Contribution of trees to the conservation of biodiversity and ecosystem services in agricultural landscapes

References

• Altieri MA. 1995. Agroecology: the science of sustainable agriculture. 2nd ed. London (UK): Intermediate Technology Publications (ITP).
   Google Scholar
• Anderson JM, Ingram JSI. 1993. Tropical soil biology and fertility: a handbook of methods. 2nd ed. Wallingford: CAB International.
   Google Scholar
• Balvanera P, Pfisterer AB, Buchmann N, He J-S, Nakashizuka T, Raffaelli D, Schmid B. 2006. Quantifying the evidence for biodiversity effects on ecosystem functioning and services. Ecol Lett. 9:1146–1156.
   PubMed Web of Science ®Google Scholar
• Balvanera P, Quijas S, Martín-López B, Barrios E, Dee L, Isbell F, Durance I, White P, Blanchard R, De Groot R. 2016. The links between biodiversity and ecosystem services. In: Potschin M, Haines-Young R, Fish R, Turner RK, editors. Routledge handbook of ecosystem services. London (UK): Routledge, Taylor & Francis Group; p. 45–49.
   Google Scholar
• Bardgett RD, van der Putten WH. 2014. Belowground biodiversity and ecosystem functioning. Nature. 515:505–511.
   PubMed Web of Science ®Google Scholar
• Barrios E. 2007. Soil biota, ecosystem services and land productivity. Ecol Econ. 64:269–285.
   Web of Science ®Google Scholar
• Barrios E, Cobo JG, Rao IM, Thomas RJ, Amezquita E, Jimenez JJ, Rondon MA. 2005. Fallow management for soil fertility recovery in tropical Andean agroecosystems in Colombia. Agric Ecosyst Envir. 110:29–42.
   Web of Science ®Google Scholar
• Barrios E, Shepherd K, Sinclair F. 2015. Soil health and agricultural sustainability: the role of soil biota. In: FAO, editor. Agroecology for food security and nutrition. Rome (Italy): Proceedings of the FAO International Symposium; p. 104–122.
   Google Scholar
• Barrios E, Sileshi GW, Shepherd KD, Sinclair F. 2012. Agroforestry and soil health: linking trees, soil biota and ecosystem services. In: Wall DH, Bardgett RD, Behan- Pelletier V, Herrick JE, Jones TH, Ritz K, Six J, Strong DR, Van der Putten WH, editors. Soil ecology and ecosystem services. Oxford (UK): Oxford University Press; p. 315–330.
   Google Scholar
• Beare MH, Coleman DC, Crossley DA Jr, Hendrix PF, Odum EP. 1995. A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling. Plant Soil. 170:5–22.
   Web of Science ®Google Scholar
• Beer J, Muschler R, Kass D, Somarriba E. 1998. Shade management in coffee and cacao plantations. Agroforestry Syst. 38:139–164.
   Web of Science ®Google Scholar
• Bhagwat S, Willis KJ, Birks HJB, Whittaker RJ. 2008. Agroforestry: a refuge for tropical biodiversity? Trends in Ecol Evol. 23:261–267.
   PubMed Web of Science ®Google Scholar
• Bligh EG, Dyer WJ. 1959. A rapid method of total lipid extraction and purification. Can J Biochem Physiol. 37:911–917.
   PubMedGoogle Scholar
• Bommarco R, Kleijn D, Potts SG. 2013. Ecological intensification: harnessing ecosystem services for food security. Trends Ecol Evol. 28:230–238.
   PubMed Web of Science ®Google Scholar
• Brussaard L, Caron P, Campbell B, Lipper L, Mainka S, Rabbinge R, Babin D, Pulleman M. 2010. Reconciling biodiversity conservation and food security: scientific challenges for a new agriculture. Curr Opin Environ Sustain. 2:34–42.
   Web of Science ®Google Scholar
• Chambon B, Ruf F, Kongmanee C, Angthong S. 2016. Can the cocoa cycle model explain the continuous growth of the rubber (Hevea brasiliensis) sector for more than a century in Thailand? J Rural Stud. 44:87–197.
   Web of Science ®Google Scholar
• Coe R, Sinclair FL, Barrios E. 2014. Scaling up agroforestry requires research ‘in’ rather than ‘for’ development. Curr Opin Environ Sustain. 6:73–77.
