Rhizobium spp. strains with biofertilizer potential: Multivariate selection and their tolerance to critical conditions of tropical soils
DOI:
https://doi.org/10.22458/urj.v18i1.6363Keywords:
nitrogen, phosphorus, siderophores, abiotic stress, tropical soilsAbstract
Introduction: Leguminous plants establish symbiotic relationships with bacteria of the genus Rhizobium, which represent an important source of organic nitrogen in sustainable production. However, successful bacterial colonization remains a challenge due to the variability of soil conditions and current agronomic practices. Objective: To select Rhizobium spp. strains based on their tolerance to salinity and aluminum toxicity, and to evaluate their effect on the foliar mineral content of common bean (Phaseolus vulgaris). Methods: We did triplicate assays on Rhizobium spp. strains, from a Costa Rican laboratory, selected for siderophore production, phosphorus solubilization, and tolerance to salinity and aluminum toxicity. In greenhouse, we filled 4-L pots with soil that had been autoclaved twice. We inoculated seeds of the Guaymí and Cabécar varieties at sowing with the selected strains at a concentration of 10⁸ CFU. We established five treatments: T1 (CIAT899), T2 (CR4019B), T3 (CIAT899 + CR4019B), T4 (urea), and T5 (control), with four replicates in a randomized design. We terminated the experiment at flowering and analyzed foliar tissue chemistry. Results: Salinity was a major limiting factor for most strains, and aluminum exposure restricted growth. The strains CIAT899 and CR4019B had high phosphorus solubilization and lower siderophore production. Inoculation increased foliar nitrogen content in both varieties and resulted in significant differences in calcium, zinc, and boron in the Guaymí variety, with no differences in foliar nitrogen compared to the urea treatment. Conclusion: Responses depend on cultivar, emphasizing the need to select compatible strains and genotypes. Overall, Rhizobium spp. offers a sustainable alternative because inoculation with selected strains (particularly CIAT899 and CR4019B), enhances phosphorus solubilization and siderophore production, improving the availability and uptake of essential nutrients in P. vulgaris, including foliar nitrogen levels comparable to those achieved with synthetic fertilizers (urea), as well as good levels of calcium, zinc, and boron.
References
Alexander, D. B., & Zuberer, D. A. (1991). Use of chrome azurol S reagents to evaluate siderophore production by rhizosphere bacteria. Biology and Fertility of Soils, 12(1), 39–45. https://doi.org/10.1007/BF00369386
Ammar, E. E., Rady, H. A., Khattab, A. M., Amer, M. H., Mohamed, S. A., Elodamy, N. I., AL-Farga, A., & Aioub, A. A. A. (2023). A comprehensive overview of eco-friendly bio-fertilizers extracted from living organisms. Environmental Science and Pollution Research International, 30(53), 113119. https://doi.org/10.1007/s11356-023-30260-x
Artigas Ramírez, M. D., Silva, J. D., Ohkama-Ohtsu, N., & Yokoyama, T. (2018). In vitro rhizobia response and symbiosis process under aluminum stress. Canadian Journal of Microbiology, 64(8), 511–526. https://doi.org/10.1139/cjm-2018-0019
Ballhorn, D. J., Wolfe, E. R., Tyler, J., Ronan, W., & Sands-Gouner, S. (2018). Quantitative Effects of Soil Salinity on the Symbiosis of Wild Lima Bean (Phaseolus lunatus L.) and Bradyrhizobium in Costa Rica. Journal of Applied Botany and Food Quality, (91), 304–309. https://doi.org/10.5073/JABFQ.2018.091.039
Bardin, S., Dan, S., Osteras, M., & Finan, T. M. (1996). A phosphate transport system is required for symbiotic nitrogen fixation by Rhizobium meliloti. Journal of Bacteriology, 178(15), 4540–4547. https://doi.org/10.1128/JB.178.15.4540-4547.1996
