Search

Coffee professionals have long known that the roast profile, i.e., the temperature versus time inside the roaster, strongly affects the flavor and quality of the coffee. A particularly important attribute of brewed coffee is the perceived sourness, which is known to be strongly correlated to the total titratable acidity (TA). Most prior work has focused on laboratory-scale roasters with little control over the roast profile, so the relationship between roast profile in a commercial-scale roaster and the corresponding development of TA to date remains unclear. Here we investigate roast profiles of the same total duration but very different dynamics inside a 5-kg commercial drum roaster, and we show that the TA invariably peaks during first crack and then decays to its original value by second crack. Although the dynamics of the TA development varied with roast profile, the peak TA surprisingly exhibited almost no statistically significant differences among roast profiles. Our results provide insight on how to manipulate and achieve desired sourness during roasting.

Introduction: ZenoTOF is new class of high-resolution mass spectrometer that combines resolution and sensitivity. This mass spectrometer is well designed to perform metabolomics. Methods: In this context, we compared the performance of ZenoTOF 7600 system (Sciex) with QTOF6520 (Agilent Technologies) through the leaf metabolome analysis of two Coffea species, namely C. anthonyi and C. arabica. Results: Both species were used to compare both TOF systems. Our results showed that the ZenoTOF 7600 system provided more features (3146 vs 2326 metabolites) and more nodes (1410 vs 379 metabolites) by molecular network in only one injection. Conclusion: These performances were attributed to the scan speed and sensitivity of the ZenotTOF and demonstrates its added value in the context of metabolomics. [ABSTRACT FROM AUTHOR]

Coffee is one of the most important beverages in the world and is produced from Coffea spp. beans. Diterpenes with ent-kaurane backbones have been described in this genus, and substances such as cafestol and kahweol have been widely investigated, along with their derivatives and biological properties. Other coffee ent-kaurane diterpenoids have been reported with new perspectives on their biological activities. The aim of this review is to update the chemical diversity of ent-kaurane diterpenoids in green and roasted coffee, detailing each new compound and reporting its biological potential. A systematic review was performed using the bibliographic databases (SciFinder, Web of Science, ScienceDirect) and specific keywords such as "coffea diterpenes", "coffee diterpenes", "coffee ent-kaurane diterpenes" and "coffee diterpenoids". Only articles related to the isolation of coffee ent-kaurane compounds were considered. A total of 146 compounds were related to Coffea spp. since the first report in 1932. Different chemical skeletons were observed, and these compounds were grouped as furan-type, oxidation-type, rearrangement-type, lacton-type, and lactam-type, among others. In general, the new coffee diterpenoids showed potential as antidiabetic, antidiapogenic, α-glucosidade inhibition, antiplatelet activity, and Cav.3 inhibitors agents, revealing the possibilities for the design, discovery, and development of new drugs. [ABSTRACT FROM AUTHOR]

During surveys in the centres of origin of the coffee leaf rust (CLR), Hemileia vastatrix in Africa, as well as in its exotic range in Brazil, 23 isolates of the genus Cladosporium were obtained from uredinial pustules. Using a phylogenetic analysis of all isolates involving a combination of partial sequences of the internal transcribed spacer region of rDNA (ITS) and two gene regions: actin (act) and translation elongation factor-1a (tef1), 12 species were delimited; including four new species - Cladosporium chlamydosporiformans, C. hemileiicola, C. mucilaginosum and C. setoides. GCPSR criteria were employed for species recognition, supported by morphological and cultural characters. The potential of these purported mycoparasites is discussed in the context of biological control of CLR in Latin America. [ABSTRACT FROM AUTHOR]

Background and Aims Leaf traits are known to be strong predictors of plant performance and can be expected to (co)vary along environmental gradients. We investigated the variation, integration, environmental relationships and evolutionary history of leaf functional traits in the genus Coffea , typically a rainforest understorey shrub, across Africa. A better understanding of the adaptive processes involved in leaf trait evolution can inform the use and conservation of coffee genetic resources in a changing climate. Methods We used phylogenetic comparative methods to investigate the evolution of six leaf traits measured from herbarium specimens of 58 African Coffea species. We added environmental data and data on maximum plant height for each species to test trait–environment correlations in various (sub)clades, and we compared continuous trait evolution models to identify variables driving trait diversification. Key Results Substantial leaf trait variation was detected across the genus Coffea in Africa, which was mostly interspecific. Of these traits, stomatal size and stomatal density exhibited a clear trade-off. We observed low densities of large stomata in early-branching lineages and higher densities of smaller stomata in more recent taxa, which we hypothesize to be related to declining CO2 levels since the mid-Miocene. Brownian motion evolution was rejected in favor of white noise or Ornstein–Uhlenbeck models for all traits, implying these traits are adaptively significant rather than driven by pure drift. The evolution of leaf area was likely driven by precipitation, with smaller leaves in drier climates across the genus. Conclusions Generally, Coffea leaf traits appear to be evolutionarily labile and governed by stabilizing selection, though evolutionary patterns and correlations differ depending on the traits and clades considered. Our study highlights the importance of a phylogenetic perspective when studying trait relationships across related taxa, as well as the consideration of various taxonomic ranges. [ABSTRACT FROM AUTHOR]

Coffea spp. are remarkable sources of phytochemicals, but the lack of a well-defined culture medium aimed at the induction of non-embryogenic and friable callus hampers the establishment of plant cell suspension cultures for large-scale production of valuable compounds. In this paper, we describe a one-medium protocol suitable to obtain both callus and cell suspension cultures from leaves of two elite cultivars of C. arabica. The protocol was developed through an iterative process involving the determination of the best concentration of auxin and cytokinin, their optimal ratio, as well as the most effective molecule of either hormone class. Young leaves were found to be a good and easy-to-use explant source for callus induction and proliferation, provided that a cytokinin was present in association with a chlorinated auxin in a full strength, semi-solid MS medium. The best results were obtained by hormone concentration and combination of 1 mg/L of both kinetin and 2,4,5-trichlorophenoxyacetic acid. The same ratio of these growth regulators was conveniently used for the development and stabilization of cell suspension cultures in liquid MS medium. When grown in darkness, stabilized suspension cultures showed a fine and homogeneous texture, with a 10-fold biomass increase within 25 days and a cell viability > 90%. In addition, the phytochemical profile revealed the presence of the most widely studied coffee compounds. The protocol can be applied to obtain adequate amounts of cell biomass for use in physiological studies concerning the production of secondary metabolites.Key messages: A protocol for callus induction and undifferentiated cell suspensions establishment in Coffea arabica was developed. This technique represents a useful tool for in vitro production of remarkable phytochemicals from coffee. [ABSTRACT FROM AUTHOR]

