Landscape context and scale differentially impact coffee leaf rust, coffee berry borer, and coffee root-knot nematodes

Tree Effects on Coffee Leaf Rust at Field and Landscape Scales

Although integrating trees into agricultural systems (i.e., agroforestry systems) provides many valuable ecosystem services, the trees can also interact with plant diseases. We demonstrate that a detailed understanding of how plant diseases interact with trees in agroforestry systems is necessary to identify key tree canopy characteristics, leaf traits, spatial arrangements, and management options that can help control plant diseases at different spatial scales. We focus our analysis on how trees affect coffee leaf rust, a major disease affecting one of the world's most significant crop commodities. We show that trees can both promote and discourage the development of coffee leaf rust at the plot scale via microclimate modifications in the understory. Based on our understanding of the role of tree characteristics in shaping the microclimate, we identify several canopy characteristics and leaf traits that can help manage coffee leaf rust at the plot scale: namely, thin canopies with high openness, short base height, horizontal branching, and small, dentate leaves. In contrast, at the edge of coffee farms, having large trees with high canopy volume and small, thick, waxy leaves is more useful to reduce throughflow wind speeds and intercept the airborne dispersal of urediniospores, an important consideration to control disease at the landscape scale. Seasonal pruning can help shape trees into the desired form, and trees can be spatially arranged to optimize desired effects. This case study demonstrates the added value of combining process-based epidemiology studies with functional trait ecology to improve disease management in agroforestry systems.

Contrasting coffee leaf rust epidemics between forest coffee and semi-forest coffee agroforestry systems in SW-Ethiopia

Ethiopian Arabica coffee is produced in different agroforestry systems which differ in forest management intensity. In forest coffee systems (FC), coffee shrubs grow naturally in the understory of Afromontane forests with little human intervention, whereas in semi-forest coffee systems (SFC) thinning of the canopy and removal of the understory is applied. Coffee leaf rust (CLR) disease is a growing concern for coffee agroforestry, but to what extent infection pressure is affected by management intensity is poorly known. Here we assessed CLR infection through time across FC and SFC systems in SW-Ethiopia. CLR infection was significantly higher for SFC, with a gradual reduction of this difference during the beginning of dry season (November) through main rainy season of (July). Our findings also demonstrated that CLR infections were significantly lower in the FC system as compared to SFC system in both years 2015/16 and 2020/21. The higher CLR infection was partly explained by lower crown cover and higher human impact. We expect that reduced wind speed and droplet penetration under closed canopies and reduced human-facilitated spore dispersal are the dominating mechanisms behind lower CLR infection in FC systems, yet lower coffee density in FC may also play a role. Overall, our results indicate that although higher management intensity still generally results in higher total yields per hectare, proportionally larger losses due to CLR infection can be expected. Therefore, introducing more coffee genetic diversity, screening resistant coffee varieties and increasing canopy cover in the SFC will mitigate the CLR disease pressure and guarantee the sustainability of higher yields of the system in the future. Also, lower yields in the FC will be rewarded through providing price premiums so that farmers instantly get a higher price for their lower yield, guaranteeing livelihoods.

Spatiotemporal Variability of Human Disturbance Impacts on Ecosystem Services in Mining Areas

Human activities pose significant impacts on ecosystem services (ESs) in mining areas, which will continually increase over time and space. However, the mechanism of ES change on spatiotemporal scales post-disturbance remains unclear, especially in the context of global climate change. Here, we conducted a global literature review on the impact of two of the most frequent disturbance factors (mining and restoration) on 27 different ESs, intending to synthesize the impacts of human disturbance on ESs in mining areas via a meta-analysis, and analyze the spatiotemporal variability of ESs after disturbance. We screened 3204 disturbance studies published on the Web of Science between 1950 and 2020 and reviewed 340 in detail. The results of independence test showed that human disturbance had a significant impact on ESs in the mining areas (p < 0.001). The impacts (positive and/or negative) caused by mining and restoration differed considerably among ESs (even on the same ESs). Additionally, spatiotemporal scales of human disturbance were significantly related to spatiotemporal scales of ES change (p < 0.001). We found that the positive and negative impacts of disturbances on ESs may be interconversion under specific spatiotemporal conditions. This seems to be associated with spatiotemporal variability, such as the temporal lag, spatial spillover, and cumulative spatiotemporal effects. Climate changes can lead to further spatiotemporal variability, which highlights the importance of understanding the changes in ESs post-disturbance on spatiotemporal scales. Our research presents recommendations for coping with the twofold pressure of climate change and spatiotemporal variability, to understand how ESs respond to human disturbance at spatiotemporal scales in the future, and manage disturbances to promote sustainable development in mining areas.