Bashan, Y., Kamnev, A. A., & de-Bashan, L. E. (2013a). A proposal for isolating and testing phosphate-solubilizing bacteria that enhance plant growth. Biology and Fertility of Soils, 49(1), 1–2. https://doi.org/10.1007/s00374-012-0756-4
Bashan, Y., Kamnev, A. A., & de-Bashan, L. E. (2013b). Tricalcium phosphate is inappropriate as a universal selection factor for isolating and testing phosphate-solubilizing bacteria that enhance plant growth: a proposal for an alternative procedure. Biology and Fertility of Soils, 49(4), 465–479. https://doi.org/10.1007/s00374-012-0737-7
Ben Romdhane, S., De Lajudie, P., Fuhrmann, J. J., & Mrabet, M. (2022). Potential role of rhizobia to enhance chickpea-growth and yield in low fertility-soils of Tunisia. Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, 115, 921–932. https://doi.org/10.1007/s10482-022-01745-5
Bērtiņš, M., Klūga, A., Dubova, L., Petrēvics, P., Alsiņa, I., & Vīksna, A. (2021). Study of Rhizobia Impact on Nutritional Element Concentration in Legumes. Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences, 75(6), 457–462. https://doi.org/10.2478/prolas-2021-0068
Bindraban, P. S., Dimkpa, C. O., & Pandey, R. (2020). Exploring phosphorus fertilizers and fertilization strategies for improved human and environmental health. In Biology and Fertility of Soils (Vol. 56, pp. 299–317). Springer. https://doi.org/10.1007/s00374-019-01430-2
Castillo R, C. G., Rubio H, R., Urzúa S, H., & Borie B, F. (2008). Interacción Rhizobium leguminosarum bv trifolii y hongos micorrícicos en un andisol con diferentes niveles de saturación de aluminio. Idesia (Arica), 26(3), 7–19. https://doi.org/10.4067/S0718-34292008000300002
Das, K., Prasanna, R., & Saxena, A. K. (2017). Rhizobia: a potential biocontrol agent for soilborne fungal pathogens. In Folia Microbiologica (Vol. 62, pp. 425–435). Springer Netherlands. https://doi.org/10.1007/s12223-017-0513-z
Fahde, S., Boughribil, S., Sijilmassi, B., & Amri, A. (2023). Rhizobia: A Promising Source of Plant Growth-Promoting Molecules and Their Non-Legume Interactions: Examining Applications and Mechanisms. In Agriculture (Switzerland) (Vol. 13). Multidisciplinary Digital Publishing Institute (MDPI). https://doi.org/10.3390/agriculture13071279
Fernandez-Aunión, C., Hamouda, T. Ben, Iglesias-Guerra, F., Argandoña, M., Reina-Bueno, M., Nieto, J. J., Aouani, M. E., & Vargas, C. (2010). Biosynthesis of compatible solutes in rhizobial strains isolated from Phaseolus vulgaris nodules in Tunisian fields. BMC Microbiology, 10(1), 192. https://doi.org/10.1186/1471-2180-10-192
Ferreira, P. A. A., Bomfeti, C. A., Soares, B. L., & de Souza Moreira, F. M. (2012). Efficient nitrogen-fixing Rhizobium strains isolated from amazonian soils are highly tolerant to acidity and aluminium. World Journal of Microbiology and Biotechnology, 28(5), 1947–1959. https://doi.org/10.1007/S11274-011-0997-7/TABLES/3
Fiodor, A., Singh, S., & Pranaw, K. (2021). The Contrivance of Plant Growth Promoting Microbes to Mitigate Climate Change Impact in Agriculture. Microorganisms 2021, Vol. 9, Page 1841, 9(9), 1841. https://doi.org/10.3390/microorganisms9091841
Gadagi, R. S., & Sa, T. (2002). New isolation method for microorganisms solulbilizing iron and aluminum phosphates using dyes. Soil Science and Plant Nutrition, 48(4), 615–618. https://doi.org/10.1080/00380768.2002.10409246
Galvis Serrano, N. F., Moreno, L., Galvis Serrano, N. F., & Moreno, L. (2024). Sideróforos de rizobacterias y su aplicación en la biorremediación. Ciencia En Desarrollo, 15(2), 203–211. https://doi.org/10.19053/UPTC.01217488.V15.N2.2024.16996
Garcha, S., & Garcha, S. (2023). Microbes from Wild Plants. Metabolomics, Proteomes and Gene Editing Approaches in Biofertilizer Industry, 173–187. https://doi.org/10.1007/978-981-99-3561-1_10
