Isolation and Characterization of Biofertilizer Microbes within Rice Rhizosphere of Soil Samples Collected from Different Agroecological Zones of Ebonyi State, Nigeria, for Enhanced Plant Growth

• Authors: J. N. Ukwa , O. M. C. Uda , N. P. Nweze , O. C. Okafor , C. N. Ochere , F. A. Ezeh
• Languages of publication: EN

Abstracts

EN

Rhizosphere microbial community plays a critical role in plant growth and development, serving as biofertilizer that solubilizes minerals, enhances nutrient uptake, and produces plant growth-promoting substances. Therefore, this study was caried out to isolate and characterize the microbial community structure in flooded Paddy across Ebonyi State Agroecological Zones, for Biofertizer microbes and effects on Rice plant growth. The four rice accessions (Oryza sativa) used in this study were sourced from Biotechnology Research and Development Centre, Ebonyi State University; and planted in Pots with control checks (unplanted soil), in a Greenhouse. The physicochemical parameters of the soil were determined using AOAC standard methods. The microbial community in the rhizosphere of paddy microcosms was characterized using (Colony counting machine, expressed in colony forming unit per mililitre (cfu/ml)), 16SrRNA gene amplification and three Random Amplified Polymorphic DNA (RAPD) primers namely, OPB05, OPT05, and OPB03 and resolved independently on agarose gel. Rice plant growth were measured in heights across four growth stages and across the three Agroecological Zones. The physicochemical properties showed that the soil was slightly acidic, had different fractions of sand, Organic Carbon, Organic matter and essential nutrients such as; Ca, P, and Mg. The microbial population differed significantly between planted and unplanted soils; while the microbial load decreased gradually as the plants' growth stages increased. Isolates biochemical analysis revealed mostly the presence of bacteria (Bacillus and Brevibacillus species), while confirmatory molecular identification of the bacterial isolates, showed that Aeromonas hydrophilia strain A210 16S, Pseudomonads plecoglossicida strain RJ39 16S, Aeromonas caviae 16S, Eschericha coli strain 26561, Pseudomonas otitidis strain JK79 16S, Enterobacter cloacae strain ES-2 16S, Serratia marcescens strain AL105_R2A02 16S and Aeromonas diversa strain 2478-85 16S were present in the rhizosphere of different Oryza species. Phylogenetic relatedness among the isolates showed isolates B1, B3 and B10 to be closely related. It showed that 90% of the isolates were of the gamma proteobacteria origin, while 10% belong to the Firmicutes. On 90 Day After Planting ( DAP), Faro 59 performed the highest across the zones, while Faro 52 was the least performed across the zones. The study has proven the presence of biofertilizer microbes in rice rhizosphere and that; Despite a higher absolute microbial abundance, there was no major shift in the relative abundance of microbial groups in the planted paddy, suggesting how highly adapted and relatively stable, and beneficial microbial community is to rice plants across Ebonyi State soil, and the possibilities of using them as biofertilizer source by farmers and breeders as a sustainable alternative to chemical fertilizer in promoting plants growth and yield to mitigate environmental impacts.

Keywords

EN

Agroecological zones; Biofertizer; Oryza; Paddy; Rhizosphere

Discipline

• BIOTECHNOLOGY: BIOTECHNOLOGY

• Publisher: Scientific Publishing House „DARWIN”
• Journal: World News of Natural Sciences
• Year: 2024
• Volume: 57
• Pages: 329-353

Contributors

author

J. N. Ukwa

• Department of Biotechnology, Ebonyi State University, Abakaliki, Nigeria

author

O. M. C. Uda

• Department of Science Education, Ebonyi State University, Abakaliki, Nigeria

author

N. P. Nweze

• Department of Biotechnology, Ebonyi State University, Abakaliki, Nigeria

author

O. C. Okafor

• Department of Microbiology, Evangel University Akaeze, Ebonyi State, Nigeria

author

C. N. Ochere

• Soil and Water Laboratory Unit, National Soil, Plant and Water Laboratory Research Center, Umudike Umuahia, Abia State, Nigeria

