Microorganismos asociados a la rizosfera de plantas de café: diversidad, funciones y perspectivas para la agricultura sostenible

David Portillo; Stephany Hurtado Clopatosky; Diego Andrés  Abril Herrera

doi:10.22490/21456453.9953

Vol. 17 No. 2 (2026)

Published 2026-09-26

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Microorganisms associated with the rhizosphere of coffee plants: diversity, roles and perspectives for sustainable agriculture

DOI: https://doi.org/10.22490/21456453.9953

David Portillo University of Cundinamarca

Stephany Hurtado Clopatosky University of Cundinamarca

Diego Andrés Abril Herrera University of Cundinamarca

PDF (Spanish)

Abstract
References

Contextualization: The rhizosphere, being an area of soil very close to the root, is directly influenced by the plants growing in it and by the different compounds they exude. The cultivation of coffee began between the 15^th and 16^th centuries and has since been appreciated around the world, and reaching an estimated production of 10 million tons. This requires extensive areas dedicated to coffee production that generate significant environmental, economic and social impacts.

Knowledge gap: Although coffee cultivation is of agronomic importance and is grown in many countries around the world, the rhizospheric microbiome remains understudied and an overview of the factors that influence its composition is lacking. In addition, it is important to characterize its possible functions and applications for crop management.

Objective: To analyze the microbial dynamics in the rhizosphere of the coffee plant and its implications for crop management, with a view to establishing sustainable production models.

Methodology: Information was collected on coffee cultivation focusing on the different microorganisms present in its rhizosphere. A narrative analysis was performed through a systematic review of documents indexed in recognized scientific databases such as Scopus, Scielo, ScienceDirect, SpringerLink and Web of Science, and based on the documents selected according to the established criteria.

Results and conclusions: The factors that influence the diversity of the population of microorganisms in the rhizosphere of the coffee plant were analyzed, as well as the coffee species established at the site, the geographical conditions, the physicochemical characteristics of the soil and the type of crop management. Based on these results it was possible to infer that the composition of the rhizospheric microorganism population is modulated by a complex set of factors that regulate the plant-microorganism interactions.

keywords: Microorganism, nutrients, bacteria, fungus, effects of human activities

Afridi, M. S., Schulman, P., Lacerda, V. N. C., Guimaraes, R. A., & Vasconcelos de Medeiros, F. H. (2024). Long-term benefit contribution of chemical and biological nematicide in coffee nematode management in soil microbial diversity and crop yield perspectives. Microbiological Research, 282, 127638. https://doi.org/10.1016/j.micres.2024.127638 DOI: https://doi.org/10.1016/j.micres.2024.127638

Ahmad, H. M., Fiaz, S., Hafeez, S., Zahra, S., Shah, A. N., Gul, B., Aziz, O., Mahmood-Ur-Rahman, Fakhar, A., Rafique, M., Chen, Y., Yang, S. H., & Wang, X. (2022). Plant growth-promoting rhizobacteria eliminate the effect of drought stress in plants: A review. Frontiers in Plant Science, 13, 875774. https://doi.org/10.3389/fpls.2022.875774. DOI: https://doi.org/10.3389/fpls.2022.875774

Ahmad, M., Varela Alonso, A., Koletti, A. E., Assimopoulou, A. N., Declerck, S., Schneider, C., & Molin, E. M. (2022). Transcriptional dynamics of Chitinophaga sp. Strain R-73072-mediated alkannin/shikonin biosynthesis in Lithospermum officinale. Frontiers in Microbiology, 13: 978021. https://doi.org/10.3389/fmicb.2022.978021 DOI: https://doi.org/10.3389/fmicb.2022.978021

Ala, A., Musa, Y., & Kadola, L. (2020). Effect of compost enrichment with Trichoderma sp on the growth of Arabica coffee seedlings. In IOP Conference Series: Earth and Environmental Science, 575 (1), 012145. https://doi.org/10.1088/1755-1315/575/1/012145 DOI: https://doi.org/10.1088/1755-1315/575/1/012145

Al-Arequi, A., Chliyeh, M., Sghir, F., Ouazzani Touhami, A., Benkirane, R., & Douira, A. (2013). Diversity of arbuscular mycorrhizal fungi in the rhizosphere of Coffea arabica in the Republic of Yemen. Journal of Applied Biosciences, 64(1), 4888-4901. https://doi.org/10.4314/jab.v64i1.88478 DOI: https://doi.org/10.4314/jab.v64i1.88478

Alves, J. R., Celestino, F. N., de Moraes, A. G., dos Reis, R. A., & Grecco, E. D. (2023). Growth promoting fungi increase the quality of Coffea canephora seedlings Pierre ex a. Froehner. Coffee Science-ISSN 1984-3909, 18, e182089-e182089. https://doi.org/10.25186/.v18i.2089 DOI: https://doi.org/10.25186/.v18i.2089

Andrade, P. H. M., Machado, P. C., Paula, A. F., Paganin, A. C. L., Rezende, G. S., Matheucci, E., Carvalho, L. M., Freire, C. C. M., Cunha, A. F., & Lacava, P. T. (2023). 16S metabarcoding analysis reveals the influence of organic and conventional farming practices on bacterial communities from the rhizospheric of Coffea arabica L. Brazilian Journal of Biology, 83. https://doi.org/10.1590/1519-6984.274070 DOI: https://doi.org/10.1590/1519-6984.274070

Andrade, S. A. L., Silveira, A. P. D., and Mazzafera, P. (2010). Arbuscular mycorrhiza alters metal uptake and the physiological response of Coffea arabica seedlings to increasing Zn and Cu concentrations in soil. Sci. Total Environ, 408(22), 5381-5391. https://doi.org/10.1016/j.scitotenv.2010.07.064 DOI: https://doi.org/10.1016/j.scitotenv.2010.07.064

Araújo, V. C., Rossati, K. F., Xavier, L. V., Oliveira, V. A. De, Carmo, G. J. Dos S., Assis, G. A. De, & Mendes, G. De O. (2020). Enhanced growth in nursery of coffee seedlings inoculated with the rhizosphere fungus Aspergillus niger for field transplantation. Rhizosphere, 15, 100236. https://doi.org/10.1016/j.rhisph.2020.100236 DOI: https://doi.org/10.1016/j.rhisph.2020.100236

Asaf, S., Numan, M., Khan, A. L., & Al-Harrasi, A. (2020). Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth. Critical Reviews in Biotechnology, 40(2), 138-152. https://doi.org/10.1080/07388551.2019.1709793 DOI: https://doi.org/10.1080/07388551.2019.1709793

Bautista-Cruz, A., Antonio-Revuelta, B., del Carmen Martínez Gallegos, V., & Báez-Pérez, A. (2019). Phosphate-solubilizing bacteria improve Agave angustifolia Haw. Growth under field conditions. Journal of the Science of Food and Agriculture, 99(14), 6601-6607. https://doi.org/10.1002/jsfa.9946 DOI: https://doi.org/10.1002/jsfa.9946

Begum, N., Qin, C., Ahanger, M. A., Raza, S., Khan, M. I., Ashraf, M., Ahmed, N., & Zhang, L. (2019). Role of arbuscular mycorrhizal fungi in plant growth regulation: Implications in abiotic stress tolerance. Frontiers in Plant Science, 10, 1068. https://doi.org/10.3389/fpls.2019.01068 DOI: https://doi.org/10.3389/fpls.2019.01068

Behnke, G. D., Kim, N., Zabaloy, M. C., Riggins, C. W., Rodriguez-Zas, S., & Villamil, M. B. (2021). Soil microbial indicators within rotations and tillage systems. Microorganisms, 9(6), 1244. https://doi.org/10.3390/microorganisms9061244 DOI: https://doi.org/10.3390/microorganisms9061244

Bekele, G. K., Abda, E. M., Tuji, F. A., Meka, A. F., & Gemeda, M. T. (2025). Shotgun Metagenomics Reveals Metabolic Potential and Functional Diversity of Microbial Communities of Chitu and Shala Soda Lakes in Ethiopia. Microbiology Research, 16(3), 71. https://doi.org/10.3390/microbiolres16030071 DOI: https://doi.org/10.3390/microbiolres16030071

