secretions was 9.7- to 17.2-fold higher than that in three non-promoting Burkholderia strains. Exogenous application of PGPHL, but not other secretory metabolites, increased citrus seedling dry weight by 43.12%. Transcriptomic analysis showed that Burk_2H3, its cell-free supernatant, or PGPHL consistently upregulated key nutrient transporter genes in roots. Consistently, ionomic analysis confirmed higher root concentrations of nitrogen, phosphorus, and potassium. Field trials further demonstrated that PGPHL increased biomass by 21% in pepper, 15% in celery, and 18% in mustard. Together, these findings identify PGPHL as a candidate for developing plant growth stimulants and biofertilizers.

Acknowledgements

This work was supported by the National Key Research and Development Program of China (2024YFD2300800), the National Natural Science Foundation of China (32502615), Hubei Fruit Industrial Technology System Project (2025HBSTX4-08), the Fundamental Research Funds for the Central Universities (2662025YLPY010), Hubei Provincial Citrus Industry Chain Project (2024), Guangxi Science and Technology Major Project (GKAA23062085).

Ethics approval and consent to participate

No ethics approval or consent to participate was required.

Author contributions

Z.P. and H.L. first conceived the study and procured the funding to undertake it. H.L. wrote the first draft of the manuscript. Z.P. gave conceptual advice for the paper. All authors read, edited, and approved the final manuscript.

Data availability

The RNA-seq datasets deposited in SRA database under BioProject number PRJNA1272145 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1272145).

Conflicts of interest statement

The authors declare that they have no competing interests.

References

[1] Chieb M, Gachomo EW . The role of plant growth promoting rhizobacteria in plant drought stress responses. BMC Plant Biol. 2023; 23: 407

[2] Egamberdieva D, Kamilova F, Validov S, et al. High incidence of plant growth-stimulating bacteria associated with the rhizosphere of wheat grown on salinated soil in Uzbekistan. Environ Microbiol. 2008; 10: 1-9

[3] Fan Z, Wu Y, Zhao L, et al. MYB308-mediated transcriptional activation of plasma membrane H+-ATPase 6 promotes iron uptake in citrus. Hortic Res. 2022; 9: uhac088

[4] Haque M, Islam S, Sheikh MA, et al. Quorum sensing: a new prospect for the management of antimicrobial-resistant infectious diseases. Expert Rev Anti-Infect Ther. 2021; 19: 571-86

[5] Sun X, Xu Z, Xie J, et al. Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions . ISME J. 2022; 16: 774-87

[6] Wang N, Wang T, Chen Y, et al. Microbiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize. Nat Commun. 2024; 15: 839

[7] Backer R, Rokem JS, Ilangumaran G, et al. Plant growth-promoting rhizobacteria: context, mechanisms of action, and roadmap to commercialization of biostimulants for sustainable agriculture. Front Plant Sci. 2018; 9: 1473-89

[8] Harbort CJ, Hashimoto M, Inoue H, et al. Root-secreted coumarins and the microbiota interact to improve iron nutrition in Arabidopsis . Cell Host Microbe. 2020; 28: 825-837.e6

[9] Zhang L, Feng G, Declerck S . Signal beyond nutrient, fructose, exuded by an arbuscular mycorrhizal fungus triggers phytate mineralization by a phosphate solubilizing bacterium. ISME J. 2018; 12: 2339-51

[10] Imran A, Mirza MS, Shah TM, et al. Differential response of kabuli and desi chickpea genotypes toward inoculation with PGPR in different soils. Front Microbiol. 2015; 6: 859

[11] Hakim S, Naqqash T, Nawaz MS, et al. A sma imran rhizosphere engineering with plant growth-promoting microorganisms for agriculture and ecological sustainability. Front Sustain Food Syst. 2021; 5: 7157

[12] Hanif MK, Malik KA, Hameed S, et al. Growth stimulatory effect of AHL producing Serratia spp. from potato on homologous and non-homologous host plants . Microbiol Soc. 2020; 238: 126506

[13] Sharma SB, Sayyed RZ, Trivedi MH, et al. Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. Springer Plus. 2013; 2: 587

[14] Ghosh SK, Bera T, Chakrabarty AM . Microbial siderophore-a boon to agricultural sciences. Biol Control. 2020; 144: 104214

[15] Kumar V, Singh P, Jorquera MA, et al. Isolation of phytase-producing bacteria from Himalayan soils and their effect on growth and phosphorus uptake of Indian mustard (Brassica juncea) . J Microbiol Biotechnol. 2013; 29: 1361-9

[16] Mukherjee A, Mazumder M, Verma A, et al. A bacterial signal coordinates plant-microbe fitness trade-off to enhance sulfur deficiency tolerance in plants. Cell Host Microbe. 2025; 33: 1748-1764.e6

[17] Liu Y, Kyle S, Straight PD . Antibiotic stimulation of a Bacillus subtilis migratory response . mSphere. 2018; 3: e0058617

[18] Mun BG, Lee WH, Kang SM, et al. LH 4 promotes plant growth and resistance against Sclerotinia sclerotiorum in cucumber via modulation of enzymatic and defense pathways . Plant Soil. 2020; 448: 87-103

