1. Abdul Hamid, N. W., & Nadarajah, K. (2022). Microbe Related Chemical Signalling and Its Application in Agriculture. International Journal of Molecular Sciences, 23, 1- 25. [DOI:10.3390/ijms23168998] [PMID] [PMCID]

2. Ahmed, A., & Hasnain, S. (2014). Auxins as one of the factors of plant growth improvement by plant growth promoting rhizobacteria. Polish Journal of Microbiology, 63(3), 261.11-24. PMID: 25546935 [DOI:10.33073/pjm-2014-035] [PMID]

3. Asha, B. B., Nayaka, C. S., Shankar, U. A., Srinivas, C., & Niranjana, S. R. (2011). Biological control of F. oxysporum f. sp. lycopersici causing wilt of tomato by Pseudomonas fluorescens. International Journal of Microbiology Research, 3(2), 79. 1-8. [DOI:10.9735/0975-5276.3.2.79-84]

4. Bakki, M., Banane, B., Marhane, O., Esmaeel, Q., Hatimi, A., Barka, E. A., Azim, K., & Bouizgarne, B. (2024). Phosphate solubilizing Pseudomonas and Bacillus combined with rock phosphates promoting tomato growth and reducing bacterial canker disease. Frontiers in microbiology, 15, 1289466. [DOI:10.3389/fmicb.2024.1289466] [PMID] [PMCID]

5. Baptista, J. P., Teixeira, G. M., de Jesus, M. L. A., Bertê, R., Higashi, A., Mosela, M., da Silva, D. V., de Oliveira, J. P., Sanches, D. S., & Brancher, J. D. (2022). Antifungal activity and genomic characterization of the biocontrol agent Bacillus velezensis CMRP 4489. Scientific reports, 12(1), 17401. [DOI:10.1038/s41598-022-22380-0] [PMID] [PMCID]

6. Barillot, C. D., Sarde, C.-O., Bert, V., Tarnaud, E., & Cochet, N. (2013). A standardized method for the sampling of rhizosphere and rhizoplan soil bacteria associated to a herbaceous root system. Annals of microbiology, 63(2), 471-4. doi: [DOI:10.1007/s13213-012-0491-y]

7. Beneduzi, A., Ambrosini, A., & Passaglia, L. M. (2012). Plant growth-promoting rhizobacteria (PGPR): their potential as antagonists and biocontrol agents. Genetics and molecular biology, 35(4 suppl 1), 1044-1051. https://doi.org/10.1590/S1415-47572012000600020 [DOI:10.1590/s1415-47572012000600020] [PMID] [PMCID]

8. Bent, E., Tuzun, S., Chanway, C. P., & Enebak, S. (2001). Alterations in plant growth and in root hormone levels of lodgepole pines inoculated with rhizobacteria. Canadian Journal of Microbiology, 47(9), 793-800. [DOI:10.1139/w01-080] [PMID]

9. Bolwerk, A., Lagopodi, A. L., Wijfjes, A. H., Lamers, G. E., Chin-A-Woeng, T. F., Lugtenberg, B. J., & Bloemberg, G. V. (2003). Interactions in the tomato rhizosphere of two Pseudomonas biocontrol strains with the phytopathogenic fungus Fusarium oxysporum f. sp. radicis-lycopersici. Molecular Plant-Microbe Interactions, 16(11), 983-993. [DOI:10.1094/MPMI.2003.16.11.983] [PMID]

10. Chaudhary, P., Bhattacharjee, A., Shivay, Y. S., Dalal, R. C., & Sharma, S. (2025). Farming practices affect soil's suppressiveness towards phytopathogens. Applied soil ecology, 209, 106012. [DOI:10.1016/j.apsoil.2025.106012]

11. Chin‐A‐Woeng, T. F., Bloemberg, G. V., & Lugtenberg, B. J. (2003). Phenazines and their role in biocontrol by Pseudomonas bacteria. New phytologist, 157(3), 503-523. [DOI:10.1046/j.1469-8137.2003.00686.x] [PMID]

12. Chin-A-Woeng, T. F., de Priester, W., van der Bij, A. J., & Lugtenberg, B. J. (1997). Description of the colonization of a gnotobiotic tomato rhizosphere by Pseudomonas fluorescens biocontrol strain WCS365, using scanning electron microscopy. Molecular plant-microbe interactions, 10(1), 79-86. http://dx.doi.org/10.1094/MPMI.1997.10.1.79 [DOI:10.1094/MPMI.1997.10.1.79]