   Web of Science ®Google Scholar
• Dafni A, Kevan PG, Husband BC, editors. 2005. Practical pollination ecology. Cambridge (Canada): Enviroquest.
   Google Scholar
• Das A, Tomar J, Ramesh T, Munda G, Ghosh P, Patel D. 2010. Productivity and economics of lowland rice as influenced by incorporation of N-fixing tree biomass in mid-altitude subtropical Meghalaya, North East India. Nutr Cycl Agroecosyst. 87:9–19.
   Web of Science ®Google Scholar
• De Bello F, Lavorel S, Díaz S, Harrington R, Cornelissen JHC, Bardgett RD, Berg MP, Cipriotti P, Feld CK, Hering D, et al. 2010. Towards an assessment of multiple ecosystem processes and services via functional traits. Biodiv Conserv. 19:2873–2893.
   Web of Science ®Google Scholar
• De Deyn GB, Cornelissen JHC, Bardgett RD. 2008. Plant functional traits and soil carbon sequestration in contrasting biomes. Ecol Lett. 11:516–531.
   PubMed Web of Science ®Google Scholar
• De Groot RS, Wilson MA, Boumans RMJ. 2002. A typology for the classification, description and valuation of ecosystem functions, goods and services. Ecol Econ. 41:393–408.
   Web of Science ®Google Scholar
• Dewi WS, Hairiah K, Yanuwiyadi B, Suprayogo D. 2006. Can agroforestry systems maintain earthworm diversity after conversion of forest to agricultural land? Agrivita. 28:198–220.
   Google Scholar
• Dewi WS, Senge M. 2015. Earthworm diversity and ecosystem services under threat. Rev Agric Sci. 3:25–35.
   Google Scholar
• Diaz S, Lavorel S, De Bello F, Quétier F, Grigulis K, Robson TM. 2007. Incorporating plant functional diversity effects in ecosystem service assessments. Pnas. 104:20684–20689.
   PubMed Web of Science ®Google Scholar
• Díaz S, Quétier F, Cáceres DM, Trainor SF, Pérez-Harguindeguy N, Bret-Harte MS, Finegan B, Peña-Claros M, Poorter L. 2011. Linking functional diversity and social actor strategies in a framework for interdisciplinary analysis of nature’s benefits to society. Pnas. 108:895–902.
   PubMed Web of Science ®Google Scholar
• Diedhiou-Sall S, Dossa EL, Diedhiou I, Badiane AN, Assigbetsé KB, Ndiaye Samba SA, Khouma M, Sène M, Dick R. 2013. Microbiology and macrofaunal activity in soil beneath shrub canopies during residue decomposition in agroecosystems of the Sahel. Soil Sci Soc Am J. 77:501–511.
   Web of Science ®Google Scholar
• Donaldson J, Nänni I, Zachariades C, Kemper J. 2002. Effects of habitat fragmentation on pollinator diversity and plant reproductive success in Renosterveld shrublands of South Africa. Conserv Biol. 5:1267–1276.
   Google Scholar
• Dore T, Makowski D, Malezieux E, Munier-Jolain N, Tchamitchian M, Tittonell P. 2011. Facing up to the paradigm of ecological intensification in agronomy: revisiting methods, concepts and knowledge. Eur J Agron. 34:197–210.
   Web of Science ®Google Scholar
• Foley JA, DeFries R, Asner GP, Barford C, Bonan G, Carpenter SR, Chapin FS, Coe MT, Daily GC, Gibbs HK, et al. 2005. Global consequences of land use. Science. 305:570–574.
   Google Scholar
• Fonte SJ, Barrios E, Six J. 2010. Earthworms, soil fertility and aggregate-associated soil organic matter dynamics in the Quesungual agroforestry system. Geoderma. 155:320–328.
   Web of Science ®Google Scholar
• Food and Agriculture Organization (FAO). 2007. The state of food and agriculture 2007. Paying farmers for environmental services. Rome: FAO.
   Google Scholar
• Frostegåd Å, BåÅh E. 1996. The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol Fertil Soils. 22:59–65.
