Soil microbial communities and soil quality drive Arabica coffee yield in pine-coffee agroforestry under varying management intensities
Article Sidebar
Abstract Views: 38
File Views: 16
Main Article Content
Abstract
Abstract. Wicaksono KP, Permanasari PN, Saitama A, Widaryanto E, Prayogo C, Adianingsih OR, Murtini ES, Tarno H. 2026. Soil microbial communities and soil quality drive Arabica coffee yield in pine-coffee agroforestry under varying management intensities. Biodiversitas 27 (2): d270240. https://doi.org/10.13057/biodiv/d270240. Pine-coffee agroforestry systems provide important ecological and economic benefits; however, the effects of management intensity on soil quality, microbial communities, and coffee productivity remain poorly understood. This study evaluated the effects of varying management intensities in a pine-coffee agroforestry system, focusing on soil quality, microbial populations, and coffee productivity and quality. Field observations and laboratory analyses were conducted to assess canopy cover, light intensity, litter accumulation, soil bulk density, particle density, porosity, infiltration rate, total nitrogen, organic carbon, and populations of cellulolytic bacteria, fungi, Nitrobacter, and Nitrosomonas. Coffee productivity and fruit quality attributes were also evaluated. The results showed that higher management intensities, specifically best management practices (BMP), positively enhanced soil physical and chemical properties, thereby directly improving coffee yield and quality. The result revealed that BMP management effectively reduced soil bulk density and increased porosity and infiltration rates, creating an optimal environment for coffee plant growth. BMP can offer soil media with good physical characteristics and high nutrient content. However, MC management can provide a more favorable ecosystem for the growth of soil microbial populations. The more stable abiotic factors of the ecosystem under non-intensive management can support the development of microorganisms through succession. It was also observed that BMP practices led to larger berry sizes, heavier bean weights, and higher sugar content in coffee beans, which are critical quality indicators. The study demonstrates that management intensity strongly influences the interactions among soil quality, microbial communities, and coffee performance in pine-coffee agroforestry systems. Moderate to intensive management can improve productivity, but balanced practices are required to maintain soil microbial diversity and long-term ecosystem sustainability.
Article Details
Issue
Section
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
References
Abu El Haija K, Chiang YW, Santos RM. 2024. On-site determination of soil organic carbon content: A photocatalytic approach. Clean Technol 6 (2): 784-801. https://doi.org/10.3390/cleantechnol6020040.
Abu-hashim M, Lilienthal H, Schnug E, Lasaponara R, Mohamed ES. 2023. Can a change in agriculture management practice improve soil physical properties. Sustainability 15 (4): 3573. https://doi.org/10.3390/su15043573.
Ahmed S, Brinkley S, Smith E, Sela A, Theisen M, Thibodeau C, Warne T, Anderson E, Van Dusen N, Giuliano P, Ionescu KE, Cash SB. 2021. Climate change and coffee quality. Front Plant Sci 12: 708013. https://doi.org/10.3389/fpls.2021.708013.
Amoozegar A, Heitman JL, Kranz CN. 2023. Comparison of soil particle density determined by a gas pycnometer. Soil Sci Soc Am J 87 (1): 1-12. https://doi.org/10.1002/saj2.20476.
Araujo ASF, Leite LFC, Freitas Iwata BdF, Lira Jr MdA, Xavier GR, Figueiredo MdVB. 2012. Microbiological processes in agroforestry systems. Agron Sustain Dev 32: 215-226. https://doi.org/10.1007/s13593-011-0026-0.
Barros-Rodríguez A, Rangseekaew P, Lasudee K, Pathom-aree W, Manzanera M. 2021. Impacts of agriculture on soil microbial biodiversity. Plants 10 (11): 2325. https://doi.org/10.3390/plants10112325
Beule L, Vaupel A, Moran-Rodas VE. 2022. Soil microorganisms in temperate alley-cropping agroforestry systems: A review. Microorganisms 10 (3): 616. https://doi.org/10.3390/microorganisms10030616.
Cerda R, Avelino J, Harvey CA, Gary C, Tixier P, Allinne C. 2020. Coffee agroforestry systems. Crop Prot 134: 105149. https://doi.org/10.1016/j.cropro.2020.105149.
Colombo MC. 2023. Coffee agroforestry system effects on soil. Res Square. https://doi.org/10.21203/rs.3.rs-3398325/v1.
De Beenhouwer M, Aerts R, Honnay O. 2013. A global meta-analysis of coffee and cacao agroforestry. Agric Ecosyst Environ 175: 1-7. https://doi.org/10.1016/j.agee.2013.05.003.
Ehrenbergerová L, Klimková M, Cano YG, Habrová H, Lvončík S, Volařík D, Khum W, Němec P, Kim S, Jelínek P, Maděra P. 2021. Does shade impact coffee yield. Sustainability 13 (24): 13823. https://doi.org/10.3390/su132413823.
Ekblad A. 2015. The Influence of Agroforestry on Soil Fertility in Coffee Cultivations. [MSc thesis]. Örebro Universitet, Sweden.
