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Soil quality and microbial diversity in relation to the severity of coffee leaf rust disease in Karnataka, India
Abstract
Soil physico-chemical properties significantly influence the quality, growth, productivity, and flavor of coffee. The current study estimates the soil nutritional properties and microbial diversity with the severity of coffee leaf rust disease. A total of twenty-nine localities were surveyed in the major coffee-growing district of Karnataka, mainly Chikkamagaluru, Kodagu, and Hassan, covering the canopies of arabica and robusta coffee plantations. The study on soil quality evaluation determines the sustainability and practices of land management in this region. The physico-chemical properties and microbial diversity of the soil were analysed. Twenty-nine soil parameters were analyzed using principal component analysis, which accounts for five principal components with eigenvalues>1 explaining 9 % of the total variance. The nine principal components together explain 82.24 % of the total variance. According to K-means clustering, soil analysis can be classified into four clusters. Soil microbial communities primarily control the complex ecosystems of soil, including root- and rhizosphere-associated beneficial microbes, and play a vital role as key components in crop production and sustainable agriculture. The present study revealed that the fertility level of the soil and the diverse taxa of rhizospheric microflora from various soil samples, characterized by an abundant diversity of beneficial microbes, such as Trichoderma sp., Bacillus sp., Penicillium sp., and Pseudomonas sp. Furthermore, this work gives insights into the sustainable soil quality and disease management practices that can help farmers to adopt better soil management practices for improving the quality and quantity of coffee production in Karnataka, India.
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Abdel-Fattah, M. K., Mohamed, E. S., Wagdi, E. M., Shahin, S. A., Aldosari, A. A., Lasaponara, R., & Alnaimy, M. A. (2021). Quantitative Evaluation of Soil Quality Using Principal Component Analysis: The Case Study of El-Fayoum Depression Egypt. Sustainability, 13(4), 1824. https://doi.org/10.3390/su13041824
Afrin, S., Tamanna, T., Shahajadi, U. F., Bhowmik, B., Jui, A. H., Miah, M. A. S., & Bhuiyan, M. N. I. (2024). Characterization of protease-producing bacteria from garden soil and antagonistic activity against pathogenic bacteria. The Microbe, 4, 100123. https://doi.org/10.1016/j.microb.2024.100123
Al-Dhabaan, F. A. M., & Bakhali, A. H. (2017). Analysis of the bacterial strains using Biolog plates in the contaminated soil from Riyadh community. Saudi Journal of Biological Sciences, 24(4), 901-906. https://doi.org/10.1016/j.sjbs.2016.01.043
Chaubey, A. N., Singh, V., Singh, S., Shukla, R. D., & Hetram. (2019). Effect of nitrogen and phosphorus levels on white rust disease of mustard [Brassica juncea (L.) Czern and Coss.]. Journal of Oilseeds Research, 36(1). https://doi.org/10.56739/jor.v36i1.126063
Chen, R., Senbayram, M., Blagodatsky, S., Myachina, O., Dittert, K., Lin, X., . . . Kuzyakov, Y. (2014). Soil C and N availability determine the priming effect: microbial N mining and stoichiometric decomposition theories. Global Change Biology, 20(7), 2356-2367. https://doi.org/10.1111/gcb.12475
da Silva Aragão, O. O., de Oliveira-Longatti, S. M., Santos de Castro Caputo, P., Rufini, M., Rodrigues Carvalho, G., Soares de Carvalho, T., & de Souza Moreira, F. M. (2020). Microbiological indicators of soil quality are related to greater coffee yield in the Brazilian Cerrado region. Ecological Indicators, 113, 106205. https://doi.org/10.1016/j.ecolind.2020.106205
Daivasikamani, S., & Rajanaika, R. (2009). Effect of some abiotic factors on germination of urediospore of the coffee leaf rust fungus, Hemileia vastatrix (Berkeley & Broome). Journal of Biopesticide, 2(1), 15-17. https://doi.org/10.57182/jbiopestic.2.1.15-17