   Web of Science ®Google Scholar
• Giller KE, Bignell DE, Lavelle P, Swift MJ, Barrios E, Moreira F, Van Noordwijk M, Barois I, Karanja N, Huising J. 2005. Soil biodiversity in rapidly changing tropical landscapes: scaling down and scaling up. In: Bardgett RD, Usher MB, Hopkins DW, editors. Biological diversity and function in soils. Cambridge (UK): Cambridge University Press; p. 295–318.
   Google Scholar
• Gliessman SR. 2007. Agroecology: the ecology of sustainable food systems. Boca Raton (FL): CRC Press; p. 384.
   Google Scholar
• Golinska P, Dahm H. 2011. Occurrence of actinomycetes in forest soil. Dendrobiology. 66:3–13.
   Web of Science ®Google Scholar
• Gonzalez-Espinosa M, Meave J, Lorea-Hernandez F, Ibarra-Manriquez G, Newton A, editors. 2011. The red list of Mexican cloud forest trees. Fauna & Flora International. [accessed 2012 Apr 24]. http://www.globaltrees.org/rl_mexican_cloudforest.htm.
   Google Scholar
• Hairiah K, Sitompul SM, Van Noordwijk M, Palm CA. 2001. Methods for sampling carbon stocks above and below ground. ASB_LN 4B. In: VanNoordwijk M, Williams SE, Verbist B, editors. Towards integrated natural resource management in forest margins of the humid tropics: local action and global concerns. ASB-Lecture Notes 1–12. Bogor (Indonesia): International Centre for Research in Agroforestry (ICRAF). http://www.icraf.cgiar.org/sea/Training/Materials/ASB-TM/ASB-ICRAFSEA-LN.htm.
   Google Scholar
• Hairiah K, Sulistyani H, Suprayogo D, Widianto, Purnomosidhi P, Widodo RH, Van Noordwijk M. 2006. Litter layer residence time in forest and coffee agroforestry systems in Sumberjaya, West Lampung. Forest Ecol Mgmt. 224:45–57.
   Web of Science ®Google Scholar
• IUCN. 2013. IUCN red list of threatened species. Version 2013.1. http://www.iucnredlist.org/search.
   Google Scholar
• Jackson LE, Pulleman MM, Brussaard L, Bawa KW, Brown GG, Cardoso IM, De Ruiter PC, Garcia-Barrios L, Hollander AD, Lavelle P, et al. 2012. Social-ecological and regional adaptation of agrobiodiversity management across a global set of research regions. Global Environ Change. 22:623–639.
   Web of Science ®Google Scholar
• Janzen DH. 1976. Why bamboos wait so long to flower. Ann Rev Ecol Syst. 7:347–391.
   Google Scholar
• Jaramillo J, Chabi-Olaye A, Kamonjo C, Jaramillo A, Vega FE, Poehling H-M, Borgemeister C. 2009. Thermal tolerance of the Coffee berry borer Hypothenemus hampei: predictions of climate change impact on a tropical insect pest. PloS One. 4:e6487.
   PubMed Web of Science ®Google Scholar
• Jaramillo J, Setamou M, Muchugu E, Chabi-Olaye A, Jaramillo A, Mukabana J, Maina J, Gatharan S, Borgemeister C. 2013. Climate change or urbanization? Impacts on a traditional coffee production system in East Africa over the last 80 years. PloS One. 8:e51815.
   PubMed Web of Science ®Google Scholar
• Jha S, Bacon CM, Philpott SM, Ernesto Méndez VE, Läderach P, Rice RA. 2014. Shade coffee: update on a disappearing refuge for biodiversity. BioScience. 64:416–428.
   Web of Science ®Google Scholar
• Jing X, Sanders NJ, Shi Y, Chu H, Classen AT, Zhao K, Chen L, Shi Y, Jiang Y, He J-S. 2015. The links between ecosystem multifunctionality and above- and belowground biodiversity are mediated by climate. Nat Commun. 6:8159.
   PubMed Web of Science ®Google Scholar
• Jonsson M, Raphael IA, Ekbom B, Kyamanywa S, Karungi-Tumutegyereize J. 2015. Contrasting effects of shade level and altitude on two important coffee pests. J Pest Sci. 88:281–287.
   Web of Science ®Google Scholar
• Kamau S, Barrios E, Karanja N, Ayuke F, Lehmann J. 2017. Soil macrofauna abundance under dominant tree species increases along a soil degradation gradient. Soil Biol Biochem. 112:35–46.
