Some like it hot: the influence and implications of climate change on coffee berry borer (Hypothenemus hampei) and coffee production in East Africa

Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology

BACKGROUND

Chemoreception is crucial for insect fitness, underlying for instance food-, host-, and mate finding. Chemicals in the environment are detected by receptors from three divergent gene families: odorant receptors (ORs), gustatory receptors (GRs), and ionotropic receptors (IRs). However, how the chemoreceptor gene families evolve in parallel with ecological specializations remains poorly understood, especially in the order Coleoptera. Hence, we sequenced the genome and annotated the chemoreceptor genes of the specialised ambrosia beetle Trypodendron lineatum (Coleoptera, Curculionidae, Scolytinae) and compared its chemoreceptor gene repertoires with those of other scolytines with different ecological adaptations, as well as a polyphagous cerambycid species.

RESULTS

We identified 67 ORs, 38 GRs, and 44 IRs in T. lineatum ('Tlin'). Across gene families, T. lineatum has fewer chemoreceptors compared to related scolytines, the coffee berry borer Hypothenemus hampei and the mountain pine beetle Dendroctonus ponderosae, and clearly fewer receptors than the polyphagous cerambycid Anoplophora glabripennis. The comparatively low number of chemoreceptors is largely explained by the scarcity of large receptor lineage radiations, especially among the bitter taste GRs and the 'divergent' IRs, and the absence of alternatively spliced GR genes. Only one non-fructose sugar receptor was found, suggesting several sugar receptors have been lost. Also, we found no orthologue in the 'GR215 clade', which is widely conserved across Coleoptera. Two TlinORs are orthologous to ORs that are functionally conserved across curculionids, responding to 2-phenylethanol (2-PE) and green leaf volatiles (GLVs), respectively.

CONCLUSIONS

Trypodendron lineatum reproduces inside the xylem of decaying conifers where it feeds on its obligate fungal mutualist Phialophoropsis ferruginea. Like previous studies, our results suggest that stenophagy correlates with small chemoreceptor numbers in wood-boring beetles; indeed, the few GRs may be due to its restricted fungal diet. The presence of TlinORs orthologous to those detecting 2-PE and GLVs in other species suggests these compounds are important for T. lineatum. Future functional studies should test this prediction, and chemoreceptor annotations should be conducted on additional ambrosia beetle species to investigate whether few chemoreceptors is a general trait in this specialized group of beetles.

Predicting the dispersal and invasion dynamics of ambrosia beetles through demographic reconstruction and process-explicit modeling

Evaluating potential routes of invasion of pathogens and vectors of sanitary importance is essential for planning and decision-making at multiple scales. An effective tool are process-explicit models that allow coupling environmental, demographic and dispersal information to evaluate population growth and range dynamics as a function of the abiotic conditions in a region. In this work we simulate multiple dispersal/invasion routes in Mexico that could be taken by ambrosia beetles and a specific symbiont, Harringtonia lauricola, responsible for a severe epiphytic of Lauraceae in North America. We used Xyleborus bispinatus Eichhoff 1868 as a study subject and estimated its demography in the laboratory in a temperature gradient (17, 20, 26, 29, 35 °C), which we then used to parameterize a process-based model to estimate its metapopulation dynamics. The maximum intrinsic growth rate of X. bispinatus is 0.13 with a thermal optimum of 26.2 °C. The models suggest important regions for the establishment and dispersal the states of Veracruz, Chiapas and Oaxaca (high host and secondary vectors diversity), the Isthmus of Tehuantepec (connectivity region), and Michoacán and Jalisco (important avocado plantations). The use of hybrid process-based models is a promising tool to refine the predictions applied to the study of biological invasions and species distributions.

Naturally Occurring Vegetation Connectivity Facilitates Ant-Mediated Coffee Berry Borer Removal

Vegetation connectivity is an essential aspect of the habitat complexity that impacts species interactions at local scales. However, agricultural intensification reduces connectivity in agroforestry systems, including coffee agroecosystems, which may hinder the movement of natural enemies and reduce the ecosystem services that they provide. Ants play an important role in regulating the coffee berry borer (CBB), which is the most damaging coffee pest. For arboreal ant communities, the connections between trees are important structures that facilitate ant mobility, resource recruitment, foraging success, and pest control ability. To better understand how connectivity impacts arboreal ants in coffee agroecosystems, we conducted an experiment to assess the impact of artificial (string) and naturally occurring vegetation (vines, leaves, branches) connectivity on Azteca sericeasur behavior on coffee plants. We compared ant activity, resource recruitment, and CBB removal rates across three connectivity treatments connecting coffee plants to A. sericeasur nest trees: vegetation connectivity, string, and control (not connected) treatments. We found higher rates of ant activity, resource recruitment, and CBB removal on plants with naturally occurring vegetation connections to A. sericeasur nest trees. Artificial connectivity (string) increased the rates of resource recruitment and CBB removal but to a lesser extent than vegetation connectivity. Moreover, vegetation connectivity buffered reductions in ant activity with distance from the ant nest tree. These results reinforce how habitat complexity in the form of vegetation connectivity impacts interspecific interactions at the local scale. Our results also suggest that leaving some degree of vegetation connectivity between coffee plants and shade trees can promote ant-mediated biological pest control in coffee systems.

Coffee Berry Borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae): Activity and Infestation in the High Mountain and Blue Mountain Regions of Jamaica

Jamaica produces coffee marketed as Blue Mountain and high mountain (grown outside the Blue Mountains). Since the discovery of the coffee berry borer (CBB; Hypothenemus hampei) in Jamaica in 1978, chemical control has traditionally been the primary approach used to protect the crop from the pest. However, in the last 20 years, there has been an effort to shift towards more sustainable management strategies. The study was conducted to determine CBB activity (trap catch) and field infestation on coffee farms in the high mountains and Blue Mountains of Jamaica, over a crop cycle. A total of 27,929 and 12,921 CBBs were captured at high mountain and Blue Mountain farms, respectively. Peak CBB activity occurred in April in the high mountain region (365 CBBs/trap/month) and February in the Blue Mountain region (129 CBBs/trap/month). The highest levels of infestation were in November (33%) and October (34%) in the high mountain region and Blue Mountain region, respectively. There was no significant difference in the patterns of CBB activity and infestation between the study locations, and neither were related to the temperature or relative humidity. However, there was a significant relationship with rainfall. These data suggest that the population dynamics of the CBB may involve complex interactions among weather conditions, berry development, and agronomic practices.