Benedek, T., Pápai, M., Gharieb, K., Bedics, A., Táncsics, A., Tóth, E., Daood, H., Maróti, G., Wirth, R., Menashe, O., Bóka, K., & Kriszt, B. (2022). Nocardioides carbamazepini sp. nov., an ibuprofen degrader isolated from a biofilm bacterial community enriched on carbamazepine. Systematic and Applied Microbiology, 45(4). https://doi.org/10.1016/j.syapm.2022.126339 DOI: https://doi.org/10.1016/j.syapm.2022.126339

Bertolini, V., Montaño, N. M., Chimal Sánchez, E., Varela Fregoso, L., Gómez Ruiz, J., & Martínez Vázquez, J. M. (2018). Abundance and richness of arbuscular mycorrhizal fungi in coffee plantations from Soconusco, Chiapas, Mexico. Revista de Biología Tropical, 66(1), 91 -105. https://doi.org/10.15517/rbt.v66i1.27946 DOI: https://doi.org/10.15517/rbt.v66i1.27946

Bertrand, B., Ramirez, G., Topart, P., & Anthony, F. (2002). Resistance of cultivated coffee (Coffea arabica and C. canephora) trees to corky-root caused by Meloidogyne arabicida and Fusarium oxysporum, under controlled and field conditions. Crop Protection, 21(9), 713-719. https://doi.org/10.1016/S0261-2194(02)00028-5 DOI: https://doi.org/10.1016/S0261-2194(02)00028-5

Bez, C., Esposito, A., Musonerimana, S., Nguyen, T. H., Navarro-Escalante, L., Tesfaye, K., Turello, L., Navarini, L., Piazza, S., & Venturi, V. (2023). Comparative study of the rhizosphere microbiome of Coffea arabica grown in different countries reveals a small set of prevalent and keystone taxa. Rhizosphere, 25, 100652. https://doi.org/10.1016/j.rhisph.2022.100652 DOI: https://doi.org/10.1016/j.rhisph.2022.100652

Bresciani, L., Freitas, C. C. G., Barros, F. M. Do R., Andreote, F. D., & Dini-Andreote, F. (2024). Partitioning the effects of coffee-Urochloa intercropping on soil microbial properties at a centimeter-scale. Applied Soil Ecology, 195, 105264. https://doi.org/10.1016/j.apsoil.2023.105264 DOI: https://doi.org/10.1016/j.apsoil.2023.105264

Broeckling, C. D., Paschke, M. W., Vivanco, J. M., & Manter, D. (2019). Rhizosphere Ecology. Encyclopedia of Ecology, 3, 574-578). https://doi.org/10.1016/B978-0-12-409548-9.11132-7 DOI: https://doi.org/10.1016/B978-0-12-409548-9.11132-7

Brtnicky, M., Kintl, A., Hammerschmiedt, T., Mustafa, A., Elbl, J., Kucerik, J., Vyhnanek, T., Skladanka, J., Hunady, I., & Holatko, J. (2021). Clover species specific influence on microbial abundance and associated enzyme activities in rhizosphere and non-rhizosphere soils. Agronomy, 11(11), 2214. https://doi.org/10.3390/agronomy11112214 DOI: https://doi.org/10.3390/agronomy11112214

Bullergahn, V. B., Menezes, K. M. S., Veloso, T. G. R., da Luz, J. M. R., Castanheira, L. F., Pereira, L. L., & Soares da Silva, M. d. C. (2024). Diversity of potential nitrogen-fixing bacteria from rhizosphere of the Coffea arabica L. and Coffea canephora L. 3 Biotech, 14(1), 27. https://doi.org/10.1007/s13205-023-03875-7 DOI: https://doi.org/10.1007/s13205-023-03875-7

Cabrera, R., García-López, H., Aguirre-von-Wobeser, E., Orozco-Avitia, J. A., & Gutiérrez-Saldaña, A. H. (2020). Amycolatopsis BX17: An actinobacterial strain isolated from soil of a traditional milpa agroecosystem with potential biocontrol against Fusarium graminearum. Biological Control, 147, 104285. https://doi.org/10.1016/j.biocontrol.2020.104285 DOI: https://doi.org/10.1016/j.biocontrol.2020.104285

Cain, C. C., Henry, A. T., Waldo, R. H., Casida, J., & Falkinham, J. O. (2000). Identification and characteristics of a novel Burkholderia strain with broad-spectrum antimicrobial activity. Applied and Environmental Microbiology, 66(9), 4139-4141. https://doi.org/10.1128/AEM.66.9.4139-4141.2000 DOI: https://doi.org/10.1128/AEM.66.9.4139-4141.2000

Caldwell, A. C., Silva, L. C. F., da Silva, C. C., & Ouverney, C. C. (2015). Prokaryotic Diversity in the Rhizosphere of Organic, Intensive, and Transitional Coffee Farms in Brazil. PLoS ONE, 10(6), e0106355. https://doi.org/10.1371/journal.pone.0106355 DOI: https://doi.org/10.1371/journal.pone.0106355

Campos Trigoso, J.-A., Murga Valderrama, N. L., Rituay Trujillo, P. A., & García Rosero, L. M. (2021). Sostenibilidad del café: revisión sistemática de la literatura. Revista Venezolana de Gerencia, 26(95), 943-961. https://doi.org/10.52080/rvgluz.27.95.30 DOI: https://doi.org/10.52080/rvgluz.27.95.30

Cao, M., Huang, J., Li, J., Qiao, Z., & Wang, G. (2017). Edaphobaculum flavum gen. nov., sp. nov., a member of family Chitinophagaceae, isolated from grassland soil. International Journal of Systematic and Evolutionary Microbiology, 67(11), 4475-4481. https://doi.org/10.1099/ijsem.0.002316 DOI: https://doi.org/10.1099/ijsem.0.002316

Carrasco-Espinosa, K., Avitia, M., Barrón-Sandoval, A., Abbruzzini, T. F., Salazar Cabrera, U. I., Arroyo-Lambaer, D., Uscanga, A., Campo, J., Benítez, M., Wegier, A., Rosell, J. A., Reverchon, F., Hernández, G., Boege, K. & Escalante, A. E. (2022). Land-Use Change and Management Intensification Is Associated with Shifts in Composition of Soil Microbial Communities and Their Functional Diversity in Coffee Agroecosystems. Microorganisms, 10(9), 1763. https://doi.org/10.3390/microorganisms10091763 DOI: https://doi.org/10.3390/microorganisms10091763

Carrión, V. J., Cordovez, V., Tyc, O., Etalo, D. W., de Bruijn, I., de Jager, V. C. L., Medema, M. H., Eberl, L., & Raaijmakers, J. M. (2018). Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils. The ISME Journal, 12(9), 2307-2321. https://doi.org/10.1038/s41396-018-0186-x DOI: https://doi.org/10.1038/s41396-018-0186-x

Chopra, A., Bobate, S., Rahi, P., Banpurkar, A., Mazumder, P. B., & Satpute, S. (2020). Pseudomonas aeruginosa RTE4: A Tea Rhizobacterium with Potential for Plant Growth Promotion and Biosurfactant Production. Frontiers in Bioengineering and Biotechnology, 8, 861. https://doi.org/10.3389/fbioe.2020.00861 DOI: https://doi.org/10.3389/fbioe.2020.00861

Colombi, E., Hill, Y., Lines, R., Sullivan, J. T., Kohlmeier, M. G., Christophersen, C. T., Ronson, C. W., Terpolilli, J. J., & Ramsay, J. P. (2023). Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer. Microbial Genomics, 9(1). https://doi.org/10.1099/mgen.0.000918 DOI: https://doi.org/10.1099/mgen.0.000918

Corazon-Guivin, M. A., Romero-Cachique, G., Del Aguila, K. M., Padilla-Domínguez, A., Hernández-Amasifuen, A. D., Cerna-Mendoza, A., Coyne, D., & Oehl, F. (2023). Rhizoglomus variabile and Nanoglomus plukenetiae, Native to Peru, Promote Coffee Growth in Western Amazonia. Microorganisms, 11(12), 2883. https://doi.org/10.3390/microorganisms11122883 DOI: https://doi.org/10.3390/microorganisms11122883