Das, S. K., Avasthe, R., Roy, A., & Singh, N. (2020). Soil sample analysis methods: A ready reckoner for soil testing. Research on Crops, 17(1), 151-156. https://www.kiran.nic.in/pdf/publications/2020/Soil%20Sample%20Analysis%20Methods%20Shaon%20Kumar%20Das.pdf
Devadas, R., Simpfendorfer, S., Backhouse, D., & Lamb, D. W. (2014). Effect of stripe rust on the yield response of wheat to nitrogen. The Crop Journal, 2(4), 201-206. https://doi.org/10.1016/j.cj.2014.05.002
Devi, V., & Sumathy, V. J. H. (2017). Production of biofertilizer from fruit wastes. European Journal of Pharmaceutical and Medical Research, 4, 436-443. https://www.ejpmr.com/home/abstract_id/2900
Dordas, C. (2008). Role of nutrients in controlling plant diseases in sustainable agriculture. A review. Agronomy for Sustainable Development, 28(1), 33-46. https://doi.org/10.1051/agro:2007051
Ezeonuegbu, B. A., Abdullahi, M. D., Whong, C. M. Z., Sohunago, J. W., Kassem, H. S., Yaro, C. A., . . . Batiha, G. E.-S. (2022). Characterization and phylogeny of fungi isolated from industrial wastewater using multiple genes. Scientific Reports, 12(1), 2094. https://doi.org/10.1038/s41598-022-05820-9
Ganapathi, Niranjana, K. S., Jayaprakash, S. M., & Harshitha, S. (2019). Effect of Granulated Liming Material on Soil Properties and Yield of Paddy in Acid Soil of Bramhavara. International Journal of Current Microbiology and Applied Sciences, 8(4). https://doi.org/10.20546/ijcmas.2019.804.201
Grazia Bonelli, M., & Manni, A. (2019). Principal Components Analysis and spatial analysis integration for enhanced assessment of pollution emission sources. IOP Conference Series: Earth and Environmental Science, 227(6), 062013. https://doi.org/10.1088/1755-1315/227/6/062013
Indoria, A. K., Sharma, K. L., & Reddy, K. S. (2020). Chapter 18 - Hydraulic properties of soil under warming climate. In M. N. V. Prasad & M. Pietrzykowski (Eds.), Climate Change and Soil Interactions (pp. 473-508). Elsevier. https://doi.org/10.1016/B978-0-12-818032-7.00018-7
Jacoby, R., Peukert, M., Succurro, A., Koprivova, A., & Kopriva, S. (2017). The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions [Review]. Frontiers in Plant Science, Volume 8 - 2017. https://doi.org/10.3389/fpls.2017.01617
Kiani, T., Mehboob, F., Hyder, M. Z., Zainy, Z., Xu, L., Huang, L., & Farrakh, S. (2021). Control of stripe rust of wheat using indigenous endophytic bacteria at seedling and adult plant stage. Scientific Reports, 11(1), 14473. https://doi.org/10.1038/s41598-021-93939-6
Luo, C., Ma, L., Zhu, J., Guo, Z., Dong, K., & Dong, Y. (2021). Effects of Nitrogen and Intercropping on the Occurrence of Wheat Powdery Mildew and Stripe Rust and the Relationship With Crop Yield [Original Research]. Frontiers in Plant Science, Volume 12 - 2021. https://doi.org/10.3389/fpls.2021.637393
Maione, C., Luíza da Costa, N., Barbosa Jr, F., & Barbosa, R. M. (2022). A Cluster Analysis Methodology for the Categorization of Soil Samples for Forensic Sciences Based on Elemental Fingerprint. Applied Artificial Intelligence, 36(1), 2010941. https://doi.org/10.1080/08839514.2021.2010941
Mari, A. H., Panhwar, R. N., Kaloi, G. M., Chohan, M., Zai, A. A. Y., Brohi, M. A., & Bhutto, M. A. (2009). Assessing zinc status of sugarcane in Taluka Nawabshah through soil and plant analysis. Journal of Applied Sciences, 6, 206-210. https://doi.org/10.3923/jas.2006.206.210
Marple, R. L., & LaCourse, W. R. (2019). Potentiometry: pH and Ion-Selective Electrodes. In N. Grinberg & S. Rodriguez (Eds.), Ewing's Analytical Instrumentation Handbook, Fourth Edition (pp. 491-508). CRC Press. https://doi.org/10.1201/9781315118024-16
Marschner, P. (Ed.). (2012). Marschner's mineral nutrition of higher plants. Academic press. https://doi.org/10.1016/C2009-0-63043-9.
