Articles | Volume 12, issue 2
https://doi.org/10.5194/soil-12-999-2026
© Author(s) 2026. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/soil-12-999-2026
© Author(s) 2026. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Original research article
| 
19 Oct 2026
Original research article |
| 19 Oct 2026
| 19 Oct 2026
Fertilizer regimes reshape microbial interaction networks without altering sugarcane rhizosphere diversity
Leonardo Zamora-Leiva
Laboratory of Metagenomics, Bionostra Chile Research Foundation, San Miguel, Santiago, Chile
Jorge Soto
Laboratory of Metagenomics, Bionostra Chile Research Foundation, San Miguel, Santiago, Chile
Ignacio Ramos-Tapia
Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 330, Santiago, Chile
Laboratory of Bioenergy and Environmental Biotechnology, Department of Environmental Sciences and Natural Resources, Faculty of Agricultural Sciences, University of Chile, La Pintana, Santiago, Chile
Cited articles
Abarenkov, K., Nilsson, R. H., Larsson, K. H., Taylor, A. F. S., May, T. W., Frøslev, T. G., Pawlowska, J., Lindahl, B., Põldmaa, K., Truong, C., Vu, D., Hosoya, T., Niskanen, T., Piirmann, T., Ivanov, F., Zirk, A., Peterson, M., Cheeke, T. E., Ishigami, Y., Jansson, A. T., Jeppesen, T. S., Kristiansson, E., Mikryukov, V., Miller, J. T., Oono, R., Ossandon, F. J., Paupério, J., Saar, I., Schigel, D., Suija, A., Tedersoo, L., and Kõljalg, U.: The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: Sequences, taxa and classifications reconsidered, Nucleic Acids Res., 52, D791–D797, https://doi.org/10.1093/nar/gkad1039, 2024.
Akter, S., Mahmud, U., Shoumik, B. A. A., and Khan, M. Z.: Although invisible, fungi are recognized as the engines of a microbial powerhouse that drives soil ecosystem services, Arch. Microbiol., 207, 79, https://doi.org/10.1007/s00203-025-04285-4, 2025.
Andam, C. P., Doroghazi, J. R., Campbell, A. N., Kelly, P. J., Choudoir, M. J., and Buckley, D. H.: A latitudinal diversity gradient in terrestrial bacteria of the genus Streptomyces, mBio, 7, e02200-15, https://doi.org/10.1128/mbio.02200-15, 2016.
Andrews, S.: FastQC: A quality control tool for high-throughput sequence data, Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (last access: September 2024), 2010.
Antoszewski, M., Mierek-Adamska, A., and Dąbrowska, G. B.: The importance of microorganisms for sustainable agriculture: A review, Metabolites, 12, 1100, https://doi.org/10.3390/metabo12111100, 2022.
Bastian, M., Heymann, S., and Jacomy, M.: Gephi: An open source software for exploring and manipulating networks, Proc. Int. AAAI Conf. Web Soc. Media, 3, 361–362, https://doi.org/10.1609/icwsm.v3i1.13937, 2009.
Berger, A., Gatt Harari, M., Gross, A., and Erez, A.: Diversity loss in microbial ecosystems undergoing gradual environmental changes, Cell Rep. Sustain., 1, 100242, https://doi.org/10.1016/j.crsus.2024.100242, 2024.
Callahan, B. J., McMurdie, P. J., and Holmes, S. P.: Exact sequence variants should replace operational taxonomic units in marker-gene data analysis, ISME J., 11, 2639–2643, https://doi.org/10.1038/ismej.2017.119, 2017.
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., and Holmes, S. P.: DADA2: High-resolution sample inference from Illumina amplicon data, Nat. Methods, 13, 581–583, https://doi.org/10.1038/nmeth.3869, 2016.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J. E., Ley, R. E., Lozupone, C. A., McDonald, D., Muegge, B. D., Pirrung, M., Reeder, J., Sevinsky, J. R., Turnbaugh, P. J., Walters, W. A., Widmann, J., Yatsunenko, T., Zaneveld, J., and Knight, R.: QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335–336, https://doi.org/10.1038/nmeth.f.303, 2010.
Centella, A., Lapinel, B., Solano, O., Vázquez, R., Fonseca, C., Cutié, V., Baéz, R., González, S., Sille, J., Rosario, P., and Duarte, L.: La sequía meteorológica y agrícola en la República de Cuba y la República Dominicana [Meteorological and agricultural drought in the Republic of Cuba and the Dominican Republic], Proyecto PNUD/ACDI Desarrollo y Adaptación al Cambio Climático, 172 pp., https://www.undp.org/es/cuba/publicaciones/la-sequia-meteorologica-y-agricola-tomos-i-y-ii (last access: September 2024), 2007.
