Tree diversity, structure and composition in coffee agroforestry with varying shade systems, coffee species, and landscape settings in Malang, Indonesia

Main Article Content

LUCHMAN HAKIM
MUHAMMAD YUSUF
FITRA D. WIRATANTRA
BRIAN RAHARDI
WENNY B. SUNARHARUM
AGUS NURROFIK

Abstract

Abstract. Hakim L, Yusuf M, Wiratantra FD, Rahardi B, Sunarharum WB, Nurrofik A. 2026. Tree diversity, structure and composition in coffee agroforestry with varying shade systems, coffee species, and landscape settings in Malang, Indonesia. Biodiversitas 27 (5): d270509. https://doi.org/10.13057/biodiv/d270509. Coffee agroforestry in Malang Region, East Java, Indonesia has been widely recognized as a multifunctional land-use system that integrates economic, and social benefits; however, its comprehensive ecological characteristics remain poorly documented. This study examines tree diversity and ecological indicators in coffee agroforestry systems in Malang, East Java, across four landscape settings, three coffee species (arabica, robusta, and liberica) and shade systems typology (shaded monoculture, commercial polyculture, traditional polyculture and rustic). Field surveys were conducted at 64 sites to document shade-tree diversity, composition (Important Value Index) and ecological indices (Shannon-Wiener Diversity Index (H), Evenness Index (E), and Simpson Dominance Index (D)). In total, there were 40 species of shade trees across all sites and primarily composed of Fabaceae and Malvaceae which contribute to soil fertility, habitat provision, and raw material resources. Results indicated that among shaded systems in averages includes, rustic-type exhibited the highest tree species diversity, high evenness, and low dominance (H′ = 2.02, E = 0.97, D = 0.19), followed by traditional polyculture systems (H′ = 1.23, E = 0.91, and D = 0.3), commercial polyculture (H′ = 0.8, E = 0.89, D = 0.46), and shaded monoculture (H′ = 0.17, E = 0.29, and D = 0.83). Liberica coffee agroforestry tended to show higher diversity index of shade trees with less dominance of few species compared to the other two. However, although its diversity assessments belong low to moderate scores, the presence of shade tree diversity has been shown to have a practical impact on the dynamics of coffee agroforestry, allowing farmers to increase food security while generating additional income beyond coffee. Therefore, to support ecological sustainability and community well-being in the Malang Region, conservation strategies and policy frameworks should prioritize biodiversity-friendly agroforestry management.

Article Details

Section

Articles

References

Abdelzaher RAE. 2025. Expanding coffee cultivation beyond traditional boundaries: Challenges, innovations, and sustainability in non-traditional regions: A review. J Plant Food Sci 3 (1): 67-76. https://doi.org/10.21608/jpfs.2025.374988.1034.

Albertin A, Nair PKR. 2004. Farmers’ perspectives on the role of shade trees in coffee production systems: An assessment from the Nicoya Peninsula, Costa Rica. Hum Ecol 32: 443-463. https://doi.org/10.1023/B:HUEC.0000043515.84334.76.

Alves V, Goulart FF, Jacobson TKB, de Miranda Filho RJ, Ribas CEDC. 2016. Shade's benefit: Coffee production under shade and full sun. J Agric Sci 8 (11): 11-21. http://dx.doi.org/10.5539/jas.v8n11p11.

Atkins JW, Bhatt P, Carrasco L, Francis E, Garabedian JE, Hakkenberg CR, Hardiman BS, Jung J, Koirala A, LaRue EA, Oh S. 2023. Integrating forest structural diversity measurement into ecological research. Ecosphere 14 (9): e04633. https://doi.org/10.1002/ecs2.4633.

Avelino J, Gagliardi S, Perfecto I, Isaac ME, Liebig T, Vandermeer J, Merle I, Hajian-Forooshani Z, Motisi N. 2023. Tree effects on coffee leaf rust at field and landscape scales. Plant Dis 107: 247-261. DOI: https://doi.org/10.1094/PDIS-08-21-1804-FE.

