Impact of Plant Growth Promoting Rhizobacteria (PGPR) on Nitrogen Uptake and Yield of Palu Local Shallots
DOI:
10.29303/jppipa.v12i6.14802Published:
2026-06-25Downloads
Abstract
Plant Growth-Promoting Rhizobacteria (PGPR) play an important role in improving soil microbial populations and enhancing plant growth and nutrient uptake. This study aimed to evaluate the effect of different PGPR concentrations on bacterial colony populations, growth performance, biomass production, and nitrogen uptake of Palu Valley shallot plants. The experiment consisted of four treatments: control (F0), PGPR 10 mL (F1), PGPR 15 mL (F2), and PGPR 20 mL (F3). The observed variables included bacterial colony population, number of shallot bulbs, fresh biomass, dry biomass, and nitrogen uptake. The results showed that PGPR application increased the bacterial colony population in soil, with the highest population recorded in treatment F3 (3.90 × 10⁶ CFU g⁻¹ soil). The average number of shallot bulbs increased from 9 bulbs plant⁻¹ in the control to 12 bulbs plant⁻¹ in treatments F2 and F3. Fresh biomass and dry biomass also increased with higher PGPR concentrations, reaching 11.95 g and 2.42 g respectively in F3. Nitrogen uptake showed a gradual increase from 1.61% in the control to 1.69% in F3. These findings indicate that PGPR application improves soil microbial populations, plant growth, biomass accumulation, and nitrogen uptake in Palu Valley shallot plants, with the 20 mL PGPR (F3) treatment providing the most effective results.
Keywords:
Nitrogen uptake PGPR Rhizobacteria Palu Valley Shallot Soil Microbial PopulationReferences
AbuQamar, S. F., El-Saadony, M. T., Saad, A. M., Desoky, E. S. M., Elrys, A. S., El-Mageed, T. A. A., Semida, W. M., Abdelkhalik, A., Mosa, W. F. A., Al Kafaas, S. S., Naser, S., Ibrahim, E. H., Alshamsi, F. M. K., Mathew, B. T., & El-Tarabily, K. A. (2024). Halotolerant plant growth-promoting rhizobacteria improve soil fertility and plant salinity tolerance for sustainable agriculture—A review. Plant Stress, 12(February), 100482. https://doi.org/10.1016/j.stress.2024.100482 DOI: https://doi.org/10.1016/j.stress.2024.100482
Aditya, I., Santoso, J., & Saefurrohman. (2025). The Effect of the Composition of Planting Media and the Concentration of Plant Growth-Promoting Rhizobacteria (PGPR) on the Growth and Yield of Bird’s Eye Chili (Capsicum frutescens L.). Jurnal Penelitian Pendidikan IPA, 11(12), 194–204. https://doi.org/10.29303/jppipa.v11i12.12966 DOI: https://doi.org/10.29303/jppipa.v11i12.12966
Agustiyani, D. (2016). Penapisan dan Karakterisasi Rhizobakteria serta Uji Aktivitasnya dalam Mendukung Perkecambahan dan Pertumbuhan Benih Jagung ( Zea mays L .) ( Screening and Characterization of Rhizobacteria and its Activities in Supporting Germination and Seedlings Growth. Jurnal Biologi Indonesia, 12(2), 241–248.