Chen, S., Gao, J., Chen, H., Zhang, Z., Huang, J., Lv, L., Tan, J., and Jiang, X.: The role of long-term mineral and manure fertilization on P species accumulation and phosphate-solubilizing microorganisms in paddy red soils, SOIL, 9, 101–116, https://doi.org/10.5194/soil-9-101-2023, 2023.
Cheng, C., Li, G., Yang, X., Zhao, J., Liu, J., Zheng, A., and Zhang, Z.: High diversity, close genetic relatedness, and favorable living conditions benefit species co-occurrence of gut microbiota in Brandt's vole, Front. Microbiol., 15, 1337402, https://doi.org/10.3389/fmicb.2024.1337402, 2024.
Cherubin, M. R., Oliveira, D. M. S., Feigl, B. J., Pimentel, L. G., Lisboa, I. P., Gmach, M. R., Varanda, L. L., Morais, M. C., Satiro, L. S., Popin, G. V., Paiva, S. R., Klebson, A. K. B., Vasconcelos, A. L. S., Melo, P. L. A., Cerri, C. E. P., Cerri, C. C., Cerri, E. P., and Cerri, C. C.: Crop residue harvest for bioenergy production and its implications on soil functioning and plant growth: A review, Sci. Agric., 75, 255–272, https://doi.org/10.1590/1678-992x-2016-0459, 2018.
Cherubin, M. R., Lisboa, I. P., Silva, A. G. B., Varanda, L. L., Bordonal, R. O., Carvalho, J. L. N., Otto, R., Pavinato, P. S., Soltangheisi, A., and Cerri, C. E. P.: Sugarcane Straw Removal: Implications to Soil Fertility and Fertilizer Demand in Brazil, Sugar, 12, 888–900, https://doi.org/10.1007/s12155-019-10021-w, 2019.
Datta, R., Kelkar, A., Baraniya, D., Molaei, A., Moulick, A., Meena, R. S., and Formanek, P.: Enzymatic degradation of lignin in soil: A review, Sustainability, 9, 1163, https://doi.org/10.3390/su9071163, 2017.
de Castro, S. G. Q., Magalhães, P. S. G., de Castro, S. A. Q., Kölln, O. T., and Franco, H. C. J.: Optimizing nitrogen fertilizer rates at distinct in-season application moments in sugarcane, Int. J. Plant Prod., 16, 137–152, https://doi.org/10.1007/s42106-021-00175-z, 2022.
Dinesh Babu, K. S., Janakiraman, V., Palaniswamy, H., Kasirajan, L., Gomathi, R., and Ramkumar, T. R.: A short review on sugarcane: Its domestication, molecular manipulations and future perspectives, Genet. Resour. Crop Evol., 69, 2623–2643, https://doi.org/10.1007/s10722-022-01430-6, 2022.
Du, J., Gao, Q., Sun, F., Liu, B., Jiao, Y., and Liu, Q.: Agricultural soil microbiomes at the climate frontier: Nutrient-mediated adaptation strategies for sustainable farming, Ecotoxicol. Environ. Saf., 295, 118161, https://doi.org/10.1016/j.ecoenv.2025.118161, 2025.
Durán, I.: Comportamiento de la precipitación en estaciones meteorológicas seleccionadas de Cuba [Precipitation behavior at selected meteorological stations in Cuba], Ph.D. Thesis, Universidad de La Habana, https://www.researchgate.net/publication/322235859_Comportamiento_de_la_Precipitacion_en_Estaciones_Meteorologicas_Seleccionadas_de_Cuba (last access: September 2024), 2012.
FAO [Food and Agriculture Organization of the United Nations]: Fertilizer use by crop in Cuba, Land and Plant Nutrition Management Service and Land and Water Development Division, FAO, Rome, 39 pp., https://openknowledge.fao.org/handle/20.500.14283/y4801e (last access: September 2024), 2003.
FAO [Food and Agriculture Organization of the United Nations]: Sugar cane production, Our World in Data, https://archive.ourworldindata.org/20251014-161652/grapher/sugar-cane-production.html (last access: September 2024), 2025.
Fabian, J., Zlatanovic, S., Mutz, M., and Premke, K.: Fungal–bacterial dynamics and their contribution to terrigenous carbon turnover in relation to organic matter quality, ISME J., 11, 415–425, https://doi.org/10.1038/ismej.2016.131, 2017.
Filippidou, S., Wunderlin, T., Junier, T., Jeanneret, N., Dorador, C., Molina, V., Johnson, D. R., and Junier, P.: A combination of extreme environmental conditions favor the prevalence of endospore-forming Firmicutes, Front. Microbiol., 7, 1707, https://doi.org/10.3389/fmicb.2016.01707, 2016.