Costa, O. Y. A., Pijl, A., & Kuramae, E. E. (2020). Dynamics of active potential bacterial and fungal interactions in the assimilation of acidobacterial EPS in soil. Soil Biology and Biochemistry, 148, 107916. https://doi.org/10.1016/j.soilbio.2020.107916 DOI: https://doi.org/10.1016/j.soilbio.2020.107916

das Neves, T. T., de Jesus Cassimiro, D. M., de Souza, J. G. D. L., de Souza Castro, C. R., Schwan, R. F., Batista, L. R., & Silva, C. F. (2024). Inhibition of Aspergillus spp. growth and ochratoxin A production in Conilon and Arabica coffees based-medium by Saccharomyces cerevisiae. International Journal of Food Microbiology, 425, 110875. https://doi.org/10.1016/j.ijfoodmicro.2024.110875 DOI: https://doi.org/10.1016/j.ijfoodmicro.2024.110875

Davis, A. P., Govaerts, R., Bridson, D. M., & Stoffelen, P. (2006). An annotated taxonomic conspectus of the genus Coffea (Rubiaceae). Botanical Journal of the Linnean Society, 152(4), 465-512. https://doi.org/10.1111/j.1095-8339.2006.00584.x DOI: https://doi.org/10.1111/j.1095-8339.2006.00584.x

de Beenhouwer, M., Van Geel, M., Ceulemans, T., Muleta, D., Lievens, B., & Honnay, O. (2015). Changing soil characteristics alter the arbuscular mycorrhizal fungi communities of Arabica coffee (Coffea arabica) in Ethiopia across a management intensity gradient. Soil Biology and Biochemistry, 91, 133-139. https://doi.org/10.1016/j.soilbio.2015.08.037 DOI: https://doi.org/10.1016/j.soilbio.2015.08.037

de Oliveira-Longatti, S. M., Martins de Sousa, P., Marciano Marra, L., Avelar Ferreira, P. A., & de Souza Moreira, F. M. (2015). Burkholderia fungorum promotes common bean growth in a dystrophic oxisol. Annals of Microbiology, 65(4), 1825-1832. https://doi.org/10.1007/s13213-014-1020-y DOI: https://doi.org/10.1007/s13213-014-1020-y

de Oliveira Mendes, G., Moreira de Freitas, A.L., Liparini Pereira, O. et al. (2014). Mechanisms of phosphate solubilization by fungal isolates when exposed to different P sources. Ann Microbiol, 64, 239-249. https://doi.org/10.1007/s13213-013-0656-3 DOI: https://doi.org/10.1007/s13213-013-0656-3

de Sousa, L. P., Filho, O. G., & Mondego, J. M. C. (2023). Age-Related Rhizosphere Analysis of Coffea arabica Plants. Current Microbiology, 80(4), 130. https://doi.org/10.1007/s00284-023-03236-w DOI: https://doi.org/10.1007/s00284-023-03236-w

de Sousa, L. P., Guerreiro-Filho, O., & Mondego, J. M. C. (2022). The Rhizosphere Microbiomes of Five Species of Coffee Trees. Microbiology Spectrum, 10(2). https://doi.org/10.1128/spectrum.00444-22 DOI: https://doi.org/10.1128/spectrum.00444-22

Drever, J. I., & Stillings, L. L. (1997). The role of organic acids in mineral weathering. Colloids and Surfaces A: Physicochemical and Engineering Aspects, 120(1-3), 167-181. DOI: https://doi.org/10.1016/S0927-7757(96)03720-X

Duong, B., Nguyen, H. X., Phan, H. V., Colella, S., Trinh, P. Q., Hoang, G. T., Nguyen, T. T., Marraccini, P., Lebrun, M., & Duponnois, R. (2021). Identification and characterization of Vietnamese coffee bacterial endophytes displaying in vitro antifungal and nematicidal activities. Microbiological Research, 242, 126613. https://doi.org/10.1016/j.micres.2020.126613 DOI: https://doi.org/10.1016/j.micres.2020.126613

El‐Shatnawi, M. K. J., & Makhadmeh, I. M. (2001). Ecophysiology of the Plant–Rhizosphere System. Journal of Agronomy and Crop Science, 187(1), 1-9. https://doi.org/10.1046/j.1439-037X.2001.00498.x DOI: https://doi.org/10.1046/j.1439-037X.2001.00498.x

Farha, A., Fatimah, I. N., Ade, M. A., Hidayati, R. F., Lili, D., Merry, M. G., & Aidil, A. (2024). Colonization of arbuscular mycorrhizal fungi (AMF) in the rhizosphere of robusta coffee plant (Coffea canephora). E3S Web of Conferences, 577, 02018). EDP Sciences. https://doi.org/10.1051/e3sconf/202457702018 DOI: https://doi.org/10.1051/e3sconf/202457702018

Franzin, M. L., Moreira, C. C., da Silva, L. N., Martins, E. F., Fadini, M. A., Pallini, A., ... & Venzon, M. (2022). Metarhizium associated with coffee seedling roots: positive effects on plant growth and protection against Leucoptera coffeella. Agriculture, 12(12), 2030. https://doi.org/10.3390/agriculture12122030 DOI: https://doi.org/10.3390/agriculture12122030

Gaete, A., Mandakovic, D., & González, M. (2020). Isolation and identification of soil bacteria from extreme environments of Chile and their plant beneficial characteristics. Microorganisms, 8(8), 1-13. https://doi.org/10.3390/microorganisms8081213 DOI: https://doi.org/10.3390/microorganisms8081213

Ge, Y., Zhang, F., Xie, C., Qu, P., Jiang, K., Du, H., Zhao, M., Lu, Y., Wang, B., Shi, X., Li, X., & Zhang, C. (2023). Effects of Different Altitudes on Coffea arabica Rhizospheric Soil Chemical Properties and Soil Microbiota. Agronomy, 13(2), 471. https://doi.org/10.3390/agronomy13020471 DOI: https://doi.org/10.3390/agronomy13020471

Gebers, R. (1981). Enrichment, Isolation, and Emended Description of Pedomicrobium ferrugineum Aristovskaya and Pedomicrobium manganicum Aristovskaya. International Journal of Systematic Bacteriology, 31(3) DOI: https://doi.org/10.1099/00207713-31-3-302

Gomes, W. d. S., Partelli, F. L., Veloso, T. G. R., Soares da Silva, M. d. C., Moreli, A. P., Moreira, T. R., Pereira, L. L., & Louwzada Pereira, L. (2024). Effects of Coffea canephora genotypes on the microbial community of soil and fruit. Scientific Reports, 14, 29035. https://doi.org/10.1038/s41598-024-80403-4 DOI: https://doi.org/10.1038/s41598-024-80403-4

Green, S. J., Prakash, O., Jasrotia, P., Overholt, W. A., Cardenas, E., Hubbard, D., Tiedje, J. M., Watson, D. B., Schadt, C. W., Brooks, S. C., & Kostka, J. E. (2012). Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site. Applied and Environmental Microbiology, 78(4), 1039-1047. https://doi.org/10.1128/AEM.06435-11 DOI: https://doi.org/10.1128/AEM.06435-11

Groß, V., Reinhard, A., Petters, S., Pichler, M., & Urich, T. (2023). Adding complexity to soil food webs: Myxobacteria have broad predation spectra with bacteria, yeasts and filamentous fungi in vitro. European Journal of Soil Biology, 117. https://doi.org/10.1016/j.ejsobi.2023.103508 DOI: https://doi.org/10.1016/j.ejsobi.2023.103508

Gu, Y., Wang, Y., Lu, S., Xiang, Q., Yu, X., Zhao, K., Zou, L., Chen, Q., Tu, S., & Zhang, X. (2017). Long-term fertilization structures bacterial and archaeal communities along soil depth gradient in a paddy soil. Frontiers in Microbiology, 8. https://doi.org/10.3389/fmicb.2017.01516 DOI: https://doi.org/10.3389/fmicb.2017.01516