Angst, G., Potapov, A., Joly, F. X., Angst, Š., Frouz, J., Ganault, P., & Eisenhauer, N. (2024). Conceptualizing soil fauna effects on labile and stabilized soil organic matter. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-49240-x DOI: https://doi.org/10.1038/s41467-024-49240-x
Aragie, E., Alemayehu, M., & Abate, A. (2023). Influences of Seedling Age and Variety on the Growth and Bulb Yield of Onion in Northwest Ethiopia. International Journal of Agronomy, 2023. https://doi.org/10.1155/2023/9132446 DOI: https://doi.org/10.1155/2023/9132446
Bangkele, L. I., Basir-Cyio, M., Tjoa, A., & Tellu, A. T. (2019). Rattan root morphology under different inorganic nitrogen fertilization. IOP Conference Series: Earth and Environmental Science, 260(1). https://doi.org/10.1088/1755-1315/260/1/012126 DOI: https://doi.org/10.1088/1755-1315/260/1/012126
Bangkele, L. I., Basir-cyio, M., Tjoa, A., & Tellu, T. (2020). Nitrogen and Phosphorus Acquisition of Rattan Seeds Grown in Rizoboxes. Haya: The Saudi Journal of Life Sciences, 05(03), 18–22. https://doi.org/10.36348/sjls.2020.v05i03.001 DOI: https://doi.org/10.36348/sjls.2020.v05i03.001
Chauhan, P., Sharma, N., Tapwal, A., Kumar, A., Verma, G. S., Meena, M., Seth, C. S., & Swapnil, P. (2023). Soil Microbiome: Diversity, Benefits and Interactions with Plants. Sustainability (Switzerland), 15(19). https://doi.org/10.3390/su151914643 DOI: https://doi.org/10.3390/su151914643
Chen, L., & Liu, Y. (2024). The Function of Root Exudates in the Root Colonization by Beneficial Soil Rhizobacteria. Biology, 13(2), 1–18. https://doi.org/10.3390/biology13020095 DOI: https://doi.org/10.3390/biology13020095
Chiaranunt, P and White, J. (2023). Vertical Farming Systems. 12(400), 2–27. DOI: https://doi.org/10.3390/plants12020400
Dal Lago, P., Vavlas, N., Kooistra, L., & De Deyn, G. B. (2024). Estimation of nitrogen uptake, biomass, and nitrogen concentration, in cover crop monocultures and mixtures from optical UAV images. Smart Agricultural Technology, 9(September), 100608. https://doi.org/10.1016/j.atech.2024.100608 DOI: https://doi.org/10.1016/j.atech.2024.100608
Eichmann, R., Richards, L., & Schäfer, P. (2021). Hormones as go-betweens in plant microbiome assembly. Plant Journal, 105(2), 518–541. https://doi.org/10.1111/tpj.15135 DOI: https://doi.org/10.1111/tpj.15135
El-Saadony, M. T., Saad, A. M., Mohammed, D. M., Fahmy, M. A., Elesawi, I. E., Ahmed, A. E., Algopishi, U. B., Elrys, A. S., Desoky, E. S. M., Mosa, W. F. A., Abd El-Mageed, T. A., Alhashmi, F. I., Mathew, B. T., AbuQamar, S. F., & El-Tarabily, K. A. (2024). Drought-tolerant plant growth-promoting rhizobacteria alleviate drought stress and enhance soil health for sustainable agriculture: A comprehensive review. Plant Stress, 14(July). https://doi.org/10.1016/j.stress.2024.100632 DOI: https://doi.org/10.1016/j.stress.2024.100632
Elias, D. M. O., Mason, K. E., Goodall, T., Taylor, A., Zhao, P., Otero-Fariña, A., Chen, H., Peacock, C. L., Ostle, N. J., Griffiths, R., Chapman, P. J., Holden, J., Banwart, S., McNamara, N. P., & Whitaker, J. (2024). Microbial and mineral interactions decouple litter quality from soil organic matter formation. Nature Communications , 15(1). https://doi.org/10.1038/s41467-024-54446-0 DOI: https://doi.org/10.1038/s41467-024-54446-0
Hakim, S., Naqqash, T., Nawaz, M. S., Laraib, I., Siddique, M. J., Zia, R., Mirza, M. S., & Imran, A. (2021). Rhizosphere Engineering With Plant Growth-Promoting Microorganisms for Agriculture and Ecological Sustainability. Frontiers in Sustainable Food Systems, 5(February), 1–23. https://doi.org/10.3389/fsufs.2021.617157 DOI: https://doi.org/10.3389/fsufs.2021.617157
