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For the first time, the dual effect of coffee cherry sanitization methods to control the microbial load in processing and the influence of fermentation time on coffee quality parameters was evaluated. Two assays were carried out by wet processing: I) Sanitization of the coffee cherry (ST1: Unclassified processed cherries; ST2: Classified and sanitized cherries with drinking water; ST3: Classified and sanitized cherries with a chemical agents and II) Fermentation times (FT1: 12 h; FT2: 24 h; FT3: 48 h; FT4: 72 h and FT5: 96 h). pH, temperature, and dissolved oxygen were monitored during fermentation. Counts of Lactic Acid Bacteria - LAB, mesophiles, and yeasts were carried out on the coffee mass before and after fermentation. Caffeine and chlorogenic acid contents were determined by HPLC-DAD and the sensory profile by methodology for specialty coffees (SCA). The main findings showed that: sanitization with Timsen® did not significantly influence the evolution of pH during fermentation (p > 0.05), but it can reduce to a small extent the action of LAB at the end of the process. It was observed that the temperature of the coffee mass tends to balance with the ambient temperature, with significant effects (p < 0.05) of sanitization (ST2 and ST3) on the stability of this variable during fermentation. Timsen® as a disinfectant affected microbial populations and improved the sensory profile in the cup. In prolonged coffee fermentations (FT3, FT4 and FT5), the pH of the coffee mass tended to stabilize after 36 h, regardless of the process time. Likewise, a correlation was evident between a higher microbial load correlated with better sensory profiles in FT4 and FT5. Neither the sanitization process nor the fermentation time significantly affected the caffeine and chlorogenic acid contents of the coffee, both in its green and roasted states. Consequently, the sanitization of cherry coffee with Timsen® and prolonged fermentation times favor the safety and coffee final quality in the cup.

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Somatic embryogenesis (SE) is a clear example of cellular totipotency. The SE of the genus Coffea has become a model for in vitro propagation for woody species and for the large-scale production of disease-free plants that provide an advantage for modern agriculture. Temporary immersion systems (TIS) are in high demand for the propagation of plants. The success of this type of bioreactor is based on the alternating cycles of immersion of the plant material in the culture medium, usually a few minutes, and the permanence outside the medium of the tissues for several hours. Some bioreactors are very efficient for propagating one species but not another. The efficiency of bioreactors depends on the species, the tissue used to propagate, the species' nutritional needs, the amount of ethylene produced by the tissue, and many more. In this protocol, we show how we produce C. canephora plants that are being taken to the field.

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Since the term proteomics was coined by Marc Wilkins in 1994, there has been an explosion in the number of articles reporting the use of the proteomics technique. As the layers of biological organization and their regulation increase, the complexity of living beings increases. Thus, we go from the genome to tissues, cells, cellular compartments, and phenotypes and the complexity of the tools used to study this complexity also increases. Unlike the genome study, in the case of the proteome, we have a more complex panorama. We have a spatial and temporal proteome. Proteomics helps to answer complex biological questions since proteins' function depends on their molecular structure, subcellular localization, and posttranslational modifications. In this protocol, we describe a methodology to extract proteins using different methods, separating proteins by electrophoresis in double-dimensional gels and analyzing the gels using specialized software that allows obtaining information on the number and abundance of the proteins from the gels.

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Omic tools have changed the way of doing research in experimental biology. The somatic embryogenesis (SE) study has not been immune to this benefit. The transcriptomic tools have been used to compare the genes expressed during the induction of SE with the genes expressed in zygotic embryogenesis or to compare the development of the different stages embryos go through. It has also been used to compare the expression of genes during the development of calli from which SE is induced, as well as many other applications. The protocol described here is employed in our laboratory to extract RNA and generate several transcriptomes for the study of SE on Coffea canephora.