Guo, L., Zheng, S., Cao, C., & Li, C. (2016). Tillage practices and straw-returning methods affect topsoil bacterial community and organic C under a rice-wheat cropping system in central China. Scientific Reports, 6, 33155. https://doi.org/10.1038/srep33155 DOI: https://doi.org/10.1038/srep33155

Haldar, S., & Sengupta, S. (2015). Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential. The Open Microbiology Journal, 9(1), 1-7. https://doi.org/10.2174/1874285801509010001 DOI: https://doi.org/10.2174/1874285801509010001

Han, S., Luo, X., Liao, H., Nie, H., Chen, W., & Huang, Q. (2017). Nitrospira are more sensitive than Nitrobacter to land management in acid, fertilized soils of a rapeseed-rice rotation field trial. Science of the Total Environment, 599-600, 135-144. https://doi.org/10.1016/j.scitotenv.2017.04.086 DOI: https://doi.org/10.1016/j.scitotenv.2017.04.086

Hernández-Acosta, E., Trejo-Aguilar, D., Ferrera-Cerrato, R., Rivera-Fernández, & González-Chávez, M. C. (2018). Hongos micorrízicos arbusculares en el crecimiento de café (Coffea arabica L.) Variedades Garnica, Catimor, Caturra y Catuaí. Agroproductividad, 11(4), 61-67. https://mail.revista-agroproductividad.org/index.php/agroproductividad/es/article/view/352

Hindersah, R., & Asyiah, I. N. (2023). Abundance of Beneficial Soil Microbes in the Rhiosphere of Coffee Plants Infected by Pratylenchus coffeae. Biosaintifika: Journal of Biology & Biology Education, 15(2), 220-229. https://doi.org/10.15294/biosaintifika.v15i2.43085 DOI: https://doi.org/10.15294/biosaintifika.v15i2.43085

Hwang, Y. J., Son, J. S., Lee, S. Y., He, Y., Jo, Y., Shin, J. H., & Ghim, S. Y. (2020). Nocardioides sambongensis sp. Nov., isolated from dokdo islands soil. International Journal of Systematic and Evolutionary Microbiology, 70(1), 16-22. https://doi.org/10.1099/ijsem.0.003689 DOI: https://doi.org/10.1099/ijsem.0.003689

Islam, M. T., Tabrez, S., Jabir, N. R., Ali, M., Kamal, M. A., da Silva Araujo, L., De Oliveira Santos, J. V., Da Mata, A. M. O. F., De Aguiar, R. P. S., & de Carvalho Melo Cavalcante, A. A. (2018). An Insight into the Therapeutic Potential of Major Coffee Components. Current Drug Metabolism, 19(6), 544-556. https://doi.org/10.2174/1389200219666180302154551 DOI: https://doi.org/10.2174/1389200219666180302154551

Jan-Roblero, J., Cruz-Maya, J. A., & Cancino-Diaz, J. C. (2024). Novel Molecular Techniques for Identifying Agricultural Microorganisms. Agriculture, 14(7), 987. https://doi.org/10.3390/agriculture14070987 DOI: https://doi.org/10.3390/agriculture14070987

Jasso-Arreola, Y., Ibarra, J. A., Rosas-Cárdenas, F. d. F., & Estrada-de los Santos, P. (2025). Beneficial Effects of ACC Deaminase-Producing Rhizobacteria on the Drought Stress Resistance of Coffea arabica L. Plants, 14(7), 1084. https://doi.org/10.3390/plants14071084 DOI: https://doi.org/10.3390/plants14071084

Jiang, H., Chen, Y., Hu, Y., Wang, Z., & Lu, X. (2021). Soil bacterial communities and diversity in alpine grasslands on the Tibetan Plateau based on 16S rRNA gene sequencing. Frontiers in Ecology and Evolution, 9, 630722. https://doi.org/10.3389/fevo.2021.630722 DOI: https://doi.org/10.3389/fevo.2021.630722

Jones, B., Goodall, T., George, P. B. L., Gweon, H. S., Puissant, J., Read, D. S., Emmett, B. A., Robinson, D. A., Jones, D. L., & Griffiths, R. I. (2021). Beyond Taxonomic Identification: Integration of Ecological Responses to a Soil Bacterial 16S rrna Gene Database. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.682886 DOI: https://doi.org/10.3389/fmicb.2021.682886

Jones, F. P., Clark, I. M., King, R., Shaw, L. J., Woodward, M. J., & Hirsch, P. R. (2016). Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes - A genome comparison. Scientific Reports, 6, 25858. https://doi.org/10.1038/srep25858 DOI: https://doi.org/10.1038/srep25858

Jurburg, S. D., Shek, K. L., & mcguire, K. (2020). Soil microbial composition varies in response to coffee agroecosystem management. FEMS Microbiology Ecology, 96(9). https://doi.org/10.1093/femsec/fiaa164 DOI: https://doi.org/10.1093/femsec/fiaa164

Kalam, S., Basu, A., Ahmad, I., Sayyed, R. Z., El-Enshasy, H. A., Dailin, D. J., & Suriani, N. L. (2020). Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.580024 DOI: https://doi.org/10.3389/fmicb.2020.580024

Kartika, E., & Duaja, M. D. (2019). Diversity of Arbuscular Mycorrhizal Fungi from Liberica Tungkal Jambi Coffee Plant Rhizosphere on Peatland. IOP Conference Series: Earth and Environmental Science, 391(1), 012058). IOP Publishing. https://doi.org/10.1088/1755-1315/391/1/012058 DOI: https://doi.org/10.1088/1755-1315/391/1/012058

Kejela, T., Thakkar, V. R., & Thakor, P. (2016). Bacillus species (BT42) isolated from Coffea arabica L. rhizosphere antagonizes Colletotrichum gloeosporioides and Fusarium oxysporum and also exhibits multiple plant growth promoting activity. BMC Microbiology, 16, 277. https://doi.org/10.1186/s12866-016-0897-y DOI: https://doi.org/10.1186/s12866-016-0897-y

Khalil, Z. G., Salim, A. A., Vuong, D., Crombie, A., Lacey, E., Blumenthal, A., & Capon, R. J. (2017). Amycolatopsins A-C: Antimycobacterial glycosylated polyketide macrolides from the Australian soil Amycolatopsis sp. MST-108494. Journal of Antibiotics, 70(12), 1097-1103. https://doi.org/10.1038/ja.2017.119 DOI: https://doi.org/10.1038/ja.2017.119

Kim, D. U., Lee, H., Kim, H., Kim, S. G., & Ka, J. O. (2016). Dongia soli sp. Nov., isolated from soil from Dokdo, Korea. International Journal of General and Molecular Microbiology, 109(10), 1397-1402. https://doi.org/10.1007/s10482-016-0738-x DOI: https://doi.org/10.1007/s10482-016-0738-x

Kim, D. Y., Han, J. W., Lee, J. W., Kim, B., Kim, Y. S., Kim, H. T., Choi, G. J., & Kim, H. (2023). Biocontrol potential of Chitinophaga flava HK235 producing antifungal-related peptide chitinocin. Frontiers in Microbiology, 14, 1170673. https://doi.org/10.3389/fmicb.2023.1170673 DOI: https://doi.org/10.3389/fmicb.2023.1170673

Knežević, M., Berić, T., Buntić, A., Jovković, M., Avdović, M., Stanković, S., Delić, D., & Stajković-Srbinović, O. (2022). Native Mesorhizobium strains improve yield and nutrient composition of the common bird’s-foot trefoil grown in an acid soil. Rhizosphere, 21, 100487. https://doi.org/10.1016/j.rhisph.2022.100487 DOI: https://doi.org/10.1016/j.rhisph.2022.100487

Kostka, J. E., Green, S. J., Rishishwar, L., Prakash, O., Katz, L. S., Mariño-Ramírez, L., King Jordan, I., Munk, C., Ivanova, N., Mikhailova, N., Watson, D. B., Brown, S. D., Palumbo, A. V., & Brooks, S. C. (2012). Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities. Journal of Bacteriology, 194(16), 4461-4462). https://doi.org/10.1128/JB.00871-12 DOI: https://doi.org/10.1128/JB.00871-12