Freilich, S., Zarecki, R., Eilam, O., Segal, E. S., Henry, C. S., Kupiec, M., Gophna, U., Sharan, R., and Ruppin, E.: Competitive and cooperative metabolic interactions in bacterial communities, Nat. Commun., 2, 589, https://doi.org/10.1038/ncomms1597, 2011.
Gao, C., Xu, L., Montoya, L., Madera, M., Hollingsworth, J., Chen, L., Purdom, E., Singan, V., Vogel, J., Hutmacher, R. B., Dahlberg, J. A., Coleman-Derr, D., Lemaux, P. G., and Taylor, J. W.: Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities, Nat. Commun., 13, 3867, https://doi.org/10.1038/s41467-022-31343-y, 2022.
Gao, C., Bezemer, T. M., de Vries, F. T., and van Bodegom, P. M.: Trade-offs in soil microbial functions and soil health in agroecosystems, Trends Ecol. Evol., 39, 895–903, https://doi.org/10.1016/j.tree.2024.05.013, 2024.
Gonçalves, O. S., Fernandes, A. S., Tupy, S. M., Ferreira, T. G., Almeida, L. N., Creevey, C. J., and Santana, M. F.: Insights into plant interactions and the biogeochemical role of the globally widespread Acidobacteriota phylum, Soil Biol. Biochem., 192, 109369, https://doi.org/10.1016/j.soilbio.2024.109369, 2024.
Guo, J. and Chen, J.: The impact of heavy rainfall variability on fertilizer application rates: Evidence from maize farmers in China, Int. J. Environ. Res. Publ. Hth., 19, 15906, https://doi.org/10.3390/ijerph192315906, 2022.
Guo, Z., Wan, S., Hua, K., Yin, Y., Chu, H., Wang, D., and Guo, X.: Fertilization regime has a greater effect on soil microbial community structure than crop rotation and growth stage in an agroecosystem, Appl. Soil Ecol., 149, 103510, https://doi.org/10.1016/j.apsoil.2020.103510, 2020.
Hakim, F. K., Sofyan, E. T., Sudirja, R., Joy, B., Yuniarti, A., and Herdiyantoro, D.: The application of slow release NPK fertilizer on inceptisols to changes of soil chemical properties and growth of sweet corn (Zea mays L. saccharata), Int. J. Environ., Agric. Biotechnol., 7, 18–24, https://doi.org/10.22161/ijeab.73.3, 2022.
Hernández, A., Pérez, J., Bosch, D., and Castro, N.: Clasificación de los suelos de Cuba 2015 [Classification of Cuban soils 2015], Mayabeque, Cuba, Ediciones INCA, 93 pp., SBN 978-959-7023-77-7, 2015.
Hernández-Jiménez, A., Pérez-Jiménez, J., Bosch-Infante, D., and Castro, N.: La clasificación de suelos de Cuba: Énfasis en la versión de 2015 [The soil classification of Cuba: emphasis in the 2015 version], Cult. Trop., 40, 31, ISSN 0258-5936, 2019.
Hou, Z., Lv, G., and Jiang, L.: Functional diversity can predict ecosystem functions better than dominant species: The case of desert plants in the Ebinur Lake Basin, Sustainability, 13, 2858, https://doi.org/10.3390/su13052858, 2021.
Huang, R., Li, W., Qiu, S., Long, Y., Zeng, Z., Tang, J., and Huang, Q.: Impact of land use types on soil microbial community structure and functional structure in Baihualing Village, China, Glob. Ecol. Conserv., 57, e03379, https://doi.org/10.1016/j.gecco.2024.e03379, 2025.
INICA [Instituto Nacional de Investigaciones de la Caña de Azúcar]: Normas metodológicas del departamento de suelos y agroquímica [Methodological standards of the Department of Soils and Agrochemistry], INICA-MINAZ, Tomo 1, La Habana, Cuba, 100 pp., 1990.
Jiménez-Venegas, J., Zamora-Leiva, L., Univaso, L., Soto, J., Tapia, Y., and Paneque, M.: Profile of Bacterial Communities in Copper Mine Tailings Revealed through High-Throughput Sequencing, Microorganisms, 12, 1820, https://doi.org/10.3390/microorganisms12091820, 2024.
Jiménez-Venegas, J., Zamora-Leiva, L., Román-Figueroa, C., Tapia, Y., and Paneque, M.: Metals and Extremophilic Bacteria in Mining Environments: A Systematic Review, Microorganisms, 14, 1312, https://doi.org/10.3390/microorganisms14061312, 2026.