Genomic Evaluation of Coffea arabica and Its Wild Relative Coffea racemosa in Mozambique: Settling Resilience Keys for the Coffee Crop in the Context of Climate Change

Climate change is negatively affecting the coffee value chain, with a direct effect on approximately 100 million people from 80 countries. This has been attributed to the high vulnerability of the two-mainstream species, Coffea arabica and Coffea canephora, to extreme weather events, with notable uneven increases in market prices. Taking into account the narrow genetic plasticity of the commercial coffee cultivars, wild-relatives and underutilized Coffea species are valuable genetic resources. In this work, we have assessed the occurrence of Coffea species in to understand the degree of genetic relationships between Coffea species in the country, as well as the patterns of genetic diversity, differentiation, and genetic structure. Only one wild species was found, C. racemosa, which showed a high level of genetic separation with C. arabica, based on plastid, as well as SSR and SNP analysis. C. arabica presented low levels of diversity likely related to their autogamous nature, while the allogamous C. racemosa presented higher levels of diversity and heterozygosity. The analysis of the functional pathways based on SNPs suggests that the stress signaling pathways are more robust in this species. This novel approach shows that it is vital to introduce more resilient species and increase genomic diversity in climate-smart practices.

Molecular Species Delimitation Using COI Barcodes of Mealybugs (Hemiptera: Pseudococcidae) from Coffee Plants in Espírito Santo, Brazil

Mealybugs are insects belonging to the family Pseudococcidae. This family includes many plant-pest species with similar morphologies, which may lead to errors in mealybug identification and delimitation. In the present study, we employed molecular-species-delimitation approaches based on distance (ASAP) and coalescence (GMYC and mPTP) methods to identify mealybugs collected from coffee and other plant hosts in the states of Espírito Santo, Bahia, Minas Gerais, and Pernambuco, Brazil. We obtained 171 new COI sequences, and 565 from the BOLD Systems database, representing 26 candidate species of Pseudococcidae. The MOTUs estimated were not congruent across different methods (ASAP-25; GMYC-30; mPTP-22). Misidentifications were revealed in the sequences from the BOLD Systems database involving Phenacoccus solani × Ph. solenopsis, Ph. tucumanus × Ph. baccharidis, and Planacoccus citri × Pl. minor species. Ten mealybug species were collected from coffee plants in Espírito Santo. Due to the incorrect labeling of the species sequences, the COI barcode library of the dataset from the database needs to be carefully analyzed to avoid the misidentification of species. The systematics and taxonomy of mealybugs may be improved by integrative taxonomy which may facilitate the integrated pest management of these pests.

Integrating temperature-dependent development and reproduction models for predicting population growth of the coffee berry borer, Hypothenemus hampei Ferrari

The coffee berry borer, Hypothenemus hampei Ferrari (Coleoptera: Curculionidae, Scolytinae), is the most devastating insect pest of coffee worldwide. It feeds on the beans inside the berries leading to significant crop losses and unmarketable products. This study aims to model the impact of temperature on H. hampei fecundity and population growth parameters, as a contribution to the prediction of infestation risk. The fecundity was assessed on fresh coffee beans at six constant temperatures in the range 15-30°C, with RH 80 ± 5% and photoperiod 12:12 L:D. Nonlinear models were fitted to the relationship between fecundity and temperature using the ILCYM software. The best fecundity model was combined to development models obtained for immature stages in a previous study in order to simulate life table parameters at different constant temperatures. Females of H. hampei successfully oviposited in the temperature range 15-30°C, with the highest fecundity observed at 23°C (106.1 offspring per female). Polynomial function 8 model was the best fitted to the relationship between fecundity and temperature. With this model, the highest fecundity was estimated at 23°C, with 110 eggs per female. The simulated net reproductive rate (R₀) was maximal at 24°C, with 50.08 daughters per female, while the intrinsic rate of increase (r_m) was the highest at 26°C, with a value of 0.069. Our results will help understand H. hampei population dynamics and develop an ecologically sound management strategy based on a better assessment of infestation risk.

A Systematic Review on the Impacts of Climate Change on Coffee Agrosystems

Coffee production is fragile, and the Intergovernmental Panel on Climate Change (IPCC) reports indicate that climate change (CC) will reduce worldwide yields on average and decrease coffee-suitable land by 2050. This article adopted the systematic review approach to provide an update of the literature available on the impacts of climate change on coffee production and other ecosystem services following the framework proposed by the Millenium Ecosystem Assessment. The review identified 148 records from literature considering the effects of climate change and climate variability on coffee production, covering countries mostly from three continents (America, Africa, and Asia). The current literature evaluates and analyses various climate change impacts on single services using qualitative and quantitative methodologies. Impacts have been classified and described according to different impact groups. However, available research products lacked important analytical functions on the precise relationships between the potential risks of CC on coffee farming systems and associated ecosystem services. Consequently, the manuscript recommends further work on ecosystem services and their interrelation to assess the impacts of climate change on coffee following the ecosystem services framework.

Genetic composition and diversity of Arabica coffee in the crop's center of origin and its impact on four major fungal diseases

Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the sixty sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels.

Modeling coffee (Coffea arabica L.) climate suitability under current and future scenario in Jimma zone, Ethiopia

Climate suitability is important for coffee (Coffea arabica L.) production in climate variability-prone regions like Ethiopia. The aim of this study was to assess the current and future climate suitability for the species in the Jimma zone under moderate (RCP4.5) and worst (RCP8.5) climate change scenarios. Field surveys and Worldclim and Paleoclim databases were used to capture 224 C. arabica species' location points and 9 bioclimatic data, respectively. The MaxEnt model with integration of ArcGis was used to simulate and characterize these data. The diagnostic outcome of the model showed that the anticipated climate change will increase the areas of suitability in the first and third coffee sub-zones, while there will be a decrease in the second sub-zone. Net suitability under the RCP4.5 would be decreased by 4.75 and 6.09% in the 2050s and 2070s, respectively. Indeed, under the RCP8.5, total suitability will be expected to be increased by 2.52% and 2.25% in the 2050s and 2070s, respectively. For the 2050s and 2070s, the suitability gap between RCP4.5 and RCP8.5 was estimated to be 401 km² and 1567 km², respectively. To summarize, with the exemption of RCP 8.5 within the 2070s, the suitability would be improved and come up short in all circumstances. To keep Arabica coffee in its original habitat, we suggest that the entire climate change adjustment procedures that are prearranged under the RCP4.5 ought to be executed to sustain the crop trees in its origin. Otherwise, moving the crop plant from impeded areas to suitable ones is crucial.

