Skip to main content

Advertisement

SpringerLink
Log in

Spatially explicit models predict coffee rust spread in fragmented landscapes

  • Research Article
  • Published:
Landscape Ecology Aims and scope Submit manuscript

Abstract

Context

Landscape structure influences the spread of plant pathogens, including coffee leaf rust, a fungal disease affecting the coffee industry. Rust transmission is likely affected by landscape structure through the dispersal of wind-borne spores. Previous studies found positive associations between rust incidence and the proportion of pasture cover, suggesting deforestation may facilitate spore dispersal.

Objectives

We explored the links between landscape structure and coffee rust by modeling the spread of rust transmission. We investigated how (1) spatial clustering of coffee farms, (2) proportion of landscape deforestation, and (3) clustering of deforestation affects the speed of rust transmission.

Methods

We developed a probabilistic model to simulate within-patch and between-patch transmission in simulated and real landscapes. We modeled within-patch transmission using a probabilistic cellular automata model and between-patch transmission using a random walk with spore movement inhibited by canopy cover.

Results

Clustering of coffee farms is the primary driver of rust transmission. Deforestation is a secondary driver of rust spread: outbreaks spread more rapidly in landscapes where deforested areas are evenly dispersed throughout the landscape. When applied to real landscapes in Costa Rica, the model yields the same trends as simulated landscapes and suggests increased amounts of coffee near the starting location of the outbreak are correlated with more rapid rust spread.

Conclusions

It is essential to consider landscape structure when managing the spread of crop diseases. Increasing the spacing between coffee farms and reducing forest fragmentation in coffee-growing regions can benefit biodiversity conservation and reduce the economic impacts of coffee rust.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Data availability

Not applicable.

Code availability

All code and model outputs are archived on Zenodo at https://zenodo.org/record/6760264#.Yrm2o3bMJdg.

References

  • 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

    Article  Google Scholar 

  • Amico AL, Ituarte-Lima C, Elmqvist T (2020) Learning from social–ecological crisis for legal resilience building: multi-scale dynamics in the coffee rust epidemic. Sustain Sci 15:485–501

    Article  Google Scholar 

  • Avelino J, Cristancho M, Georgiou S et al (2015) The coffee rust crises in Colombia and Central America (2008–2013): impacts, plausible causes and proposed solutions. Food Sec 7:303–321

    Article  Google Scholar 

  • Avelino J, Romero-Gurdián A, Cruz-Cuellar HF, Declerck FAJ (2012) Landscape context and scale differentially impact coffee leaf rust, coffee berry borer, and coffee root-knot nematodes. Ecol Appl 22:584–596

    Article  PubMed  Google Scholar 

  • Avelino J, Willocquet L, Savary S (2004) Effects of crop management patterns on coffee rust epidemics. Plant Pathol 53:541–547

    Article  Google Scholar 

  • Avelino J, Zelaya H, Merlo A et al (2006) The intensity of a coffee rust epidemic is dependent on production situations. Ecol Model 197:431–447

    Article  Google Scholar 

  • Baker P (2014) The “Big Rust”: an update on the coffee leaf rust situation. Coffee Cocoa Int 40:37–39

    Google Scholar 

  • Bassanezi RB, Montesino LH, Gimenes-Fernandes N et al (2013) Efficacy of area-wide inoculum reduction and vector control on temporal progress of Huanglongbing in young sweet orange plantings. Plant Dis 97:789–796

    Article  PubMed  Google Scholar 

  • Becker S, Mulinge SK, Kranz J (1975) Evidence that uredospores of Hemileia vastatrix Berk. and Br. are wind-borne. Phytopathol Z 82:359–360

    Article  Google Scholar 

  • Boudrot A, Pico J, Merle I et al (2016) Shade effects on the dispersal of airborne Hemileia vastatrix Uredospores. Phytopathology 106:572–580

    Article  PubMed  Google Scholar 

  • Brévault T, Clouvel P (2019) Pest management: reconciling farming practices and natural regulations. Crop Prot 115:1–6