Shaded-Coffee: A Nature-Based Strategy for Coffee Production Under Climate Change? A Review

Coffee is deemed to be a high-risk crop in light of upcoming climate changes. Agroforestry practices have been proposed as a nature-based strategy for coffee farmers to mitigate and adapt to future climates. However, with agroforestry systems comes shade, a highly contentious factor for coffee production in terms of potential yield reduction, as well as additional management needs and interactions between shade trees and pest and disease. In this review, we summarize recent research relating to the effects of shade on (i) farmers' use and perceptions, (ii) the coffee microenvironment, (iii) pest and disease incidence, (iv) carbon assimilation and phenology of coffee plants, (v) coffee quality attributes (evaluated by coffee bean size, biochemical compounds, and cup quality tests), (vi) breeding of new Arabica coffee F1 hybrids and Robusta clones for future agroforestry systems, and (vii) coffee production under climate change. Through this work, we begin to decipher whether shaded systems are a feasible strategy to improve the coffee crop sustainability in anticipation of challenging climate conditions. Further research is proposed for developing new coffee varieties adapted to agroforestry systems (exhibiting traits suitable for climate stressors), refining extension tools by selecting locally-adapted shade trees species and developing policy and economic incentives enabling the adoption of sustainable agroforestry practices.

Interactions between Geomorphology and Production Chain of High-Quality Coffee in Costa Rica

High-altitude coffee has an international reputation due to its high quality, especially in countries with a long production history, such as Costa Rica. Specific geographical characteristics determine the regions where high-altitude coffee can be cultivated. Over the last two decades, new production conditions have promoted the growth of smallholder coffee farms in the Upper Buenavista Catchment (UBC) in the South of Costa Rica. To understand this phenomenon’s process, we initially performed a detailed geomorphological mapping of the high-elevation production sites in the UBC. Then, we used remote sensing to determine the coffee land cover (2005, 2012, and 2018) to compare their landforms. Furthermore, we analyzed the production–processing–market chain that has promoted coffee plantations since 2005. Our results show that coffee farmers chose more unstable and erosive areas with short-term production prospects to cultivate premium-priced coffee. Moreover, farmers have changed their role in the coffee sector, evolving from small producers to entrepreneurs with specialized knowledge. These actions may reduce economic risks and improve the household incomes of smallholder coffee producers. However, limited research has been conducted along the tropics about the relationships between landforms, socioeconomic drivers, and high-altitude coffee yield. Therefore, our results are essential to present geomorphology and applied geography as baselines in land-use planning for agricultural landscapes.

Towards integrated pest and pollinator management in tropical crops

Biotic pollination and pest control are two critical insect-mediated ecosystem services that support crop production. Although management of both services is usually treated separately, the new paradigm of Integrated Pest and Pollinator Management (IPPM) suggests synergetic benefits by considering them together. We reviewed the management practices in two major tropical perennial crops: cocoa and coffee, to assess IPPM applications under the tropics. We found potential synergies and antagonisms among crop pest and pollination management, however, very few studies considered these interactions. Interestingly, we also found management practices focusing mainly on a single service mediated by insects although species can show multiple ecological functions as pests, natural enemies, or pollinators. The tropics represent a promising area for the implementation of IPPM and future research should address this concept to move towards a more sustainable agriculture.