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Coffee (Coffea arabica) cultivation is vital to the global economic, social and cultural life of farmers. However, senescent and disease-susceptible plantations affect coffee productivity. Therefore, it is crucial to improve biotechnological strategies such as micropropagation to increase the number of plants for replanting. In this study, the dark condition (T1) and different light qualities (T0-white light 400-700 nm; T2-red light 660 nm and T3-blue light 460 nm) were evaluated to optimize the in vitro propagation of 4 and 9 month-old coffee seeds. The results showed that red light had the highest percentage, an outstanding germination rate index, which may suggest that in the case of coffee seeds could be involved phytochromes that promote germination in a red light quality. In summary, the ideal conditions for in vitro micropropagation of coffee are under white and red light condition.

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The maturation of Arabica coffee fruits is influenced by both endogenous and external factors. The stage of fruit maturation affects the chemical composition of the beans, which in turn impacts the quality of the coffee beverage. During maturation, the fruit peel changes colour from green to red (cherry), signalling the optimal harvest time and suggesting high fruit quality. However, the degree of redness can vary, indicating different levels of maturity. This study aimed to explore the variation in soluble sugar accumulation in relation to the redness of coffee fruit tissues. We classified ripe fruits into six ripeness categories based on the intensity of the red colour of the epicarp, measured using a colourimeter. We analysed total soluble sugar, sucrose, and starch in three parts: coat (exocarp + mesocarp), coat juice (obtained by squeezing the coat), and beans. Our findings reveal that the variation in sugar in the endosperm does not correspond to changes in the coat, suggesting separate regulation of sugar accumulation, particularly sucrose, which is crucial for coffee quality. Our data indicate that there is no transfer of sucrose and reducing sugars from the red coat to the bean.

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Consumers are increasingly looking for healthy foods without the addition of synthetic additives. The aim of this study was to evaluate the efficiency of coffee extracts as a natural antioxidant in fresh pork sausage. Firstly, the conditions for obtaining coffee green extracts were optimized (Central Composite Rotatable Design 23, variables: extraction time, ethanol-water ratio, and sample-solvent ratio) in an ultrasound bath (70 °C). The response variables were the bioactive compounds levels and antioxidant activity. Valid models were obtained (p ≤ 0.05, R2 > 0.751), with higher bioactive content and antioxidant activity in the central point region. Extracts of Robusta and Arabica coffee green (RG and AG) and medium roast (RR and AR) obtained, and central point (10 min, an ethanol concentration of 30%, and a sample-solvent ratio of 10 g/100 mL) and optimized (14.2 min, 34.2%, and 5.8 g/100 mL) parameters were characterized. The RG presented a significantly (p ≤ 0.05) higher content of caffeine (3114.8 ± 50.0 and 3148.1 ± 13.5 mg/100 g) and 5-CQA (6417.1 ± 22.0 and 6706.4 ± 23.5 mg/100 g) in both extraction conditions, respectively. The RG and RR coffee presented the highest antioxidant activity. Two concentrations of RG and RR coffee extracts were tested in fresh pork sausage. The Robusta coffee extract presented the highest antioxidant activity in both roasted and green states. However, when applied to a meat product, the extract prepared with RG coffee showed better results, with efficiency in replacing synthetic antioxidants (content of malonaldehyde/kg of sample below 0.696 ± 0.059 in 20 days of storage), without altering the sensory attributes of the product (average scores above 7.16 ± 1.43 for all attributes evaluated). Therefore, the RG coffee extract was a suitable alternative as a natural antioxidant applied to fresh pork sausage.

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Cancer is the second leading cause of death worldwide, despite the many treatments available, cancer patients face side effects that reduce their quality of life. Therefore, there is a need to develop novel strategies to increase the efficacy of treatments. In this study, gold nanoparticles obtained by green synthesis with Coffea arabica green bean extract were loaded with Doxorubicin, (a highly effective but non-specific drug) by direct interaction and using commercial organic ligands that allow colloidal dispersion at physiological and tumor pH. Conjugation of these components resulted in stable nanohybrids at physiological pH and a tumor pH release dependent, with a particle size less than 40 nm despite having the ligands and Doxorubicin loaded on their surface, which gave them greater specificity and cytotoxicity in H69 tumor cells.