Martinelli, F., Scalenghe, R., Davino, S., Panno, S., Scuderi, G., Ruisi, P., . . . Dandekar, A. M. (2015). Advanced methods of plant disease detection. A review. Agronomy for Sustainable Development, 35(1), 1-25. https://doi.org/10.1007/s13593-014-0246-1
McCook, S. (2006). Global rust belt: Hemileia vastatrix and the ecological integration of world coffee production since 1850. Journal of Global History, 1(2), 177-195. https://doi.org/10.1017/S174002280600012X
Medina-Sauza, R. M., Álvarez-Jiménez, M., Ortíz-Huerta, Y., Ruiz-Sayago, E., Blouin, M., Villain, L., . . . Barois, I. (2022). Bulk and rhizosphere soil properties under two Coffea species influenced by the earthworm Pontoscolex corethrurus. Rhizosphere, 21, 100458. https://doi.org/10.1016/j.rhisph.2021.100458
Moutassem, D., Belabid, L., Bellik, Y., Rouag, N., Abed, H., Ziouche, S., & Baali, F. (2019). Role of soil physicochemical and microbiological properties in the occurrence and severity of chickpea's Fusarium wilt disease. Eurasian Journal of Soil Science, 8(4), 304-312. https://doi.org/10.18393/ejss.585160
Nair, K. P. P. (2010). 6 - Coffee. In K. P. P. Nair (Ed.), The Agronomy and Economy of Important Tree Crops of the Developing World (pp. 181-208). Elsevier. https://doi.org/10.1016/B978-0-12-384677-8.00006-0
Ndolo, D., Njuguna, E., Adetunji, C. O., Harbor, C., Rowe, A., Den Breeyen, A., . . . Hospet, R. (2019). Research and Development of Biopesticides: Challenges and Prospects. Outlooks on Pest Management, 30(6), 267-276. https://doi.org/10.1564/v30_dec_08
Niranjana, K., Yogendra, K., & Mahadevan, K. (2019). Assessment of soil quality index under coffee land use system of hilly zone of Karnataka, India. Journal of Pharmacognosy and Phytochemistry, 8(1), 2548-2553. https://www.phytojournal.com/archives/2019/vol8issue1/PartAQ/8-1-379-598.pdf
Panigatti, S., Thangadurai, D., Sangeetha, J., Hospet, R., Yadav, G. G., Shinde, S., . . . Soytong, K. (2025). Soil physico-chemical properties and microbial diversity on chilli anthracnose disease severity in Northern Karnataka, India. Sains Tanah Journal of Soil Science and Agroclimatology, 22(1), 14. https://doi.org/10.20961/stjssa.v22i1.94015
Pereira, L. L., Guarçoni, R. C., Moreli, A. P., Pinheiro, P. F., Pinheiro, C. A., Moreira, T. R., . . . ten Caten, C. S. (2021). Physicochemical parameters of arabica fermented coffee in different altitudes. Coffee Science - ISSN 1984-3909, 16, e161877. https://doi.org/10.25186/.v16i.1877
Pérez, C. D. P., Pozza, E. A., Pozza, A. A. A., de Freitas, A. S., Silva, M. G., & da Silva Gomes Guimarães, D. (2019). Impact of nitrogen and potassium on coffee rust. European Journal of Plant Pathology, 155(1), 219-229. https://doi.org/10.1007/s10658-019-01765-4
Pham, Y., Reardon-Smith, K., Mushtaq, S., & Cockfield, G. (2019). The impact of climate change and variability on coffee production: a systematic review. Climatic Change, 156(4), 609-630. https://doi.org/10.1007/s10584-019-02538-y
Pinheiro, J. B., Pozza, E. A., Pozza, A. A. A., Moreira, A. d. S., & Alves, M. C. (2011). Effect of potassium and calcium supplied via nutrient solution on the severity of Asian soybean rust. Revista Ceres, 58, 43-50. https://doi.org/10.1590/S0034-737X2011000100007
Rutherford, M. A., & Phiri, N. (2006). Pests and diseases of coffee in Eastern Africa: A technical and advisory manual. Wallingford, UK: CAB International. https://assets.publishing.service.gov.uk/media/57a08c1b40f0b64974000fcc/U3071CoffeeManual.pdf