Harahap, E. J., Junita, D., Chairudin, C., Agustinur, A., & Afrillah, M. (2023). Pengenalan Hidroponik DFT (Deep Flow Technique) pada Tanaman Pakcoy (Brassica rapa L.) untuk Pencegahan Stunting di Desa Kuta Blang Kecamatan Samadua Kabupaten Aceh Selatan. Jurnal Pengabdian Agro and Marine Industry, 3(1), 41. https://doi.org/10.35308/jpami.v3i1.7576 DOI: https://doi.org/10.35308/jpami.v3i1.7576
Hasan, A., Tabassum, B., Hashim, M., & Khan, N. (2024). Role of Plant Growth Promoting Rhizobacteria (PGPR) as a Plant Growth Enhancer for Sustainable Agriculture: A Review. Bacteria, 3(2), 59–75. https://doi.org/10.3390/bacteria3020005 DOI: https://doi.org/10.3390/bacteria3020005
Hiremath, S. S., Prasanna, N. L., S, S., M, A., C.K., A., Nigam, R., Kumar, S., & Elangovan, M. (2024). A Review on Role of Root Exudates in Shaping Plant-Microbe-Pathogen Interactions. Journal of Advances in Microbiology, 24(12), 1–17. https://doi.org/10.9734/jamb/2024/v24i12868 DOI: https://doi.org/10.9734/jamb/2024/v24i12868
Ikiz, B., Dasgan, H. Y., & Gruda, N. S. (2024). Utilizing the power of plant growth promoting rhizobacteria on reducing mineral fertilizer, improved yield, and nutritional quality of Batavia lettuce in a floating culture. Scientific Reports, 14(1). https://doi.org/10.1038/s41598-024-51818-w DOI: https://doi.org/10.1038/s41598-024-51818-w
Iqbal, B., Li, G., Alabbosh, K. F., Hussain, H., Khan, I., Tariq, M., Javed, Q., Naeem, M., & Ahmad, N. (2023). Advancing environmental sustainability through microbial reprogramming in growth improvement, stress alleviation, and phytoremediation. Plant Stress, 10(October), 100283. https://doi.org/10.1016/j.stress.2023.100283 DOI: https://doi.org/10.1016/j.stress.2023.100283
Ishaq, L. F., Manehat, I. J. A., Tae, A. S. J. A., & Benggu, Y. I. (2023). Dual Inoculation of Rhizobium and Arbuscular Mycorrhizal Fungi Increases Soil-Total Nitrogen, Available Phosphorus, and Yield of Soybean in Vertisols. Jurnal Penelitian Pendidikan IPA, 9(5), 2444–2451. https://doi.org/10.29303/jppipa.v9i5.3162 DOI: https://doi.org/10.29303/jppipa.v9i5.3162
Kalasari, R., Marlina, N., Marlina, M., Husna, N., & Irnady, I. (2023). Application of Organic Fertilizer Cow Dung and Biofertilizer in Shallots (Allium Acalonicum L.) in Lowland. Jurnal Lahan Suboptimal : Journal of Suboptimal Lands, 12(1), 95–101. https://doi.org/10.36706/jlso.12.1.2023.620 DOI: https://doi.org/10.36706/jlso.12.1.2023.620
Koza, N. A., Adedayo, A. A., Babalola, O. O., & Kappo, A. P. (2022). Microorganisms in Plant Growth and Development: Roles in Abiotic Stress Tolerance and Secondary Metabolites Secretion. Microorganisms, 10(8), 1–20. https://doi.org/10.3390/microorganisms10081528 DOI: https://doi.org/10.3390/microorganisms10081528
Lestari, V. H., Suryaningtyas, D. T., & Mulatsih, S. (2025). Integrated Evaluation Land Suitability and Local Land Management Shallot in Larangan District, Brebes Regency: An Applied Agricultural Science Approach. Jurnal Penelitian Pendidikan IPA, 11(8), 444–457. https://doi.org/10.29303/jppipa.v11i8.11719 DOI: https://doi.org/10.29303/jppipa.v11i8.11719
Lopes, M. J. dos S., Dias-Filho, M. B., & Gurgel, E. S. C. (2021). Successful Plant Growth-Promoting Microbes: Inoculation Methods and Abiotic Factors. Frontiers in Sustainable Food Systems, 5(February), 1–13. https://doi.org/10.3389/fsufs.2021.606454 DOI: https://doi.org/10.3389/fsufs.2021.606454
Mahmud, K., Missaoui, A., Lee, K., Ghimire, B., Presley, H. W., & Makaju, S. (2021). Rhizosphere microbiome manipulation for sustainable crop production. Current Plant Biology, 27(June), 100210. https://doi.org/10.1016/j.cpb.2021.100210 DOI: https://doi.org/10.1016/j.cpb.2021.100210