A Comprehensive Review of the Coffee Leaf Miner Leucoptera coffeella (Lepidoptera: Lyonetiidae)-A Major Pest for the Coffee Crop in Brazil and Others Neotropical Countries

Simple Summary

Coffee is produced in more than 60 countries by 25 million coffee producers, most of whom are smallholders in emergent countries. More than a beverage intake, coffee has become a ritual for an increasing number of consumers across the globe. This rising market demands modern management to improve grain quality, environment protecting, and produce pesticide-free products. Among several challenges to overcome, the coffee leaf miner (CLM) pest is one of the most severe threats to the coffee crop, especially in neotropical countries, such as Brazil, the world’s largest producer. Responsible for losses ranging from 30–70%, the CLM impairs the grain production and quality, which negatively reflects on the coffee production chain. Drawback aspects caused by chemical control with pesticides, such as the harmful effects to human health and environment and the selection of resistant-insect populations, prompt scientists to improve integrated pest management (IPM) tools. Therefore, the development of new resistant cultivars, biological control, nano-biopesticide products and other approaches are important strategies to a sustainable CLM control design. This review addresses basic knowledge of the insect L. coffeella and proposes novel insights for an IPM view.

Abstract

The coffee leaf miner (CLM) Leucoptera coffeella moth is a major threat to coffee production. Insect damage is related to the feeding behavior of the larvae on the leaf. During the immature life stages, the insect feeds in the mesophyll triggering necrosis and causing loss of photosynthetic capacity, defoliation and significant yield loss to coffee crops. Chemical control is used to support the coffee production chain, though market requirements move toward conscious consumption claiming for more sustainable methods. In this overview, we discuss aspects about the CLM concerning biology, history, geographical distribution, economic impacts, and the most relevant control strategies in progress. Insights to develop an integrated approach for a safer and eco-friendly control of the CLM are discussed here, including bio-extracts, nanotechnology, pheromones, and tolerant cultivars.

Demography and perturbation analyses of the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): Implications for management

The coffee berry borer (CBB) Hypothenemus hampei Ferrari is the most serious pest of coffee worldwide. Management of the CBB is extremely difficult because its entire life cycle occurs inside the fruit, where it is well protected. Knowing which life stages contribute most to population growth, would shed light on the population dynamics of this pest and help to improve CBB management programs. Two staged-classified matrices were constructed for CBB populations reared in the lab on artificial diets and CBB populations from artificial infestations in the field. Matrices were used to determine demographic parameters, to conduct elasticity analyses, and to perform prospective perturbation analysis. Higher values of the intrinsic rate of natural increase (r_m) and population growth rate (λ): were observed for CBB populations growing in the lab than in the field (r_m: 0.058, λ: 1.74 lab; r_m: 0.053, λ: 1.32 field). Sensitivity values for both CBB populations were highest for the transitions from larva to pupa (G₂: 0.316 lab, 0.352 field), transition from pupa to juvenile (G₃: 0.345 lab, 0.515 field) and survival of adult females (P₅: 0.324 lab, 0.389 field); these three vital rates can be important targets for CBB management. Prospective perturbation analyses indicated that an effective management for the CBB should consider multiple developmental stages; perturbations of >90% for each transition are necessary to reduce λ to <1. However, when the three vital rates with highest sensitivity are impacted at the same time, the percentage of perturbation is reduced to 25% for each transition; with these reductions in survival of larvae, pupae and adult females the value of λ was reduced from 1.32 to 0.96. Management programs for CBB should be focused on the use of biological and cultural measures that are known to affect these three important targets.

Climate-induced outbreaks in high-elevation pines are driven primarily by immigration of bark beetles from historical hosts

Warming temperatures are allowing native insect herbivores to expand into regions that previously exceeded their thermal tolerance, encounter new host species, and pose significant threats to native communities. However, the dynamics of these expansions remain poorly understood, particularly in the extent to which outbreaks remain reliant on emigration from historical hosts or are driven by local reproduction within novel hosts in the expanded range. We tested these non-mutually exclusive hypotheses using spatially explicit data on mountain pine beetle (Dendroctonus ponderosae), which historically undergoes intermittent outbreaks in low-elevation lodgepole pine (Pinus contorta), but is now causing severe mortality in a high-elevation endangered species, whitebark pine (Pinus albicaulis). We compiled data from 2000 to 2019 across British Columbia, Canada, at 1-km² resolution, and analyzed spatiotemporal patterns of beetle infestations, lodgepole pine distributions, expansion into habitats dominated by whitebark pine, and the likelihood of future outbreaks in all pine communities under simulated conditions. Overall, we found strong support for the hypothesis of emigration from the historical host species continuing to be a major driver of outbreaks in the more recently accessed host. First, beetle population pressure was consistently the best predictor of infestation severity in both lodgepole and whitebark pine, and appeared to be mostly unidirectional from lodgepole to whitebark pine. Second, infestations in lodgepole pine were of a longer duration than those in whitebark pine, which appeared too brief to sustain transitions from endemic to eruptive dynamics. Furthermore, resource depletion appears to drive emigration from lodgepole pine, whereas in whitebark pine drought appears to favor establishment of immigrants although bioclimatic factors and stand structure preclude self-sustaining outbreaks. Finally, we project that most pine in British Columbia will be at risk in the event of a new major outbreak. We describe implications for conserving and protecting whitebark pine and to other climate-driven range expansions.

Evaluating management strategies for sustainable crop production under changing climate conditions: A system dynamics approach

The increasing frequency and severity of drought pose significant threats to sustainable agricultural production across the world. Managing drought risks is challenging given the complexity of the interdependencies and feedback between climate drivers and socio-economic and ecological systems. To better understand the dynamics that drive the impacts of drought and water scarcity on crop production, a system dynamics model has been developed to explore complex interactions between factors in associated with drought and agricultural production, and examine how these might impact agricultural sustainability, using a case study in a coffee production system in Viet Nam. The model shows that water- and land-use drivers and their interactions with ecological and socio-economic factors play a more significant role than drought in determining the sustainability of coffee production. Results of policy scenario analyses indicate that drought conditions might exacerbate problems related to water shortages for irrigation but their impacts could be substantially minimized through applying intervention strategies, including restriction of the total area of land available for coffee production (to ~ 190,000 ha) and a 25% reduction in the irrigation amount per hectare of coffee compared to the common practices. Overall, the model findings add significant insight into drought and water resources management for sustainable crop production and the developed model can serve as a decision-support tool to inform strategic policy-making.