author

F. A. Ezeh

• Department of Animal Science, Ebonyi State University, Abakaliki, Nigeria

References

• [1] Aulakh, M.S., Kabba, B.S., Baddesha, H.S., Bahl, G.S. and Gill, M.P.S. (2003). Crop yields and Phosphorus fertilizer transformation after 25 years of applications to a subtropical soil under groundnut – based cropping system. Field Crops Research. 83: 283-296
• [2] Aizebeokhai, A.P., Okenwa, N.U., Oyeyemi, K.D., Kayode, O.T. and Adeyemi, G.A. (2005). Soil characterization using remote sensing in Southwestern Nigeria: implications for precise agriculture. Earth and Environmental Science 173: 1-6
• [3] Babalola, O.O. (2010). Beneficial bacteria of agricultural importance. Biotechnology Letters, 32: 1559-1570
• [4] Babalola, O.O. and Akindolire, A.M. (2011). Identification of native Rhizobacteria peculiar to selected food crops in Mmabatho municipality of South Africa. Biological Agriculture and Horticulture, 27: 294-309
• [5] Barea, J.M., Pozo, M.J., Azcón, R. and Azcón-Aguilar, C. (2005). Microbial co-operation in the rhizosphere. Journal of Experimental Botany, 56, 1761–1778
• [6] Bernhard, A.E., Colbert, D., McManus, J. and Field, K.G. (2005). Microbiological community dynamics based on 16SrRNA Gene profiles in a Pacific Northwest Estuary and its tributaries. FEMS Microbiology Ecology. 52 (1): 115-128
• [7] Boden, R., Hutt, L.P. and Rae, A.W. (2017). Reclassification of Thiobacillus aquaesulis (Wood and Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales o the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the "Proteobacteria", and four new families within the orders Nitrosomonadales and Rhodocyclales. International Journal of Systematic and Evolutionary Microbiology, 67(5): 1191-1205
• [8] Breidenbach, B. and Conrad, R. (2014). Seasonal dynamics of bacterial and archeal methanogenic communities in flooded rice fields and effects of drainage. Frontiers in Microbiology. 5: 752
• [9] Brune, A., Frenzel, P. and Cypionka, H. (2000). Life at the oxic-anoxic interface: microbial activities and adaptations. Microbiology Review, 24: 691-710
• [10] Buir, T.J. and Caesar, A. (1984). Beneficial Plant Bacteria. Critical Review. Plant Science 2: 1-20
• [11] Butler, R.B., Kelley, M.L., Powell, W.H., Hahn,M.E. and Van Beneden, R.J.(2001). An aryl hydrocarbon receptor homologue from the soft – shell clam, Mya arenaria: evidence that invertebrate AHR homologues lack TCDD and BNF binding. Gene, 278(1-2 ): 223-234
• [12] Chen, Y., Tu, P., Yang, Y. et al. Diversity of rice rhizosphere microorganisms under different fertilization modes of slow-release fertilizer. Sci Rep 12, 2694 (2022). https://doi.org/10.1038/s41598-022-06155-1
• [13] Cheesbrough, M. (2006). District Laboratory Practice in Tropical Countries. Cambridge University Press. 62.
• [14] Chiara, B.,Carlo, G., Alluvione, F. and Laura, Z.(2012) Field plots and crop yields under innovative methods of Carbon sequestration in soil. In: Carbon Sequestration in Agricultural Soils. Editor: Alessandro Piccolo. Springer Heidelberg. Pp. 39-60.
• [15] Compant, S., Gangl, H. and Sessitsch, A. (2013). Visualization of niches of colonization of firmicutes with Bacillus spp. in the rhizosphere, rhizoplane, and endorhiza of grapevine plants at flowering stage of development by FISH microscopy. Molecular Microbial Ecology of the Rhizosphere, 1, 423-427
• [16] Di Cello, F., Bevivo, A., Chiarini, Fani, R., Paffetti, D. and Tabacchi, S. (1997). Biodiversity of Burkholderia cepacia population isolated from Maize rhizosphere at different plant growth stages. Applied Environmental Microbiology 63: 4485-4493
• [17] Edwards, J., Johnson, C., Santos-Medellín, C., Lurie, E., Podishetty, N. K. and Bhatnagar, S. (2015). Structure, variation, and assembly of the root associated microbiomes of rice. Proceedings of National Academy of Science of United States of America, 112: 911-920
• [18] Firmanda, A., Fahma, F., Syamsu, K. et al. (2023). Factors Influencing the Biodegradability of Agro-biopolymer Based Slow or Controlled Release Fertilizer. J Polym Environ, 31, 1706–1724. https://doi.org/10.1007/s10924-022-02718-5