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Specialty coffee beans are those produced, processed, and characterized following the highest quality standards, toward delivering a superior final product. Environmental, climatic, genetic, and processing factors greatly influence the green beans' chemical profile, which reflects on the quality and pricing. The present study focuses on the assessment of eight major health-beneficial bioactive compounds in green coffee beans aiming to underscore the influence of the geographical origin and post-harvesting processing on the quality of the final beverage. For that, we examined the non-volatile chemical profile of specialty Coffea arabica beans from Minas Gerais state, Brazil. It included samples from Cerrado (Savannah), and Matas de Minas and Sul de Minas (Atlantic Forest) regions, produced by two post-harvesting processing practices. Trigonelline, theobromine, theophylline, chlorogenic acid derivatives, caffeine, caffeic acid, ferulic acid, and p-coumaric acid were quantified in the green beans by high-performance liquid chromatography with diode array detection. Additionally, all samples were roasted and subjected to sensory analysis for coffee grading. Principal component analysis suggested that Cerrado samples tended to set apart from the other geographical locations. Those samples also exhibited higher levels of trigonelline as confirmed by two-way ANOVA analysis. Samples subjected to de-pulping processing showed improved chemical composition and sensory score. Those pulped coffees displayed 5.8% more chlorogenic acid derivatives, with an enhancement of 1.5% in the sensory score compared to unprocessed counterparts. Multivariate logistic regression analysis pointed out altitude, ferulic acid, p-coumaric acid, sweetness, and acidity as predictors distinguishing specialty coffee beans obtained by the two post-harvest processing. These findings demonstrate the influence of regional growth conditions and post-harvest treatments on the chemical and sensory quality of coffee. In summary, the present study underscores the value of integrating target metabolite analysis with statistical tools to augment the characterization of specialty coffee beans, offering novel insights for quality assessment with a focus on their bioactive compounds.

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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.

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Despite the important role that flower-visiting insects play in agricultural production, none of the previous studies of coffee pollinators in Colombia have incorporated functional diversity into their analysis. Therefore, this study aimed to quantify the abundance, richness, and functional diversity of insects that visit flowers in coffee crops. Twenty-eight plots were selected among five sites in the north, center, and south of Colombia. In each plot, coffee flower insect visitors were collected and recorded on 90 trees at eight-minute intervals per tree, at three different times over three days. All sampling was carried out during two flowering events per year, over three years, resulting in a total of 1240 h of observations. Subsequently, the insects were taxonomically identified, and the number of individuals and species, as well as the diversity of the order q, were estimated. Functional diversity was also characterized in the bee community. The results: (a) 23,735 individuals belonging to 566 species were recorded; of them, 90 were bees, with the native species being the most abundant during 10:30 and 13:00 h; (b) bees formed five functional groups, with corbiculate and long-tongued non-corbiculate bees being the most abundant and occupying the largest regions of functional space; (c) potential pollinators in coffee crops are Apis mellifera, Nannotrigona gaboi, Tetragonisca angustula, Geotrigona cf. tellurica, and Partamona cf. peckolti. Coffee crops host a wide diversity of flower visitors, especially bees, which could be beneficial for productivity and contribute to the maintenance of plant species that accompany coffee cultivation.

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A simple method set for assessing biochemical changes associated with osmotic stress responses was developed using coffee (Coffea arabica L.) leaf disks. Stress was induced by polyethylene glycol (PEG) exposure. Quantitative evaluation of tissue physiological stress parameters was carried out using analytical methods to validate the conversion of classic qualitative histochemical tests for localizing lipid peroxidation, hydrogen peroxide, and total xanthine alkaloids into semi-quantitative assays. Relative electrolyte leakage (EL%) and chlorophyll content (SPAD index) were also recorded. EL% levels of treated disks were higher than those of control ones, whereas SPAD indexes were comparable. Histochemical localization indicated that levels of lipid peroxidation, H2O2, and total xanthines were also higher under osmotic stress than in control conditions. Semi-quantitative data obtained by image processing of histochemical staining consistently matched quantitative evaluations. Chromatographic analyses revealed that theophylline and caffeine concentrations increased in the presence of PEG, whereas theobromine remained constant in relation to the control. The methods herein described can be useful to rapidly acquire initial data regarding biochemical osmotic stress responses in coffee tissues based on simple staining and imaging steps. Moreover, it is likely that the same method may be applicable to other types of stresses and plant species upon minor adjustments.