Determination of temperature thresholds for the parasitoid Diachasmimorpha longicaudata (Hymenoptera: Braconidae), using life cycle simulation modeling: Implications for effective field releases in classical biological control of fruit flies

The braconid parasitoid Diachasmimorpha longicaudata (Ashmead) (Hymenoptera: Braconidae) is one of the most important natural enemies in classical biological control programs against tephritid fruit flies worldwide. In light of the spread of the invasive fruit fly species, Bactrocera dorsalis in Africa and beyond, there is a need to implement classical biological control. The current study aimed to determine temperature thresholds for D. longicaudata reared on B. dorsalis, using life cycle simulation modeling to guide informed parasitoid releases in Africa. Simulated parameters included thermal requirements, population growth parameters at different temperature requirements, suitable areas for the establishment, and the number of generations per year under projected climatic conditions. The lower thermal threshold for the development was estimated at 10.0°C, with a thermal constant (k) of 333.3-degree days, while the maximum temperature threshold was estimated at 33.69°C. Fecundity was highest at 25°C, with 177.3 eggs per female. Temperature significantly affected the population growth parameters of D. longicaudata, and the maximum value of the intrinsic rate of increase (rm) was 0.145 at 27°C. Results indicate that D. longicaudata could successfully establish in tropical and sub-tropical regions under current and future climatic conditions. However, a slight change in the suitable areas is expected by the year 2050 due to a slight and gradual rise in temperature. Our findings provide important information for further release of this parasitoid in Africa as well as designing pest management strategies to limit the spread and reduce the impact of fruit flies sustainably.

Climate Change, Land, Water, and Food Security: Perspectives From Sub-Saharan Africa

The current and projected warming of the earth is unequivocal with humans playing a strong role as both perpetrators and victims. The warming on the African continent is projected to be greater than the global average with an increased average temperature of 3–6°C by the end of the century under a high Representative Concentration Pathway. In Africa, the Sub-Saharan region is identified as the most vulnerable to the changing climate due to its very low capacity to adapt to or mitigate climate change. While it is common to identify studies conducted to assess how climate change independently impacts water, land, or food resources, very limited studies have sought to address the interlinkages, synergies, and trade-offs existing between climate change, water, land, and food (WLF) resources as a system in Sub-Saharan Africa (SSA). The climate change and WLF security nexus, therefore, seeks to address this shortfall in literature and subsequently serve as a relevant source of information for decision-making and policy implementation concerning climate change mitigation and adaptation. In this study, 41 relevant studies were selected from Web of Science, Google Scholar, ResearchGate, and institutional websites. We provide information on the independent relationships between climate change and WLF resources, and further discuss the existing inter-linkages between climate change and the WLF security in SSA using the nexus approach, with recommendations on how decision making and policy implementations should be done using the climate change and WLF security nexus approach.

Coffee Berry Borer (Hypothenemus hampei) Emergence from Ground Fruits Across Varying Altitudes and Climate Cycles, and the Effect on Coffee Tree Infestation

During coffee harvest, picked berries fall to the ground where they serve as a reservoir for the coffee berry borer (CBB) which then infest coffee berries on the trees. This study tested the effect of fallen CBB-infested coffee berries on the infestation of coffee trees (Coffea arabica). Three-year-old trees were treated with either 0, 1, 5, 10, 15, or 20 CBB-infested berries placed on the root vicinity. The CBB infestation of coffee trees was sampled every 30 days during 6 months for four coffee productive cycles. The experiment was set up at four different locations comprising different altitudes (1,218; 1,381; 1,470; and 1,700 m.a.s.l.) and the measurements were taken during 4 years where the climatic events of El Niño, La Niña, Neutral, and transitions El Niño/La Niña were present. The results show that CBB-infested berries left on the ground are a reservoir of CBB for 140 ± 8.2 days and infest developing healthy coffee berries. In a climate Neutral year, one CBB-infested ground berry left on the ground infested on average 590.2 ± 142.2 berries in coffee trees grown at 1,218 m.a.s.l. At the same altitude, one CBB-infested ground berry resulted in 151.5 ± 29.1 infested tree berries during La Niña year and 959.0 ± 89.6 during El Niño year. The CBB infestation was positively correlated with temperature and negatively correlated with altitude (R²= 0.99 and R²= -0.96, respectively). This study highlights the importance of careful harvesting practices to prevent berries from falling to the ground, followed by ground sanitation to limit later infestation of the coffee crop.

Organic Farming Practices and Shade Trees Reduce Pest Infestations in Robusta Coffee Systems in Amazonia

Coffee agroforestry systems could reconcile agricultural and environmental objectives. While pests and diseases can reduce yield, their interactions with shade and nutrition have been rarely researched, and are particularly lacking in perennial systems. We hypothesized that intermediate shade levels could reduce coffee pests while excess shade could favor fungal diseases. We hypothesized that organic rather than mineral fertilization would better synchronize with nutrient uptake and higher nutrient inputs would be associated with reduced pest and disease damage due to higher plant vigor, yet effects would be less obvious in shaded plots as coffee growth would be light-limited. Using three-year-old trees of Coffea canephora var. Robusta (robusta coffee) in the Ecuadorian Amazon, we compared a full-sun system with four shading methods creating different shade levels: (1) Myroxylon balsamum; (2) Inga edulis; (3) Erythrina spp.; or, (4) Erythrina spp. plus Myroxylon balsamum. Conventional farming at either (1) moderate or (2) intensified input and organic farming at (3) low or (4) intensified input were compared in a split-plot design with shade as the main plot factor and farming practice as the sub-plot factor. The infestation of the following pests and disease incidences were evaluated monthly during the dry season: brown twig beetle (Xylosandrus morigerus), coffee leaf miner (Leucoptera coffeella), coffee berry borer (Hypothenemus hampei), anthracnose disease (Colletotrichum spp.), thread blight (Pellicularia koleroga), and cercospora leaf spot (Cercospora coffeicola). Coffee berry borer and brown twig beetle infestation were both reduced by 7% in intensified organic treatments compared to intensified conventional treatments. Colonization of coffee berry borer holes in coffee berries by the entomopathogenic fungus Beauveria bassiana was also assessed. Brown twig beetle infestation was significantly higher under full sun than under Inga edulis, yet no other shade effects were detected. We demonstrate for the first time how intensified input use might promote pest populations and thus ultimately lead to robusta coffee yield losses.