13. Chu, T. N., Bui, L. V., & Hoang, M. T. T. (2020). Pseudomonas PS01 isolated from maize rhizosphere alters root system architecture and promotes plant growth. Microorganisms, 8(4), 471. [DOI:10.3390/microorganisms8040471] [PMID] [PMCID]

14. Eichmann, R., Richards, L., & Schäfer, P. (2021). Hormones as go‐betweens in plant microbiome assembly. The Plant Journal, 105(2), 518-541. [DOI:10.1111/tpj.15135] [PMID] [PMCID]

15. Fattahi, E., Ostovar, N., & Kaboosi, H. (2017). Isolation and characterization of chlorpyrifos-degrading bacteria from rice field soils in Amol City, Iran. Scientific Journal of School of Public Health and Institute of Public Health Research 15(1), 73-82. http://sjsph.tums.ac.ir/article-1-5480-en.html

16. Ghazy, N., & El-Nahrawy, S. (2021). Siderophore production by Bacillus subtilis MF497446 and Pseudomonas koreensis MG209738 and their efficacy in controlling Cephalosporium maydis in maize plant. Archives of microbiology, 203(3), 1195-1209. [DOI:10.1007/s00203-020-02113-5] [PMID] [PMCID]

17. Ghoreshizadeh, S., Calvo-Peña, C., Ruiz-Muñoz, M., Dobrajc, M., Radišek, S., Coque, J. J. R., & Cobos, R. (2025). Isolation and characterization of Pseudomonas sp. HX1, Streptomyces luteogriseus HR40, and Streptomyces Flavofungini HR77 as promising biocontrol agents against verticillium wilt in hops affected by Verticillium nonalfalfae. Horticulturae, 11(5), 459. [DOI:10.3390/horticulturae11050459]

18. Hnini, M., & Aurag, J. (2024). Genetic diversity, stress tolerance and phytobeneficial potential in rhizobacteria of Vachellia tortilis subsp. raddiana. Environmental Microbiome, 19, 1- 21. [DOI:10.1186/s40793-024-00611-3] [PMID] [PMCID]

19. Hou, Q., Wang, C., Guo, H., Xia, Z., Ye, J., Liu, K., & Ding, Y. (2015). Draft genome sequence of Delftia tsuruhatensis MTQ3, a strain of plant growth-promoting rhizobacterium with antimicrobial activity. Genome announcements, 3(4), 10-1128. [DOI:10.1128/genomeA.00822-15] [PMID] [PMCID]

20. Hultberg, M., Alsberg, T., Khalil, S., & Alsanius, B. (2010). Suppression of disease in tomato infected by Pythium ultimum with a biosurfactant produced by Pseudomonas koreensis. BioControl, 55(3), 435-444. https://link.springer.com/article/10.1007/s10526-009-9261-6 [DOI:10.1007/s10526-009-9261-6]

21. Kumar, S., Stecher, G., Suleski, M., Sanderford, M., Sharma, S., & Tamura, K. (2024). MEGA12: Molecular Evolutionary Genetic Analysis version 12 for adaptive and green computing. Molecular biology and evolution, 41(12), msae263. [DOI:10.1093/molbev/msae263] [PMID] [PMCID]

22. Lehman, D. (2005). Triple sugar iron agar protocols. American society for microbiology, 1-7.

23. Li, B., Sun, Q., Shi, J., Zhang, W., Zhou, H., Wang, Y., Wang, P., Tang, M., Du, Y., & Liu, B. (2025). Pseudomonas chlororaphis YTBTa14 as a Multifunctional Biocontrol Agent: Simultaneous Growth Enhancement and Systemic Resistance Induction in Vitis vinifera Against Downy Mildew. Agriculture, 15(17), 1822. [DOI:10.3390/agriculture15171822]

24. Louden, B. C., Haarmann, D., & Lynne, A. M. (2011). Use of blue agar CAS assay for siderophore detection. Journal of microbiology & biology education, 12(1), 51-53. PMID: 23653742 [DOI:10.1128/jmbe.v12i1.249] [PMID] [PMCID]

25. Maake, T. W., & Sibisi, P. (2025). Microbial Antagonists for the Control of Plant Diseases in Solanaceae Crops: Current Status, Challenges, and Global Perspectives. Bacteria, 4. 29. ; [DOI:10.3390/bacteria4030029]