The use of transcriptomic data to make inferences about plant metabolomes is a useful tool to help the discovery of important compounds in the available biodiversity. To unveil previously undiscovered metabolites of Coffea, of phytotherapeutic and economic value, we employed 24 RNAseq libraries. These libraries were sequenced from leaves exposed to a diverse range of environmental conditions. Subsequently, the data were meticulously processed to create models of putative metabolic networks, which shed light on the production of potential natural compounds of significant interest. Then, we selected one of the predicted compounds, the L-3,4-dihydroxyphenylalanine (L-DOPA), to be analyzed by LC-MS/MS using three biological replicates of flowers, leaves, and fruits from Coffea arabica and Coffea canephora. We were able to identify metabolic pathways responsible for producing several compounds of economic importance. One of the identified pathways involved in isoquinoline alkaloid biosynthesis was found to be active and producing L-DOPA, which is a common product of POLYPHENOL OXIDASES (PPOs, EC 1.14.18.1 and EC 1.10.3.1). We show that coffee plants are a natural source of L-DOPA, a widely used medicine for treatment of the human neurodegenerative condition called Parkinsons disease. In addition, dozens of other compounds with medicinal significance were predicted as potential natural coffee products. By further refining analytical chemistry techniques, it will be possible to enhance the characterization of coffee metabolites, enabling a deeper understanding of their properties and potential applications in medicine.

Summary: The root-knot nematode Meloidogyne izalcoensis was described parasitising coffee trees and causing damage in the Izalco volcano region, Sonsonate, El Salvador. In Brazil, it was detected in coffee roots in the municipality of Indianópolis, Minas Gerais state (MG). Intercropping cover crops is a traditional practice in Brazilian coffee orchards, and the use of plants that are non-hosts or antagonistic to the nematodes is a very promising strategy for coffee in infested areas. Due to the scarce information on the host status of M. izalcoensis , the aim of this study was to evaluate 24 plants of different species of cover crops and select the non-hosts or poor hosts. Two assays were conducted at different times, and all plants were inoculated with 10 000 eggs. After 90 days, the following parameters were determined: fresh root weight, reproduction factor (RF) and final reaction. Plants with RF < 1.0 were classified as non-hosts (NH), those with RF > 1.0 were classified as hosts and using statistical analyses as: good host (GH), intermediate host (IH) and poor host (PH). Most of the botanical species tested were classified as NH or PH to M. izalcoensis : cotton, rice, white oat, black oat, ryegrass, corn, three species of grass, two cultivars of millet, two wheat cultivars, Crotalaria breviflora , C. ochroleuca , C. spectabilis , jack bean, gray mucuna bean and two species of rice grass. Only tomato and bean were classified as GH, and C. juncea and soybean were classified as IH. The plants identified as non-hosts or poor hosts can be recommended for intercropping or for crop rotation in Brazilian coffee orchards in regions infested by M. izalcoensis. [ABSTRACT FROM AUTHOR]

Coffee leaf rust, caused by the fungus Hemileia vastatrix , has become a major concern for coffee-producing countries. Additionally, there has been an increase in the resistance of certain races of the fungus to fungicides and breeding cultivars, making producers use alternative control methods. In this work, we transplanted the leaf surface microbiota of rust-resistant coffee species (Coffea racemosa and Coffea stenophylla) to Coffea arabica and tested whether the new microbiota would be able to minimize the damage caused by H. vastatrix. It was seen that the transplant was successful in controlling rust, especially from C. stenophylla , but the protection depended on the concentration of the microbiota. Certain fungi, such as Acrocalymma, Bipolaris, Didymella, Nigrospora, Setophaeosphaeria, Simplicillium, Stagonospora and Torula , and bacteria, such as Chryseobacterium, Sphingobium and especially Enterobacter , had their populations increased and this may be related to the antagonism seen against H. vastatrix. Interestingly, the relative population of bacteria from genera Pantoea, Methylobacterium and Sphingomonas decreased after transplantation, suggesting a positive interaction between them and H. vastatrix development. Our findings may help to better understand the role of the microbiota in coffee leaf rust, as well as help to optimize the development of biocontrol agents. [ABSTRACT FROM AUTHOR]

Caffeine biosynthesis in Coffea evolved independently through tandem gene duplication and subsequent neofunctionalization of ancestral N-methyltransferases (NMTs). The bulk of our understanding of this process in Coffea is centered on two species: C. arabica and C. canephora. To gain a wider perspective of caffeine biosynthesis in Coffea, this study focused on the less popular but commercially available C. liberica var. liberica, locally known as "kapeng barako." This study aimed to determine the genomic and coding sequences of the three NMTs -- mainly, xanthosine methyltransferase (XMT), 7-methylxanthine-N-methyltransferase (MXMT), and dimethylxanthine methyltransferase (DXMT) -- through Sanger sequencing. Relative expression levels of these NMTs in the leaves, flower bud, green fruit, and red fruit stages were also determined through polymerase chain reaction amplification of synthesized cDNA and then gel electrophoresis. Results reveal that the genetic sequences of NMTs of C. liberica were similar to the C. eugenioides-derived NMTs of C. arabica. Results also indicate that there is a possibility that more than one NMT gene for each NMT cluster (XMT, MXMT, DXMT) exists. This study has also identified genomic sequences and transcripts, whose sequences were in between the XMT and MXMT gene clusters. The function of these novel sequences is yet to be determined. NMT expression levels in C. liberica were similar to those observed in C. arabica and C. canephora, wherein expression peaks at the green fruit stage and then diminishes, as the fruit ripens fully. Although the NMTs of C. liberica have a lot of similarities with C. arabica and C. canephora, discovering the function and role in caffeine biosynthesis of these novel genomic sequences and transcripts will help us further understand the evolution of caffeine biosynthesis in Coffea. [ABSTRACT FROM AUTHOR]