García-Berumen, J. A., Flores de la Torre, J. A., de los Santos-Villalobos, S., Espinoza-Canales, A., Echavarría-Cháirez, F. G., & Gutiérrez-Bañuelos, H. (2024). Phosphorus dynamics and sustainable agriculture: The role of microbial solubilization and innovations in nutrient management. Current Research in Microbial Sciences, 8, 100326. https://doi.org/10.1016/J.CRMICR.2024.100326
Johan, P. D., Ahmed, O. H., Omar, L., & Hasbullah, N. A. (2021). Phosphorus Transformation in Soils Following Co-Application of Charcoal and Wood Ash. Agronomy 2021, Vol. 11, Page 2010, 11(10), 2010. https://doi.org/10.3390/AGRONOMY11102010
Jones, D. L., & Oburger, E. (2011). Solubilization of Phosphorus by Soil Microorganisms (pp. 169–198). https://doi.org/10.1007/978-3-642-15271-9_7
Mamalakis, A., Randerson, J. T., Yu, J. Y., Pritchard, M. S., Magnusdottir, G., Smyth, P., Levine, P. A., Yu, S., & Foufoula-Georgiou, E. (2021). Zonally contrasting shifts of the tropical rain belt in response to climate change. Nature Climate Change, 11, 143–151. https://doi.org/10.1038/s41558-020-00963-x
Masjedi, S. K., Kazemi, A., Moeinnadini, M., Khaki, E., & Olsen, S. I. (2024). Urea production: An absolute environmental sustainability assessment. Science of The Total Environment, 908, 168225. https://doi.org/10.1016/J.SCITOTENV.2023.168225
Milagres, A. M. F., Machuca, A., & Napoleão, D. (1999). Detection of siderophore production from several fungi and bacteria by a modification of chrome azurol S (CAS) agar plate assay. Journal of Microbiological Methods, 37(1), 1–6. https://doi.org/10.1016/S0167-7012(99)00028-7
Mmayi, M. P., & Musyimi, D. M. (2025). Effects of Aluminium Application and Rhizobium Inoculation on Aluminium Accumulation, Nodulation and Yields of Soy beans Grown in Kenya. Agriculture Archives, 4(2), 7–19. https://doi.org/10.51470/AGRI.2025.4.2.07
Montes de Oca, P., Mata, R., & Chaves, M. A. (1996). Estudios de salinidad en la provincia de Guanacaste (Costa Rica) y caracterización de algunos suelos con influencia salina. Agronomía Mesoamericana, 7(2), 77. https://doi.org/10.15517/am.v7i2.24766
Osorio, N. W., & Habte, M. (2001). Synergistic Influence of an Arbuscular Mycorrhizal Fungus and a P Solubilizing Fungus on Growth and P Uptake of Leucaena leucocephala in an Oxisol. Arid Land Research and Management, 15(3), 263–274. https://doi.org/10.1080/15324980152119810
Pahalvi, H. N., Rafiya, L., Rashid, S., Nisar, B., & Kamili, A. N. (2021). Chemical fertilizers and their impact on soil health. In Microbiota and Biofertilizers, Vol 2: Ecofriendly Tools for Reclamation of Degraded Soil Environs (pp. 1–20). Springer International Publishing. https://doi.org/10.1007/978-3-030-61010-4_1
Pla Sentís, I. (2020). Overview of salt-affected areas in Latin America: Physical, social and economic perspectives. In Saline and Alkaline Soils in Latin America: Natural Resources, Management and Productive Alternatives (pp. 3–36). Springer International Publishing. https://doi.org/10.1007/978-3-030-52592-7_1
Portillaϯ, J., Ramírez, R., & Lozano, Z. (2025). Fósforo liberado por bacterias nativas de las rocas fosfóricas de Riecito (Estado Falcón) y Navay (Estado Táchira) en Venezuela. Bioagro, 37(1), 111–122. https://doi.org/10.51372/bioagro371.10
Rees, D. C., Akif Tezcan, F., Haynes, C. A., Walton, M. Y., Andrade, S., Einsle, O., & Howard, J. B. (2005). Structural basis of biological nitrogen fixation. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 363(1829), 971–984. https://doi.org/10.1098/rsta.2004.1539
Reyes, I., Bernier, L., Simard, R. R., & Antoun, H. (1999). Effect of nitrogen source on the solubilization of different inorganic phosphates by an isolate of Penicillium rugulosum and two UV-induced mutants. FEMS Microbiology Ecology, 28(3), 281–290. https://doi.org/10.1111/J.1574-6941.1999.TB00583.X