Brazilian Coffee Production and the Future Microbiome and Mycotoxin Profile Considering the Climate Change Scenario

Brazil holds a series of favorable climatic conditions for agricultural production including the hours and intensity of sunlight, the availability of agricultural land and water resources, as well as diverse climates, soils and biomes. Amidst such diversity, Brazilian coffee producers have obtained various standards of qualities and aromas, between the arabica and robusta species, which each present a wide variety of lineages. However, temperatures in coffee producing municipalities in Brazil have increased by about 0.25 °C per decade and annual precipitation has decreased. Therefore, the agricultural sector may face serious challenges in the upcoming decades due to crop sensitivity to water shortages and thermal stress. Furthermore, higher temperatures may reduce the quality of the culture and increase pressure from pests and diseases, reducing worldwide agricultural production. The impacts of climate change directly affect the coffee microbiota. Within the climate change scenario, aflatoxins, which are more toxic than OTA, may become dominant, promoting greater food insecurity surrounding coffee production. Thus, closer attention on the part of authorities is fundamental to stimulate replacement of areas that are apt for coffee production, in line with changes in climate zoning, in order to avoid scarcity of coffee in the world market.

Climate change and specialty coffee potential in Ethiopia

Current climate change impact studies on coffee have not considered impact on coffee typicities that depend on local microclimatic, topographic and soil characteristics. Thus, this study aims to provide a quantitative risk assessment of the impact of climate change on suitability of five premium specialty coffees in Ethiopia. We implement an ensemble model of three machine learning algorithms to predict current and future (2030s, 2050s, 2070s, and 2090s) suitability for each specialty coffee under four Shared Socio-economic Pathways (SSPs). Results show that the importance of variables determining coffee suitability in the combined model is different from those for specialty coffees despite the climatic factors remaining more important in determining suitability than topographic and soil variables. Our model predicts that 27% of the country is generally suitable for coffee, and of this area, only up to 30% is suitable for specialty coffees. The impact modelling showed that the combined model projects a net gain in coffee production suitability under climate change in general but losses in five out of the six modelled specialty coffee growing areas. We conclude that depending on drivers of suitability and projected impacts, climate change will significantly affect the Ethiopian speciality coffee sector and area-specific adaptation measures are required to build resilience.

Coffee Berry Borer (Hypothenemus hampei), a Global Pest of Coffee: Perspectives from Historical and Recent Invasions, and Future Priorities

Coffee berry borer (Hypothenemus hampei (Ferrari), CBB) has invaded nearly every coffee-producing country in the world, and it is commonly recognized as the most damaging insect pest of coffee. While research has been conducted on this pest in individual coffee-growing regions, new insights may be gained by comparing and contrasting patterns of invasion and response across its global distribution. In this review, we explore the existing literature and focus on common themes in the invasion biology of CBB by examining (1) how it was introduced into each particular region and the response to its invasion, (2) flight activity and infestation patterns, (3) economic impacts, and (4) management strategies. We highlight research conducted over the last ten years in Hawaii as a case study for the development and implementation of an effective integrated pest management (IPM) program for CBB, and also discuss biosecurity issues contributing to incursion and establishment. Potential areas for future research in each of the five major components of CBB IPM (monitoring and sampling, cultural, biological, chemical, and physical controls) are also presented. Finally, we emphasize that outreach efforts are crucial to the successful implementation of CBB IPM programs. Future research programs should strive to include coffee growers as much as possible to ensure that management options are feasible and cost-effective.

Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

Intensive coffee production is accompanied by several environmental issues, including soil degradation, biodiversity loss, and pollution due to the wide use of agrochemical inputs and wastes generated by processing. In addition, climate change is expected to decrease the suitability of cultivated areas while potentially increasing the distribution and impact of pests and diseases. In this context, the coffee microbiota has been increasingly studied over the past decades in order to improve the sustainability of the coffee production. Therefore, coffee associated microorganisms have been isolated and characterized in order to highlight their useful characteristics and study their potential use as sustainable alternatives to agrochemical inputs. Indeed, several microorganisms (including bacteria and fungi) are able to display plant growth-promoting capacities and/or biocontrol abilities toward coffee pests and diseases. Despite that numerous studies emphasized the potential of coffee-associated microorganisms under controlled environments, the present review highlights the lack of confirmation of such beneficial effects under field conditions. Nowadays, next-generation sequencing technologies allow to study coffee associated microorganisms with a metabarcoding/metagenomic approach. This strategy, which does not require cultivating microorganisms, now provides a deeper insight in the coffee-associated microbial communities and their implication not only in the coffee plant fitness but also in the quality of the final product. The present review aims at (i) providing an extensive description of coffee microbiota diversity both at the farming and processing levels, (ii) identifying the “coffee core microbiota,” (iii) making an overview of microbiota ability to promote coffee plant growth and to control its pests and diseases, and (iv) highlighting the microbiota potential to improve coffee quality and waste management sustainability.

Shade trees preserve avian insectivore biodiversity on coffee farms in a warming climate

AIM

Coffee is an important export for many developing countries, with a global annual trade value of $100 billion, but it is threatened by a warming climate. Shade trees may mitigate the effects of climate change through temperature regulation that can aid in coffee growth, slow pest reproduction, and sustain avian insectivore diversity. The impact of shade on bird diversity and microclimate on coffee farms has been studied extensively in the Neotropics, but there is a dearth of research in the Paleotropics.

LOCATION

East Africa.

METHODS

We created current and future regional Maxent models for avian insectivores in East Africa using Worldclim temperature data and observations from the Global Biodiversity Information Database. We then adjusted current and future bioclimatic layers based on mean differences in temperature between shade and sun coffee farms and projected the models using these adjusted layers to predict the impact of shade tree removal on climatic suitability for avian insectivores.

RESULTS

Existing Worldclim temperature layers more closely matched temperatures under shade trees than temperatures in the open. Removal of shade trees, through warmer temperatures alone, would result in reduction of avian insectivore species by over 25%, a loss equivalent to 50 years of climate change under the most optimistic emissions scenario. Under the most extreme climate scenario and removal of shade trees, insectivore richness is projected to decline from a mean of 38 to fewer than 8 avian insectivore species.