Coffea canephora × C. arabica-crossing direction has shown to have a complete post-zygotic barrier. The study sought to unravel the degree of seed failure of paternal excess interspecific hybridization of C. canephora × C. arabica. The present research was conducted at the Pakuwon Experimental Station, Indonesian Industrial and Beverage Crops Research Institute (IBCRI), from August 2019 until March 2022. The C. canephora “Sidodadi” hand pollination used freshly collected pollen from C. arabica “Mangening” and C. arabica “AGK,” as well as from C. canephora “Kriting” and C. liberica. The fruit set was observed three months after anthesis (MAP) and six MAP. Cherry fruit and seed morphometric traits were measured at harvest time, with the number of seeds with collapsed endosperm (empty seed) also recorded. The surviving healthy seeds subsequently were sown to observe germination percentage. The number of leaf pairs on developing seedlings was recorded at a 2-month interval. Results showed that paternal excess had generated larger fruit and seeds but mostly contained collapsed endosperm. Few healthy developed seeds could germinate and subsequently develop into seedlings that are more vigorous. Interestingly, the interspecific homoploid crossing of C. canephora × C. liberica also exhibited a robust post-zygotic barrier. [ABSTRACT FROM AUTHOR]

Introduction. Anthropogenic activities are one of the causes of the increase in global temperature, which affects agro-environmental, ecological and socioeconomic processes. The contributions of agricultural production systems in the capture and storage of greenhouse gases have been little studied. Still, the literature indicates that the inclusion of trees on farms is an option to capture and store some greenhouse gases. Objective. To evaluate the relationship between floristic and structural diversity of coffee production systems and soil organic carbon storage (SOC). Materials and methods. The study was carried out during the period 2019-2020, in three localities Sandoná, San Pablo and Buesaco, Nariño-Colombia. Twelve agroecosystems with coffee were visited, where Shannon-Weiner and Simpson indices, tree density and complete soil analysis with samples at 30 cm depth were evaluated. An analysis of variance and principal components was sufficient for the analysis of the information. Results. The SOC was not presented statistical differences (p>0.05), which ranged between 38.55 Mg ha-1 in the full sun coffee arrangement in Buesaco and 96.63 Mg ha-1 in the coffee arrangement with miscellaneous in the same municipality, which presented the highest species diversity. Conclusions. It was proved that the coffee harvest associated with agroforestal systems (T3 and T4) with higher diversity and abundance of species, is higher than carbon accumulated in the soil compared to the monoculture arrangement (80,43 Mg ha-1 vs 58,32 Mg ha-1, severally), this diversification give to the family and enviroment some services and goods, contributing to the mitigation of climate change.

Background: Robusta green coffee bean extract toothpaste was an alternative product for preventing caries and periodontal disease. As a product, a hedonic test to determine consumer acceptance and satisfaction was needed. This research assessed the preference level for Robusta green coffee bean extract toothpaste among students at the University of Jember, Indonesia. Methods: This is an experimental and analytical observational study. The Robusta green coffee bean was extracted using the maceration method with 96% ethanol. The toothpaste was made by mixing placebo paste ingredients with Robusta green coffee bean extract at concentrations of 0.0625%, 0.125%, 0.25%, and 0.5%. The hedonic test included color, aroma, and texture parameters with a Likert scale and was carried out in the period August-November 2023 by 30 students from the Faculty of Dentistry, University of Jember, who were healthy, without allergies, and did not smoke SPSS vr26 was used and the mean score was calculated as the level of preference. Statistical test with Kruskal Wallis followed by Mann Whitney with p-value0.05). Conclusion: Robusta green coffee bean extract toothpaste with concentrations of 0.25% and 0.5% were preferred by consumers.

Beverage color significantly affects perceived sensory quality and consumer preference. Although the color of coffee beans is well known to vary strongly with roast level, little work has examined how roast level and brewing conditions affect the color of the final beverage. Here, we report that the color of full immersion brewed coffee is significantly affected by both roast level and brewing temperature. Coffees from three different origins were each roasted to three different levels (light, medium, and dark) and then brewed at three different temperatures (4, 22, and 92°C). Each sample was brewed toward full extraction and then diluted to precisely 2% total dissolved solids so that differences in concentration would not confound color measurements. Absorbance spectra (UV-vis) and color tristimulus values (L*a*b*) were then collected and analyzed. We find that roast level had the strongest impact on brew color, and that brew temperature had a significant impact on color for light and medium roasts, with less impact on dark roasts. Qualitatively, the cold brewed coffees tended to be redder, while the hot brewed coffees were blacker. The results suggest that there is an opportunity to manipulate and brand brewed coffee color through judicious choices of roast level and brewing temperature. PRACTICAL APPLICATION: Color serves as an indicator of coffee quality and potentially could affect perceived sensory characteristics. Our results suggest that appropriate control of roast level and brew temperature could yield desired colors for novel coffee products.

Background: The consumption of coffee has been associated with beneficial effects when it comes to Alzheimer's disease (AD). However, to the best of our knowledge, there are no studies on Conilon coffee consumption in elderly people with AD. Objective: Evaluate the effects of Conilon coffee consumption in elderly with AD. Methods: The study was carried out with 9 participants who consumed a minimum of 2 cups (200 mL cup) of Conilon coffee per day for 90 days. Cognitive assessment was done before (T0) and after 90 days (T90). Blood analysis was conducted at T0 and T90, as well as the assessment of advanced oxidation protein products (AOPP) and thiobarbituric acid reactive species (TBARS). The levels of chlorogenic acids and caffeine in the coffee beverage were quantified by liquid chromatography. Results: During the treatment, the participants consumed at least 550 mg and 540 mg of CGAs and caffeine, respectively. A significant improvement in cognition between T0 and T90 was observed as per MMSE, CTP, and clock drawing tests. Furthermore, there was a significant reduction in AOPP (37%) and TBARS (60%), indicating a reduction in oxidative stress. The consumption of the coffee did not significantly alter any blood parameter, which confirms the safety of the coffee treatment during the 90 days. Conclusions: Our study demonstrated for the first time that regular consumption of coffee with high amounts of CGAs and caffeine improves cognitive functions and reduces oxidative stress, without altering blood parameters that indicate possible signs of toxicity in classical target organs. [ABSTRACT FROM AUTHOR]