Bandeira FP, Martorell C, Meave JA, Caballero J. 2005. The role of rustic coffee plantations in the conservation of wild tree diversity in the Chinantec Region of Mexico. Biodivers Conserv 14: 1225-1240. https://doi.org/10.1007/s10531-004-7843-2.

Bharucha Z, Pretty J. 2010. The roles and values of wild foods in agricultural systems. Philos Trans R Soc B Biol Sci 365 (1554): 2913-2926. https://doi.org/10.1098/rstb.2010.0123.

BPS Kabupaten Malang. 2020. Kabupaten Malang Satu Data Edisi 2020. Dinas Komunikasi dan Informatika Kabupaten Malang, Malang. https://malangkab.go.id. [Indonesian]

BPS Kabupaten Malang. 2025. Kabupaten Malang dalam Angka 2025. Badan Pusat Statistik Kabupaten Malang, Malang. [Indonesian]

BPS Kota Batu. 2025. Kota Batu dalam Angka 2025. Badan Pusat Statistik Kota Batu, Batu. [Indonesian]

Budiaman A, Hardjanto. 2023. Harvesting systems of private forests in Indonesia: A review. Jurnal Manajemen Hutan Tropika 29 (3): 219-233. https://doi.org/10.7226/jtfm.29.3.219.

Cerda R, Avelino J, Gary C, Tixier P, Lechevallier E, Allinne C. 2017. Primary and secondary yield losses caused by pests and diseases: Assessment and modeling in coffee. PLoS One 12 (1): e0169133. https://doi.org/10.1371/journal.pone.0169133.

Cerda R, Avelino J, Harvey CA, Gary C, Tixier P, Allinne C. 2020. Coffee agroforestry systems capable of reducing disease-induced yield and economic losses while providing multiple ecosystem services. Crop Prot 134: 105149. DOI: https://doi.org/10.1016/j.cropro.2020.105149.

Cramer PJS. 1957. A Review of Literature of Coffee Research in Indonesia. IICA Biblioteca Venezuela, Venezuela.

Da-Costa-Rocha I, Bonnlaender B, Sievers H, Pischel I, Heinrich M. 2014. Hibiscus sabdariffa L. - A phytochemical and pharmacological review. Food Chem 165: 424-443. https://doi.org/10.1016/j.foodchem.2014.05.002.

De Beenhouwer M, Aerts R, Honnay O. 2013. A global meta-analysis of the biodiversity and ecosystem service benefits of coffee and cacao agroforestry. Agric Ecosyst Environ 175: 1-7. https://doi.org/10.1016/j.agee.2013.05.003.

Demko J, Machava J. 2022. Tree resin, a macroergic source of energy, a possible tool to lower the rise in atmospheric CO₂ levels. Sustainability 14 (6): 3506. https://doi.org/10.3390/su14063506.

Escobar-Ramírez S, Grass I, Armbrecht I, Tscharntke T. 2019. Biological control of the coffee berry borer: Main natural enemies, control success, and landscape influence. Biol Control 136: 103992. https://doi.org/10.1016/j.biocontrol.2019.05.011.

Evizal R, Sugiatno, Prasmatiwi FE, Nurmayasari I. 2016. Shade tree species diversity and coffee productivity in Sumberjaya, West Lampung, Indonesia. Biodiversitas 17 (1): 234-240. https://doi.org/10.13057/biodiv/d170134.

Fox GA, Negrete-Yankelevich S, Sosa VJ. 2015. Ecological Statistics: Contemporary Theory and Application. Oxford University Press, Oxford. https://doi.org/10.1093/acprof:oso/9780199672547.001.0001.

Gillison AN, Liswanti N, Budidarsono S, van Noordwijk M, Tomich TP. 2004. Impact of cropping methods on biodiversity in coffee agroecosystems in Sumatra, Indonesia. Ecol Soc 9 (2): 7. https://doi.org/10.5751/ES-00657-090207.

Góngora CE, Gil ZN, Constantino LM, Benavides P. 2023. Sustainable strategies for the control of pests in coffee crops. Agronomy 13 (12): 2940. https://doi.org/10.3390/agronomy13122940.