    Article  Google Scholar 

  • Cerda R, Avelino J, Gary C et al (2017) Primary and secondary yield losses caused by pests and diseases: assessment and modeling in coffee. PLoS ONE 12:e0169133

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cunniffe NJ, Koskella BE, Metcalf CJ et al (2015) Thirteen challenges in modelling plant diseases. Epidemics 10:6–10

    Article  PubMed  Google Scholar 

  • Delignette-Muller ML, Dutang C (2015) fitdistrplus: an R package for fitting distributions. J Stat Softw 64:1–31

    Article  Google Scholar 

  • Ellwanger JH, Kulmann-Leal B, Kaminski VL et al (2020) Beyond diversity loss and climate change: impacts of Amazon deforestation on infectious diseases and public health. An Acad Bras Ciênc 92:e20191375

    Article  CAS  PubMed  Google Scholar 

  • Etherington TR, Holland EP, O’Sullivan D (2015) NLMpy: a python software package for the creation of neutral landscape models within a general numerical framework. Methods Ecol Evol 6:164–168

    Article  Google Scholar 

  • Fabre F, Coville J, Cunniffe NJ (2019) Optimising reactive disease management using spatially explicit models at the landscape scale. https://arxiv.org/191112131 [math, q-bio]

  • Fahrig L (2003) Effects of habitat fragmentation on biodiversity. Annu Rev Ecol Evol Syst 34:487–515

    Article  Google Scholar 

  • Fahrig L (2013) Rethinking patch size and isolation effects: the habitat amount hypothesis. J Biogeogr 40:1649–1663

    Article  Google Scholar 

  • Gagliardi S, Avelino J, Beilhe LB, Isaac ME (2020) Contribution of shade trees to wind dynamics and pathogen dispersal on the edge of coffee agroforestry systems: a functional traits approach. Crop Prot 130:105071

    Article  Google Scholar 

  • Gagliardi S, Avelino J, Virginio Filho EM, Isaac ME (2021) Shade tree traits and microclimate modifications: implications for pathogen management in biodiverse coffee agroforests. Biotropica 53:1356–1367

    Article  Google Scholar 

  • Gavish Y, Ziv Y, Rosenzweig ML (2012) Decoupling fragmentation from habitat loss for spiders in patchy agricultural landscapes. Conserv Biol 26:150–159

    Article  PubMed  Google Scholar 

  • Gibb R, Redding DW, Chin KQ et al (2020) Zoonotic host diversity increases in human-dominated ecosystems. Nature 584:398–402

    Article  CAS  PubMed  Google Scholar 

  • Gilligan CA (2008) Sustainable agriculture and plant diseases: an epidemiological perspective. Phil Trans R Soc B 363:741–759

    Article  PubMed  Google Scholar 

  • Gilligan CA, Truscott JE, Stacey AJ (2007) Impact of scale on the effectiveness of disease control strategies for epidemics with cryptic infection in a dynamical landscape: an example for a crop disease. J R Soc Interface 4:925–934

    Article  PubMed  PubMed Central  Google Scholar 

  • Haddad NM, Brudvig LA, Clobert J et al (2015) Habitat fragmentation and its lasting impact on Earth’s ecosystems. Sci Adv 1:e1500052

    Article  PubMed  PubMed Central  Google Scholar 

  • Hagenaars TJ, Donnelly CA, Ferguson NM (2004) Spatial heterogeneity and the persistence of infectious diseases. J Theor Biol 229:349–359

    Article  CAS  PubMed  Google Scholar 

  • Hajian-Forooshani Z, Vandermeer J (2021) Emergent spatial structure and pathogen epidemics: the influence of management and stochasticity in agroecosystems. Ecol Complex 45:100872

    Article  Google Scholar 

  • He HS, DeZonia BE, Mladenoff DJ (2000) An aggregation index (AI) to quantify spatial patterns of landscapes. Landscape Ecol 15:591–601