   Web of Science ®Google Scholar
• Karp DS, Mendenhall CD, Sandi RF, Chaumont N, Ehrlich PR, Hadly EA, Daily GC. 2013. Forest bolsters bird abundance, pest control and coffee yield. Ecol Lett. 16:1339–1347.
   PubMed Web of Science ®Google Scholar
• Kearns CA, Inouye DW. 1993. Techniques for pollination biologists. Niwot (CO): University Press of Colorado.
   Google Scholar
• Kibblewhite MG, Ritz K, Swift MJ. 2008. Soil health in agricultural systems. Philos Trans Royal Soc B Biol Sci. 363:685–701.
   PubMed Web of Science ®Google Scholar
• Klein A-M, Cunningham SA, Bos M, Steffan-Dewenter I. 2008. Advances in pollination ecology from tropical plantation crops. Ecology. 89:935–943.
   PubMed Web of Science ®Google Scholar
• Klein A-M, Vaissiere BE, Cane JH, Steffan-Dewenter I, Cunningham SA, Kremen C, Tscharntke T. 2007. Importance of pollinators in changing landscapes for world crops. Proc Royal Soc B Biol Sci. 274:303–313.
   PubMed Web of Science ®Google Scholar
• Kremen C. 2005. Managing ecosystem services: what do we need to know about their ecology. Ecol Lett. 8:468–479.
   PubMed Web of Science ®Google Scholar
• Kutywayo D, Chemura A, Kusena W, Chidoko P, Mahoya C. 2013. The impact of climate change on the potential distribution of agricultural pests: the case of the Coffee white stem borer (Monochamus leuconotus P.) in Zimbabwe. PLoS One. 8:e73432.
   PubMed Web of Science ®Google Scholar
• Kuyah S, Oborn I, Jonsson M, Dahlin AS, Barrios E, Muthuri C, Malmer A, Nyaga J, Magaju C, Namirembe S, et al. 2016. Trees in agricultural landscapes enhance provision of ecosystem services in Sub-Saharan Africa. Int J Biodiv Sci Eco Serv Mgmt. 12:255–273.
   Google Scholar
• Lavelle P, Rodriguez N, Arguello O, Bernal J, Botero C, Chaparro P, Gomez Y, Gurierrez A, Hurtado MP, Loaiza S, et al. 2014. Soil ecosystem services and land use in the rapidly changing Orinoco River Basin of Colombia. Agric Ecosyst Environ. 185:107–116.
   Web of Science ®Google Scholar
• Legname E, Brauman A, Poulain J, Razafimbelo T, Pablo A-L, Brüls T, O’Donohue M, Razafindrakoto M, Blanchart E, Chapuis-Lardy L, et al. 2012. Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil. ISME J. 6:213–222.
   PubMed Web of Science ®Google Scholar
• Maestre FT, Quero JL, Gotelli NJ, Escudero A, Ochoa V, Delgado-Baquerizo M, García-Gómez M, Bowker MA, Soliveres S, Escolar C, et al. 2012. Plant species richness and ecosystem multifunctionality in global drylands. Science. 335:214–218.
   PubMed Web of Science ®Google Scholar
• Marichal E, Feijoo Martinez A, Praxedes C, Ruiz D, Carvajal AF, Oszwald J, Hurtado MP, Brown GG, Grimaldi M, Desjandins T. 2010. Invasion of Pontoscolex corethrurus (Glossoscolecidae, Oligochaeta) in landscapes of the Amazonian deforestation arc. Appl Soil Ecol. 46(3):443–449.
   Web of Science ®Google Scholar
• Matson PA, Parton WJ, Power AG, Swift MJ. 1997. Agricultural intensification and ecosystem properties. Science. 277:504–509.
   PubMed Web of Science ®Google Scholar
• McGregor SE. 1976. Insect pollination of cultivated crop plants. United States Department of Agriculture. https://www.ars.usda.gov/SP2UserFiles/Place/20220500/OnlinePollinationHandbook.pdf.
   Google Scholar
• Mortimer PE, Gui H, Xu J, Zhang C, Barrios E, Hyde KD. 2015. Alder trees enhance crop productivity and soil microbial biomass in tea plantations. Appl Soil Ecol. 96:25–32.