Habibah LN, Hakim L, Pangestuti E, Siswanto D, Rahardi B. 2024. Vegetation diversity, structure and composition in nature-based recreation sites as a potential tourist attraction in Banyuwangi, Indonesia. Biodiversitas 25 (9): 3273-3285. https://doi.org/10.13057/biodiv/d250950.

Haggar J, Barrios M, Bolaños M, Merlo M, Moraga P, Munguia R, Ponce A, Romero S, Soto G, Staver C, Virginio E. 2011. Coffee agroecosystem performance under full sun, shade, and organic management regimes in Central America. Agrofor Syst 82: 285-301. https://doi.org/10.1007/s10457-011-9392-5.

Hairiah K, Arifin J, Berlian, Prayogo C, van Noordwijk M. 2002. Carbon stock assessment for a forest-to-coffee conversion landscape in Malang (East Java) and Sumber-Jaya (Lampung, Indonesia). International Symposium on Forest Carbon Sequestration and Monitoring 28-36. Taipei, Taiwan 2002. https://www.cifor-icraf.org.

Hakim L. 2011. Cultural landscapes of the Tengger Highland, East Java. In: Hong SK, Kim JE, Wu J, Nakagoshi N (eds). Landscape Ecology in Asian cultures. Ecological Research Monographs. Springer, Tokyo. https://doi.org/10.1007/978-4-431-87799-8_6.

Hasyim MA, Qurrotaayunina RP, Nayomi M, Suheriyanto D, Prahardika BA. 2024. The diversity of aerial insects in coffee agroforestry, Dampit and Purwodadi District, East Java, Indonesia. IOP Conf Ser Earth Environ Sci 1312 (1): 012010. https://doi.org/10.1088/1755-1315/1312/1/012010.

Hidayat AS, Laili S, Zayadi H. 2021. Studi persepsi masyarakat tentang agroforestri tanaman kopi di Desa Patokpicis, Kecamatan Wajak, Kabupaten Malang. e-Jurnal Ilmiah Biosaintropis 6 (Special Edition): 1-7. [Indonesian]

IUCN. 2025. The IUCN Red List of Threatened Species. Version 2025-2. https://www.iucnredlist.org.

Jose S. 2009. Agroforestry for ecosystem services and environmental benefits: An overview. Agrofor Syst 76 (1): 1-10. https://doi.org/10.1007/s10457-009-9229-7.

Kementerian Lingkungan Hidup dan Kehutanan Republik Indonesia. 2020. The State of Indonesia’s Forests 2020. Kementerian Lingkungan Hidup dan Kehutanan Republik Indonesia, Jakarta. [Indonesian]

Kementerian Pertanian. 2023. Analisis Kinerja Perdagangan Kopi. Pusat Data dan Sistem Informasi Pertanian, Kementerian Pertanian, Jakarta. [Indonesian]

Ketsa S, Wisutiamonkul A, Palapol Y, Paull R. 2020. The durian: Botany, horticulture, and utilization. In: Warrington I (eds.). Horticultural Reviews Volume 47. John Wiley & Sons, Hoboken. https://doi.org/10.1002/9781119625407.ch4.

Konaté N, Ouattara Y, Kouakou AK, Barima YS. 2024. Effects of traditional agroforestry practices on cocoa yields in Côte d'Ivoire. Sustainability 16 (22): 9927. https://doi.org/10.3390/su16229927.

Koutouleas A, Sarzynski T, Bordeaux M, Bosselmann AS, Campa C, Etienne H, Turreira-García N, Rigal C, Vaast P, Ramalho JC, Marraccini P, Ræbild A. 2022. Shaded coffee: A nature-based strategy for coffee production under climate change? A review. Front Sustain Food Syst 6: 877476. https://doi.org/10.3389/fsufs.2022.877476.

Küfeoğlu S. 2022. SDG-13: Climate Action. Emerging technologies. Sustainable Development Goals Series. Springer, Cham. https://doi.org/10.1007/978-3-031-07127-0_15.

Kumar BM, Kunhamu TK. 2022. Nature-based solutions in agriculture: A review of the coconut (Cocos nucifera L.)-based farming systems in Kerala, “the land of coconut trees”. Nature-Based Solutions 2: 100012. https://doi.org/10.1016/j.nbsj.2022.100012.