Agro-Ecological Management of Coffee Pests in Brazil

Coffee plants host several herbivorous species, but only few are considered pests. Brazil is the largest coffee producer of the world, and the two key coffee pests of the crop in the country are the coffee leaf miner Leucoptera coffeella and the coffee berry borer Hypothenemus hampei. However, in some regions or on specific conditions, species of mites and scales can also cause damage to coffee plants. Conventional management of coffee pests relies on chemical pesticides, and it is the most commonly used strategy in Brazil, but environmental problems, pest resistance, and toxicity-related issues have led coffee growers to search for alternatives for pest control. Agro-ecological strategies suitable to coffee cultivation can be adopted by farmers, based on plant diversification, in order to provide resources for natural enemies, such as nectar, pollen, shelter, microclimate conditions, and oviposition sites, thereby promoting conservation biological control. Here I revise these strategies and report the results from research in Brazil. I include results on agroforestry, use of cover crops, and non-crop plant management. These are complemented by curative measures based on the use of organic farming-approved pesticides that can be employed when the agro-ecological practices are not yet consolidated. I also present the cultural control method used by several coffee producers in Brazil to decrease coffee berry borer damage.

Better outcomes for pest pressure, insecticide use, and yield in less intensive agricultural landscapes

Agricultural systems have been continuously intensified to meet rising demand for agricultural products. However, there are increasing concerns that larger, more connected crop fields and loss of seminatural areas exacerbate pest pressure, but findings to date have been inconclusive. Even less is known about whether increased pest pressure results in measurable effects for farmers, such as increased insecticide use and decreased crop yield. Using extensive spatiotemporal data sampled every 2 to 3 d throughout five growing seasons in 373 cotton fields, we show that pests immigrated earlier and were more likely to occur in larger cotton fields embedded in landscapes with little seminatural area (<10%). Earlier pest immigration resulted in earlier spraying that was further linked to more sprays per season. Importantly, crop yield was the lowest in these intensified landscapes. Our results demonstrate that both environmental conservation and production objectives can be achieved in conventional agriculture by decreasing field sizes and maintaining seminatural vegetation in the surrounding landscapes.

Temperature-dependent development and survival of immature stages of the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae)

Although the coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae: Scolytinae) is the most destructive insect pest of coffee worldwide, there is much to learn about its thermal biology. This study aimed to develop temperature-based models for H. hampei development and to provide the thermal requirements of immature stages in the laboratory. Using a new observation method, larval development and survival were monitored daily on fresh Arabica coffee seeds, under seven constant temperatures in the range 15-35°C, with 80 ± 5% RH and 12:12 L:D photoperiod. Linear and non-linear functions were fitted to the development data plotted against temperature, using Insect Life Cycle Modelling software (ILCYM). Temperature significantly affected the development time of all immature stages. Egg incubation period ranged 4.6-16.8 days, under temperature between 30 and 15°C. No development occurred at 35°C and the larval stage did not develop to pupa at 15°C. The minimum temperature threshold (Tmin) estimated from linear regression was 10.5, 13.0, 15.0 and 13.0°C, for egg, larva, pupa and the total development from egg to adult, respectively. The maximum temperature threshold (Tmax) estimated from the Sharpe and DeMichele function was 32°C for egg to adult development. The thermal constant (k) was estimated at 78.1, 188.7, 36.5 and 312.5 degree days, for egg, larva, pupa and for egg to adult, respectively. Our results will help understand and predict the pest population dynamics and distribution in coffee plantations as impacted by temperature, and as such, will contribute to a more efficient management of the pest.

The Community Ecology of Herbivore Regulation in an Agroecosystem: Lessons from Complex Systems

Whether an ecological community is controlled from above or below remains a popular framework that continues generating interesting research questions and takes on especially important meaning in agroecosystems. We describe the regulation from above of three coffee herbivores, a leaf herbivore (the green coffee scale, Coccus viridis), a seed predator (the coffee berry borer, Hypothenemus hampei), and a plant pathogen (the coffee rust disease, caused by Hemelia vastatrix) by various natural enemies, emphasizing the remarkable complexity involved. We emphasize the intersection of this classical question of ecology with the burgeoning field of complex systems, including references to chaos, critical transitions, hysteresis, basin or boundary collision, and spatial self-organization, all aimed at the applied question of pest control in the coffee agroecosystem.