   Web of Science ®Google Scholar
• Muhamad D. 2013. Socio-ecological assessment of ecosystem services in relation to biodiversity along a gradient from forest to agricultural landscape in West Java, Indonesia [ PhD dissertation]. Department of Ecosystem Studies, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Japan.
   Google Scholar
• Myers N, Mittermeler RA, Mittermeler CG, Gab DF, Kent J. 2000. Biodiversity hotspots for conservation priorities. Nature. 403(6772):853–858.
   PubMed Web of Science ®Google Scholar
• Ong CK, Kho RM, Radersma S. 2004. Ecological interactions in multispecies agroecosystems: concepts and rules. In: Van Noordwijk M, Cadisch G, Ong CK, editors. Below-ground interactions in tropical agroecosystems – concepts and models with multiple plant components. Wallingford (UK): CAB International; p. 1–15.
   Google Scholar
• Pauli N, Barrios E, Conacher AJ, Oberthur T. 2011. Soil macrofauna in agricultural landscapes dominated by the Quesungual Slash-and-Mulch Agroforestry System, western Honduras. Appl Soil Ecol. 47:119–132.
   Web of Science ®Google Scholar
• Pauli N, Barrios E, Conacher AJ, Oberthur T. 2012. Farmer knowledge of the relationships among soil macrofauna, soil quality, and tree species in a small holder agroforestry system of western Honduras. Geoderma. 189–190:186–198.
   Web of Science ®Google Scholar
• Pauli N, Oberthur T, Barrios E, Conacher AJ. 2010. Fine-scale spatial and temporal variation in earthworm surface casting activity in agroforestry fields, western Honduras. Pedobiologia. 53:127–139.
   Web of Science ®Google Scholar
• Peacock AD, Mullen MD, Ringelberg DB, Tyler DD, Hedrick DB, Gale PM, White DC. 2001. Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol Biochem. 33:1011–1019.
   Web of Science ®Google Scholar
• Peeters LYK, Soto-Pinto L, Perales H, Montoya G, Ishiki M. 2003. Coffee production, timber, and firewood in traditional and Inga-shaded plantations in Southern Mexico. Agric Ecosyst Environ. 95:481–493.
   Web of Science ®Google Scholar
• Perfecto I, Rice RA, Greenberg R, van der Voort ME. 1996. Shade coffee: a disappearing refuge for biodiversity. Bioscience. 46:598–608.
   Web of Science ®Google Scholar
• Perfecto I, Vandermeer J. 2002. Quality of agroecological matrix in a tropical montane landscape: ants in coffee plantations in southern Mexico. Conserv Biol. 16:174–182.
   PubMed Web of Science ®Google Scholar
• Perfecto I, Vandermeer J. 2008. Biodiversity conservation in tropical agroecosystems: a new conservation paradigm. Annals NY Acad Sci. 1134:173–200.
   PubMed Web of Science ®Google Scholar
• Perfecto I, Vandermeer J, Lopez Bautista G, Nuñez G, Greenberg R, Bichier P, Langridge S. 2004. Greater predation in shaded coffee farms: the role of resident neotropical birds. Ecology. 85:2677–2681.
   Web of Science ®Google Scholar
• Philpott SM, Dietsch T. 2003. Coffee and conservation: a global context and the value of farmer involvement. Conserv Biol. 17:1844–1846.
   Web of Science ®Google Scholar
• Potts SG, Biesmeijer JC, Kremen C, Neumann P, Schweiger O. 2010. Global pollinator declines: trends, impacts and drivers. Trends Ecol Evol. 25:345–353.
   PubMed Web of Science ®Google Scholar
• Prabhu R, Barrios E, Bayala J, Diby L, Donovan J, Gyau A, Graudal L, Jamnadass R, Kahia J, Kehlenbeck K, et al. 2015. Agroforestry: realizing the promise of an agroecological approach. In: FAO, editor. Agroecology for food security and nutrition. Rome (Italy): Proceedings of the FAO International Symposium; p. 201–224.
   Google Scholar
• Prescott CE, Grayston SJ. 2013. Tree species influence on microbial communities in litter and soil: current knowledge and research needs. Forest Ecol Mgmt. 309:19–27.