Coffea arabica, C. canephora, and C. liberica's coexistence in one location or proximity areas could promote interspecific pollination. However, information related to floral phenology and flower structure of these three coffee species is insufficient. This research aimed to identify the divergence of flowering phenology and flower morphometrics among C. arabica, C. canephora, and C. liberica. Flowering phenology observations continued daily from July to October 2020, extending to two locations of parapatric populations of three coffee species. Flower morphometric measurements ensued at the peak period of flowering. The results showed some co-anthesis periods among the three coffee species, with C. liberica starting to flower early. Moreover, C. liberica var liberica had the broadest flower diameter and the highest petal number, whereas the tetraploid C. arabica had the lowest. Consequences of flowering phenology and flower structure on a pre-zygotic barrier of spontaneous, as well as, controlled interspecific hybridization among the three coffee species were the discussion focus. [ABSTRACT FROM AUTHOR]

The objective was to develop cappuccino-flavored dulce de leche (DL), and to evaluate the effect of the different contents of instant coffee and cocoa powder on the proximate composition, physicochemical and sensorial characteristics. Six cappuccino sweet formulations were produced, differing in concentrations of instant coffee (2.5, 5.0 and 7.5 g) and cocoa powder (50, 100 and 150 g). The addition of cocoa powder and instant coffee added value to DL-based formulations. Calories ranged from 300.80 to 302.88 kcal 100 g−1, which is equivalent to approximately 15% of a balanced diet at 2000 kcal day−1 (100 g portion). The calories parameter was also positively correlated (p 90%) and purchase intentions, represented by the term “would certainly buy” > 60%. The elaboration of cappuccino sweet was feasible, being able to be a nutritious and tasty gastronomic option for the tables of different social classes.

Coffee (Coffea spp.) is one of the most popular refreshing beverages globally. Coffee lipid diversity has untapped potential for improving coffee marketability because lipids contribute significantly to both the health benefits and cup quality of coffee. However, in spite of its potential importance, there have not been extensive studies of lipids among C. canephora genotypes. In this study, ultra-performance liquid chromatography coupled with mass spectrometry (UPLC-MS) profiling of lipid molecules was performed for 30 genotypes consisting of 15 cultivated and 15 conserved genotypes of C. canephora in Southwestern Nigeria. We identified nine classes of lipids in the 30 genotypes which belong to the 'Niaouli', 'Kouillou' and 'Java Robusta' group: among these, the most abundant lipid class was the triacylglycerols, followed by the fatty acyls group. Although 'Niaouli' diverged from the 'Kouillou' and 'Java Robusta' genotypes when their lipid profiles were compared, there was greater similarity in their lipid composition by multivariate analysis, compared to that observed when their primary metabolites and especially their secondary metabolite profiles were examined. However, distinctions could be made among genotypes. Members of the fatty acyls group had the greatest power to discriminate among genotypes, however, lipids that were low in abundance e.g. a cholesterol ester (20:3), and phosphotidylethanolamine (34:0) were also helpful to understand the relationships among C. canephora genotypes. The divergent lipid profiles identified among the C. canephora genotypes, correlated with their Single Nucleotide Polymorphism grouping as assessed by genotype-by-sequencing, and will be exploited to improve coffee cup quality.

Coffee, after petroleum, is the most valuable commodity globally in terms of total value (harvest to coffee cup). Here, our bioeconomic analysis considers the multitude of factors that influence coffee production. The system model used in the analysis incorporates realistic field models based on considerable new field data and models for coffee plant growth and development, the coffee/coffee berry borer (CBB) dynamics in response to coffee berry production and the role of the CBB parasitoids and their interactions in control of CBB. Cultural control of CBB by harvesting, cleanup of abscised fruits, and chemical sprays previously considered are reexamined here to include biopesticides for control of CBB such as entomopathogenic fungi (Beauveria bassiana, Metarhizium anisopliae) and entomopathogenic nematodes (Steinernema sp., Heterorhabditis). The bioeconomic analysis estimates the potential of each control tactic singly and in combination for control of CBB. The analysis explains why frequent intensive harvesting of coffee is by far the most effective and economically viable control practice for reducing CBB infestations in Colombia and Brazil.

Aims Elucidating the identity of an isolate of Aspergillus sp. obtained during searches for anti-coffee leaf rust (CLR) biocontrol agents, from healthy coffee berry samples, preliminarily verify whether it is an aflatoxin-producer, confirm its ability to grow as an endophyte in healthy coffee tissues and assess its biocontrol potential against CLR. Methods and results One, among hundreds of fungal isolates fungus were obtained from healthy coffee tissues belonged to Aspergillus (isolate COAD 3307). A combination of morphology features and molecular analyses; including four regions—internal transcribed spacer, second-largest subunit of RNA polymerase (RPB2), β-tubulin (BenA) and calmodulin (CAL)—identified COAD 3307 as Aspergillus flavus. Inoculations of healthy Coffea arabica with COAD 3307 confirmed its establishment as an endophyte in leaves, stems, and roots. Treatment of C. arabica plants by combinated applications of COAD 3307 on aerial parts and in the soil, significantly (P  > .0001) reduced CLR severity as compared to controls. Thin-layer chromatography indicated that COAD 3307 is not an aflatoxin-producing isolate. In order to confirm this result, the extract was injected into high-performance liquid chromatography system equipped with a fluorescence detector, and no evidence of aflatoxin was found. Conclusions COAD 3307 is an endophytic isolate of A. flavus —a species that has never been previously recorded as an endophyte of Coffea spp. It is a non-aflatoxin producing strain that has an anti-CLR effect and merits further evaluation as a biocontrol agent. [ABSTRACT FROM AUTHOR]

Consumption of coffee is still high, and consumers demand high-quality coffee. Quality of coffee is a complex term. Moisture content (mc), water activity (aw), textural features, and the color of green coffee are one of the many attributes of the quality. In the research, we focused on these parameters and analyzed 21 samples of green Coffea arabica from different locations in Central America. Our results proved that moisture content did not exceed 14% in any samples. However, some samples had slightly lower values of moisture content. Water activity ranged from 0.391 to 0.582. Pearson's correlation was fairly positive at 0.70 between mc and aw. Regarding textural analysis, we focused on hardness and fracturability. In this case, we observed a low negative correlation between water activity and fracturability. This might suggest that the higher the aw (to a certain point), the lower the fracturability. The color parameter shows no significant difference, which might be caused due to the same post-harvest processing (wet processing), which is crucial for obtaining relatively same color quality despite different harvesting locations. Since coffee is a hygroscopic matrix, the results might have great use regarding storage and minimalizing textural changes and color concerning further roasting and grinding. [ABSTRACT FROM AUTHOR]