• [19] Gaur, R., Shani, N., Kawaljeet, Johri, B. N., Rossi, P. and Aragno, M. (2004). Diacetylphloroglucinol-producing pseudomonads do not influence AM fungi in wheat rhizosphere. Current Science, 86: 453-457
• [20] Guo, Y., Kuzyakov, Y., Li, N. et al. Rice rhizosphere microbiome is more diverse but less variable along environmental gradients compared to bulk soil. Plant Soil (2024). https://doi.org/10.1007/s11104-024-06728-1
• [21] Hernandez, M., Dumont, M.G., Yuan, Q. and Conrad, R. (2015). Different bacterial populations associated with the root and rhizosphere of rice incorporate plant – derived carbon. Applied Environmental Microbiology. 81: 2244-2253
• [22] Idris, A., Labuschagne, N. and Korsten, L. (2009). Efficacy of rhizobacteria for growth promotion in sorghum under greenhouse conditions and selected modes of action studies. Journal of Agricultural Science 147: 17-30
• [23] Knief, C., Delmotte, N., Chaffron, S., Stark, M., Innerebner, G., Wassmann, R., von Mering, C. and Vorholt, J.A. (2011). Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. Multidisciplinary Journal of Microbial Ecology 11: 1-13
• [24] Miller, I.M. (1990). Bacterial leaf nodule symbiosis. Advanced Botanty Research, 17: 163-234
• [25] Ode, F.F. (2008). Seed inoculation with Bacillus subtilis, formulated with oyster meal and growth of corn, soybean and cotton. Ciencia Agrotecnologia. 32: 456-462
• [26] Onweremadu,E. U. and Oti, N.N. (2005). Soil colour as an indicator of soil quality in soils formed over coastal plain sands of owerri agricultural area, Southeastern Nigeria. Internal Journal of Natural and Applied Science 1(2): 118-121
• [27] Ren, G., Zhang, H., Lin,X., Zhu, J. and Jia, Z. (2014). Response of phyllosphere bacterial community to elvate CO2 during rice growing season. Applied Microbiology and Biotechnology. 98: 9459-9471
• [28] Seiphepo, L., Kodisang, L., Mobolaji, F.A., Ayodele, A.S., Anthony, I.O. and Olubukola, O.B. (2013). Genotypic and phenotypic diversity of culturable rhizobacteria from fieldgrown crops in Mahikeng, South Africa. Journal of Food, Agriculture and Environment, 11(2): 583-590
• [29] Shibagaki, S.T., Nakayama, Y., Matsuya, K., Kimura, M. and Asakawa, S. (2006). Phylogenetic study on a bacterial community in the floodwater of a Japanese paddy field estimated by sequencing 16S rRNA fragments after denaturing gradient gel electrophosis. Biology and Fertility of Soil. 42(4): 362-365
• [30] Shrestha, B., Anderson, T. A., Acosta-Martinez, V., Payton, P. and Cañas-Carrell, J. E. (2015). The influence of multiwalled carbon nanotubes on polycyclic aromatic hydrocarbon (PAH) bioavailability and toxicity to soil microbial communities in alfalfa rhizosphere. Ecotoxicology and Environmental Safety, 116, 143-149
• [31] Singh, B.K., Milard, P., Whitely, A.S. and Murrell, J.C. (2004). Unravelling rhizosphere-microbial interactions: opportunities and limitations. Trends Microbiology. 12: 386-393
• [32] Tian, J., Dippold, M., and Pausch, J. ( 2013). Microbial response to rhizodeposition depending on water regimes in paddy soils. Soil Biology and Biochemistry. 65: 195-203
• [33] WU Qiong, Yu-hui WANG, Yan-feng DING, Wei-ke TAO, Shen GAO, Quan-xin LI, Wei-wei LI, Zheng-hui LIU, Gang-hua LI. Effects of different types of slow- and controlled-release fertilizers on rice yield. Journal of Integrative Agriculture, Volume 20, Issue 6, (2021) 1503-1514, https://doi.org/10.1016/S2095-3119(20)63406-2
• [34] Wu, J.H., Miller,S., Hall, H., and Mooney,P. (2003) In vitro initiation, culture and propagation of Rubus selections from HortResearch breeding programmes. Programme and Abstracts, 15th Biennial Meeting of the New Zealand Branch of the International Association of Plant Tissue Culture and Biotechnology. 25-28
• [35] Xin, F. et al. Large increases of paddy rice area, gross primary production, and grain production in Northeast China during 2000–2017. Sci. Total Environ. 711 (2020) 135-183. https:// doi. org/ 10. 1016/j. scito tenv. 2019. 135183
• [36] Zhang, H. M., Sun, Y., Xie, X. T., Kim, M.S., Dowd, S.E. and Pare, P.W. (2009). A soil bacterium regulates plant acquisition of iron via deficiency-inducible mechanisms. Plant Journal. 58: 568-577

• Document Type: article