Fahad S, Chavan SB, Chichaghare AR, Uthappa AR, Kumar M, Kakade V, Pradhan A, Jinger D, Rawale G, Yadav DK, Kumar V. 2022. Agroforestry systems for soil health improvement. Sustainability 14 (22): 14877. https://doi.org/10.3390/su142214877.
Fitch A, Rowe RL, McNamara NP, Prayogo C, Ishaq RM, Prasetyo RD, Mitchell Z, Oakley S, Jones L. 2022. The coffee compromise: Is agricultural expansion into tree plantations a sustainable option? Sustainability 14 (5): 3019. https://doi.org/10.3390/su14053019.
Gu F, Chen Xj, Su Za, Zhang Xb, Zhou Mh. 2022. Variation of soil organic carbon and bulk density. J Mt Sci 19: 2322-2332. https://doi.org/10.1007/s11629-021-7291-4.
Hamza MA, Anderson WK. 2005. Soil compaction in cropping systems. Soil Tillage Res 82 (2): 121-145. https://doi.org/10.1016/j.still.2004.08.009.
Haruna SI, Anderson SH, Udawatta RP, Gantzer CJ, Phillips NC, Cui S, Gao Y. 2020. Improving soil physical properties. Agrosyst Geosci Environ 3 (1): e20105. https://doi.org/10.1002/agg2.20105.
Jurburg SD, Shek KL, McGuire K. 2020. Soil microbial composition in coffee agroecosystems. FEMS Microbiol Ecol 96 (9): fiaa164. https://doi.org/10.1093/femsec/fiaa164.
Kielak AM, Scheublin TR, Mendes LW, van Veen JA, Kuramae EE. 2016. Bacterial community succession in pine-wood decomposition. Front Microbiol 7: 231. https://doi.org/10.3389/fmicb.2016.00231.
Kiup E, Swan T, Field D. 2025. Soil management practices in coffee farming systems. Soil Use Manag 41 (2): e70068. https://doi.org/10.1111/sum.70068.
Kurniawan S, Nugroho RMYAP, Ustiatik R, Nita I, Nugroho GA, Prayogo C, Anderson CWN. 2024. Soil nitrogen dynamics in coffee-based agroforestry. Agrofor Syst 98: 1323-1341. https://doi.org/10.1007/s10457-024-01004-8.
Lee SA, Kim JM, Kim Y, Joa JH, Kang SS, Ahn JH, Ahn JH, Kim M, Song J, Weon HY. 2020. Agricultural land use and soil bacterial communities. Sci Rep 10: 17469. https://doi.org/10.1038/s41598-020-74193-8.
Li S, Gong S, Hou Y, Li X, Wang C. 2022. Agroforestry impacts on soil multi-functionality. Sci Total Environ 847: 157438. https://doi.org/10.1016/j.scitotenv.2022.157438.
Lori M, Symnaczik S, Mäder P, De Deyn G, Gattinger A. 2017. Organic farming enhances soil microbial abundance. PLoS One 12 (7): e0180442. https://doi.org/10.1371/journal.pone.0180442.
Maharjan M, Ayer S, Timilsina S, Ghimire P, Bhatta S, Thapa N, Timilsina YP, Lama S, Yadav VK, Okolo CC. 2024. Impact of agroforestry on carbon stock and soil quality. Soil Secur 16: 100164. https://doi.org/10.1016/j.soisec.2024.100164.
Martinez HEP, de Andrade SAL, Santos RHS, Baptistella JLC, Mazzafera P. 2024. Agronomic practices toward coffee sustainability. Sci Agric 81: e20220277. https://doi.org/10.1590/1678-992X-2022-0277.
Matistic M, Dugan I, Bugonovic I. 2024. Challenges in sustainable agriculture—the role of organic amendments. Agriculture 14 (4): 643. https://doi.org/10.3390/agriculture14040643.
Moi DA, García-Ríos R, Hong Z, Daquila BV, Mormul RP. 2020. Intermediate disturbance hypothesis in ecology. Ann Zool Fennici 57: 67-78. https://doi.org/10.5735/086.057.0108.
Nahon SM, Trindade FC, Yoshiura CA, Martins GC, Costa IR, Costa PH, Herrera H, Balestrin D, Godinho TD, Marchiori BM, Valadares RB. 2024. Impact of agroforestry practices on soil microbial diversity. Intl J Mol Sci 25 (21):11345. https://doi.org/10.3390/ijms252111345.
Osorio Pérez V, Matallana Pérez LG, Fernandez-Alduenda MR, Alvarez Barreto CI, Gallego Agudelo CP, Montoya Restrepo EC. 2023. Chemical composition and sensory quality of coffee fruits at different stages of maturity. Agronomy 13 (2): 341. https://doi.org/10.3390/agronomy13020341.