    Article  Google Scholar 

  • Irey M, Gottwald TR, Graham JH et al (2006) Post-hurricane analysis of citrus canker spread and progress towards the development of a predictive model to estimate disease spread due to catastrophic weather events. Plant Health Progress 7:16

    Article  Google Scholar 

  • Jha S, Bacon CM, Philpott SM et al (2014) Shade coffee: update on a disappearing refuge for biodiversity. Bioscience 64:416–428

    Article  Google Scholar 

  • Keane RE, Holsinger LM, Pratt SD (2006) Simulating historical landscape dynamics using the landscape fire succession model LANDSUM version 4.0. U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station, Ft. Collins, CO

  • Koen EL, Garroway CJ, Wilson PJ, Bowman J (2010) The effect of map boundary on estimates of landscape resistance to animal movement. PLoS ONE 5:e11785

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kushalappa AC, Eskes AB (1989) Coffee rust: epidemiology, resistance, and management. CRC Press, Boca Raton

    Google Scholar 

  • Legg J, Ndalahwa M, Yabeja J et al (2017) Community phytosanitation to manage cassava brown streak disease. Virus Res 241:236–253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Levin SA (1992) The problem of pattern and scale in ecology: the Robert H. MacArthur award lecture. Ecology 73:1943–1967

    Article  Google Scholar 

  • Macfadyen S, Gibson RH, Symondson WOC, Memmott J (2011) Landscape structure influences modularity patterns in farm food webs: consequences for pest control. Ecol Appl 21:516–524

    Article  PubMed  PubMed Central  Google Scholar 

  • Martinez JA, Palazzo DA, Karazawa M, et al (1975) Presenca de esporos de Hemileia vastatrix Berk Br. agente causal de ferrugem do cafeeiro, em diferentes altitudes nas principais areas cafeeiras dos Estados de Sao Paulo e Parana, Brasil. Biologico 41:

  • McCook S, Vandermeer J (2015) The big rust and the red queen: long-term perspectives on coffee rust research. Phytopathology 105:1164–1173

    Article  CAS  PubMed  Google Scholar 

  • Merle I, Tixier P, de Virginio Filho EM et al (2020) Forecast models of coffee leaf rust symptoms and signs based on identified microclimatic combinations in coffee-based agroforestry systems in Costa Rica. Crop Prot 130:105046

    Article  CAS  Google Scholar 

  • Moran PAP (1950) Notes on a continuous stochastic phenomena. Biometricka 37:178–181

    Article  CAS  Google Scholar 

  • Narayana MR (2013) Do coffee varieties and shade trees matter for management of leaf rust disease in India? Evidence for household farmers. Forests, Trees Livelih 22:275–288

    Article  Google Scholar 

  • Oliphant TE (2006) A guide to NumPy. Trelgol Publishing, USA

    Google Scholar 

  • Perfecto I, Jiménez-Soto ME, Vandermeer J (2019) Coffee landscapes shaping the anthropocene: forced simplification on a complex agroecological landscape. Curr Anthropol 60:S236–S250

    Article  Google Scholar 

  • Perfecto I, Rice RA, Greenberg R, Van der Voort ME (1996) Shade coffee: a disappearing refuge for biodiversity: shade coffee plantations can contain as much biodiversity as forest habitats. Bioscience 46:598–608

    Article  Google Scholar 

  • Pham Y, Reardon-Smith K, Mushtaq S, Cockfield G (2019) The impact of climate change and variability on coffee production: a systematic review. Clim Change 156:609–630

    Article  CAS  Google Scholar 

  • Plantegenest M, Le May C, Fabre F (2007) Landscape epidemiology of plant diseases. J R Soc Interface 4:963–972

    Article  PubMed  PubMed Central  Google Scholar 

  • Putz FE, Redford KH (2010) The importance of defining ‘forest’: tropical forest degradation, deforestation, long-term phase shifts, and further transitions. Biotropica 42:10–20

    Article  Google Scholar 

  • Python Software Foundation (2018) Version 3.7.1

  • R Core Team (2020) R: a language and environment for statistical computing. Version 4.0.0. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/