Katoh, K. and Standley, D. M.: MAFFT multiple sequence alignment software version 7: Improvements in performance and usability, Mol. Biol. Evol., 30, 772–780, https://doi.org/10.1093/molbev/mst010, 2013.
Kaur, S., Bedi, M., Singh, S., Kour, N., Bhatti, S. S., Bhatia, A., Kumar, M., and Kumar, R.: Monoculture of crops: A challenge in attaining food security, in: Environmental Challenges in Attaining Food Security, Advances in Food Security and Sustainability, 9, edited by: Sharma, A., Kumar, M., and Sharma, P., Elsevier, 197–213, https://doi.org/10.1016/bs.af2s.2024.07.008, 2024.
Khan, A., Wei, Y., Adnan, M., Ali, I., and Zhang, M.: Dynamics of rhizosphere bacterial communities and soil physiochemical properties in response to consecutive ratooning of sugarcane, Front. Microbiol., 14, 1197246, https://doi.org/10.3389/fmicb.2023.1197246, 2023.
Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., and Glöckner, F. O.: Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies, Nucleic Acids Res., 41, e1–e1, https://doi.org/10.1093/nar/gks808, 2013.
Kostin, J. E., Cesarz, S., Lochner, A., Schädler, M., Macdonald, C. A., and Eisenhauer, N.: Land-use drives the temporal stability and magnitude of soil microbial functions and modulates climate effects, Ecol. Appl., 31, e02325, https://doi.org/10.1002/eap.2325, 2021.
Kracmarova, M., Uhlik, O., Strejcek, M., Szakova, J., Cerny, J., Balik, J., Tlustos, P., Kohout, P., Demnerova, K., and Stiborova, H.: Soil microbial communities following 20 years of fertilization and crop rotation practices in the Czech Republic, Environ. Microbiome, 17, 13, https://doi.org/10.1186/s40793-022-00406-4, 2022.
Kumar, V., Raghuvanshi, N., Pandey, A. K., Kumar, A., Thoday-Kennedy, E., and Kant, S.: Role of halotolerant plant growth-promoting rhizobacteria in mitigating salinity stress: Recent advances and possibilities, Agriculture, 13, 168, https://doi.org/10.3390/agriculture13010168, 2023.
Lahlali, R., Ibrahim, D. S. S., Belabess, Z., Kadir Roni, M. Z., Radouane, N., Vicente, C. S. L., Menéndez, E., Mokrini, F., Barka, E. A., Galvão de Melo E Mota, M., and Peng, G.: High-throughput molecular technologies for unraveling the mystery of soil microbial community: Challenges and future prospects, Heliyon, 7, e08142, https://doi.org/10.1016/j.heliyon.2021.e08142, 2021.
Li, J., Yuan, X., Ge, L., Li, Q., Li, Z., Wang, L., and Liu, Y.: Rhizosphere effects promote soil aggregate stability and associated organic carbon sequestration in rocky areas of desertification, Agric., Ecosyst. Environ., 304, 107126, https://doi.org/10.1016/j.agee.2020.107126, 2020.
Liao, H., Zhang, Y., Wang, K., Hao, X., Chen, W., and Huang, Q.: Complexity of bacterial and fungal network increases with soil aggregate size in an agricultural inceptisol, Appl. Soil Ecol., 154, 103640, https://doi.org/10.1016/j.apsoil.2020.103640, 2020.
Liu, C., Cui, Y., Li, X., and Yao, M.: Microeco: An R package for data mining in microbial community ecology, FEMS Microbiol. Ecol., 97, fiaa255, https://doi.org/10.1093/femsec/fiaa255, 2021a.
Liu, Q., Zhao, X., Liu, Y., Xie, S., Xing, Y., Dao, J., Wei, B., Peng, Y., Duan, W., and Wang, Z.: Response of sugarcane rhizosphere bacterial community to drought stress, Front. Microbiol., 12, 716196, https://doi.org/10.3389/fmicb.2021.716196, 2021b.
Liu, Y., Liang, D., Xing, J., Xue, Z., and Zhang, Z.: Interactions between sugarcane leaf return and fertilizer reduction in soil bacterial network in Southern China red soil, Microorganisms, 12, 1788, https://doi.org/10.3390/microorganisms12091788, 2024.
Looney, S. W. and Hagan, J. L.: Statistical methods for assessing biomarkers and analyzing biomarker data, in: Handbook of Statistics, 27, edited by: Rao, C. R., Miller, J. P., and Rao, D. C., Elsevier, 27–65, https://doi.org/10.1016/B978-0-444-53737-9.50005-0, 2011.