Kusumawati IA, Mardiani MO, Purnamasari E, Batoro J, van Noordwijk M, Hairiah K. 2022. Agrobiodiversity and plant use categories in coffee-based agroforestry in East Java, Indonesia. Biodiversitas 23 (10): 5412-5422. https://doi.org/10.13057/biodiv/d231051.

Kutos S, Bennett RE, Rao MV, Fleischer RC, Rice RA, Muletz-Wolz CR. 2024. Farm management and shade tree species influence coffee soil microbiomes in Central and South America. Appl Soil Ecol 202: 105571. https://doi.org/10.1016/j.apsoil.2024.105571.

Leakey RRB. 1996. Definition of agroforestry revisited. Agroforestry Today 8 (1): 5-7.

Lugo-Pérez J, Hajian-Forooshani Z, Perfecto I, Vandermeer J. 2023. The importance of shade trees in promoting carbon storage in coffee agroforest systems. Agric Ecosyst Environ 355: 108594. https://doi.org/10.1016/j.agee.2023.108594.

Majeed F, Raza A, Munir A, Hensel O. 2022. Batch-type solar roaster-an innovative decentralized system for coffee roasting. Sustainability 14: 2217. DOI: https://doi.org/10.3390/su14042217.

Manson S, Nekaris KAI, Nijman V, Campera M. 2024. Effect of shade on biodiversity within coffee farms: A meta-analysis. Sci Total Environ 914: 169882. https://doi.org/10.1016/j.scitotenv.2024.169882.

Mihrete TB, Mihretu FB. 2025. Crop diversification for ensuring sustainable agriculture, risk management and food security. Glob Chall 9 (2): 2400267. https://doi.org/10.1002/gch2.202400267.

Misgana Z, Garedew W, Alemayehu Y, Bekeko Z, Nebiyu A. 2024. The influence of shade tree species and coffee varieties on selected soil physicochemical properties in coffee-based farming systems of Southwestern Ethiopia. Trees For People 17: 100650. https://doi.org/10.1016/j.tfp.2024.100650.

Morais H, Caramori PH, Ribeiro AMDA, Gomes JC, Koguishi MS. 2006. Microclimatic characterization and productivity of coffee plants grown under shade of pigeon pea in Southern Brazil. Pesqui Agropecu Bras 41 (5): 763-770. https://doi.org/10.1590/S0100-204X2006000500007.

Moura XO, Jedlicka JA, Oliveira SL, Johnson MD. 2025. Effects of native and non-native shade trees on insect predation pressure on Kenyan coffee farms. Front Conserv Sci 6: 1529450. https://doi.org/10.3389/fcosc.2025.1529450.

Muñoz-Villers LE, Geris J, Alvarado-Barrientos MS, Holwerda F, Dawson T. 2020. Coffee and shade trees show complementary use of soil water in a traditional agroforestry ecosystem. Hydrol Earth Syst Sci 24 (4): 1649-1663. https://doi.org/10.5194/hess-24-1649-2020.

Nair PKR. 1993. An Introduction to Agroforestry. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-1608-4.

Nasiro K. 2024. The benefits of agroforestry coffee production systems: A review. World J Food Sci Technol 8 (4): 86-105. https://doi.org/10.11648/j.wjfst.20240804.13.

Noponen MRA, Healey JR, Soto G, Haggar JP. 2013. Sink or source—The potential of coffee agroforestry systems to sequester atmospheric CO2 into soil organic carbon. Agric Ecosyst Environ 175: 60-68. https://doi.org/10.1016/j.agee.2013.04.012.

Odum EP. 1971. Fundamentals of Ecology. 3rd Edition. W.B. Saunders, Philadelphia.

Perfecto I, Rice RA, Greenberg R, Van der Voort M. 1996. Shade coffee: A disappearing refuge for biodiversity. BioScience 46 (8): 598-608. https://doi.org/10.2307/1312989.