  • Rayner RW (1961a) Germination and penetration studies on coffee rust (Hemileia vastatrix B. & Br.). Ann Appl Biol 49:497–505

    Article  Google Scholar 

  • Rayner RW (1961b) Spore liberation and dispersal of coffee rust Hemileia vastatrix B. et Br. Nature 191:725–725

    Article  Google Scholar 

  • Rimbaud L, Dallot S, Gottwald T et al (2015) Sharka epidemiology and worldwide management strategies: learning lessons to optimize disease control in perennial plants. Annu Rev Phytopathol 53:357–378

    Article  CAS  PubMed  Google Scholar 

  • Riva F, Fahrig L (2022) The disproportionately high value of small patches for biodiversity conservation. Conserv Lett. https://doi.org/10.1111/conl.12881

    Article  Google Scholar 

  • Romero-Alvarado Y, Soto-Pinto L, García-Barrios L, Barrera-Gaytán JF (2002) Coffee yields and soil nutrients under the shades of Inga sp. vs. multiple species in Chiapas. Mexico Agroforestry Systems 54:215–224

    Article  Google Scholar 

  • Saura S, Martınez-Millan J (2000) Landscape patterns simulation with a modified random clusters method. Landscape Ecol 15:661–678

    Article  Google Scholar 

  • Sherman J, Burke JM, Gent DH (2019) Cooperation and coordination in plant disease management. Phytopathology 109:1720–1731

    Article  PubMed  Google Scholar 

  • Soto-Pinto L, Perfecto I, Caballero-Nieto J (2002) Shade over coffee: its effects on berry borer, leaf rust and spontaneous herbs in Chiapas, Mexico. Agrofor Syst 55:37–45

    Article  Google Scholar 

  • Tracey JA, Bevins SN, VandeWoude S, Crooks KR (2014) An agent-based movement model to assess the impact of landscape fragmentation on disease transmission. Ecosphere 5:art119

    Article  Google Scholar 

  • UNFCCC (2006) FCCC/KP/CMP/2005/8/Add.1: report of the conference of the parties on its first session, held at Berlin from 28 March to 7 April 1995. Addendum. Part two: action taken by the conference of the parties at its first session. Geneva, Switzerland

  • Valencia V, García-Barrios L, Sterling EJ et al (2018) Smallholder response to environmental change: impacts of coffee leaf rust in a forest frontier in Mexico. Land Use Policy 79:463–474

    Article  Google Scholar 

  • Valencia V, West P, Sterling EJ et al (2015) The use of farmers’ knowledge in coffee agroforestry management: implications for the conservation of tree biodiversity. Ecosphere 6:art122

    Article  Google Scholar 

  • van der Vossen H, Bertrand B, Charrier A (2015) Next generation variety development for sustainable production of arabica coffee (Coffea arabica L.): a review. Euphytica 204:243–256

    Article  CAS  Google Scholar 

  • Vandermeer J, Hajian-Forooshani Z, Perfecto I (2018) The dynamics of the coffee rust disease: an epidemiological approach using network theory. Eur J Plant Pathol 150:1001–1010

    Article  Google Scholar 

  • Vandermeer J, Rohani P (2014) The interaction of regional and local in the dynamics of the coffee rust disease. https://arxiv.org/14078247 [q-bio]

  • Vandermeer J, Rohani P, Perfecto I (2015) Local dynamics of the coffee rust disease and the potential effect of shade. https://arxiv.org/151005849 [q-bio]

  • Viguera B, Alpízar F, Harvey CA et al (2019) Percepciones de cambio climático y respuestas adaptativas de caficultores costarricenses de pequeña escala1. Agronomía Mesoamericana 30:333–351

    Article  Google Scholar 

  • Vilchez-Mendoza S, Romero-Gurdián A, Avelino J et al (2022) Assessing the joint effects of landscape, farm features and crop management practices on berry damage in coffee plantations. Agr Ecosyst Environ 330:107903