Lori, M., Hartmann, M., Kundel, D., Mayer, J., Mueller, R. C., Mäder, P., and Krause, H. M.: Soil microbial communities are sensitive to differences in fertilization intensity in organic and conventional farming systems, FEMS Microbiol. Ecol., 99, fiad046, https://doi.org/10.1093/femsec/fiad046, 2023.
Luo, J., Liao, G., Banerjee, S., Gu, S., Liang, J., Guo, X., Zhao, H., Liang, Y., and Li, T.: Long-term organic fertilization promotes the resilience of soil multifunctionality driven by bacterial communities, Soil Biol. Biochem., 177, 108922, https://doi.org/10.1016/j.soilbio.2022.108922, 2023.
Martiny, J. B. H.: History leaves its mark on soil bacterial diversity, mBio, 7, e00784-16, https://doi.org/10.1128/mBio.00784-16, 2016.
Matazimov, M. T., Sidametova, Z. E., Olimov, N. K., Abdullaeva, M. U., Rakhimova, D. O., Rustamov, I. X., and Umurzakova, N. S.: Ecological roles of fungal networks: Integrating nutrient cycling, soil health, and climate resilience – A systematic review, Microb. Bioact., 8, 1–8, https://doi.org/10.25163/microbbioacts.8110420, 2025.
McDonald, M. D., Lewis, K. L., Blazier, J. C., and Gentry, T. J.: Semi-arid soil bacterial communities are refined by altered plant selection pressure under conservation management practices, Appl. Soil Ecol., 194, 105191, https://doi.org/10.1016/j.apsoil.2023.105191, 2024.
Meena, S. K., Dwivedi, B. S., Meena, M. C., Datta, S. P., Singh, V. K., Mishra, R. P., Chakraborty, D., Dey, A., and Meena, V. S.: Impact of long-term nutrient supply options on soil aggregate stability after nineteen years of rice–wheat cropping system, Land, 11, 1465, https://doi.org/10.3390/land11091465, 2022.
Mitter, E. K., Tosi, M., Obregón, D., Dunfield, K. E., and Germida, J. J.: Rethinking crop nutrition in times of modern microbiology: Innovative biofertilizer technologies, Front. Sustain. Food Syst., 5, 606815, https://doi.org/10.3389/fsufs.2021.606815, 2021.
Moneda, A. P. C., de Carvalho, L. A. L., Teheran-Sierra, L. G., Funnicelli, M. I. G., and Pinheiro, D. G.: Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure, Sci. Rep., 12, 19174, https://doi.org/10.1038/s41598-022-23562-6, 2022.
Mu, P., Ding, G., Zhang, Y., Jin, Q., Liu, Z., Guan, Y., Zhang, L., Liang, C., Zhou, F., and Liu, N.: Interactions between arbuscular mycorrhizal fungi and phosphate-soluble bacteria affect ginsenoside compositions by modulating the C:N:P stoichiometry in Panax ginseng, Front. Microbiol., 15, 1426440, https://doi.org/10.3389/fmicb.2024.1426440, 2024.
Naylor, D., Sadler, N., Bhattacharjee, A., Graham, E. B., Anderton, C. R., McClure, R., Lipton, M., Hofmockel, K. S., and Jansson, J. K.: Soil microbiomes under climate change and implications for carbon cycling, Annu. Rev. Environ. Resour., 45, 29–59, https://doi.org/10.1146/annurev-environ-012320-082720, 2020.
Niu, Z., An, F., Su, Y., Liu, T., Yang, R., Du, Z., and Chen, S.: Effect of long-term fertilization on aggregate size distribution and nutrient accumulation in aeolian sandy soil, Plants, 11, 909, https://doi.org/10.3390/plants11070909, 2022.
Núñez Salazar, R., Aguirre, C., Soto, J., Salinas, P., Salinas, C., Prieto, H., and Paneque, M.: Physicochemical parameters affecting the distribution and diversity of the water column microbial community in the high-altitude Andean lake system of la Brava and la Punta, Microorganisms, 8, 1181, https://doi.org/10.3390/microorganisms8081181, 2020.
Oishy, M. N., Shemonty, N. A., Fatema, S. I., Mahbub, S., Mim, E. L., Hasan Raisa, M. B., and Anik, A. H.: Unravelling the effects of climate change on the soil-plant-atmosphere interactions: A critical review, Soil Environ. Health, 3, 100130, https://doi.org/10.1016/j.seh.2025.100130, 2025.
Orgiazzi, A., Lumini, E., Nilsson, R. H., Girlanda, M., Vizzini, A., Bonfante, P., and Bianciotto, V.: Unravelling soil fungal communities from different Mediterranean land-use backgrounds, PLoS One, 7, e34847, https://doi.org/10.1371/journal.pone.0034847, 2012.