Mokoginta, R. F., Tumbelaka, S., & Nangoi, R. (2022). Pengaruh Pemberian Pupuk Hayati PGPR (Plant Growth Promoting Rhizobacteria) Terhadap Pertumbuhan Dan Hasil Tanaman Selada (Lactuca sativa L.). Jurnal Agroteknologi Terapan, 3(1), 43–51. https://talenta.usu.ac.id/joa/article/view/2485/1871
Munser, L., Sathyanarayanan, K. K., Raecke, J., Mansour, M. M., Uland, M. E., & Streif, S. (2025). Precise and Continuous Biomass Measurement for Plant Growth Using a Low-Cost Sensor Setup. Sensors, 25(15), 1–24. https://doi.org/10.3390/s25154770 DOI: https://doi.org/10.3390/s25154770
Pantigoso, H. A., Newberger, D., & Vivanco, J. M. (2022). The rhizosphere microbiome: Plant–microbial interactions for resource acquisition. Journal of Applied Microbiology, 133(5), 2864–2876. https://doi.org/10.1111/jam.15686 DOI: https://doi.org/10.1111/jam.15686
Priyashantha, A. K. H., Dai, D. Q., Bhat, D. J., Stephenson, S. L., Promputtha, I., Kaushik, P., Tibpromma, S., & Karunarathna, S. C. (2023). Plant–Fungi Interactions: Where It Goes? Biology, 12(6). https://doi.org/10.3390/biology12060809 DOI: https://doi.org/10.3390/biology12060809
Purwanto, Agustono, T., Mujiono, Widiatmoko, T., & Widjonarko, B. R. (2019). The Effect of Plant Growth Promotion Rhizobacteria Inoculation to Agronomic Traits of Aromatic Rice (Oryza sativa CV. Inpago Unsoed 1). IOP Conference Series: Earth and Environmental Science, 255(1). https://doi.org/10.1088/1755-1315/255/1/012023 DOI: https://doi.org/10.1088/1755-1315/255/1/012023
Rahmawati, N., & Ladewa, I. (2023). Analysis of Shallot Growth and Production With Organic Fertilizer and Zeolite in Beach Sand Media. Agrosains : Jurnal Penelitian Agronomi, 25(1), 13. https://doi.org/10.20961/agsjpa.v25i1.72729 DOI: https://doi.org/10.20961/agsjpa.v25i1.72729
Saeed, Q., Xiukang, W., Haider, F. U., Kučerik, J., Mumtaz, M. Z., Holatko, J., Naseem, M., Kintl, A., Ejaz, M., Naveed, M., Brtnicky, M., & Mustafa, A. (2021). Rhizosphere bacteria in plant growth promotion, biocontrol, and bioremediation of contaminated sites: A comprehensive review of effects and mechanisms. International Journal of Molecular Sciences, 22(19). https://doi.org/10.3390/ijms221910529 DOI: https://doi.org/10.3390/ijms221910529
Santos, B. D. M. S. Dos, Silva, M. S. D. R. D. A., Chávez, D. W. H., & Rigobelo, E. C. (2021). Bacillus subtilis - capacity for enzymatic degradation, resistance to trace elements, antagonisms and siderophore production. Australian Journal of Crop Science, 15(5), 787–795. https://doi.org/10.21475/ajcs.21.15.05.p3206 DOI: https://doi.org/10.21475/ajcs.21.15.05.p3206
Sudewi, S., Ala, A., Patandjengi, B., BDR, M. F., & Saleh, A. R. (2021). Scereening of Plant Growth Promotion Rhizobacteria (PGPR) to increase local aromatic rice plant growth. International Journal of Pharmaceutical Research, 13(01), 924–931. https://doi.org/10.31838/ijpr/2021.13.01.151 DOI: https://doi.org/10.31838/ijpr/2021.13.01.151
Sulandjari, S., Triharyanto, E., Purnomo, D., Muliawati, E. S., & Sabrina, H. R. (2025). Growth and Yield of Three Varieties of True Shallot Seed with Application of Plant Growth Regulators and Boron Formulations. 9(1), 1–8. https://doi.org/10.20961/agrotechresj.v9i1.94895 DOI: https://doi.org/10.20961/agrotechresj.v9i1.94895
Sun, W., Li, Q., Qiao, B., Jia, K., Li, C., & Zhao, C. (2024). Advances in Plant–Soil Feedback Driven by Root Exudates in Forest Ecosystems. Forests, 15(3). https://doi.org/10.3390/f15030515 DOI: https://doi.org/10.3390/f15030515