Samago, T. Y., & Dakora, F. D. (2024). Combined use of Rhizobium inoculation and low phosphorus application increased plant growth, root nodulation and grain yield of common bean (Phaseolus vulgaris) in Ethiopia. Frontiers of Agricultural Science and Engineering, 0(0), 0. https://doi.org/10.15302/J-FASE-2024556
Sanga, D. L., Mwamahonje, A. S., Mahinda, A. J., & Kipanga, E. A. (2024). Soil salinization under irrigated farming: A threat to sustainable food security and environment in semi-arid tropics. Journal of Agricultural Science and Practice, 9(3), 32–47. https://doi.org/10.31248/JASP2024.468
Shome, S., Barman, A., & Solaiman, Z. M. (2022). Rhizobium and Phosphate Solubilizing Bacteria Influence the Soil Nutrient Availability, Growth, Yield, and Quality of Soybean. Agriculture, 12(8), 1136. https://doi.org/10.3390/agriculture12081136
Sigma-Aldrich. (2013). P1602 Pikovskaya’s Agar. Product Information. https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/191/794/p1602dat.pdf
Silva, C. R., Pereira, R. B., & Sabadini, E. (2001). Color changes in indicator solutions: An intriguing and elucidative general chemistry experiment. Journal of Chemical Education, 78(7), 939–940. https://doi.org/10.1021/ED078P939/SUPPL_FILE/JCE2001P0939W.ZIP
Singh, M., Jha, S., Pathak, D., & Maisnam, G. (2025). Advancing biofertilizers: the evolution from single-strain formulations to synthetic microbial communities (SynCom) for sustainable agriculture. Discover Plants 2025 2:1, 2(1), 226-. https://doi.org/10.1007/s44372-025-00318-w
Singh, P., Kumar, V., & Agrawal, S. (2014). Evaluation of phytase producing bacteria for their plant growth promoting activities. International Journal of Microbiology, 2014. https://doi.org/10.1155/2014/426483
Sulistiyani, T. R., Meliah, S., -, M., Kusmiati, M., Budiyanto, A., & Muslichah, D. A. (2024). Molecular Approach and Preliminary Screening of Culturable Free-Living Rhizobium as Plant Growth Enhancer. Malaysian Journal of Science, 43(2), 21–29. https://doi.org/10.22452/mjs.vol43no2.3
Timofeeva, A. M., Galyamova, M. R., & Sedykh, S. E. (2023). Plant Growth-Promoting Soil Bacteria: Nitrogen Fixation, Phosphate Solubilization, Siderophore Production, and Other Biological Activities. Plants 2023, Vol. 12, Page 4074, 12(24), 4074. https://doi.org/10.3390/PLANTS12244074
Utsumi, N., & Kim, H. (2022). Observed influence of anthropogenic climate change on tropical cyclone heavy rainfall. Nature Climate Change, 12, 436–440. https://doi.org/10.1038/s41558-022-01344-2
Verma, D. K., Pandey, A. K., Mohapatra, B., Srivastava, S., Kumar, V., Talukdar, D., Yulianto, R., Zuan, A. T. K., Jobanputra, A. H., & Asthir, B. (2019). Plant Growth-Promoting Rhizobacteria: An Eco-Friendly Approach for Sustainable Agriculture and Improved Crop Production. In Microbiology for Sustainable Agriculture, Soil Health, and Environmental Protection (pp. 3–80). Apple Academic Press. https://doi.org/10.1201/9781351247061-1
Waring, B. G., De Guzman, M. E., Du, D. V., Dupuy, J. M., Gei, M., Gutknecht, J., Hulshof, C., Jelinski, N., Margenot, A. J., Medvigy, D., Pizano, C., Salgado-Negret, B., Schwartz, N. B., Trierweiler, A. M., Van Bloem, S. J., Vargas G., G., & Powers, J. S. (2021). Soil biogeochemistry across Central and South American tropical dry forests. Ecological Monographs, 91. https://doi.org/10.1002/ecm.1453
Wekesa, C., Asudi, G. O., Okoth, P., Reichelt, M., Muoma, J. O., Furch, A. C. U., & Oelmüller, R. (2022). Rhizobia Contribute to Salinity Tolerance in Common Beans (Phaseolus vulgaris L.). Cells, 11. https://doi.org/10.3390/cells11223628
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