Kruczyńska, A., Kuźniar, A., Podlewski, J., Słomczewski, A., Grządziel, J., Marzec-Grządziel, A., Gałązka, A., & Wolińska, A. (2023). Bacteroidota structure in the face of varying agricultural practices as an important indicator of soil quality – a culture independent approach. Agriculture, Ecosystems and Environment, 342, 108252. https://doi.org/10.1016/j.agee.2022.108252 DOI: https://doi.org/10.1016/j.agee.2022.108252

Kutos, S., Bennett, R., Rao, M. V., Fleischer, R. C., Rice, R., & Muletz-Wolz, C. (2024). Farm management and shade tree species influence coffee soil microbiomes in Central and South America. Applied Soil Ecology, 202, 105571. https://doi.org/10.1016/j.apsoil.2024.105571 DOI: https://doi.org/10.1016/j.apsoil.2024.105571

Lashermes, P., Andrade, A. C., & Etienne, H. (2008.). Genomics of Coffee One of the World’s Largest Traded Commodities. Genomics of Tropical Crop Plants (pp. 203–226). https://doi.org/10.1007/978-0-387-71219-2_9 DOI: https://doi.org/10.1007/978-0-387-71219-2_9

Li, C., Hu, H. W., Chen, Q. L., Chen, D., & He, J. Z. (2019). Comammox Nitrospira play an active role in nitrification of agricultural soils amended with nitrogen fertilizers. Soil Biology and Biochemistry, 138, 107609. https://doi.org/10.1016/j.soilbio.2019.107609 DOI: https://doi.org/10.1016/j.soilbio.2019.107609

Li, J., Wang, C., Liang, W., & Liu, S. (2021). Rhizosphere Microbiome: The Emerging Barrier in Plant-Pathogen Interactions. Frontiers in Microbiology, 12, 772420. https://doi.org/10.3389/fmicb.2021.772420 DOI: https://doi.org/10.3389/fmicb.2021.772420

Liao, H.-L. (2021). The plant-growth-promoting fungus, Mortierella elongata: Its biology, ecological distribution, and growth-promoting activities (SS679/SL466). EDIS, 2021(2). University of Florida Institute of Food and Agricultural Sciences (UF/IFAS). https://ask.ifas.ufl.edu/publication/SS679 DOI: https://doi.org/10.32473/edis-ss679-2021

Ling, N., Wang, T., & Kuzyakov, Y. (2022). Rhizosphere bacteriome structure and functions. Nature Communications, 13, 836. https://doi.org/10.1038/s41467-022-28448-9 DOI: https://doi.org/10.1038/s41467-022-28448-9

Lu, X., Taylor, A. E., Myrold, D. D., & Neufeld, J. D. (2020). Expanding perspectives of soil nitrification to include ammonia-oxidizing archaea and comammox bacteria. Soil Science Society of America Journal, 84, 287-302. John Wiley and Sons Inc. https://doi.org/10.1002/saj2.20029 DOI: https://doi.org/10.1002/saj2.20029

Lv, Y. Y., Gao, Z. H., Xia, F., Chen, M. H., & Qiu, L. H. (2017). Puia dinghuensis gen. Nov., sp. Nov., isolated from monsoon evergreen broad-leaved forest soil. International Journal of Systematic and Evolutionary Microbiology, 67(11), 4639-4645. https://doi.org/10.1099/ijsem.0.002346 DOI: https://doi.org/10.1099/ijsem.0.002346

Ma, Y., Wang, J., Liu, Y., Wang, X., Zhang, B., Zhang, W., Chen, T., Liu, G., Xue, L., & Cui, X. (2023). Nocardioides: “Specialists” for Hard-to-Degrade Pollutants in the Environment. Molecules, 28(21), 7433. https://doi.org/10.3390/molecules28217433 DOI: https://doi.org/10.3390/molecules28217433

Meliah, S., Indah Kusumawati, D., & Lisdiyani, P. (2018). The Genus Chitinophaga Isolated from Wanggameti National Park and Their Lytic Activities. Journal Biologi Indonesia, 14(2), 165-174. https://doi.org/10.47349/jbi/14022018/165 DOI: https://doi.org/10.47349/jbi/14022018/165

Menéndez, E., Pérez-Yépez, J., Hernández, M., Rodríguez-Pérez, A., Velázquez, E., & León-Barrios, M. (2020). Plant growth promotion abilities of phylogenetically diverse Mesorhizobium strains: Effect in the root colonization and development of tomato seedlings. Microorganisms, 8(3), 412. https://doi.org/10.3390/microorganisms8030412 DOI: https://doi.org/10.3390/microorganisms8030412

Mertz, F. P., & Yao, R. C. (1993). Amycolatopsis alba sp. Nov., Isolated from Soil. In International Journal of Systematic Bacteriology, 43(4), 715-720. https://pubmed.ncbi.nlm.nih.gov/8240953/ DOI: https://doi.org/10.1099/00207713-43-4-715

Mng’ong’o, M. E., Ojija, F., & Aloo, B. N. (2023). The role of Rhizobia toward food production, food and soil security through microbial agro-input utilization in developing countries. Case Studies in Chemical and Environmental Engineering, 8, 100404. https://doi.org/10.1016/j.cscee.2023.100404 DOI: https://doi.org/10.1016/j.cscee.2023.100404

Moher D., Liberati A., Tetzlaff J., Altman D. G., The PRISMA Group (2009). Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement. PLoS Med 6(7): e1000097. https://doi.org/10.1371/journal.pmed.100009 DOI: https://doi.org/10.1371/journal.pmed.1000097

Moreira, S. D., França, A. C., Rocha, W. W., Tibães, E. S. R., & Neiva Júnior, E. (2018). Inoculation with mycorrhizal fungi on the growth and tolerance to water deficit of coffee plants. Revista Brasileira de Engenharia Agrícola e Ambiental, 22(11), 747-752. https://doi.org/10.1590/1807-1929/agriambi.v22n11p747-752 DOI: https://doi.org/10.1590/1807-1929/agriambi.v22n11p747-752

Mulatu, A., Megersa, N., Abena, T., Kanagarajan, S., Liu, Q., Tenkegna, T. A., & Vetukuri, R. R. (2022). Biodiversity of the Genus Trichoderma in the Rhizosphere of Coffee (Coffea arabica) Plants in Ethiopia and Their Potential Use in Biocontrol of Coffee Wilt Disease. Crops, 2(2), 120-141. https://doi.org/10.3390/crops2020010 DOI: https://doi.org/10.3390/crops2020010

Mulaw, T. B., Kubicek, C. P., & Druzhinina, I. S. (2010). The rhizosphere of Coffea arabica in its native highland forests of Ethiopia provides a niche for a distinguished diversity of Trichoderma. Diversity, 2(4), 527. https://doi.org/10.3390/d2040527 DOI: https://doi.org/10.3390/d2040527

Muleta, A., Tesfaye, K., Haile Selassie, T. H., Cook, D. R., & Assefa, F. (2021). Phosphate solubilization and multiple plant growth promoting properties of Mesorhizobium species nodulating chickpea from acidic soils of Ethiopia. Archives of Microbiology, 203(5), 2129-2137. https://doi.org/10.1007/s00203-021-02189-7 DOI: https://doi.org/10.1007/s00203-021-02189-7

Muok, A. R., Claessen, D., & Briegel, A. (2021). Microbial hitchhiking: how Streptomyces spores are transported by motile soil bacteria. The ISME Journal, 15(9), 2591-2600. https://doi.org/10.1038/s41396-021-00952-8 DOI: https://doi.org/10.1038/s41396-021-00952-8