Orrù, L., Canfora, L., Trinchera, A., Migliore, M., Pennelli, B., Marcucci, A., Farina, R., and Pinzari, F.: How tillage and crop rotation change the distribution pattern of fungi, Front. Microbiol., 12, 634325, https://doi.org/10.3389/fmicb.2021.634325, 2021.
Otto, R., Ferraz-Almeida, R., Sanches, G. M., Lisboa, I. P., and Cherubin, M. R.: Nitrogen fertilizer consumption and nitrous oxide emissions associated with ethanol production – A national-scale comparison between Brazilian sugarcane and corn in the United States, J. Clean. Prod., 350, 131482, https://doi.org/10.1016/j.jclepro.2022.131482, 2022.
Pan, Y., Cassman, N., de Hollander, M., Mendes, L. W., Korevaar, H., Geerts, R. H. E. M., van Veen, J. A., and Kuramae, E. E.: Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil, FEMS Microbiol. Ecol., 90, 195–205, https://doi.org/10.1111/1574-6941.12384, 2014.
Peng, Z., Qian, X., Liu, Y., Li, X., Gao, H., An, Y., Qi, J., Jiang, L., Zhang, Y., Chen, S., Pan, H., Chen, B., Liang, C., van der Heijden, M. G. A., Wei, G., and Jiao, S.: Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally, Nat. Commun., 15, 3624, https://doi.org/10.1038/s41467-024-47348-8, 2024.
Philippot, L., Griffiths, B. S., and Langenheder, S.: Microbial community resilience across ecosystems and multiple disturbances, Microbiol. Mol. Biol. Rev., 85, e00026-20, https://doi.org/10.1128/mmbr.00026-20, 2021.
Price, M. N., Dehal, P. S., and Arkin, A. P.: FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix, Mol. Biol. Evol., 26, 1641–1650, https://doi.org/10.1093/molbev/msp077, 2009.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., and Glöckner, F. O.: The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools, Nucleic Acids Res., 41, D590–D596, https://doi.org/10.1093/nar/gks1219, 2013.
Ramos-Tapia, I., Nuñez, R., Salinas, C., Salinas, P., Soto, J., and Paneque, M.: Study of wetland soils of the Salar de Atacama with different azonal vegetative formations reveals changes in the microbiota associated with hygrophile plant type on the soil surface, Microbiol. Spectr., 10, e0053322, https://doi.org/10.1128/spectrum.00533-22, 2022.
Ramos-Tapia, I., Salinas, P., Nuñez, R., Cortez, D., Soto, J., and Paneque, M.: Compositional changes in sediment microbiota are associated with seasonal variation of the water column in high-altitude hyperarid Andean lake systems, Microbiol. Spectr., 11, e0520022, https://doi.org/10.1128/spectrum.05200-22, 2023.
Rashid, H., Sun, X., Wu, F., and Ni, X.: Nutrient leaching after subtropical forest conversions and its implications for soil fertility, Forest Ecol. Manage., 566, 122044, https://doi.org/10.1016/j.foreco.2024.122044, 2024.
R Core Team: R: A Language and Environment for Statistical Computing (Version 4.3.2), R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/ (last access: September 2024), 2023.
Ritchie, H., Rosado, P., and Roser, M.: Agricultural production, Our World in Data, https://ourworldindata.org/agricultural-production (last access: September 2024), 2023.
Robeson, M. S., O'Rourke, D. R., Kaehler, B. D., Ziemski, M., Dillon, M. R., Foster, J. T., and Bokulich, N. A.: RESCRIPt: Reproducible sequence taxonomy reference database management, PLoS Comput. Biol., 17, e1009581, https://doi.org/10.1371/journal.pcbi.1009581, 2021.
Sanchez, P. A.: Soils of the tropics, in: Properties and management of soils in the tropics, Cambridge University Press, 82–119, https://doi.org/10.1017/9781316809785.006, 2019.
Semenov, M. V., Krasnov, G. S., Semenov, V. M., and van Bruggen, A.: Mineral and organic fertilizers distinctly affect fungal communities in the crop rhizosphere, J. Fungi, 8, 251, https://doi.org/10.3390/jof8030251, 2022.
Shaw, G. T.-W., Liu, A.-C., Weng, C.-Y., Chen, Y.-C., Chen, C.-Y., Weng, F. C.-H., Wang, D., and Chou, C.-Y.: A network-based approach to deciphering a dynamic microbiome's response to a subtle perturbation, Sci. Rep., 10, 19530, https://doi.org/10.1038/s41598-020-73920-5, 2020.