26. Mavrodi, D. V., Blankenfeldt, W., & Thomashow, L. S. (2006). Phenazine compounds in fluorescent Pseudomonas spp. biosynthesis and regulation. Annu. Rev. Phytopathol., 44(1), 417-445. [DOI:10.1146/annurev.phyto.44.013106.145710] [PMID]

27. Mazuecos-Aguilera, I., Anta-Fernández, F., Crespo-Barreiro, A., Martínez-Quesada, A., Lombana-Larrea, L., & González-Andrés, F. (2025). Plant growth-promoting rhizobacteria enhanced induced systemic resistance of tomato against Botrytis cinerea phytopathogen. Frontiers in plant science, 16, 1570986. [DOI:10.3389/fpls.2025.1570986] [PMID] [PMCID]

28. Michielse, C. B., van Wijk, R., Reijnen, L., Manders, E. M., Boas, S., Olivain, C., & Rep, M. (2009). The nuclear protein Sge1 of Fusarium oxysporum is required for parasitic growth. PLoS pathogens, 5(10), e1000637. [DOI:10.1371/journal.ppat.1000637] [PMID] [PMCID]

29. Nautiyal, C. S. (1999). An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS microbiology letters, 170(1), 265-270. [DOI:10.1111/j.1574-6968.1999.tb13383.x] [PMID]

30. Pan, L., & Cai, B. (2023). Phosphate-solubilizing bacteria: advances in their physiology, molecular mechanisms and microbial community effects. Microorganisms, 11(12), 2904. [DOI:10.3390/microorganisms11122904] [PMID] [PMCID]

31. Pastor, N., Carlier, E., Andrés, J., Rosas, S. B., & Rovera, M. (2012). Characterization of rhizosphere bacteria for control of phytopathogenic fungi of tomato. Journal of Environmental Management, 95, S332-S337. doi.org/10.1016/j.jenvman.2011.03.037 [DOI:10.1016/j.jenvman.2011.03.037] [PMID]

32. Peng, J., Hou, J., Liu, H., Mavrodi, D. V., Mavrodi, O. V., Sun, F., Shen, M., Wang, X., Dang, K., & Yan, M. (2025). Changes in the soil and rhizosphere microbiomes associated with bacterial wilt decline in the tomato monoculture field. Geoderma, 457, 117273. [DOI:10.1016/j.geoderma.2025.117273]

33. Rahman, M. M., Almasoudi, N. M., Asiry, K. N., & Abo‑Elyousr, K. A. M. (2025). Evaluation of bacterial bioagents for controlling gray mold disease in tomatoes and promoting crop health. Egyptian Journal of Biological Pest Control, 35. [DOI:10.1186/s41938-025-00843-6]

34. Reinhold-Hurek, B., Bünger, W., Burbano, C. S., Sabale, M., & Hurek, T. (2015). Roots shaping their microbiome: global hotspots for microbial activity. Annual Review of Phytopathology, 53(1), 403-424. [DOI:10.1146/annurev-phyto-082712-102342] [PMID]

35. Sehrawat, A., Sindhu, S. S., & Glick, B. R. (2022). Hydrogen cyanide production by soil bacteria: Biological control of pests and promotion of plant growth in sustainable agriculture. Pedosphere, 32(1), 15-38. [DOI:10.1016/S1002-0160(21)60058-9]

36. Serafim, B., Bernardino, A. R., Freitas, F., & Torres, C. A. (2023). Recent developments in the biological activities, bioproduction, and applications of Pseudomonas spp. phenazines. Molecules, 28(3), 1368. [DOI:10.3390/molecules28031368] [PMID] [PMCID]

37. Singh, V. K., Singh, A. K., & Kumar, A. (2017). Disease management of tomato through PGPB: current trends and future perspective. 3 Biotech, 7(4), 255. [DOI:10.1007/s13205-017-0896-1] [PMID] [PMCID]

38. Smalla, K., Wieland, G., Buchner, A., Zock, A., Parzy, J., Kaiser, S., Roskot, N., Heuer, H., & Berg, G. (2001). Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Applied and environmental microbiology, 67(10), 4742-4751. doi:10.1128/AEM.67.10.4742-4751.2001 [DOI:10.1128/AEM.67.10.4742-4751.2001] [PMID] [PMCID]

39. Sonkar, P., Purwar, S., Bhargva, P., Singh, R. P., Alkahtani, J., Al-Hashimi, A., and Khan, S. (2024). In silico profiling, docking analysis, and protein interactions of secondary metabolites in Musa spp. Against the SGE1 protein of Fusarium oxysporum f. sp. cubense. Computational Biology and Chemistry, 113, 108230. [DOI:10.1016/j.compbiolchem.2024.108230] [PMID]