Nakayasu, M., Takamatsu, K., Kanai, K., Masuda, S., Yamazaki, S., Aoki, Y., Shibata, A., Suda, W., Shirasu, K., Yazaki, K., & Sugiyama, A. (2023). Tomato root-associated Sphingobium harbors genes for catabolizing toxic steroidal glycoalkaloids. Mbio, 14, e00599-23. https://doi.org/10.1128/MBIO.00599-23 DOI: https://doi.org/10.1128/mbio.00599-23

Navarro, G. V. D., Quirong, D. D., Maghanoy, G. A., & Cortes, A. D. (2023). Characterization and identification of rhizobacteria associated with Liberica and Robusta coffee rhizosphere. Technology in Horticulture, 3, 24. https://doi.org/10.48130/tih-2023-0024 DOI: https://doi.org/10.48130/TIH-2023-0024

Ochoa-Henriquez, V. H., Faggioli, V., Gómez-Godínez, L. J., Rivarola, M., & Cristancho, M. (2024). Colombian coffee (Coffea arabica L.) Plantations: a taxonomic and functional survey of soil fungi. Frontiers in Sustainable Food Systems, 8, 1345383. https://doi.org/10.3389/fsufs.2024.1345383 DOI: https://doi.org/10.3389/fsufs.2024.1345383

Olal, S., Bitalo, D. N., Olango, N. D., Mulindwa, J., Ochwo, S., Opiyo, S. O., ... & Ogwok, E. (2019). De novo genome sequence of a Fusarium xylarioides race pathogenic to Robusta coffee (Coffea canephora) in Uganda. Microbiology Resource Announcements, 8(31), 10-1128. https://doi.org/10.1128/mra.00520-19 DOI: https://doi.org/10.1128/MRA.00520-19

Oliveira, C., Shakiba, E., North, D., McGraw, M., Ballard, E., Barrett-D’Amico, M., Glazko, G., & Rahmatallah, Y. (2022). 16S rRNA gene-based metagenomic analysis of rhizosphere soil bacteria in Arkansas rice crop fields. Agronomy, 12(1), 222. https://doi.org/10.3390/agronomy12010222 DOI: https://doi.org/10.3390/agronomy12010222

Oliveira, M. C. O., Alves, A., Fidalgo, C., de Freitas, J. G. R., & Pinheiro de Carvalho, M. A. A. (2024). Variations in the structure and function of the soil fungal communities in the traditional cropping systems from Madeira Island. Frontiers in Microbiology, 15, 1426957. https://doi.org/10.3389/fmicb.2024.1426957 DOI: https://doi.org/10.3389/fmicb.2024.1426957

Oliveira-Longatti, S. M. De, Marra, L. M., & Moreira, F. M. D. S. (2013). Evaluation of plant growth-promoting traits of Burkholderia and Rhizobium strains isolated from Amazon soils for their co-inoculation in common bean. African Journal of Microbiology Research, 7(11), 948-959. https://doi.org/10.5897/AJMR12.1055 DOI: https://doi.org/10.5897/AJMR12.1055

Oshkin, I. Y., Kulichevskaya, I. S., Rijpstra, W. I. C., Damste, J. S. S., Rakitin, A. L., Ravin, N. V., & Dedysh, S. N. (2019). Granulicella sibirica sp. Nov., a psychrotolerant acidobacterium isolated from an organic soil layer in forested tundra, West Siberia. International Journal of Systematic and Evolutionary Microbiology, 69(4), 1195-1201. https://doi.org/10.1099/ijsem.0.003290 DOI: https://doi.org/10.1099/ijsem.0.003290

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

Patay, É. B., Bencsik, T., & Papp, N. (2016). Phytochemical overview and medicinal importance of Coffea species from the past until now. Asian Pacific Journal of Tropical Medicine, 9(12), 1127-1135. https://doi.org/10.1016/j.apjtm.2016.11.008 DOI: https://doi.org/10.1016/j.apjtm.2016.11.008

Peterson, S. W., Vega, F. E., Posada, F., & Nagai, C. (2005). Penicillium coffeae, a new endophytic species isolated from a coffee plant and its phylogenetic relationship to P. fellutanum, P. thiersii and P. brocae based on parsimony analysis of multilocus DNA sequences. Mycologia, 97(3), 659-666. https://doi.org/10.3852/mycologia.97.3.659 DOI: https://doi.org/10.1080/15572536.2006.11832796

Petters, S., Groß, V., Söllinger, A., Pichler, M., Reinhard, A., Bengtsson, M. M., & Urich, T. (2021). The soil microbial food web revisited: Predatory myxobacteria as keystone taxa? The ISME Journal, 15(9), 2665-2675. https://doi.org/10.1038/s41396-021-00958-2 DOI: https://doi.org/10.1038/s41396-021-00958-2

Pino, A. F. S., Espinosa, Z. Y. D., & Cabrera, E. V. R. (2023). Characterization of the rhizosphere bacterial microbiome and coffee bean fermentation in the Castillo-Tambo and Bourbon varieties in the Popayán-Colombia Plateau. BMC Plant Biology, 23, 217. https://doi.org/10.1186/s12870-023-04182-2

Prashanthi, R., Shreevatsa, G. K., Krupalini, S., & Manoj, L. (2021). Isolation, characterization, and molecular identification of soil bacteria showing antibacterial activity against human pathogenic bacteria. Journal of Genetic Engineering and Biotechnology, 19(1), 120. https://doi.org/10.1186/s43141-021-00219-x DOI: https://doi.org/10.1186/s43141-021-00219-x

Purwaningsih, S., Agustiyani, D., & Antonius, S. (2021). Diversity, activity, and effectiveness of Rhizobium bacteria as plant growth promoting rhizobacteria (PGPR) isolated from Dieng, central Java (Vol. 13, Issue 1). https://doi.org/10.3390/plants10040779 DOI: https://doi.org/10.18502/ijm.v13i1.5504

Rao, M. V., Rice, R. A., Fleischer, R. C., & Muletz-Wolz, C. R. (2020). Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador. PLoS ONE, 15(4), e0231875. https://doi.org/10.1371/journal.pone.0231875 DOI: https://doi.org/10.1371/journal.pone.0231875

Razafinarivo, N. J., Guyot, R., Davis, A. P., Couturon, E., Hamon, S., Crouzillat, D., Rigoreau, M., Dubreuil-Tranchant, C., Poncet, V., De Kochko, A., Rakotomalala, J. J., & Hamon, P. (2013). Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites. Annals of Botany, 111(2), 229-248. https://doi.org/10.1093/aob/mcs283 DOI: https://doi.org/10.1093/aob/mcs283

Renzi, S., Nenciarini, S., & Cavalieri, D. (2023). Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome. Microbiome Research Reports, 3(2). https://doi.org/10.20517/mrr.2023.27 DOI: https://doi.org/10.20517/mrr.2023.27

Richter, D. D., Oh, N.-H., Fimmen, R., & Jackson, J. (2007). The Rhizosphere and Soil Formation. The Rhizosphere (179-200). Elsevier Inc. https://doi.org/10.1016/B978-012088775-0/50010-0 DOI: https://doi.org/10.1016/B978-012088775-0/50010-0

Sah, S., & Singh, R. (2016). Phylogenetical coherence of Pseudomonas in unexplored soils of Himalayan region. 3 Biotech, 6(2), 170. https://doi.org/10.1007/s13205-016-0493-8 DOI: https://doi.org/10.1007/s13205-016-0493-8

Sattler, M. C., de Oliveira, S. C., Mendonça, M. A. C., & Clarindo, W. R. (2022). Coffea cytogenetics: from the first karyotypes to the meeting with genomics. Planta, 255(6), 112.. https://doi.org/10.1007/s00425-022-03898-z DOI: https://doi.org/10.1007/s00425-022-03898-z

Sasan, R. K., & Bidochka, M. J. (2012). The insect‐pathogenic fungus Metarhizium robertsii (Clavicipitaceae) is also an endophyte that stimulates plant root development. American journal of botany, 99(1), 101-107. https://doi.org/10.3732/ajb.1100136 DOI: https://doi.org/10.3732/ajb.1100136