Sieiro, G. L. and Pablos, P.: Índice de calidad para un suelo Pardo Sialítico monocultivado con Saccharum officinarum L. [Quality index for a Sialitic Brown soil monocultured with Saccharum officinarum L.], Rev. Agric. Trop., 7, 1–11, 2021.
Singavarapu, B., Du, J., Beugnon, R., Cesarz, S., Eisenhauer, N., Xue, K., Wang, Y., Bruelheide, H., and Wubet, T.: Functional potential of soil microbial communities and their subcommunities varies with tree mycorrhizal type and tree diversity, Microbiol. Spectr., 11, e0457822, https://doi.org/10.1128/spectrum.04578-22, 2023.
Skidmore, M., Andarge, T., and Foltz, J.: The impact of extreme precipitation on nutrient runoff, J. Agric. Appl. Econ. Assoc., 2, 769–785, https://doi.org/10.1002/jaa2.90, 2023.
Sofyan, E. T., Yuniarti, A., and Alparidzy, M.: Effect of liquid and single compound NPK fertilizer on soil and plant nitrogen content and yield of sweet corn (Zea mays L. saccharata) in inceptisols of Jatinangor, Asian J. Soil Sci. Plant Nutr., 10, 407–414, https://doi.org/10.9734/ajsspn/2024/v10i3352, 2024.
Soil Survey Staff [United States Department of Agriculture]: Illustrated guide to soil taxonomy, version 2, U.S. Department of Agriculture, Natural Resources Conservation Service, National Soil Survey Center, Lincoln, Nebraska, https://www.nrcs.usda.gov/sites/default/files/2022-06/Illustrated_Guide_to_Soil_Taxonomy.pdf (last access: September 2024), 2015.
Souza, V. S., Canisares, L. P., Schiebelbein, B. E., de Castro Santos, D., Menillo, R. B., Pinheiro Junior, C. R., and Cherubin, M. R.: Cover crops enhance soil health, crop yield and resilience of tropical agroecosystem, Field Crops Res., 322, 109755, https://doi.org/10.1016/j.fcr.2025.109755, 2025.
Stover, H. J. and Henry, H. A. L.: Soil homogenization and microedges: Perspectives on soil-based drivers of plant diversity and ecosystem processes, Ecosphere, 9, 6, https://doi.org/10.1002/ecs2.2289, 2018.
Sui, B., Wang, L., Wang, H., Zhao, X., Jin, F., Wang, H., Guo, J., and Xu, Q.: Deep tillage inhibits microbial species interactions and exhibits contrasting roles in bacterial and fungal assembly, Agric. Ecosyst. Environ., 357, 108679, https://doi.org/10.1016/j.agee.2023.108679, 2023.
Suman, J., Rakshit, A., Ogireddy, S. D., Singh, S., Gupta, C., and Chandrakala, J.: Microbiome as a key player in sustainable agriculture and human health, Front. Soil Sci., 2, 1–13, https://doi.org/10.3389/fsoil.2022.821589, 2022.
Syamsiyah, J., Sumarno, S., Suryono, S., Sari, W., and Anwar, M.: Chemical properties of inceptisol and rice yields applied with mixed source fertilizer (MSF), J. Trop. Soils, 23, 1–9, https://doi.org/10.5400/jts.2018.v23i1.1-9, 2018.
Tamayo-Isaac, M., Piñón-Gómez, D. R., Ramos-Tapia, I., Soto-Winckler, J., Reynosa-Rodríguez, G., and Paneque, M.: Diversidad microbiana en estudios de fertilización mineral de larga duración en caña de azúcar [Microbial diversity in long-term mineral fertilization studies in sugarcane], Rev. U.D.C.A Actual. Divulg. Cient., 26, 2, https://doi.org/10.31910/rudca.v26.n2.2023.2511, 2023.
Tamayo-Isaac, M., Piñón-Gómez, D., Puchades-Izaguirre, Y., Pablos-Reyes, P., and Pérez-Silva, R.: Biological activity of the microbial population associated with the rhizosphere of Saccharum officinarum L., Rev. Cub. Quím., 36, 1–12, 2024.
Tang, R., Li, S., Lang, X., Huang, X., and Su, J.: Rare species contribute greater to ecosystem multifunctionality in a subtropical forest than common species due to their functional diversity, Forest Ecol. Manage., 538, 120981, https://doi.org/10.1016/j.foreco.2023.120981, 2023.
Tedersoo, L. and Bahram, M.: Mycorrhizal types differ in ecophysiology and alter plant nutrition and soil processes, Biol. Rev. Camb. Philos. Soc., 94, 1857–1880, https://doi.org/10.1111/brv.12538, 2019.