Acrylamide (AA) has been classified as a toxic, harmful, and carcinogenic substance since 2002, and therefore it is currently widely studied. When functional amino and carbonyl groups of asparagine and reducing sugars are condensed into Schiff bases, they are transformed into AA molecules at temperatures >120 °C. This mechanism is known as the Maillard reaction and is considered the main AA pathway. Simultaneously, desired browning and sensory properties are developed. However, changes in chemical composition of the matrix, properties, and secondary reactions trigger intermediary synthesis, destabilizing the medium and leading to new AA molecules. Coffee has become the most consumed beverage worldwide. Therefore, the World Health Organization established recommended benchmark levels of AA concentrations that could be detected in roasted coffee beans and by-products (<850 μg/kg). Trace levels of AA can differ between samples due to roasting and brewing conditions, and the analytical and extraction methods chosen for sample analysis. • Acrylamide (AA) is a neurotoxic, genotoxic, carcinogenic, and reprotoxic compound. • AA is detected in different food sources subjected to thermal treatments. • Deep eutectic solvents show minimal volatility, good ionic conductivity, low flammability. • The chemical composition of green coffee after roasting leads to AA formation. • Treatments with asparaginase could reduce AA presence. [ABSTRACT FROM AUTHOR]

A cafeicultura vem crescendo cada vez mais no Brasil e, diante disso, tecnologias são desenvolvidas constantemente para obtenção de maiores produtividades. Nesse contexto, vem sendo estudado o efeito do mulching de polietileno e fontes de adubo na cafeicultura. O objetivo desse trabalho foi avaliar a incidência de bicho-mineiro e ácaro-vermelho em cafeeiro em função do uso do mulching de polietileno e adubos (liberação controlada e convencional). A pesquisa foi realizada na área experimental da Universidade Federal de Uberlândia – Campus Monte Carmelo, Minas Gerais, com a cultivar de Coffea arabica IPR 100, com delineamento em blocos casualizados e quatro repetições. Foram testados os seguintes tratamentos: T1 - mulching dupla face branco/preto com adubo convencional; T2 – mulching dupla face branco/preto com adubo de liberação controlada; T3 – mulching dupla face prata/preto com adubo convencional; T4 – mulching dupla face prata/preto com adubo de liberação controlada; T5 – Sem mulching com adubo convencional; T6 – Sem mulching com adubo de liberação controlada. As avaliações ocorreram quinzenalmente de julho de 2020 a dezembro de 2020, mediante a constatação da presença ou ausência de ácaro-vermelho e de lagartas de bicho-mineiro. Os picos de densidade populacional para bicho-mineiro ocorreram no período de julho a outubro de 2020, e para ácaro-vermelho no mês de agosto, devido à baixa umidade relativa do ar e precipitação. Assim, conclui-se que a utilização do mulching dupla face prata/preto proporcionou maior atratividade do bicho-mineiro-do-cafeeiro. Já as fontes de adubo não influenciaram na probabilidade de ocorrência deste inseto-praga. Além disso, os adubos convencionais, bem como os de liberação controlada, e a ausência/presença de coberturas do solo, não influenciaram na incidência de ácaro-vermelho em cafeeiros da região do Cerrado Mineiro.

Ant community assembly is driven by many factors including species interactions (e.g., competition, predation, parasitism), habitat filtering (e.g., vegetation differences, microclimate, food and nesting resources), and dispersal. Canopy ant communities, including dominant and twig-nesting ants, are structured by all these different factors, but we know less about the impacts of species interactions and habitat filters acting at the colonization or recruitment stage. We examined occupation of artificial twig nests placed in shade trees in coffee agroecosystems. We asked whether species interactions-aggression from the dominant canopy ant, Azteca sericeasur Longino (Hymenoptera: Formicidae)-or habitat filtering-species of tree where nests were placed or surrounding vegetation-influence colonization, species richness, and community composition of twig-nesting ants. We found 20 species of ants occupying artificial nests. Nest occupation was lower on trees with A. sericeasur, but did not differ depending on tree species or surrounding vegetation. Yet, there were species-specific differences in occupation depending on A. sericeasur presence and tree species. Ant species richness did not vary with A. sericeasur presence or tree species. Community composition varied with A. sericeasur presence and surrounding vegetation. Our results suggest that species interactions with dominant ants are important determinants of colonization and community composition of twig-nesting ants. Habitat filtering at the level of tree species did not have strong effects on twig-nesting ants, but changes in coffee management may contribute to differences in community composition with important implications for ant conservation in agricultural landscapes, as well as biological control of coffee pests.

As both coffee quality and sustainability become increasingly important, there is growing interest in understanding how ecological quality affects coffee quality. Here we analyze, for the first time, the state of evidence that ecological quality, in terms of biodiversity and ecosystem functions, impacts the quality of Coffea arabica and C. canephora, based on 78 studies. The following ecosystem functions were included: pollination; weed, disease, and pest control; water and soil fertility regulation. Biodiversity was described by the presence, percentage, and diversity of shade trees. Coffee quality was described by the green bean physical characteristics, biochemical compounds, and organoleptic characteristics. The presence and diversity of shade trees positively impacted bean size and weight and reduced the percentage of rejected beans, but these observations were not consistent over different altitudes. In fact, little is known about the diversity of shade trees and their influence on biochemical compounds. All biochemical compounds varied with the presence of shade, percentage of shade, and elevation. Coffee beans from more diverse tree shade plantations obtained higher scores for final total organoleptic quality than simplified tree shade and unshaded plantations. Decreasing ecological quality diminished ecosystem functions such as pollination, which in turn negatively affected bean quality. Shade affected pests and diseases in different ways, but weeds were reduced. High soil quality positively affected coffee quality. Shade improved the water use efficiency, such that coffee plants were not water stressed and coffee quality was improved. While knowledge on the influence of shade trees on overall coffee quality remains scarce, there is evidence that agroecosystem simplification is negatively correlated with coffee quality. Given global concerns about biodiversity and habitat loss, we recommend that the overall definition of coffee quality include measures of ecological quality, although these aspects are not always detectable in certain coffee quality characteristics or the final cup. [ABSTRACT FROM AUTHOR]