40. Srinivas, C., Devi, D. N., Murthy, K. N., Mohan, C. D., Lakshmeesha, T. R., Singh, B., & Srivastava, R. K. (2019). Fusarium oxysporum f. sp. lycopersici causal agent of vascular wilt disease of tomato: Biology to diversity-A review. Saudi journal of biological sciences, 26(7), 1315-1324. [DOI:10.1016/j.sjbs.2019.06.002] [PMID] [PMCID]

41. Steel, K. (1961). The oxidase reaction as a taxonomic tool. Microbiology, 25(2), 297-306. [DOI:10.1099/00221287-25-2-297]

42. Tian, J., Ge, F., Zhang, D., Deng, S., & Liu, X. (2021). Roles of phosphate solubilizing microorganisms from managing soil phosphorus deficiency to mediating biogeochemical P cycle. Biology, 10(2), 158. [DOI:10.3390/biology10020158] [PMID] [PMCID]

43. Vessey, J. K. (2003). Plant growth promoting rhizobacteria as biofertilizers. Plant and soil, 255(2), 571-586. [DOI:10.1023/A:1026037216893]

44. Villar-Moreno R, Tienda S, Gutie' rrez-Barranquero JA, Carrio' n VJ, de Vicente A, Cazorla FM, & E, A. (2022). Interplay between rhizospheric Pseudomonas chlororaphis strains lays the basis for beneficial bacterial consortia. Frontiers in plant science, 1-17. [DOI:10.3389/fpls.2022.1063182] [PMID] [PMCID]

45. Wang, Y., Zhang, G., Huang, Y., Guo, M., Song, J., Zhang, T., Long, Y., Wang, B., & Liu, H. (2022). A Potential Biofertilizer-Siderophilic Bacteria Isolated From the Rhizosphere of Paris polyphylla var. yunnanensis. Frontiers in microbiology, 13. [DOI:10.3389/fmicb.2022.870413] [PMID] [PMCID]

46. Wei, D., Zhu, D., Zhang, Y., Yang, Z., Hu, Y., Song, C., Yang, W., & Chang, X. (2024). Pseudomonas chlororaphis IRHB3 assemblies beneficial microbes and activates JA-mediated resistance to promote nutrient utilization and inhibit pathogen attack. Frontiers in microbiology, 5(15):1-15. [DOI:10.3389/fmicb.2024.1328863] [PMID] [PMCID]

47. Weisburg, W. G., Barns, S. M., Pelletier, D. A., & Lane, D. J. (1991). 16S ribosomal DNA amplification for phylogenetic study. Journal of bacteriology, 173(2), 697-703. [DOI:10.1128/jb.173.2.697-703.1991] [PMID] [PMCID]

48. Wen, T., Yu, G.-H., Hong, W.-D., Yuan, J., Niu, G.-Q., Xie, P.-H., Sun, F.-S., Guo, L.-D., Kuzyakov, Y., & Shen, Q.-R. (2022). Root exudate chemistry affects soil carbon mobilization via microbial community reassembly. Fundamental Research, 2(5), 697-707. [DOI:10.1016/j.fmre.2021.12.016] [PMID] [PMCID]

49. Zamioudis, C., Mastranesti, P., Dhonukshe, P., Blilou, I., & Pieterse, C. M. (2013). Unraveling root developmental programs initiated by beneficial Pseudomonas spp. bacteria. Plant physiology, 162(1), 304-318. [DOI:10.1104/pp.112.212597] [PMID] [PMCID]

50. Zhalnina, K., B. Louie, K., Hao, Z., Mansoori, N., da Rocha, U. N., Shi, S., Cho, H., Karaoz, U., Loqué, D., P. Bowen, B., Firestone, M., Northen, T., & Brodie, E. L. (2018). Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nature microbiology, 3, 470-480. [DOI:10.1038/s41564-018-0129-3] [PMID]

51. Zhou, J., Bruns, M. A., & Tiedje, J. M. (1996). DNA recovery from soils of diverse composition. Applied and environmental microbiology, 62(2), 316-322. doi: https://doi.org/10.1128/aem.62.2.316-322.1996 [DOI:10.1128/aem.62.2.316-322.1996. https://doi.org/10.1128/aem.62.2.316-322.1996] [PMID] [PMCID]