[19] Wang N, Pierson EA, Setubal JC, et al. The Candidatus Liberibacter-host interface: insights into pathogenesis mechanisms and disease control. Annu Rev Phytopathol. 2017; 55: 451-82

[20] Darriaut R, Lailheugue V, Masneuf-Pomarède I, et al. Grapevine rootstock and soil microbiome interactions: keys for a resilient viticulture. Hortic Res. 2022; 9: uhac019

[21] Li H, Wang Y, Deng L, et al. Microbial biobank-based strain phenotyping efficiently identifies plant growth-promoting bacteria from citrus rhizosphere. Hortic Adv. 2025; 3: 3

[22] Russ D, Fitzpatrick CR, Teixeira P, et al. Deep discovery informs difficult deployment in plant microbiome science. Cell. 2023; 186: 4496-513

[23] Schenk ST, Hernández-Reyes C, Samans B, et al. N-acyl-homoserine lactone primes plants for cell wall reinforcement and induces resistance to bacterial pathogens via the salicylic acid/oxylipin pathway. Plant Cell. 2014; 26: 2708-23

[24] Jamil F, Mukhtar H, Fouillaud M, et al. Rhizosphere signaling: insights into plant-rhizomicrobiome interactions for sustainable agronomy. Microorganisms. 2022; 10: 899

[25] Mathesius U, Mulders S, Gao M, et al. Extensive and specific responses of a eukaryote to bacterial quorum-sensing signals. Proc Natl Acad Sci USA. 2003; 100: 1444-9

[26] Babenko LM, Kosakivska IV, Romanenko KO . Molecular mechanisms of N-acyl homoserine lactone signals perception by plants. Cell Biol Int. 2022; 46: 523-34

[27] Middleton B, Rodgers HC, Cámara M, et al. Direct detection of N-acylhomoserine lactones in cystic fibrosis sputum. FEMS Microbiol Lett. 2002; 207: 1-7

[28] von Rad U, Klein I, Dobrev PI, et al. Response of Arabidopsis thaliana to N-hexanoyl-DL-homoserine-lactone, a bacterial quorum sensing molecule produced in the rhizosphere . Planta. 2008; 229: 73-85

[29] Pazarlar S, Cetinkaya N, Bor M, et al. N-acyl homoserine lactone-mediated modulation of plant growth and defense against Pseudoperonospora cubensis in cucumber . J Exp Bot. 2020; 71: 6638-54

[30] Götz-Rösch C, Sieper T, Fekete A, et al. Influence of bacterial N-acyl-homoserine lactones on growth parameters, pigments, antioxidative capacities and the xenobiotic phase II detoxification enzymes in barley and yam bean. Front Plant Sci. 2015; 6: 205

[31] Liu F, Bian Z, Jia Z, et al. The GCR1 and GPA1 participate in promotion of Arabidopsis primary root elongation induced by N-acyl-homoserine lactones, the bacterial quorum-sensing signals. Mol Plant-Microbe Interact. 2012; 25: 677-83

[32] Custódio V, Salas-González I, Gopaulchan D, et al. Individual leaf microbiota tunes a genetic regulatory network to promote leaf growth. Cell Host Microbe. 2025; 33: 436-450.e15

[33] Li J, Wang J, Liu H, et al. Application of microbial inoculants significantly enhances crop productivity: a meta-analysis of studies from 2010 to 2020. J Sustain Agric Environ. 2022; 1: 216-25

[34] Compant S, Cassan F, Kostić T, et al. Harnessing the plant microbiome for sustainable crop production. Nat Rev Microbiol. 2025; 23: 9-23

[35] Kruse S, Becker S, Pierre F, et al. Metabolic profiling of bacterial co-cultures reveals intermicrobiome interactions and dominant species. J Chromatogr A. 2023; 1694: 463911

[36] Anders S, Pyl PT, Huber W . HTSeq-a python framework to work with high-throughput sequencing data. Bioinformatics. 2015; 31: 166-9

[37] Hansen TH, Laursen KH, Persson DP, et al. Micro-scaled high-throughput digestion of plant tissue samples for multi-elemental analysis. Plant Methods. 2009; 5: 12

[38] Wu S, Zhang Y, Tian Q, et al. Biochar is superior to lime in improving acidic soil properties and fruit quality of Satsuma mandarin . Sci Total Environ. 2020; 714: 136722

[39] Sáez-Plaza P, Navas MJ, Wybraniec S, et al. An overview of the kjeldahl method of nitrogen determination. Part II. Sample preparation, working scale, instrumental finish, and quality control. Anal Chem. 2013; 43: 224-72

[40] Marguí E, Dalipi R, Sangiorgi E, et al. Determination of essential elements (Mn, Fe, Cu and Zn) in herbal teas by TXRF, FAAS and ICP-OES. X-Ray Spectrom. 2022; 51: 204-13

[41] Hodgkinson JT, Galloway WRJD, Casoli M, et al. Robust routes for the synthesis of N-acylated-L-homoserine lactone (AHL) quorum sensing molecules with high levels of enantiomeric purity. Tetrahedron Lett. 2011; 52: 3291-4