Plant diversity can enhance natural pest control in agriculture by providing resources and conditions that are not regularly available in conventional crops to natural enemies of crop pests. Extrafloral nectar-producing plants, for example, might cause reduction of pest densities on neighboring plants because the nectar can increase the performance of natural enemies. Coffee agroforestry systems often contain extrafloral-nectar-producing Inga spp. trees that serve several purposes. Recent studies suggest that they attract and arrest a diversity of natural enemies that contribute to the control of coffee pests. Mites from the Phytoseiid family are key natural enemies of coffee pest mites, but no study has investigated whether Inga extrafloral nectar increases the performance of predatory mites in coffee ecosystems. Thus, here, we assessed whether the extrafloral nectar of Inga edulis Mart. (Fabaceae) can be considered a suitable nutritional resource for the predatory mite Amblyseius herbicolus (Chant), one of the most abundant phytoseiids in coffee crops. We found that feeding on extrafloral nectar allows for development and survival, but not reproduction, of A. herbicolus. Whereas individuals that fed on a diet of nectar during their immature development could subsequently only oviposit after having fed on a pollen diet, individuals that had developed on pollen stopped ovipositing when fed nectar. Our findings suggest that interplanted Inga trees can help to conserve populations of predatory mites in crop ecosystems through the provision of nectar and may boost biological control services. Future research should investigate the effects of extrafloral nectar-producing trees on coffee pest control by these predatory mites., Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethical approval: This study did not use animal species that require ethical approval., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

In Yunnan Province, the coffee-growing regions are mainly distributed in Pu'er and Xishuangbanna. During the surveys of microfungi associated with coffee in Yunnan Province, seven taxa were isolated from coffee samples. Based on molecular phylogenetic analyses of combined ITS, LSU, SSU, rpb2, and tef1-α sequence data and morphological characteristics, four new species viz. Deniquelata yunnanensis, Paraconiothyrium yunnanensis, Pseudocoleophoma puerensis, and Pse. yunnanensis, and three new records viz. Austropleospora keteleeriae, Montagnula thailandica, and Xenocamarosporium acaciae in Pleosporales are introduced. In addition, Paracamarosporium fungicola was transferred back to Paraconiothyrium based on taxonomy and DNA sequences. Full descriptions, illustrations, and phylogenetic trees to show the placement of new and known taxa are provided. In addition, the morphological comparisons of new taxa with closely related taxa are given. [ABSTRACT FROM AUTHOR]

Coffee is a high value agricultural commodity grown in about 80 countries. Sustainable coffee cultivation is hampered by multiple biotic and abiotic stress conditions predominantly driven by climate change. The NAC proteins are plants specific transcription factors associated with various physiological functions in plants which include cell division, secondary wall formation, formation of shoot apical meristem, leaf senescence, flowering embryo and seed development. Besides, they are also involved in biotic and abiotic stress regulation. Due to their ubiquitous influence, studies on NAC transcription factors have gained momentum in different crop plant species. In the present study, NAC25 like transcription factor was isolated and characterized from two cultivated coffee species, Coffea arabica and Coffea canephora and five Indian wild coffee species for the first time. The full-length NAC25 gene varied from 2,456 bp in Coffea jenkinsii to 2,493 bp in C. arabica. In all the seven coffee species, sequencing of the NAC25 gene revealed 3 exons and 2 introns. The NAC25 gene is characterized by a highly conserved 377 bp NAM domain (N-terminus) and a highly variable C terminus region. The sequence analysis revealed an average of one SNP per every 40.92 bp in the coding region and 37.7 bp in the intronic region. Further, the non-synonymous SNPs are 8-11 fold higher compared to synonymous SNPs in the non-coding and coding region of the NAC25 gene, respectively. The expression of NAC25 gene was studied in six different tissue types in C. canephora and higher expression levels were observed in leaf and flower tissues. Further, the relative expression of NAC25 in comparison with the GAPDH gene revealed four folds and eight folds increase in expression levels in green fruit and ripen fruit, respectively. The evolutionary relationship revealed the independent evolution of the NAC25 gene in coffee. [ABSTRACT FROM AUTHOR]

Xylella fastidiosa, an economically important plant-pathogenic bacterium, infects both coffee and citrus trees in Brazil. Although X. fastidiosa in citrus is well studied, knowledge about the population structure of this bacterium infecting coffee remains unknown. Here, we studied the population structure of X. fastidiosa infecting coffee trees in São Paulo State, Brazil, in four regions where citrus is also widely cultivated. Genotyping of over 500 isolates from coffee plants using 14 genomic microsatellite markers indicated that populations were largely geographically isolated, as previously found with populations of X. fastidiosa infecting citrus. These results were supported by a clustering analysis, which indicated three major genetic groups among the four sampled regions. Overall, approximately 38% of isolates showed significant membership coefficients not related to their original geographical populations (i.e., migrants), characterizing a significant degree of genotype flow among populations. To determine whether admixture occurred between isolates infecting citrus and coffee plants, one site with citrus and coffee orchards adjacent to each other was selected; over 100 isolates were typed from each host plant. No signal of natural admixture between citrus- and coffee-infecting isolates was found; artificial cross-infection assays with representative isolates also yielded no successful cross infection. A comparison determined that X. fastidiosa populations from coffee have higher genetic diversity and allelic richness compared with citrus. The results showed that coffee and citrus X. fastidiosa populations are effectively isolated from each other and, although coffee populations are spatially structured, migration has an important role in shaping diversity.

Coffee is a high value agricultural commodity grown in about 80 countries. Sustainable coffee cultivation is hampered by multiple biotic and abiotic stress conditions predominantly driven by climate change. The NAC proteins are plants specific transcription factors associated with various physiological functions in plants which include cell division, secondary wall formation, formation of shoot apical meristem, leaf senescence, flowering embryo and seed development. Besides, they are also involved in biotic and abiotic stress regulation. Due to their ubiquitous influence, studies on NAC transcription factors have gained momentum in different crop plant species. In the present study, NAC25 like transcription factor was isolated and characterized from two cultivated coffee species, Coffea arabica and Coffea canephora and five Indian wild coffee species for the first time. The full-length NAC25 gene varied from 2,456 bp in Coffea jenkinsii to 2,493 bp in C. arabica. In all the seven coffee species, sequencing of the NAC25 gene revealed 3 exons and 2 introns. The NAC25 gene is characterized by a highly conserved 377 bp NAM domain (N-terminus) and a highly variable C terminus region. The sequence analysis revealed an average of one SNP per every 40.92 bp in the coding region and 37.7 bp in the intronic region. Further, the non-synonymous SNPs are 8-11 fold higher compared to synonymous SNPs in the non-coding and coding region of the NAC25 gene, respectively. The expression of NAC25 gene was studied in six different tissue types in C. canephora and higher expression levels were observed in leaf and flower tissues. Further, the relative expression of NAC25 in comparison with the GAPDH gene revealed four folds and eight folds increase in expression levels in green fruit and ripen fruit, respectively. The evolutionary relationship revealed the independent evolution of the NAC25 gene in coffee.