MAIN CONCLUSIONS

We found that shade trees on coffee farms already provide important cooler microclimates for avian insectivores. Future temperatures will become a regionally limiting factor for bird distribution in East Africa, which could negatively impact control of coffee pests, but the effect of climate change can be potentially mediated through planting and maintaining shade trees on coffee farms.

A Review of Potential Impacts of Climate Change on Coffee Cultivation and Mycotoxigenic Fungi

Coffee is one of the most traded commodities in the world. It plays a significant role in the global economy, employing over 125 million people. However, it is possible that this vital crop is threatened by changing climate conditions and fungal infections. This paper reviews how suitable areas for coffee cultivation and the toxigenic fungi species of Aspergillus, Penicillium, and Fusarium will be affected due to climate change. By combining climate models with species distribution models, a number of studies have investigated the future distribution of coffee cultivation. Studies predict that suitable coffee cultivation area could drop by ~50% under representation concentration pathway (RCP) 6.0 by 2050 for both Arabica and Robusta. These findings agree with other studies which also see an altitudinal migration of suitable cultivation areas to cooler regions, but limited scope for latitudinal migration owing to coffee's inability to tolerate seasonal temperature changes. Increased temperatures will see an overall increase in mycotoxin production such as aflatoxins, particularly in mycotoxigenic fungi (e.g., Aspergillus flavus) more suited to higher temperatures. Arabica and Robusta's limited ability to relocate means both species will be grown in less suitable climates, increasing plant stress and making coffee more susceptible to fungal infection and mycotoxins. Information regarding climate change parameters with respect to mycotoxin concentrations in real coffee samples is provided and how the changed climate affects mycotoxins in non-coffee systems is discussed. In a few areas where relocating farms is possible, mycotoxin contamination may decrease due to the "parasites lost" phenomenon. More research is needed to include the effect of mycotoxins on coffee under various climate change scenarios, as currently there is a significant knowledge gap, and only generalisations can be made. Future modelling of coffee cultivation, which includes the influence of atmospheric carbon dioxide fertilisation and forest management, is also required; however, all indications show that climate change will have an extremely negative effect on future coffee production worldwide in terms of both a loss of suitable cultivation areas and an increase in mycotoxin contamination.

Climate Change Adaptation, Food Security, and Attitudes toward Risk among Smallholder Coffee Farmers in Nicaragua

Farmers’ livelihoods are uniquely vulnerable to climate change, and taking adaptive measures to changing environmental conditions constitutes one of the most important pathways for protecting them. Their willingness and capacity to adopt improved practices and technologies, their cognitive and behavioural preferences, and the institutional response mechanisms will go a long way in determining their success in their adaptation to climate change. This study presents results of an analysis of the vulnerabilities of smallholder coffee producers in Nicaragua to climate change. I use descriptive analyses and experimental risk games to evaluate the preferences and attitudes of coffee producers in the context of their adaptation to climate change. I show that food insecure households are more risk-averse than food-secure households and that much work is needed in the sector to ensure equity and improve institutional capacity. For households in chronic poverty, conventional risk management strategies simply may not be enough. Institutional arrangements must be put in place to enable coffee-growing households to engage in practices that result in improved capacity for climate change adaptation.

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.

Elucidation of Hosts, Native Distribution, and Habitat of the Coffee Berry Borer (Hypothenemus hampei) Using Herbaria and Other Museum Collections

The coffee berry borer (Hypothenemus hampei) is the most damaging insect pest of global coffee production. Despite its importance, our knowledge on the insect's natural habitat, range, and wild host species remains poorly known. Using archival sources (mainly herbaria but also other museum collections), we surveyed 18,667 predominantly wild-collected herbarium specimens mostly from Africa, Madagascar, and Asia for coffee berry borer occurrence. A total of 72 incidences were confirmed for presence of the coffee berry borer, with identifications assisted by micro-CT for SEM. Of the 72 positive infestations, all were from tropical African coffee (Coffea) species, of which 32 were from wild (non-cultivated) plants. Of the 32 wild occurrences, 30 were found in C. canephora (robusta coffee), 1 in C. liberica (Liberica coffee), and 1 in C. arabica (Arabica coffee). Our herbarium survey confirms literature and anecdotal reports that the coffee berry borer is indigenous to tropical Africa, and that coffee species, and particularly robusta coffee, are important hosts. We identify the wetter type of Guineo-Congolian forest as either the preferred or exclusive native habitat of the coffee berry borer. Other than coffee, we find no evidence of other naturally occurring hosts. Characters of infestation (e.g., hole position on coffee fruits) infers a certain degree of specificity between the coffee berry borer and its host.

Climate change does not impact on Coffea arabica yield in Brazil

BACKGROUND

Brazil is the largest producer of coffee in the world. Studies on climate change estimate large impacts on the production of Coffea arabica (C. arabica). In this context, it is necessary to know the quantitative production values to provide evidence for policy makers to target the prompt answer.

RESULTS

Using data from 18 municipalities located in five Brazilian states that produce more coffee in Brazil, in an unprecedented way, in this work it is shown that although the minimum temperature is the most important climatic variable for the production, its effect, although positive, and its degree of explanation, were technically too small to explain the volume of production in Brazilian conditions. According to the model of non-stationary time series ARIMA (1, 1, 0) coffee production in the future may reach almost four million tons, and the productivity almost 2500 kg ha^-1 on average, with the advancement of technology as the main factor that should promote simultaneous increases in production and productivity. However, despite natural climate variations, which make it the most responsible for the variability of annual coffee production, the producer must increase the use of the technologies to support the Brazilian coffee agribusiness.

CONCLUSIONS

The results of this study reveal that coffee production in Brazil is due much more to productivity than to the minimum ambient temperature change over the long term; despite this, the climate variable should be considered the most influential on the production and productivity of coffee. © 2017 Embrapa. Journal of the Science of Food and Agriculture © 2019 Society of Chemical Industry.