Tian, H., Xu, R., Canadell, J. G., Thompson, R. L., Winiwarter, W., Suntharalingam, P., Davidson, E. A., Ciais, P., Jackson, R. B., Janssens-Maenhout, G., Prather, M. J., Regnier, P., Pan, N., Pan, S., Peters, G. P., Shi, H., Tubiello, F. N., Zaehle, S., Zhou, F., Arneth, A., Battaglia, G., Berthet, S., Bopp, L., Bouwman, A. F., Buitenhuis, E. T., Chang, J., Chipperfield, M. P., Dangal, S. R. S., Dlugokencky, E., Elkins, J. W., Eyre, B. D., Fu, B., Hall, B., Ito, A., Joos, F., Krummel, P. B., Landolfi, A., Laruelle, G. G., Lauerwald, R., Li, W., Lienert, S., Maavara, T., MacLeod, M., Millet, D. B., Olin, S., Patra, P. K., Prinn, R. G., Raymond, P. A., Ruiz, D. J., van der Werf, G. R., Vuichard, N., Wang, J., Weiss, R. F., Wells, K. C., Wilson, C., Yang, J., and Yao, Y.: A comprehensive quantification of global nitrous oxide sources and sinks, Nature, 586, 248–256, https://doi.org/10.1038/s41586-020-2780-0, 2020.
Tripathi, B. M., Song, W., Slik, J. W. F., Sukri, R. S., Jaafar, S., Dong, K., and Adams, J. M.: Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity, Front. Microbiol., 7, 376, https://doi.org/10.3389/fmicb.2016.00376, 2016.
Wang, C., Miao, Q., Wei, Z., Guo, Y., Li, J., Fan, Z., Hu, Y., Zhang, H., Sun, J., and Cui, Z.: Nutrient runoff and leaching under various fertilizer treatments and pedogeographic conditions: A case study in tobacco (Nicotiana tabacum L.) fields of the Erhai Lake basin, China, Eur. J. Agron., 156, 127170, https://doi.org/10.1016/j.eja.2024.127170, 2024.
Wilpiszeski, R. L., Aufrecht, J. A., Retterer, S. T., Sullivan, M. B., Graham, D. E., Pierce, E. M., Zablocki, O. D., Palumbo, A. V., and Elias, D. A.: Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales, Appl. Environ. Microbiol., 85, e00324-19, https://doi.org/10.1128/AEM.00324-19, 2019.
Yan, Q., Deng, J., Wang, F., Liu, Y., and Liu, K.: Community assembly and co-occurrence patterns underlying the core and satellite bacterial sub-communities in the Tibetan Lakes, Front. Microbiol., 12, 695465, https://doi.org/10.3389/fmicb.2021.695465, 2021.
Yang, H., Yang, Y., Zhu, H., Xiong, H., Zhang, Y., Liu, Y., Huang, X., Li, Y., and Jiang, T.: Short-term phosphorus fertilization alters soil fungal community in long-term phosphorus-deprived yellow soil paddy fields, Agriculture, 15, 280, https://doi.org/10.3390/agriculture15030280, 2025.
Zamkovaya, T., Foster, J. S., de Crécy-Lagard, V., and Conesa, A.: A network approach to elucidate and prioritize microbial dark matter in microbial communities, ISME J., 15, 228–244, https://doi.org/10.1038/s41396-020-00777-x, 2021.
Zamora-Leiva, L., Soto, J., Román-Figueroa, C., Peña, F., Univaso, L., and Paneque, M.: Characterization of bacterial diversity associated with a Salar de Atacama native plant Nitrophila atacamensis, Environ. Microbiome, 20, 100, https://doi.org/10.1186/s40793-025-00766-7, 2025.
Zeghal, E., Vaksmaa, A., Vielfaure, H., Boekhout, T., and Niemann, H.: The potential role of marine fungi in plastic degradation – A review, Front. Mar. Sci., 8, 738877, https://doi.org/10.3389/fmars.2021.738877, 2021.
Zhong, X., Li, J., Li, X., Ye, Y., Liu, S., Hallett, P. D., Ogden, M. R., and Naveed, M.: Physical protection by soil aggregates stabilizes soil organic carbon under simulated N deposition in a subtropical forest of China, Geoderma, 285, 323–332, https://doi.org/10.1016/j.geoderma.2016.09.026, 2017.
Short summary
We examined how long-term fertilizer treatments shape the microbial community around sugarcane roots. Using gene sequencing, we found that although the types of microbes stayed similar, their interactions changed with each nutrient regime. These shifts suggest that fertilizer composition influences soil functioning. The results help guide more sustainable management of soils used for sugarcane.
We examined how long-term fertilizer treatments shape the microbial community around sugarcane...