Managing the farmscape for connectivity increases conservation value for tropical bird species with different forest-dependencies

Land clearing for agricultural use is a primary driver of biodiversity loss and fragmentation of natural ecosystems. Restoring natural habitat connectivity by retaining quality habitats and increasing on-farm tree cover contributes to species' mobility and persistence in agricultural landscapes. Nonetheless, remarkably few studies have quantified the impacts of on-farm practices for species' mobility measured as functional connectivity within the context of farm and broader spatial levels of landscape organization. We tested how adding and removing trees in different configurations on a farm comprised of coffee plantations and cattle pastures can help evaluate species' mobility at the farmscape level (an area comprising the farm plus a 1.5 km buffer area). We coupled bird capture data and scenario modeling to assess species mobility of five neotropical bird species with distinct life history characteristics representing a gradient of forest dependency. We used seven years of mist-netting data to estimate species habitat affinity and to predict species mobility using the Circuitscape model across a 4371 ha farmscape in Costa Rica. Circuitscape allowed us to estimate changes in movement probability and relative changes in resistance to movement that species experience during dispersal (measured as resistance distance and passage area through which species can move) under four farmscape management scenarios. The four land-use scenarios included: (a) the 2011 farmscape land-use composition and configuration, b) converting all existing live fences to post-and-wire fence lines in the farm c) converting simplified coffee agroforests to multistrata coffee agroforests in the farm, and d) placing multistrata live fences around the perimeter of every parcel and roads on the farm. Model results suggest that existing multistrata live fences maintain the sporadic movement of all five species irrespective of forest dependence. Likewise, adding multistrata live fences around individual fields presents a more efficient strategy for increasing species mobility than multistrata coffee agroforestry systems in the assessed farmscape, by doubling the passage areas available to all species, although it created labyrinths with "dead-ends" for two species. While retaining large habitat patches remains important for conservation, managing on-farm connectivity complements these efforts by increasing movement probability and reducing dispersal resistance for forest-dependent bird species.

Importance of Remotely-Sensed Vegetation Variables for Predicting the Spatial Distribution of African Citrus Triozid (Trioza erytreae) in Kenya

Citrus is considered one of the most important fruit crops globally due to its contribution to food and nutritional security. However, the production of citrus has recently been in decline due to many biological, environmental, and socio-economic constraints. Amongst the biological ones, pests and diseases play a major role in threatening citrus quantity and quality. The most damaging disease in Kenya, is the African citrus greening disease (ACGD) or Huanglongbing (HLB) which is transmitted by the African citrus triozid (ACT), Trioza erytreae. HLB in Kenya is reported to have had the greatest impact on citrus production in the highlands, causing yield losses of 25% to 100%. This study aimed at predicting the occurrence of ACT using an ecological habitat suitability modeling approach. Specifically, we tested the contribution of vegetation phenological variables derived from remotely-sensed (RS) data combined with bio-climatic and topographical variables (BCL) to accurately predict the distribution of ACT in citrus-growing areas in Kenya. A MaxEnt (maximum entropy) suitability modeling approach was used on ACT presence-only data. Forty-seven (47) ACT observations were collected while 23 BCL and 12 RS covariates were used as predictor variables in the MaxEnt modeling. The BCL variables were extracted from the WorldClim data set, while the RS variables were predicted from vegetation phenological time-series data (spanning the years 2014–2016) and annually-summed land surface temperature (LST) metrics (2014–2016). We developed two MaxEnt models; one including both the BCL and the RS variables (BCL-RS) and another with only the BCL variables. Further, we tested the relationship between ACT habitat suitability and the surrounding land use/land cover (LULC) proportions using a random forest regression model. The results showed that the combined BCL-RS model predicted the distribution and habitat suitability for ACT better than the BCL-only model. The overall accuracy for the BCL-RS model result was 92% (true skills statistic: TSS = 0.83), whereas the BCL-only model had an accuracy of 85% (TSS = 0.57). Also, the results revealed that the proportion of shrub cover surrounding citrus orchards positively influenced the suitability probability of the ACT. These results provide a resourceful tool for precise, timely, and site-specific implementation of ACGD control strategies.