Pusat Penelitian Kopi dan Kakao Indonesia. 2023. Narasi Tunggal Kopi: Profil Industri Kopi di Indonesia Periode 2018-2023. Pusat Penelitian Kopi dan Kakao Indonesia, PT Riset Perkebunan Nusantara, Jember. [Indonesian]

Rahayu SM, Batoro J, Hakim L, Sukenti K. 2023. Plant diversity of Sasak Tribe homegardens in villages around Mandalika, Lombok Island, Indonesia. J Mar Isl Cult 12 (3): 325-350. https://doi.org/10.21463/jmic.2023.12.3.21.

Raymundo D, Prado-Junior J, de Oliveira-Neto NE, Santana LD, do Vale VS, Jacobson TB, Oliveira PEA, Carvalho FA. 2018. Persistence of Coffea arabica and its relationship with the structure, species diversity and composition of a secondary forest in Brazil. PLoS One 13 (3): e0194032. https://doi.org/10.1371/journal.pone.0194032.

Rembold K, Mangopo H, Tjitrosoedirdjo S, Kreft H. 2017. Plant diversity, forest dependency, and alien plant invasions in tropical agricultural landscapes. Biol Conserv 213: 234-242. https://doi.org/10.1016/j.biocon.2017.07.020.

Reza AD, Firdausi E, Kusuma LA, Sabrina MA, Fadhillah EN, Naim DM, Setyawan AD. 2025. Traditional knowledge and utilization of non-medicinal plants in homegardens of a tropical karst landscape in Central Java, Indonesia. Intl J Trop Drylands 9 (1): 20-35. https://doi.org/10.13057/tropdrylands/t090103.

Rindyastuti R, Abywijaya IK, Rahadiantoro A, Irawanto R, Nurfadilah S, Siahaan FA, Danarto SA, Hapsari L, Lestari DA, Damaiyani J, Ariyanti EE. 2018. Keanekaragaman Tumbuhan Pulau Sempu dan Ekosistemnya. LIPI Press, Jakarta. [Indonesian]

Royal Botanic Gardens, Kew. 2017. Plants of the World Online (POWO). https://powo.science.kew.org.

Rumicha TD, Belew S, Hasen G, Teka TA, Forsido SF. 2025. Food, feed, and phytochemical uses of wild edible plants: A systematic review. Food Sci Nutr 13 (6): e70454. https://doi.org/10.1002/fsn3.70454.

Santhyami, Yunita H. 2024. Sustainable food security: An ethnobotanical study of Dlingo Village, Grobogan Regency. IOP Conf Ser Earth Environ Sci 1357: 012013. https://doi.org/10.1088/1755-1315/1357/1/012013.

Schroth G, da Fonseca GAB, Harvey CA, Gascon C, Vasconcelos HL, Izac A-MN (eds.). 2004. Agroforestry and Biodiversity Conservation in Tropical Landscapes. Island Press, Washington, Covelo, London.

Sinu PA, Viswan G, Fahira PP, Rajesh TP, Manoj K, Hariraveendra M, Jose T. 2021. Shade tree diversity may not drive prey–predator interaction in coffee agroforests of the Western Ghats biodiversity hotspot, India. Biol Control 160: 104674. https://doi.org/10.1016/j.biocontrol.2021.104674.

Soto-Pinto L, Anzueto M, Mendoza J, Ferrer GJ, de Jong B. 2010. Carbon sequestration through agroforestry in indigenous communities of Chiapas, Mexico. Agrofor Syst 78: 39-51. https://doi.org/10.1007/s10457-009-9247-5.

Soto-Pinto L, Perfecto I, Castillo-Hernandez J, Caballero-Nieto J. 2000. Shade effect on coffee production at the Northern Tzeltal Zone of the State of Chiapas, Mexico. Agric Ecosyst Environ 80 (1-2): 61-69. https://doi.org/10.1016/S0167-8809(00)00134-1.

Sudomo A, Leksono B, Tata HL, Rahayu AAD, Umroni A, Rianawati H, Asmaliyah, Krisnawati, Setyayudi A, Utomo MMB, Pieter LAG, Wresta A, Indrajaya Y, Rahman SA, Baral H. 2023. Can agroforestry contribute to food and livelihood security for Indonesia’s smallholders in the climate change era? Agriculture 13 (10): 1896. https://doi.org/10.3390/agriculture13101896.