Rakocevic M, dos Santos-Scholz MB, Pazianotto RAA, Matsunaga FT, Ramalho JC. 2023. Variation in coffee bean attributes. Horticulturae 9 (2): 215. https://doi.org/10.3390/horticulturae9020215.
Robinson DA, Thomas A, Reinsch S, Lebron I, Feeney CJ, Maskell LC, Wood CM, Seaton FM, Emmett BA, Cosby BJ. 2022. Analytical modelling of soil porosity and bulk density. Sci Rep 12 (1): 7085. https://doi.org/10.1038/s41598-022-11099-7.
Sainju UM, Liptzin D, Jabro JD. 2022. Relating soil physical properties to crop yields. Sci Rep 12 (1): 26619. https://doi.org/10.1038/s41598-022-26619-8.
Schmidt JE, Kent AD, Brisson VL, Gaudin ACM. 2019. Agricultural management and rhizosphere microbial communities. Microbiome 7: 146. https://doi.org/10.1186/s40168-019-0756-9.
Schmidt M, Corre MD, Kim B, Morley J, Göbel L, Sharma ASI, Setriuc S, Veldkamp E. 2021. Nutrient saturation of crop monocultures. Nutr Cycl Agroecosyst 119: 69-82. https://doi.org/10.1007/s10705-020-10113-6.
Schmidt R, da Silva CA, Silva LO, Espindula MC, Rodrigues WP, Vieira HD, Tomaz MA, Partelli FL. 2023. Accumulation of nutrients in coffee robusta. Plants 12 (19): 3476. https://doi.org/10.3390/plants12193476.
Schwyter AR, Vaughan KL. 2020. Carbon/Nitrogen Ratio. In: Introduction to Soil Science Laboratory Manual. University of Wyoming.
Singavarapu B, Du J, Beugnon R, Cesarz S, Eisenhauer N, Xue K, Wang Y, Bruelheide H, Wubet T. 2023. Functional potential of soil microbial communities. Microbiol Spectr 11 (2): e04578-22. https://doi.org/10.1128/spectrum.04578-22.
Su J, Ji W, Sun X, Wang H, Kang Y, Yao B. 2023. Effects of different management practices on soil microbial community structure and function in alpine grassland. J Environ Manage 327: 116859. https://doi.org/10.1016/j.jenvman.2022.116859.
Sudharta KA, Hakim AL, Fadhilah MA, Fadzil MN, Prayogo C, Kusuma Z, Suprayogo D. 2022. Soil organic matter and nitrogen in coffee-pine agroforestry. Biodiversitas 23 (11): 5884-5891. https://doi.org/10.13057/biodiv/d231142.
Suman J, Rakshit A, Ogireddy SD, Singh S, Gupta C, Chandrakala J. 2022. Microbiome in sustainable agriculture and human health. Front Soil Sci 2: 821589. https://doi.org/10.3389/fsoil.2022.821589.
Tilden GM, Aranka JN, Curry GN. 2024. Ecosystem services in coffee agroforestry. Agroforest Syst 98: 383-400. https://doi.org/10.1007/s10457-023-00917-0.
Torrez V, Benavides-Frias C, Jacobi J, Speranza CI. 2023. Ecological quality as a coffee quality enhancer. Agron Sustain Dev 43: 19. https://doi.org/10.1007/s13593-023-00874-z.
Uhland RE, O’Neal AM. 1951. Soil Permeability Determinations. Technical Bulletin. U.S. Department of Agriculture.
Vaast P, Bertrand B, Perriot JJ, Guyot B, Génard M. 2006. Fruit thinning and shade improve coffee quality. J Sci Food Agric 86 (2): 197-204. https://doi.org/10.1002/jsfa.2338.
Wang M, He D, Shen F, Huang J, Zhang R, Liu W, Zhu M, Zhou L, Wang L, Zhou Q. 2019. Soil compaction on plant growth and root respiration. Environ Sci Pollut Res 26 (22): 22835-22845. https://doi.org/10.1007/s11356-019-05606-z.
Wang W, Ye Z, Li J, Liu G, Wu Q, Wang Z, He G, Yan W, Zhang C. 2024. Intermediate irrigation with low fertilization promotes soil nutrient cycling. J Environ Manage 351: 119688. https://doi.org/10.1016/j.jenvman.2023.119688.
Wright DR, Gordon A, Bennett RE, Selinske MJ, Lentini PE, Garrard GE, Rodewald AD, Bekessy SA. 2024. Biodiverse coffee plantations provide co-benefits. J Sustain Agric Environ 3 (3). https://doi.org/10.1002/sae2.70005.
Xu S, Liu Y, Ma F, Yang N, Virginio Filho EM, Fisk ID. 2022. Impact of agroforestry systems on coffee aroma. Front Nutr 9: 968783. https://doi.org/10.3389/fnut.2022.968783.
Xu S, Liu Y, Sun Z, Chen G, Ma F, Yang N, Filho EdMV, Fisk ID. 2023. Agroforestry effects on green coffee beans. Front Nutr 10: 1198802. https://doi.org/10.3389/fnut.2023.1198802.