    Article  Google Scholar 

  • Waller JM (1982) Coffee rust—epidemiology and control. Crop Prot 1:385–404

    Article  Google Scholar 

  • Ward R, Gonthier D, Nicholls C (2017) Ecological resilience to coffee rust: varietal adaptations of coffee farmers in Copán, Honduras. Agroecol Sustain Food Syst 41:1081–1098

    Google Scholar 

  • White ER, Hastings A (2020) Seasonality in ecology: progress and prospects in theory. Ecol Complex 44:100867

    Article  Google Scholar 

  • White ER, Smith AT (2018) The role of spatial structure in the collapse of regional metapopulations. Ecology 99:2815–2822

    Article  PubMed  Google Scholar 

  • White JW, Rassweiler A, Samhouri JF et al (2014) Ecologists should not use statistical significance tests to interpret simulation model results. Oikos 123:385–388

    Article  Google Scholar 

  • White LA, Forester JD, Craft ME (2018) Disease outbreak thresholds emerge from interactions between movement behavior, landscape structure, and epidemiology. PNAS 115:7374–7379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wiegand T, Revilla E, Moloney KA (2005) Effects of habitat loss and fragmentation on population dynamics. Conserv Biol 19:108–121

    Article  Google Scholar 

  • Wolfram S (2002) A new kind of science. Wolfram Media, Champaign, IL

    Google Scholar 

  • Zambolim L (2016) Current status and management of coffee leaf rust in Brazil. Trop Plant Pathol 41:1–8

    Article  Google Scholar 

Download references

Acknowledgements

We thank Nick Gotelli and members of the QuEST community at the University of Vermont for helpful feedback on our simulation and analysis. We thank two anonymous reviewers for constructive feedback on this manuscript. We are especially grateful to Jorge A. Ruiz-Arocho for illustrating our graphical abstract. We also thank Emily Fung and Christian Brenes P. at The Tropical Agricultural Research and Higher Education Center (CATIE) for sharing the land-use data used for the real landscape analyses.

Funding

The Quantitative and Evolutionary STEM Training (QuEST) Program financed by the University of Vermont and the National Science Foundation (Grant DGE-1735316) supported all authors. E.M. Bueno was supported by an HHMI Gilliam Fellowship for Advanced Study (Grant #GT13607).

Author information

Authors and Affiliations

  1. Department of Biology, University of Vermont, 109 Carrigan Dr, Burlington, VT, 05405, USA

    Emily M. Beasley

  2. Rubenstein School of Environment and Natural Resources, University of Vermont, 81 Carrigan Dr, Burlington, VT, 05405, USA

    Natalia Aristizábal

  3. Gund Institute for Environment, University of Vermont, 210 Colchester Ave, Burlington, VT, 05405, USA

    Natalia Aristizábal & Easton R. White

  4. Department of Plant and Soil Science, University of Vermont, 63 Carrigan Dr, Burlington, VT, 05405, USA

    Erika M. Bueno

  5. Department of Biological Sciences, University of New Hampshire, 38 Academic Way, Durham, NH, 03824, USA

    Easton R. White

Authors
  1. Emily M. Beasley
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Natalia Aristizábal
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Erika M. Bueno
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Easton R. White
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

EMB, NA, and EMB contributed equally to study conception, design, and wrote the first draft of the manuscript. EMB wrote all code for simulations and data analyses. NA obtained real landscape data. All authors read, revised, and approved subsequent drafts of the manuscript.

Corresponding author

Correspondence to Emily M. Beasley.

Ethics declarations

Conflict of interest

The authors declare no competing interests.

Ethical approval

Not applicable.

Informed consent

Not applicable.

Consent for publication

Not applicable.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 193 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Beasley, E.M., Aristizábal, N., Bueno, E.M. et al. Spatially explicit models predict coffee rust spread in fragmented landscapes. Landsc Ecol 37, 2165–2178 (2022). https://doi.org/10.1007/s10980-022-01473-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10980-022-01473-1

Keywords

Search

Navigation