The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat genes (NLRs). The products of these genes are responsible for recognizing avirulence proteins (Avr) of phytopathogens and triggering specific defense responses. Identifying NLRs in plant genomes with standard gene annotation software is challenging due to their multidomain nature, sequence diversity, and clustered genomic distribution. We present the results of a genome-wide scan and comparative analysis of NLR loci in three coffee species (Coffea canephora, Coffea eugenioides and their interspecific hybrid Coffea arabica). A total of 1311 non-redundant NLR loci were identified in C. arabica, 927 in C. canephora, and 1079 in C. eugenioides, of which 809, 562, and 695 are complete loci, respectively. The NLR-Annotator tool used in this study showed extremely high sensitivities and specificities (over 99%) and increased the detection of putative NLRs in the reference coffee genomes. The NLRs loci in coffee are distributed among all chromosomes and are organized mostly in clusters. The C. arabica genome presented a smaller number of NLR loci when compared to the sum of the parental genomes (C. canephora, and C. eugenioides). There are orthologous NLRs (orthogroups) shared between coffee, tomato, potato, and reference NLRs and those that are shared only among coffee species, which provides clues about the functionality and evolutionary history of these orthogroups. Phylogenetic analysis demonstrated orthologous NLRs shared between C. arabica and the parental genomes and those that were possibly lost. The NLR family members in coffee are subdivided into two main groups: TIR-NLR (TNL) and non-TNL. The non-TNLs seem to represent a repertoire of resistance genes that are important in coffee. These results will support functional studies and contribute to a more precise use of these genes for breeding disease-resistant coffee cultivars. [ABSTRACT FROM AUTHOR]

Coffee endophytes have been studied for almost 74 years, and several studies have demonstrated coffee-endophytic fungi with antibacterial and antifungal potential for human and plant pathogens. In this study, we isolated and identified a total of 235 strains of endophytic fungi from coffee leaf tissues collected in four coffee plantations in Pu'er city, Yunnan province, China. Molecular identification was carried out using maximum likelihood phylogenetic analysis of nuclear ribosomal internal transcribed spacer (ITS1-5.8S rDNA-ITS2) sequences, while the colonization rate and the isolation frequency were also calculated. Two pathogenic fungi (Alternaria alternata and Penicillium digitatum) and two pathogenic bacteria (Pseudomonas syringae and Salmonella enterica subsp. enterica) were used for screening the antagonistic activities of 61 strains of coffee-endophytic fungi by a dual-culture test assay while maximum likelihood phylogenetic analysis confirmed their natural classification. This is the first study of coffee-leaf-endophytic fungal diversity in China, and the results revealed that coffee-endophytic fungi from this study belong to the Ascomycota, distributed among two classes, 10 orders, and 17 families. Concurrently, endophytic fungi isolates distributed in Arthrinium, Biscogniauxia, Daldinia, Diaporthe, and Nigrospora showed strong antagonistic activities against the pathogens. For the pathogens Alternaria alternata and Pseudomonas syringae, Nigrospora XCE-7 showed the best inhibitory effects with inhibition rates of 71.76% and 61.11%, respectively. For the pathogen Penicillium digitatum, Daldinia ME-9 showed the best inhibitory effect with a 74.67% inhibition rate, while Biscogniauxia PTE-7 and Daldinia T5E-1-3 showed the best inhibitory effect with a rate of 60.42% against the pathogen Salmonella enterica subsp. enterica. Overall, our study shows the diversity of coffee endophytes in four coffee-growing areas in Pu'er city, Yunnan province, China, and their potential use as biological control agents against two fungal and two bacterial pathogens. [ABSTRACT FROM AUTHOR]

Introducción. La erosión hídrica es un fenómeno natural, acelerado por la actividad humana, que facilita la degradación de los suelos y el transporte de sedimentos a otras zonas. Objetivo. Cuantificar la escorrentía superficial y la tasa de erosión a escala de parcela, bajo eventos de precipitación natural, en un suelo Entisol sembrado con café (Coffea arabica) con sombra, y determinar la dinámica temporal y la influencia de los principales factores asociados con este proceso. Materiales y métodos. El estudio se desarrolló en Llano Brenes, Alajuela, Costa Rica. Se instalaron nueve parcelas de escorrentía, los datos fueron recolectados entre mayo de 2018 y noviembre de 2019, cada parcela tuvo un medidor de escorrentía y un contenedor para la toma de muestras de sedimentos. Se instalaron tres sensores de reflectometría de dominio temporal para las mediciones de contenido superficial de humedad del suelo. El análisis de datos se realizó a escala mensual-anual, inter-evento e intra-evento. En la escala intra-evento se utilizó el modelo de infiltración de Diskin y Nazimov. Resultados. En los años 2018 y 2019 se obtuvieron, respectivamente, los siguientes resultados anuales: a) lámina total de escorrentía de 90,99 y 102,66 mm, b) concentración de sedimentos de 2,14 y 1,88 g L-1, y c) pérdida de suelo de 1612 y 1692 g m-2. Los mayores valores de pérdida de suelo se obtuvieron en octubre de cada año; el análisis intra-evento explicó la generación de escorrentía con base la lámina de precipitación y el contenido de humedad inicial en el evento. Conclusión. La tasa de erosión y la escorrentía medias anuales fueron de 1652 g m-2 y 96,8 mm, respectivamente. La lámina de precipitación, intensidades y contenido inicial de humedad superficial del suelo tuvieron un importante rol en la generación de escorrentía y pérdida de suelo.