The Potential Global Distribution and Voltinism of the Japanese Beetle (Coleoptera: Scarabaeidae) Under Current and Future Climates

Japanese beetle, Popillia japonica (Newman), is a severe invasive insect pest of turf, landscapes, and horticultural crops. It has successfully colonized much of the United States and has recently established in mainland Europe. The distribution and voltinism of P. japonica will undoubtedly change as a consequence of climate change, posing additional challenges to the management of this species. To assess these challenges, a process-oriented bioclimatic niche model for P. japonica was developed to examine its potential global distribution under current (1981-2010) and projected climatic conditions (2040-2059) using one emission scenario (representative concentration pathway [RCP] 8.5) and two global climate models, ACCESS1-0 and CNRM-CM5. Under current climatic conditions, the bioclimatic niche model agreed well with all credible distribution data. Model projections indicate a strong possibility of further range expansion throughout mainland Europe under both current and future climates. In North America, projected increases in temperature would enable northward range expansion across Canada while simultaneously shifting southern range limits in the United States. In Europe, the suitable range for P. japonica would increase by 23% by midcentury, especially across portions of the United Kingdom, Ireland, and Scandinavia. Under the RCP 8.5 scenario, cumulative growing degree-days increased, thereby reducing the probability of biannual life cycles in northern latitudes where they can occur, including Hokkaido, Japan, northeastern portions of the United States, and southern Ontario, Canada. The results of this study highlight several regions of increasing and emerging risk from P. japonica that should be considered routinely in ongoing biosecurity and pest management surveys.

High extinction risk for wild coffee species and implications for coffee sector sustainability

Wild coffee species are critical for coffee crop development and, thus, for sustainability of global coffee production. Despite this fact, the extinction risk and conservation priority status of the world's coffee species are poorly known. Applying IUCN Red List of Threatened Species criteria to all (124) wild coffee species, we undertook a gap analysis for germplasm collections and protected areas and devised a crop wild relative (CWR) priority system. We found that at least 60% of all coffee species are threatened with extinction, 45% are not held in any germplasm collection, and 28% are not known to occur in any protected area. Existing conservation measures, including those for key coffee CWRs, are inadequate. We propose that wild coffee species are extinction sensitive, especially in an era of accelerated climatic change.

The Structure and Phenology of Non-Native Scolytine Beetle Communities in Coffee Plantations on Kaua'i

Populations and communities are known to respond to abiotic conditions, but the forces determining the distribution of particular insect pests are sometimes overlooked in the process of developing control methods. Bark and ambrosia beetles (Curculionidae: Scolytinae) are important pests of crops, forestry, and ecosystems worldwide, yet the factors that influence their success are unknown for many species. The Hawaiian archipelago is host to over three dozen invasive scolytines, many of which occur on Kauaʻi and are pests of agriculture. We analyzed scolytine community dynamics at two coffee estates: a hand-harvested site in a tropical wet forest and a mechanically harvested site in a tropical dry savanna. Our regression analyses show overall scolytine abundance was negatively correlated with rainfall, as were four species: the tropical nut borer (Hypothenemus obscurus), H. brunneus, Cryphalus longipilus, and Xyleborinus andrewesi. These relationships contributed to the compositions of the communities being markedly dissimilar despite having the same species richness. Multivariate analysis found no influence from temperature or harvest method on community dynamics. This information can be valuable for the timing of pest control methods, for predicting the success of possible new scolytine arrivals on Kauaʻi, and for forecasting how these species may spread with climate change.

Climate Change, Carbon Dioxide, and Pest Biology, Managing the Future: Coffee as a Case Study

The challenge of maintaining sufficient food, feed, fiber, and forests, for a projected end of century population of between 9–10 billion in the context of a climate averaging 2–4 °C warmer, is a global imperative. However, climate change is likely to alter the geographic ranges and impacts for a variety of insect pests, plant pathogens, and weeds, and the consequences for managed systems, particularly agriculture, remain uncertain. That uncertainty is related, in part, to whether pest management practices (e.g., biological, chemical, cultural, etc.) can adapt to climate/CO2 induced changes in pest biology to minimize potential loss. The ongoing and projected changes in CO2, environment, managed plant systems, and pest interactions, necessitates an assessment of current management practices and, if warranted, development of viable alternative strategies to counter damage from invasive alien species and evolving native pest populations. We provide an overview of the interactions regarding pest biology and climate/CO2; assess these interactions currently using coffee as a case study; identify the potential vulnerabilities regarding future pest impacts; and discuss possible adaptive strategies, including early detection and rapid response via EDDMapS (Early Detection & Distribution Mapping System), and integrated pest management (IPM), as adaptive means to improve monitoring pest movements and minimizing biotic losses while improving the efficacy of pest control.

Responses of aerial insectivorous bats to local and landscape-level features of coffee agroforestry systems in Western Ghats, India

Shade coffee has shown great promise in providing crucial habitats for biodiversity outside formal protected areas. Insectivorous bats have been understudied in coffee, although they may provide pest control services. We investigated the influence of local and landscape-level features of coffee farms on aerial insectivorous bats in Chikmagalur district in the Western Ghats biodiversity hotspot, India. Bats were monitored in 20 farm sites using ultrasound detectors, and the response of bat species richness and activity to changes in tree density, proportion of built-up area in the neighborhood, and distance of farm from forest areas quantified. We examined if models built to explain the species richness and activity could also predict them in nine additional sites. We detected nine phonic types/species in the study area. The quantified predictors had no effect on assemblage-level species richness and activity of bats. Responses of edge-space and cluttered-space forager guilds mirrored those of the overall assemblage, but some species vulnerable to forest conversion like Rhinolophus beddomei were detected rarely. Best models explained up to 20% and 15% variation in assemblage-level species richness and activity respectively, and were poor predictors of both response variables. We conclude that coffee farms in our study area offer an important commuting space for insectivorous bats across a gradient of shade management. Further research should include species-specific responses to management decisions for at-risk species and quantification of ecosystem services like natural pest control to inform biodiversity conservation initiatives in the Western Ghats coffee landscapes.

Prediction of insect pest distribution as influenced by elevation: Combining field observations and temperature-dependent development models for the coffee stink bug, Antestiopsis thunbergii (Gmelin)

The antestia bug, Antestiopsis thunbergii (Gmelin 1790) is a major pest of Arabica coffee in Africa. The bug prefers coffee at the highest elevations, contrary to other major pests. The objectives of this study were to describe the relationship between A. thunbergii populations and elevation, to elucidate this relationship using our knowledge of the pest thermal biology and to predict the pest distribution under climate warming. Antestiopsis thunbergii population density was assessed in 24 coffee farms located along a transect delimited across an elevation gradient in the range 1000-1700 m asl, on Mt. Kilimanjaro, Tanzania. Density was assessed for three different climatic seasons, the cool dry season in June 2014 and 2015, the short rainy season in October 2014 and the warm dry season in January 2015. The pest distribution was predicted over the same transect using three risk indices: the establishment risk index (ERI), the generation index (GI) and the activity index (AI). These indices were computed using simulated life table parameters obtained from temperature-dependent development models and temperature data from 1) field records using data loggers deployed over the transect and 2) predictions for year 2055 extracted from AFRICLIM database. The observed population density was the highest during the cool dry season and increased significantly with increasing elevation. For current temperature, the ERI increased with an increase in elevation and was therefore distributed similarly to observed populations, contrary to the other indices. This result suggests that immature stage susceptibility to extreme temperatures was a key factor of population distribution as impacted by elevation. In the future, distribution of the risk indices globally indicated a decrease of the risk at low elevation and an increase of the risk at the highest elevations. Based on these results, we concluded with recommendations to mitigate the risk of A. thunbergii infestation.