Sureshbabu, K., Amaresan, N., & Kumar, K. (2016). Amazing Multiple Function Properties of Plant Growth Promoting Rhizobacteria in the Rhizosphere Soil. International Journal of Current Microbiology and Applied Sciences, 5(2), 661–683. https://doi.org/10.20546/ijcmas.2016.502.074 DOI: https://doi.org/10.20546/ijcmas.2016.502.074
Tahat, M. M., Alananbeh, K. M., Othman, Y. A., & Leskovar, D. I. (2020). Soil health and sustainable agriculture. Sustainability (Switzerland), 12(12), 1–26. https://doi.org/10.3390/SU12124859 DOI: https://doi.org/10.3390/su12124859
Tahir, H. A. S., Gu, Q., Wu, H., Raza, W., Hanif, A., Wu, L., Colman, M. V., & Gao, X. (2017). Plant growth promotion by volatile organic compounds produced by Bacillus subtilis SYST2. Frontiers in Microbiology, 8(FEB). https://doi.org/10.3389/fmicb.2017.00171 DOI: https://doi.org/10.3389/fmicb.2017.00171
Tharanath, A. C., Upendra, R. S., & Rajendra, K. (2024). Soil Symphony: A Comprehensive Overview of Plant–Microbe Interactions in Agricultural Systems. Applied Microbiology (Switzerland), 4(4), 1549–1567. https://doi.org/10.3390/applmicrobiol4040106 DOI: https://doi.org/10.3390/applmicrobiol4040106
Thepbandit, W., & Athinuwat, D. (2024). Rhizosphere Microorganisms Supply Availability of Soil Nutrients and Induce Plant Defense. Microorganisms, 12(3), 1–23. https://doi.org/10.3390/microorganisms12030558 DOI: https://doi.org/10.3390/microorganisms12030558
Ulfa, A., Burhanuddin, & Purwono, J. (2024). The Intention of Using Biofertilizer Among Shallot Farmers in Nganjuk Regency, East Java Province, Indonesia. Agro Bali, 7(1), 17–23. https://doi.org/10.37637/ab.v7i1.1506 DOI: https://doi.org/10.37637/ab.v7i1.1506
Vieira, F. C. S., & Nahas, E. (2005). Comparison of microbial numbers in soils by using various culture media and temperatures. Microbiological Research, 160(2), 197–202. https://doi.org/10.1016/j.micres.2005.01.004 DOI: https://doi.org/10.1016/j.micres.2005.01.004
Wahab, A., Muhammad, M., Munir, A., Abdi, G., Zaman, W., Ayaz, A., Khizar, C., & Reddy, S. P. P. (2023). Role of Arbuscular Mycorrhizal Fungi in Regulating Growth, Enhancing Productivity, and Potentially Influencing Ecosystems under Abiotic and Biotic Stresses. Plants, 12(17). https://doi.org/10.3390/plants12173102 DOI: https://doi.org/10.3390/plants12173102
Warman, R., Santari, P. T., & Sandi, N. (2022). Performance of Shallots (Allium Ascalonicum L) in Peat Soil with Organic Fertilizer and Arbuscular Mycorrhizal Fungi (AMF). Jurnal Penelitian Pendidikan IPA, 8(SpecialIssue), 58–66. https://doi.org/10.29303/jppipa.v8ispecialissue.2482 DOI: https://doi.org/10.29303/jppipa.v8iSpecialIssue.2482
Yang, P., Condrich, A., Scranton, S., Hebner, C., Lu, L., & Ali, M. A. (2024). Utilizing Plant Growth-Promoting Rhizobacteria (PGPR) to Advance Sustainable Agriculture. Bacteria, 3(4), 434–451. https://doi.org/10.3390/bacteria3040030 DOI: https://doi.org/10.3390/bacteria3040030
Zhang, N., Zhou, Y., Ali, A., Wang, T., Wang, X., & Sun, X. (2024). Effect of Molasses Addition on the Fermentation Quality and Microbial Community during Mixed Microstorage of Seed Pumpkin Peel Residue and Sunflower Stalks. Fermentation, 10(6). https://doi.org/10.3390/fermentation10060314 DOI: https://doi.org/10.3390/fermentation10060314
Zhao, L., Li, J., Tian, N., Li, G., Sheng, L., He, C., & Bian, H. (2024). Effect of experimental warming on dissolved organic matter and bacterial diversity in a forest swamp soil. Ecological Indicators, 158(January 2023), 111375. https://doi.org/10.1016/j.ecolind.2023.111375 DOI: https://doi.org/10.1016/j.ecolind.2023.111375
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