   Web of Science ®Google Scholar
• Pretty JN, Noble AD, Bossio D, Dixon J, Hine RE, Penning de Vries FWT, Morison JIL. 2006. Resource-conserving agriculture increases yields in developing countries. Environ Sci Technol. 40:1114–1119.
   PubMed Web of Science ®Google Scholar
• Pumariño L, Sileshi GW, Gripenberg S, Kaartinen R, Barrios E, Muchane MN, Midega C, Jonsson M. 2015. Effects of agroforestry on pest, disease and weed control: a meta-analysis. Basic Appl Ecol. 16:573–582.
   Web of Science ®Google Scholar
• Rappole JH, King DI, Rivera JHV. 2003. Coffee and conservation. Conserv Biol. 17:334–336.
   Web of Science ®Google Scholar
• Ricketts TH, Daily GC, Ehrlich PR, Michener CD. 2004. Economic value of tropical forest to coffee production. Pnas. 18:12579–12582.
   Google Scholar
• Ricketts TH, Regetz J, Steffan-Dewenter I, Cunningham SA, Kremen C, Bogdanski A, Gemmill-Herren B, Greenleaf SS, Klein AM, Mayfield MM, et al. 2008. Landscape effects on crop pollination services: are there general patterns? Ecol Lett. 11:499–515.
   PubMed Web of Science ®Google Scholar
• Rockström J, Steffen W, Noone K, Persson Å, Chapin-III FS, Lambin E, Lenton TM, Scheffer M, Folke C, Schellnhuber H, et al. 2009. Planetary boundaries: exploring the safe operating space for humanity. Ecol Soc. 14(2):32. [online]. http://www.ecologyandsociety.org/vol14/iss2/art32/.
   Web of Science ®Google Scholar
• Romero-Alvarado Y, Soto-Pinto L, Garcıa-Barrios L. 2002. Coffee yields and soil nutrients under the shades of Inga sp. vs. multiple species in Chiapas, Mexico. Agroforestry Syst. 54:215–224.
   Web of Science ®Google Scholar
• Roubik DW. 1995. Pollination of cultivated plants in the tropics. FAO Agricultural Services Bulletin 118. Rome: FAO.
   Google Scholar
• Rousseau L, Fonte SJ, Tellez O, van der Hoek R, Lavelle P. 2013. Soil macrofauna as indicators of soil quality and land use impacts in smallholder agroecosystems of western Nicaragua. Ecol Indic. 27:71–82.
   Web of Science ®Google Scholar
• Rutherford MA, Phiri N, editors. 2006. Pests and diseases of coffee in Eastern Africa: a technical and advisory manual. Wallingford (UK): CAB International.
   Google Scholar
• Schroth G, Da Fonseca GAB, Harvey CA, Gascon C, Vasconcelos HL, Izac AM, editors. 2004. Agroforestry and biodiversity conservation in tropical landscapes. Washington (DC): Island Press. http://publications.cirad.fr/une_notice.php?dk=518308.
   Google Scholar
• Selmants PC, Hart SC, Boyle SI, Stark JM. 2005. Red alder (Alnus rubra) alters community-level soil microbial function in conifer forests of the Pacific Northwest, USA. Soil Biol Biochem. 37:1860–1868.
   Web of Science ®Google Scholar
• Šnajdr J, Dobiášová P, Urbanová M, Petránková M, Cajthaml T, Frouz J, Baldrian P. 2013. Dominant trees affect microbial community composition and activity in post-mining afforested soils. Soil Biol Biochem. 56:105–115.
   Web of Science ®Google Scholar
• Snapp SS, Blackie M, Gilbert RA, Bezner-Kerr R, Kanyama-Phiri GY. 2010. Biodiversity can support a greener revolution in Africa. PNAS. 107:20840–20845.
   PubMed Web of Science ®Google Scholar
• Steffan-Dewenter I, Kessler M, Barkmann J, Bos MM, Buchori D, Erasmi S, Faust H, Gerold G, Glenk K, Gradstein SR, et al. 2007. Trade-offs between income, biodiversity, and ecosystem functioning during tropical rainforest conversion and agroforestry intensification. PNAS. 104:4973–4978.