Control of American Cockroach (Periplaneta americana) in Municipal Sewage Disposal System, Central Iran

BACKGROUND

Cockroaches consists of 4000 species, of which 40 species are serious domestic pests. They have involved the mechanical transmission of various pathogenic viruses, bacteria, and protozoans to humans. This study aimed to determine different control methods of P. americana in sewage system of Esfahan City, central Iran using different insecticides recommended by WHO.

METHODS

Totally, 164 manholes with at least more than three cockroaches were selected until 2017 for this study. The species of cockroaches were identified; the adults and nymphs were counted and recorded. Each sewer shaft was assigned to one treatment method in an ascending order of number of cockroaches counted, coding the treatment method with paint on the lower part of the wall near the manhole cover. The manhole shafts were then inspected at 1 and 5 months' post-treatment. Data analyzed by statistical methods.

RESULTS

Almost all of the products (Excluding boric acid with bait formulation) resulted in appropriate control within one month of application. The appropriate products for chemical control of cockroaches were the chlorpyrifos 5% Emulsifiable Concentrate (EC), diazinon 5% (EC), diazinon 0.05% (EC) and cypermethrin 5% Fog. These pesticides achieved an optimal reduction of population providing more than 90% control of cockroaches for five consecutive months.

CONCLUSION

The emulsifiable concentrates and fog formulations in the control were more successful compared to other methods and this was penetration deep into the hiding places of cockroaches.

Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L

Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley.

Differential fine-tuning of gene expression regulation in coffee leaves by CcDREB1D promoter haplotypes under water deficit

Despite the importance of the DREB1D gene (also known as CBF4) in plant responses to water deficit and cold stress, studies analysing its regulation by transgenic approaches are lacking. In the current work, a functional study of three CcDREB1D promoter haplotypes (named HP15, HP16 and HP17) isolated from drought-tolerant and drought-sensitive clones of Coffea canephora was carried out in plants of C. arabica stably transformed by Agrobacterium tumefaciens by analysing their ability to regulate the expression of the uidA reporter gene in response to water deficit mimicked by polyethylene glycol (-2.0 MPa) and low relative humidity treatments. A deletion analysis of their corresponding 5'-upstream regions revealed increased specificity of β-glucuronidase activity in the polyethylene glycol and low relative humidity treatments, with high expression in leaf mesophyll and guard cells in full-length constructs. RT-qPCR assays also revealed that the HP16 haplotype (specific to clone tolerant to water deficit) had stronger and earlier activity compared with the HP15 and HP17 haplotypes. As most of the cis-regulatory elements involved in ABA-dependent and -independent networks, tissue specificity and light regulation are common to these haplotypes, we propose that their organization, as well as the nucleic acid polymorphisms present outside these boxes, may play a role in modulating activities of DREB1D promoters in guard cells.

Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content

A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.

The Coffee Berry Borer (Coleoptera: Curculionidae) in Puerto Rico: Distribution, Infestation, and Population per Fruit

The coffee berry borer (CBB) (Hypothenemus hampei: Ferrar) was first detected in Puerto Rico in 2007. Its distribution since then has been extensive, but not extensively documented. An island-wide survey was carried out from August to November 2014 (the coffee production season) to assess CBB distribution, infestation, and population per fruit. The CBB was well-established throughout the coffee-growing area of Puerto Rico, but was not evenly distributed. Infestation (or percentages of fruits perforated) in sites sampled ranged from 0 to 95%, and CBB number per infested fruit varied from 1 to 34 individuals. CBB infestation and total population per fruit were positively correlated with altitude. Highest infestation and total population were observed in sites located >400 masl; most of the coffee-producing area in Puerto Rico is above this altitude. Coffea arabica (L.) had higher CBB infestation and population per fruit than Coffea canephora (Pierre ex A. Froehner) (robusta coffee). Based on these results, management tools should be implemented to mitigate the severe damage that CBB is causing in Puerto Rico. These management tools should include the removal of all fruits that remain on the plants after harvest and the use of the entomopathogenic fungus Beauveria bassiana (Balls.) Vuill. for biocontrol, especially on coffee farms at higher elevations.

Towards a Collaborative Research: A Case Study on Linking Science to Farmers' Perceptions and Knowledge on Arabica Coffee Pests and Diseases and Its Management

The scientific community has recognized the importance of integrating farmer's perceptions and knowledge (FPK) for the development of sustainable pest and disease management strategies. However, the knowledge gap between indigenous and scientific knowledge still contributes to misidentification of plant health constraints and poor adoption of management solutions. This is particularly the case in the context of smallholder farming in developing countries. In this paper, we present a case study on coffee production in Uganda, a sector depending mostly on smallholder farming facing a simultaneous and increasing number of socio-ecological pressures. The objectives of this study were (i) to examine and relate FPK on Arabica Coffee Pests and Diseases (CPaD) to altitude and the vegetation structure of the production systems; (ii) to contrast results with perceptions from experts and (iii) to compare results with field observations, in order to identify constraints for improving the information flow between scientists and farmers. Data were acquired by means of interviews and workshops. One hundred and fifty farmer households managing coffee either at sun exposure, under shade trees or inter-cropped with bananas and spread across an altitudinal gradient were selected. Field sampling of the two most important CPaD was conducted on a subset of 34 plots. The study revealed the following findings: (i) Perceptions on CPaD with respect to their distribution across altitudes and perceived impact are partially concordant among farmers, experts and field observations (ii) There are discrepancies among farmers and experts regarding management practices and the development of CPaD issues of the previous years. (iii) Field observations comparing CPaD in different altitudes and production systems indicate ambiguity of the role of shade trees. According to the locality-specific variability in CPaD pressure as well as in FPK, the importance of developing spatially variable and relevant CPaD control practices is proposed.