Landscapes that work for biodiversity and people

How can we manage farmlands, forests, and rangelands to respond to the triple challenge of the Anthropocene—biodiversity loss, climate change, and unsustainable land use? When managed by using biodiversity-based techniques such as agroforestry, silvopasture, diversified farming, and ecosystem-based forest management, these socioeconomic systems can help maintain biodiversity and provide habitat connectivity, thereby complementing protected areas and providing greater resilience to climate change. Simultaneously, the use of these management techniques can improve yields and profitability more sustainably, enhancing livelihoods and food security. This approach to “working lands conservation” can create landscapes that work for nature and people. However, many socioeconomic challenges impede the uptake of biodiversity-based land management practices. Although improving voluntary incentives, market instruments, environmental regulations, and governance is essential to support working lands conservation, it is community action, social movements, and broad coalitions among citizens, businesses, nonprofits, and government agencies that have the power to transform how we manage land and protect the environment.

Landscape Effects on Reproduction of Euschistus servus (Hemiptera: Pentatomidae), a Mobile, Polyphagous, Multivoltine Arthropod Herbivore

Landscape factors can significantly influence arthropod populations. The economically important brown stink bug, Euschistus servus (Say) (Hemiptera: Pentatomidae), is a native mobile, polyphagous and multivoltine pest of many crops in southeastern United States and understanding the relative influence of local and landscape factors on their reproduction may facilitate population management. Finite rate of population increase (λ) was estimated in four major crop hosts-maize, peanut, cotton, and soybean-over 3 yr in 16 landscapes of southern Georgia. A geographic information system (GIS) was used to characterize the surrounding landscape structure. LASSO regression was used to identify the subset of local and landscape characteristics and predator densities that account for variation in λ. The percentage area of maize, peanut and woodland and pasture in the landscape and the connectivity of cropland had no influence on E. servus λ. The best model for explaining variation in λ included only four predictor variables: whether or not the sampled field was a soybean field, mean natural enemy density in the field, percentage area of cotton in the landscape and the percentage area of soybean in the landscape. Soybean was the single most important variable for determining E. servus λ, with much greater reproduction in soybean fields than in other crop species. Penalized regression and post-selection inference provide conservative estimates of the landscape-scale determinants of E. servus reproduction and indicate that a relatively simple set of in-field and landscape variables influences reproduction in this species.

Fungal diversity at fragmented landscapes: synthesis and future perspectives

Fungi are organisms with important roles in ecosystem functioning and services, but knowledge about how habitat fragmentation affect fungal diversity is biased by experimental approaches and it is spread in different trophic groups. We analyzed the empirical evidences of fungal diversity in fragmented landscapes, and proposed future perspectives for the study of these organisms under land use changes. Fungal diversity might be negatively affected by habitat fragmentation; however, this trend may differ in magnitude depending on fungal groups and their nutritional habits. In addition, due to the fact that fungal diversity at fragmented landscapes has been studied mainly through few indicators (e.g. isolation, area and edge effect); we propose incorporating the landscape structure and accurate spatio-temporal scales to the study of fungal diversity responses to fragmented landscapes. Together, this methodological refinement may allow improving knowledge on fungi when designing proper strategies for landscape management.

WITHDRAWN: Fungal diversity is negatively affected by habitat fragmentation: a meta-analysis

This article that has already been published in <Current Opinion in Microbiology, 37, June 2017 61-66>, 10.1016/j.mib.2017.03.015 has been withdrawn at the request of the editor and publisher. The publisher regrets that an error occurred which led to the premature publication of this paper. This error bears no reflection on the article or its authors. The publisher apologizes to the authors and the readers for this unfortunate error". The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.