Seipke, R. F., Kaltenpoth, M., & Hutchings, M. I. (2012). Streptomyces as symbionts: an emerging and widespread theme? FEMS Microbiology Reviews, 36(4) 862-876. https://doi.org/10.1111/j.1574-6976.2011.00313.x DOI: https://doi.org/10.1111/j.1574-6976.2011.00313.x

Shah, M. A. (2014). Mycorrhizas: An Overview. In Mycorrhizas: Novel Dimensions in the Changing World (pp. 5-12). https://doi.org/10.1007/978-81-322-1865-4_4 DOI: https://doi.org/10.1007/978-81-322-1865-4_2

Sharma, S., Kumar, S., Khajuria, A., Ohri, P., Kaur, R., & Kaur, R. (2020). Biocontrol potential of chitinases produced by newly isolated Chitinophaga sp. S167. World Journal of Microbiology and Biotechnology, 36(6), 90. https://doi.org/10.1007/s11274-020-02864-9 DOI: https://doi.org/10.1007/s11274-020-02864-9

Shayanthan, A., Ordoñez, P. A. C., & Oresnik, I. J. (2022). The Role of Synthetic Microbial Communities (SynCom) in Sustainable Agriculture. Frontiers in Agronomy, 4, 896307. https://doi.org/10.3389/fagro.2022.896307 DOI: https://doi.org/10.3389/fagro.2022.896307

Silva, E. C., Keren, A., Gusmão Acsa-, H., Guimarães, E. R., & Gonzaga De Castro Junior, L. (2019). Governança privada e sustentabilidade na indústria do café, 25, 48, 35-51. https://www.redalyc.org/journal/1992/199262942003/html/

Silveira, A. P. D., Tristão, F. S. M., Fernandes, A. O., Andrade, S. A. L., & Cipriano, M. A. P. (2023). Arbuscular mycorrhizal fungi inoculation for coffee seedling production with commercial and conventional substrates. Bragantia, 82, e20220161. https://doi.org/10.1590/1678-4499.20220161 DOI: https://doi.org/10.1590/1678-4499.20220161

Singh, A., Kumari, R., Yadav, A. N., Mishra, S., Sachan, A., & Sachan, S. G. (2020). Tiny microbes, big yields: Microorganisms for enhancing food crop production for sustainable development. New and Future Developments in Microbial Biotechnology and Bioengineering, 1-15. Elsevier. https://doi.org/10.1016/B978-0-12-820526-6.00001-4 DOI: https://doi.org/10.1016/B978-0-12-820526-6.00001-4

Solis, A. , Delgado, Z., & Ramos, E. (2023). Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau. BMC Plant Biology, 23, 217. https://doi.org/10.1186/s12870-023-04182-2 DOI: https://doi.org/10.1186/s12870-023-04182-2

Sopiana, E., Tahir, M., & Sudirman, A. (2018). Respons Viabilitas Benih Kopi Arabica (Coffea arabica) terhadap Pelumuran Jamur Trichoderma viride di Pre-nursery. Jurnal Agro Industri Perkebunan, 6(1), 9–18. https://doi.org/10.25181/jaip.v6i1.656 DOI: https://doi.org/10.25181/jaip.v6i1.656

Stopnisek, N., Zuhlke, D., Carlier, A., Barberan, A., Fierer, N., Becher, D., Riedel, K., Eberl, L., & Weisskopf, L. (2016). Molecular mechanisms underlying the close association between soil Burkholderia and fungi. ISME Journal, 10(1), 253-264. https://doi.org/10.1038/ismej.2015.73 DOI: https://doi.org/10.1038/ismej.2015.73

Su, Y., He, Z., Yang, Y., Jia, S., Yu, M., Chen, X., & Shen, A. (2020). Linking soil microbial community dynamics to straw-carbon distribution in soil organic carbon. Scientific Reports, 10, 5526. https://doi.org/10.1038/s41598-020-62198-2 DOI: https://doi.org/10.1038/s41598-020-62198-2

Sugawara, M., Shah, G. R., Sadowsky, M. J., Paliy, O., Speck, J., Vail, A. W., & Gyaneshwar, P. (2011). Expression and Functional Roles of Bradyrhizobium japonicum Genes Involved in the Utilization of Inorganic and Organic Sulfur Compounds in Free-Living and Symbiotic Conditions. / 451 MPMI, 24(4), 451-457. https://doi.org/10.1094/MPMI-08-10-0184 DOI: https://doi.org/10.1094/MPMI-08-10-0184

Suharjono, & Yuliatin, E. (2022). Bacteria communities of coffee plant rhizosphere and their potency as plant growth promoting. Biodiversitas, 23(11), 5822-5834. https://doi.org/10.13057/biodiv/d231136 DOI: https://doi.org/10.13057/biodiv/d231136

Sun, Y., Yan, L., Zhang, A., Yang, J., Zhao, Q., Lin, X., Zhang, Z., Huang, L., Wang, X., & Wang, X. (2024). Effects of grafting on the structure and function of coffee rhizosphere microbiome. Agriculture, 14(10), 1854. https://doi.org/10.3390/agriculture14101854 DOI: https://doi.org/10.3390/agriculture14101854

Sutariati, G. A. K., Rahni, N. M., Madiki, A., Mudi, L., Guyasa, I. M., & Zahrima. (2020). Characterization of endophytic-rhizobacteria from areca nut rhizosphere to dissolve phosphates, nitrogen fixation of IAA hormone synthesis. Pakistan Journal of Biological Sciences, 23(3), 240-247. https://doi.org/10.3923/pjbs.2020.240.247 DOI: https://doi.org/10.3923/pjbs.2020.240.247

Tapaça, I. D. P. E., Obieze, C. C., Pereira, G. V. D. M., Fangueiro, D., Coutinho, J., Fraga, I., Partelli, F. L., Ramalho, J. C., Marques, I., & Ribeiro-Barros, A. I. (2024). Irradiance level and elevation shape the soil microbiome communities of Coffea arabica L. Environmental Microbiome, 19, 75. https://doi.org/10.1186/s40793-024-00619-9 DOI: https://doi.org/10.1186/s40793-024-00619-9

Teshome, B., Wassie, M., & Abatneh, E. (2017). Isolation, screening and biochemical characterization of phosphate-solubilizing rhizobacteria associated with Coffea arabica L. Journal of Fertilizers & Pesticides, 8(3), 188. https://doi.org/10.4172/2471-2728.1000188 DOI: https://doi.org/10.4172/2471-2728.1000188

Tran, D. M. (2022). Rhizosphere microbiome dataset of Robusta coffee (Coffea canephora L.) grown in the Central Highlands, Vietnam, based on 16S rRNA metagenomics analysis. Data in Brief, 42, 108106. https://doi.org/10.1016/j.dib.2022.108106 DOI: https://doi.org/10.1016/j.dib.2022.108106

Vaninsberghe, D., Maas, K. R., Cardenas, E., Strachan, C. R., Hallam, S. J., & Mohn, W. W. (2015). Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils. The ISME Journal, 9(11), 2435-2441. https://doi.org/10.1038/ismej.2015.54 DOI: https://doi.org/10.1038/ismej.2015.54

Veloso, T. G. R., da Silva, M. d. C. S., Moreira, T. R., da Luz, J. M. R., Moreli, A. P., Kasuya, M. C. M., & Pereira, L. L. (2023). Microbiomes associated with Coffea arabica and Coffea canephora in four different floristic domains of Brazil. Scientific Reports, 13, 18477. https://doi.org/10.1038/s41598-023-45465-w DOI: https://doi.org/10.1038/s41598-023-45465-w

Vega, F. E., Posada, F., Peterson, S. W., Gianfagna, T. J., & Chaves, F. (2006). Penicillium species endophytic in coffee plants and ochratoxin A production. Mycologia, 98(1), 31-42. https://doi.org/10.3852/mycologia.98.1.31 DOI: https://doi.org/10.1080/15572536.2006.11832710

Vila, T., Nazir, R., Rozental, S., dos Santos, G. M. P., Calixto, R. O. R., Barreto-Bergter, E., Wick, L. Y., & van Elsas, J. D. (2016). The role of hydrophobicity and surface receptors at hyphae of Lyophyllum sp. Strain Karsten in the interaction with Burkholderia terrae BS001 - Implications for interactions in soil. Frontiers in Microbiology, 7, 1689. https://doi.org/10.3389/fmicb.2016.01689 DOI: https://doi.org/10.3389/fmicb.2016.01689