   PubMed Web of Science ®Google Scholar
• Swift MJ, Izac AM, Van Noordwijk M. 2004. Biodiversity and ecosystems services in agricultural landscapes - are we asking the right questions? Agric Ecosyst Environ. 104:113–134.
   Web of Science ®Google Scholar
• Teodoro A, Klein AM, Reis PR, Tscharntke T. 2009. Agroforestry management affects coffee pests contingent on season and developmental stage. Agric Forest Entomol. 11:295–300.
   Web of Science ®Google Scholar
• Tittonell P. 2014. Ecological intensification of agriculture - sustainable by nature. Curr Opin Environ Sustain. 8:53–61.
   Web of Science ®Google Scholar
• Tomich TP, Brodt S, Ferris H, Galt R, Horwarth WR, Kebreab E, Leveau JHJ, Liptzin D, Lubell M, Merel P, et al. 2011. Agroecology: a review from a global-change perspective. Annu Rev Environ Resour. 36:193–222.
   Web of Science ®Google Scholar
• Tscharntke T, Clough Y, Bhagwat SA, Buchori D, Faust H, Hertel D, Hölscher D, Juhrbandt J, Kessler M, Perfecto I, et al. 2011. Multifunctional shade-tree management in tropical agroforestry landscapes - a review. J Appl Ecol. 48:619–629.
   Web of Science ®Google Scholar
• Tscharntke T, Clough Y, Wanger TC, Jackson L, Motzke I, Perfecto I, Vandermeer J, Whitbread A. 2012a. Global food security, biodiversity conservation and the future of agricultural intensification. Biol Conserv. 151:53–59.
   Web of Science ®Google Scholar
• Tscharntke T, Tylianakis JM, Rand TA, Didham RK, Fahrig L, Batáry P, Bengtsson J, Clough Y, Crist TO, Dormann CF, et al. 2012b. Landscape moderation of biodiversity patterns and processes - eight hypotheses. Biol Rev. 87:661–685.
   PubMed Web of Science ®Google Scholar
• Ushio M, Kitayama K, Balser T. 2010. Tree species-mediated spatial patchiness of the composition of microbial community and physicochemical properties in the topsoils of a tropical montane forest. Soil Biol Biochem. 42:1588–1595.
   Web of Science ®Google Scholar
• Valencia V, García-Barrios L, West P, Sterling EJ, Naeem S. 2014. The role of coffee agroforestry in the conservation of tree diversity and community composition of native forests in a Biosphere Reserve. Agric Ecosyst Environ. 189:154–163.
   Web of Science ®Google Scholar
• Valencia V, Naeem S, Garcia-Barrios L, West P, Sterling EJ. 2016. Conservation of tree species of late succession and conservation concern in coffee agroforestry systems. Agric Ecosyst Environ. 219:32–41.
   Web of Science ®Google Scholar
• 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:art122.
   Web of Science ®Google Scholar
• Van der Putten WH, Bardgett R, Bever JD, Bezemer TM, Casper BB, Fukami T, Kardol P, Kliromonos JN, Kulmatski A, Schweitzer JA, et al. 2013. Plant-soil feedbacks: the past, the present and future challenges. J Ecology. 101:265–276.
   Web of Science ®Google Scholar
• Vandermeer J, Perfecto I. 2007. The agricultural matrix and a future paradigm for conservation. Conserv Biol. 21:274–277.
   PubMed Web of Science ®Google Scholar
• Vanlalhluna PC, Sahoo UK. 2009. Performance of multi-purpose trees and associated crops in agroforestry system of Mizoram. Indian J Forest. 32:191–194.
   Google Scholar
• Wall DH, Bardgett RD, Kelly EF. 2010. Biodiversity in the dark. Nat Geosci. 3:297–298.
   Web of Science ®Google Scholar
• Wardle DA, Bardgett RD, Kliromonos JN, Setala H, Van der Putten W, Wall DH. 2004. Ecological linkages between aboveground and belowground biota. Science. 304:1629–1633.
   PubMed Web of Science ®Google Scholar
• Zomer RJ, Neufeldt H, Xu J, Ahrends A, Bossio D, Trabucco A, van Noordwijk M, Wan M. 2016. Global tree cover and biomass carbon on agricultural land: the contribution of agroforestry to global and national carbon budgets. Sci Rep. 6:29987.
   PubMed Web of Science ®Google Scholar