Santiago-Santiago, M., Sánchez-Viveros, G., Hernández-Adame, L., Chiquito-Contreras, C. J., Salinas-Castro, A., Chiquito-Contreras, R. G., & Hernández-Montiel, L. G. (2023). Essential Oils and Antagonistic Microorganisms as Eco-Friendly Alternatives for Coffee Leaf Rust Control. Plants, 12(20), 3519. https://doi.org/10.3390/plants12203519
Sembiring, M., Hutahuruk, J. M., Susilowati, D. N., Yuniarti, E., Sabrina, T., & Siregar, L. A. M. (2024). Functional diversity of bacteria in various saline soil plant vegetations around Sialang Buah Coast, North Sumatra, Indonesia. Sains Tanah Journal of Soil Science and Agroclimatology, 21(2), 9. https://doi.org/10.20961/stjssa.v21i2.80075
Silva, M. d. C., Várzea, V., Guerra-Guimarães, L., Azinheira, H. G., Fernandez, D., Petitot, A.-S., . . . Nicole, M. (2006). Coffee resistance to the main diseases: leaf rust and coffee berry disease. Brazilian journal of plant physiology, 18, 119-147. https://doi.org/10.1590/S1677-04202006000100010
Silvero, N. E., Marques, J., Siqueira, D. S., Gomes, R. P., & Costa, M. M. (2018). Sampling density for characterizing the physical quality of a soil under coffee cultivation in southwestern Minas Gerais. Engenharia Agrícola, 38(5), 718-727. https://doi.org/10.1590/1809-4430-Eng.Agric.v38n5p718-727/2018
Singh, G., & Gupta, S. K. (2019). Role of temperature, relative humidity and rainfall in the development of French bean rust ( Uromyces appendiculatus). Indian Phytopathology, 72(2), 271-280. https://doi.org/10.1007/s42360-019-00133-w
Smagin, A. V., Sadovnikova, N. B., Prokopyeva, K. O., Kalnin, T. G., & Mamutov, N. K. (2024). Methodological Problems of Assessing the Salinatization of Arid Soils by the Electrical Conductivity of the Liquid Phase. Arid Ecosystems, 14(1), 25-36. https://doi.org/10.1134/S2079096124010141
Sopialena, S., Suyadi, S., & Noor, S. A. (2022). Ecosystem Monitoring on Leaves of Leaf Rust Disease of Maize (Zea mays L.). Caraka Tani: Journal of Sustainable Agriculture, 37(1), 11. https://doi.org/10.20961/carakatani.v37i1.34920
Talhinhas, P., Batista, D., Diniz, I., Vieira, A., Silva, D. N., Loureiro, A., . . . Silva, M. d. C. (2017). The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics. Molecular Plant Pathology, 18(8), 1039-1051. https://doi.org/10.1111/mpp.12512
Tinuntun, R. S. T., Dewi, W. S., Mujiyo, M., Herawati, A., Herdiansyah, G., Sumani, S., . . . Kotroczó, Z. (2025). Pedotransfer functions for soil organic carbon stock and soil porosity interpretation in diverse palm oil plantation soils. Sains Tanah Journal of Soil Science and Agroclimatology, 22(1), 13. https://doi.org/10.20961/stjssa.v22i1.93460
Velásquez, D., Sánchez , A., Sarmiento , S., Toro , M., Maiza, M., & Sierra , B. (2020). A Method for Detecting Coffee Leaf Rust through Wireless Sensor Networks, Remote Sensing, and Deep Learning: Case Study of the Caturra Variety in Colombia. Applied Sciences, 10(2), 697. https://doi.org/10.3390/app10020697
Vidya, K., & Ravindranath, N. K. (2018). Area, production and productivity of coffee in India: An enquiry. Journal of Emerging Technologies and Innovative Research, 8(5), 1217-1220.
Yan, N., Marschner, P., Cao, W., Zuo, C., & Qin, W. (2015). Influence of salinity and water content on soil microorganisms. International Soil and Water Conservation Research, 3(4), 316-323. https://doi.org/10.1016/j.iswcr.2015.11.003
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