Shade Effects on the Dispersal of Airborne Hemileia vastatrix Uredospores

Hemileia vastatrix caused a severe epidemic in Central America in 2012-13. The gradual development of that epidemic on nearly a continental scale suggests that dispersal at different scales played a significant role. Shade has been proposed as a way of reducing uredospore dispersal. The effect of shade (two strata: Erythrina poeppigiana below and Chloroleucon eurycyclum above) and full sun on H. vastatrix dispersal was studied with Burkard traps in relation to meteorological records. Annual and daily patterns of dispersal were observed, with peaks of uredospore capture obtained during wet seasons and in the early afternoon. A maximum of 464 uredospores in 1 day (in 14.4 m(3) of air) was recorded in October 2014. Interactions between shade/full sun and meteorological conditions were found. Rainfall, possibly intercepted by tree cover and redistributed by raindrops of higher kinetic energy, was the main driver of uredospore dispersal under shade. Wind gusts reversed this effect, probably by inhibiting water accumulation on leaves. Wind gusts also promoted dispersal under dry conditions in full sun, whereas they had no effect under shaded conditions, probably because the canopy blocked the wind. Our results indicate the importance of managing shade cover differentially in rainy versus dry periods to control the dispersal of airborne H. vastatrix uredospores.

Can Coffee Chemical Compounds and Insecticidal Plants Be Harnessed for Control of Major Coffee Pests?

Pests and pathogens threaten coffee production worldwide and are difficult to control using conventional methods, such as insecticides. We review the literature on the chemistry of coffee, concentrating on compounds most commonly reported from Coffea arabica and Coffea canephora. Differences in chemistry can distinguish coffee species and varieties, and plants grown under different biogeographic conditions exhibit different chemotypes. A number of chemical groups, such as alkaloids and caffeoylquinic acids, are known to be insecticidal, but most studies have investigated their effects on coffee quality and flavor. More research is required to bridge this gap in knowledge, so that coffee can be bred to be more resistant to pests. Furthermore, we report on some pesticidal plants that have been used for control of coffee pests. Locally sourced pesticidal plants have been underutilized and offer a sustainable alternative to conventional insecticides and could be used to augment breeding for resilience of coffee plants.

The Big Rust and the Red Queen: Long-Term Perspectives on Coffee Rust Research

Since 2008, there has been a cluster of outbreaks of the coffee rust (Hemileia vastatrix) across the coffee-growing regions of the Americas, which have been collectively described as the Big Rust. These outbreaks have caused significant hardship to coffee producers and laborers. This essay situates the Big Rust in a broader historical context. Over the past two centuries, coffee farmers have had to deal with the "curse of the Red Queen"-the need to constantly innovate in the face of an increasing range of threats, which includes the rust. Over the 20th century, particularly after World War II, national governments and international organizations developed a network of national, regional, and international coffee research institutions. These public institutions played a vital role in helping coffee farmers manage the rust. Coffee farmers have pursued four major strategies for managing the rust: bioprospecting for resistant coffee plants, breeding resistant coffee plants, chemical control, and agroecological control. Currently, the main challenge for researchers is to develop rust control strategies that are both ecologically and economically viable for coffee farmers, in the context of a volatile, deregulated coffee industry and the emergent challenges of climate change.

Forest bolsters bird abundance, pest control and coffee yield

Efforts to maximise crop yields are fuelling agricultural intensification, exacerbating the biodiversity crisis. Low-intensity agricultural practices, however, may not sacrifice yields if they support biodiversity-driven ecosystem services. We quantified the value native predators provide to farmers by consuming coffee's most damaging insect pest, the coffee berry borer beetle (Hypothenemus hampei). Our experiments in Costa Rica showed birds reduced infestation by ~ 50%, bats played a marginal role, and farmland forest cover increased pest removal. We identified borer-consuming bird species by assaying faeces for borer DNA and found higher borer-predator abundances on more forested plantations. Our coarse estimate is that forest patches doubled pest control over 230 km2 by providing habitat for ~ 55 000 borer-consuming birds. These pest-control services prevented US$75-US$310 ha-year(-1) in damage, a benefit per plantation on par with the average annual income of a Costa Rican citizen. Retaining forest and accounting for pest control demonstrates a win-win for biodiversity and coffee farmers.