Villamil, M. B., Kim, N., Riggins, C. W., Zabaloy, M. C., Allegrini, M., & Rodríguez-Zas, S. L. (2021). Microbial Signatures in Fertile Soils Under Long-Term N Management. Frontiers in Soil Science, 1, 765901. https://doi.org/10.3389/fsoil.2021.765901 DOI: https://doi.org/10.3389/fsoil.2021.765901

Walsh, C. M., Gebert, M. J., Delgado-Baquerizo, M., Maestre, F. T., & Fierer, N. (2019). A global survey of mycobacterial diversity in soil. Applied and Environmental Microbiology, 85, e01180-19. https://doi.org/10.1128/AEM.01180-19 DOI: https://doi.org/10.1128/AEM.01180-19

Wang, M., Xue, J., Ma, J., Feng, X., Ying, H., & Xu, H. (2020). Streptomyces lydicus M01 Regulates Soil Microbial Community and Alleviates Foliar Disease Caused by Alternaria alternata on Cucumbers. Frontiers in Microbiology, 11, 942. https://doi.org/10.3389/fmicb.2020.00942 DOI: https://doi.org/10.3389/fmicb.2020.00942

Wang, R., An, X., Lv, Y., Asad Ali Khan, R., Xue, M., Chen, J., & Liu, T. (2023). Trichoderma asperellum GD040 upregulates defense-related genes and reduces lesion size in Coffea canephora leaves inoculated with Colletotrichum cairnsense. Biological Control, 181, 105213. https://doi.org/10.1016/j.biocontrol.2023.105213 DOI: https://doi.org/10.1016/j.biocontrol.2023.105213

Weon, H. Y., Anandham, R., Kim, B. Y., Hong, S. B., Jeon, Y. A., & Kwon, S. W. (2009). Dyella soli sp. Nov. And Dyella terrae sp. Nov., isolated from soil. International Journal of Systematic and Evolutionary Microbiology, 59(7), 1685-1690. https://doi.org/10.1099/ijs.0.004838-0 DOI: https://doi.org/10.1099/ijs.0.004838-0

Weon, H. Y., Kim, B. Y., Yoo, S. H., Lee, S. Y., Kwon, S. W., Go, S. J., & Stackebrandt, E. (2006). Niastella koreensis gen. Nov., sp. Nov. and Niastella yeongjuensis sp. Nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng. International Journal of Systematic and Evolutionary Microbiology, 56(8), 1777-1782. https://doi.org/10.1099/ijs.0.64242-0 DOI: https://doi.org/10.1099/ijs.0.64242-0

Wu, Y., Zhao, X., Wang, Z., Li, X., Zhang, X., Xie, C., Du, H., Jiang, K., Qu, P., & Zhang, C. (2025). The role of coffee microbiomes in pathogen resistance across varieties and ecological niches. Microorganisms, 13(8), 1909. https://doi.org/10.3390/microorganisms13081909 DOI: https://doi.org/10.3390/microorganisms13081909

Xin, X., Liu, S., Qin, J., Ye, Z., Liu, W., Fang, S., & Yang, J. (2021). Performances of simultaneous enhanced removal of nitrogen and phosphorus via biological aerated filter with biochar as fillers under low dissolved oxygen for digested swine wastewater treatment. Bioprocess and Biosystems Engineering, 44, 1741-1753. https://doi.org/10.1007/s00449-021-02557-z DOI: https://doi.org/10.1007/s00449-021-02557-z

Yabe, S., Sakai, Y., & Yokota, A. (2016). Thermosporothrix narukonensis sp. Nov., belonging to the class Ktedonobacteria, isolated from fallen leaves on geothermal soil, and emended description of the genus Thermosporothrix. International Journal of Systematic and Evolutionary Microbiology, 66(6), 2152-2157. https://doi.org/10.1099/ijsem.0.001004 DOI: https://doi.org/10.1099/ijsem.0.001004

Yoon, J.-H., & Park, Y.-H. (2006). The Genus Nocardioides. In The Prokaryotes (1099-1113). https://doi.org/10.1007/0-387-30743-5_44 DOI: https://doi.org/10.1007/0-387-30743-5_44

Yusuf, M., Fernandes, A. A. R., Kurniawan, S., & Arisoesilaningsih, E. (2021). Spatial variation of soil bacteria communities and its alpha diversity as a potential bioindicator of land degradation. Journal of Degraded and Mining Lands Management, 8(4), 2847-2860. https://doi.org/10.15243/jdmlm.2021.084.2847 DOI: https://doi.org/10.15243/jdmlm.2021.084.2847

Zhang, H., Zhang, H., Qin, X., Wang, X., Wang, Y., Bin, Y., Xie, X., Zheng, F., & Luo, H. (2021). Biodegradation of Deoxynivalenol by Nocardioides sp. ZHH-013: 3-keto-Deoxynivalenol and 3-epi-Deoxynivalenol as Intermediate Products. Frontiers in Microbiology, 12, 658421. https://doi.org/10.3389/fmicb.2021.658421 DOI: https://doi.org/10.3389/fmicb.2021.658421

Zhang, J., Wang, N., Li, S., Wang, J., Feng, Y., Wang, E., Li, Y., Yang, T., & Chen, W. (2023a). The Effect of Different Rhizobial Symbionts on the Composition and Diversity of Rhizosphere Microorganisms of Chickpea in Different Soils. Plants, 12(19), 3421. https://doi.org/10.3390/plants12193421 DOI: https://doi.org/10.3390/plants12193421

Zhang, M., Liang, G., Ren, S., Li, L., Li, C., Li, Y., Yu, X., Yin, Y., Liu, T., & Liu, X. (2023b). Responses of soil microbial community structure, potential ecological functions, and soil physicochemical properties to different cultivation patterns in cucumber. Geoderma, 429, 116237. https://doi.org/10.1016/j.geoderma.2022.116237 DOI: https://doi.org/10.1016/j.geoderma.2022.116237

Zhao, Q., Xiong, W., Xing, Y., Sun, Y., Lin, X., & Dong, Y. (2018). Long-Term Coffee Monoculture Alters Soil Chemical Properties and Microbial Communities. Scientific Reports, 8, 6116. https://doi.org/10.1038/s41598-018-24537-2 DOI: https://doi.org/10.1038/s41598-018-24537-2

Zhao, S., Zhang, A., Zhao, Q., Dong, Y., Su, L., Sun, Y., Zhu, F., Hua, D., & Xiong, W. (2023). The impact of main Areca catechu root exudates on soil microbial community structure and function in coffee plantation soils. Frontiers in Microbiology, 14, 1257164. https://doi.org/10.3389/fmicb.2023.1257164 DOI: https://doi.org/10.3389/fmicb.2023.1257164

Zhao, Y., Yao, Y., Xu, H., Xie, Z., Guo, J., Qi, Z., & Jiang, H. (2022). Soil metabolomics and bacterial functional traits revealed the responses of rhizosphere soil bacterial community to long-term continuous cropping of Tibetan barley. Peerj, 10, e13254. https://doi.org/10.7717/peerj.13254 DOI: https://doi.org/10.7717/peerj.13254

Zhou, L., Li, H., Zhang, Y., Han, S., & Xu, H. (2016). Sphingomonas from petroleum-contaminated soils in Shenfu, China and their PAHs degradation abilities. Brazilian Journal of Microbiology, 47(2), 271-278. https://doi.org/10.1016/j.bjm.2016.01.001 DOI: https://doi.org/10.1016/j.bjm.2016.01.001

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Portillo, D., Hurtado Clopatosky, S., & Abril Herrera, D. A. (2026). Microorganisms associated with the rhizosphere of coffee plants: diversity, roles and perspectives for sustainable agriculture. Revista De Investigación Agraria Y Ambiental, 17(2), 77-119. https://doi.org/10.22490/21456453.9953

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