The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat genes (NLRs). The products of these genes are responsible for recognizing avirulence proteins (Avr) of phytopathogens and triggering specific defense responses. Identifying NLRs in plant genomes with standard gene annotation software is challenging due to their multidomain nature, sequence diversity, and clustered genomic distribution. We present the results of a genome-wide scan and comparative analysis of NLR loci in three coffee species (Coffea canephora, Coffea eugenioides and their interspecific hybrid Coffea arabica). A total of 1311 non-redundant NLR loci were identified in C. arabica, 927 in C. canephora, and 1079 in C. eugenioides, of which 809, 562, and 695 are complete loci, respectively. The NLR-Annotator tool used in this study showed extremely high sensitivities and specificities (over 99%) and increased the detection of putative NLRs in the reference coffee genomes. The NLRs loci in coffee are distributed among all chromosomes and are organized mostly in clusters. The C. arabica genome presented a smaller number of NLR loci when compared to the sum of the parental genomes (C. canephora, and C. eugenioides). There are orthologous NLRs (orthogroups) shared between coffee, tomato, potato, and reference NLRs and those that are shared only among coffee species, which provides clues about the functionality and evolutionary history of these orthogroups. Phylogenetic analysis demonstrated orthologous NLRs shared between C. arabica and the parental genomes and those that were possibly lost. The NLR family members in coffee are subdivided into two main groups: TIR-NLR (TNL) and non-TNL. The non-TNLs seem to represent a repertoire of resistance genes that are important in coffee. These results will support functional studies and contribute to a more precise use of these genes for breeding disease-resistant coffee cultivars.

Foliar spots caused by Pseudomonas coronafaciens pv. garcae (Pcg), Pseudomonas amygdali pv. tabaci (Pat) and Pseudomonas cichorii (Pch) are major bacterial diseases that can reduce coffee production. However, little is known about the genetic diversity and molecular mechanisms underlying the pathogenicity to coffee plants of these bacteria. In this study, genome sequences of Pcg, Pat and Pch strains isolated from coffee plants in Minas Gerais state, Brazil, were used to assess their variability and plasticity, and compare their type III secretion system (T3SS) and apoplastic effector repertoires as well as tabtoxin biosynthetic/detoxification genes. Genomic diversity was found for all three phytopathogens, among which Pch possesses the highest number of exclusive proteins. The Pcg genome is the most stable whereas that of Pch is the most plastic, which is related to their host ranges. When compared with those of Pseudomonas syringae pv. tomato DC3000, hrp/hrc gene sequences are more conserved in Pcg and Pat than in Pch, which also possesses the smallest T3SS and the largest apoplastic effector repertoires. The only T3SS effector family common to all three pathogens is AvrE, suggesting that, as for other plant–Pseudomonas interactions, it may play a crucial role for pathogenicity towards coffee plants. Apoplastic proteins associated with maintaining the redox balance and degrading proteins/peptides not previously described as important in plant–bacteria interactions were found. Gain/loss of the tabtoxin biosynthetic cluster with retention of the antitoxin gene was observed, indicating that tabtoxin production is not a limiting factor for the occurrence of mixed infections. [ABSTRACT FROM AUTHOR]

Introducción. La humedad del suelo es una variable muy importante en el suministro de agua para la agricultura y es su principal recurso. Sin embargo, su medición en campo suele presentar limitaciones, por lo que su predicción es necesaria para diversas actividades de planificación agrícola e investigación. Objetivo. Predecir la humedad diaria del suelo a escala de cultivo, a partir de información meteorológica mediante modelos de regresión lineal múltiple. Materiales y métodos. El estudio se desarrolló en Llano Brenes, Alajuela, Costa Rica. Se instalaron sensores de reflectometría de dominio temporal (TDR) y registraron información cada veinte minutos de humedad de suelo desde noviembre 2018 a diciembre 2019. El suelo se clasificó a nivel taxonómico como Lithic Ustorthents, en una finca con cultivo de café en producción. Se tomaron muestras de suelo no disturbadas para la calibración de los TDR y se realizó un análisis de estabilidad temporal. El primer modelo (RLM1) fue una regresión lineal múltiple con variables meteorológicas, en el segundo modelo (RLM2) además de las variables meteorológicas, se separó la precipitación en subperíodos, los cuales se introdujeron como variables “dummy”, mientras que el tercer modelo (PCA) consistió en un análisis de componentes principales y un modelo de regresión lineal. Resultados. Los modelos RLM2 (R2 = 0,838) y PCA (R2 = 0,823) presentaron un mejor desempeño en comparación con el modelo RLM1 (R2 = 0,540). Sin embargo, el modelo RLM2 se consideró más útil, debido a su simplicidad y a que presentó los mejores indicadores de bondad de ajuste. Conclusión. Los modelos de regresión lineal con variables meteorológicas permitieron estimar la humedad del suelo, debido a que esta tendió a seguir los patrones estacionales y las variaciones de la precipitación, tal como se observó en el RLM2 con la separación de subperíodos.

ABSTRACT Coffee is one of the most important commodities in the global market. Of the 130 species of Coffea, only Coffea arabica and Coffea canephora are actually cultivated on a large scale. Despite the economic and social importance of coffee, little research has been done on the coffee tree microbiome. To assess the structure and function of the rhizosphere microbiome, we performed a deep shotgun metagenomic sequencing of the rhizospheres of five different species, C. arabica, C. canephora, Coffea stenophylla, Coffea racemosa, and Coffea liberica. Our findings indicated that C. arabica and C. stenophylla have different microbiomes, while no differences were detected between the other Coffea species. The core rhizosphere microbiome comprises genera such as Streptomyces, Mycobacterium, Bradyrhizobium, Burkholderia, Sphingomonas, Penicillium, Trichoderma, and Rhizophagus, several of which are potential plant-beneficial microbes. Streptomyces and mycorrhizal fungi dominate the microbial communities. The concentration of sucrose in the rhizosphere seems to influence fungal communities, and the concentration of caffeine/theobromine has little effect on the microbiome. We also detected a possible relationship between drought tolerance in Coffea and known growth-promoting microorganisms. The results provide important information to guide future studies of the coffee tree microbiome to improve plant production and health. IMPORTANCE The microbiome has been identified as a fundamental factor for the maintenance of plant health, helping plants to fight diseases and the deleterious effects of abiotic stresses. Despite this, in-depth studies of the microbiome have been limited to a few species, generally with a short life cycle, and perennial species have mostly been neglected. The coffee tree microbiome, on the other hand, has gained interest in recent years as Coffea trees are perennial tropical species of enormous importance, especially for developing countries. A better understanding of the microorganisms associated with coffee trees can help to mitigate the deleterious effects of climate change on the crop, improving plant health and making the system more sustainable.

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.