Suprayogo D, Hairiah K, Hafidzianor, Rahayu S (eds). 2023. Agroforestri Khas Pegunungan Nusantara: Jendela Jawa Timur. Seri Katalog Agroforestri Nusantara Volume 3. World Agroforestry (ICRAF), Bogor. [Indonesian]

Tesfa E, Gudesho G, Wubie M, Awoke A. 2025. Shade tree diversity, structure, and regeneration dynamics in the Sheko semi-forest coffee agroecosystem, Southwest Ethiopia. BMC Ecol Evol 25 (1): 132. https://doi.org/10.1186/s12862-025-02470-z.

Tham-Agyekum EK, Ntem S, Sarbah E, Anno-Baah K, Asiedu P, Bakang JEA, Jones EO. 2023. Resilience against climate variability: The application of nature-based solutions by cocoa farmers in Ghana. Environ Sustain Indic 20: 100310. https://doi.org/10.1016/j.indic.2023.100310.

The Plant List. 2013. The Plant List: A working list of all known plant species. Version 1.1 (September 2013). Royal Botanic Gardens, Kew and Missouri Botanical Garden. www.theplantlist.org.

Toledo VM, Barrera-Bassols N. 2008. La memoria biocultural: La importancia ecológica de las sabidurías tradicionales. Icaria Editorial, Barcelona.

Toledo VM, Moguel P. 2012. Coffee and sustainability: The multiple values of traditional shaded coffee. J Sustain Agric 36 (3): 353-377. https://doi.org/10.1080/10440046.2011.583719.

Torquebiau EF. 2000. A renewed perspective on agroforestry concepts and classification. C R Acad Sci III Sci Vie 323 (11): 1009-1017. https://doi.org/10.1016/S0764-4469(00)01239-7.

Triwanto J, Arrofi FGR, Rahayu EM. 2022. Contribution of coffee agroforestry to the income of farmers in Tulungrejo Village, Ngantang District, Malang Regency. Jurnal Penelitian Kehutanan Wallacea 11 (2): 79-88. https://doi.org/10.18330/jwallacea.2022.vol11iss2pp79-88.

Tscharntke T, Clough Y, Bhagwat SA, Buchori D, Faust H, Hertel D, Hölscher D, Juhrbandt J, Kessler M, Perfecto I, Scherber C, Schroth G, Veldkamp E, Wanger TC. 2011. Multifunctional shade-tree management in tropical agroforestry landscapes: A review. J Appl Ecol 48 (3): 619-629. https://doi.org/10.1111/j.1365-2664.2010.01939.x.

Ullah AM, Hassan A, Hamza A. 2023. Role of clove in human medical history. SAR J Anat Physiol 4 (2): 10-19. https://doi.org/10.36346/sarjap.2023.v04i02.001.

Urugo MM, Worku M, Tola YB, Gemeded HF. 2025. Ethiopian coffee: Production systems, geographical origin traceability, and European Union deforestation regulation directive compliance. J Agric Food Res 19: 101695. https://doi.org/10.1016/j.jafr.2025.101695.

Valencia V, West P, Sterling EJ, García-Barrios L, Naeem S. 2015. The use of farmers’ knowledge in coffee agroforestry management: Implications for the conservation of tree biodiversity. Ecosphere 6 (7): 1-17. https://doi.org/10.1890/ES14-00428.1.

Waktola TU, Fekadu K. 2021. Adoption of coffee shade agroforestry technology and shade tree management in Gobu Seyo District, East Wollega, Oromia. Adv Agric 2021 (1): 8574214. https://doi.org/10.1155/2021/8574214.

Wynter V, Milner-Gulland EJ, Poore J. 2025. A global comparison of the biodiversity impacts of coffee agricultural systems-from monoculture to diverse agroforestry. Agric Syst 229: 104449. https://doi.org/10.1016/j.agsy.2025.104449.

Most read articles by the same author(s)

1 2 3 > >>