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Noncoding and coding RNAs are key regulators of plant growth, development, and stress responses. To investigate the types of transcripts accumulated during the vegetative to reproductive transition and floral development in the Coffea arabica L., we sequenced small RNA libraries from eight developmental stages, up to anthesis. We combined these data with messenger RNA and PARE sequencing of two important development stages that marks the transition of an apparent latent to a rapid growth stage. In addition, we took advantage of multiple in silico tools to characterize genomic loci producing small RNAs such as phasiRNAs, miRNAs, and tRFs. Our differential and co-expression analysis showed that some types of small RNAs such as tRNAs, snoRNAs, snRNAs, and phasiRNAs preferentially accumulate in a stage-specific manner. Members of the miR482/miR2118 superfamily and their 21-nucleotide phasiRNAs originating from resistance genes show a robust co-expression pattern that is maintained across all the evaluated developmental stages. Finally, the majority of miRNAs accumulate in a family stage-specific manner, related to modulated hormonal responses and transcription factor expression.

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Coffee fruit rot (CFR) is a well-known disease worldwide, mainly caused by Colletotrichum spp., the most important species being C. kahawae subsp. kahawae. In Puerto Rico, Colletotrichum spp. were identified as pathogens of coffee fruits. The coffee berry borer (CBB) was shown to be a dispersal agent of these fungi, and interaction of Fusarium with Colletotrichum affecting coffee fruits was suggested. In this study, we demonstrated that Fusarium spp. also cause CFR in Puerto Rico. Fusarium spp. are part of the CBB mycobiota, and this insect is responsible for spreading the pathogens in coffee fields. We identified nine Fusarium spp. (F. nirenbergiae, F. bostrycoides, F. crassum, F. hengyangense, F. solani-melongenae, F. pseudocircinatum, F. meridionale, F. concolor, and F. lateritium) belonging to six Fusarium species complexes isolated from CBBs and from rotten coffee fruits. Pathogenicity tests showed that F. bostrycoides, F. lateritium, F. nirenbergiae, F. solani-melongenae, and F. pseudocircinatum were pathogens causing CFR on green coffee fruits. F. bostrycoides was the predominant species isolated from the CBB mycobiota and coffee fruits with symptoms of CFR, suggesting a close relationship between F. bostrycoides and the CBB. To our knowledge, this is the first report of F. bostrycoides, F. solani-melongenae, F. pseudocircinatum, and F. nirenbergiae causing CFR worldwide and the first report of F. lateritium causing CFR in Puerto Rico. Understanding the CFR disease complex and how the CBB contributes to dispersing different Fusarium spp. on coffee farms is important to implement disease management practices in Puerto Rico and in other coffee-producing countries.

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Microorganisms are important indicators of soil quality due to their sensitivity to changes, reflecting the impacts caused by different land uses. The objective of this study was to evaluate the microbiological and physical-chemical attributes of the soil in areas cultivated with coffee under three different management systems (shaded coffee and full sun coffee with two spacings), as well as in adjacent areas under pasture and native forest, in Bahia, Brazil. The microbiological and physicochemical indicators evaluated were basal soil respiration (MBR), soil total organic carbon (TOC), microbial biomass carbon (MBC), metabolic quotient (qCO2), microbial quotient (qMic), enzyme activities (urease, acid phosphatase and fluorescein diacetate hydrolysis (FDA)). Physical and chemical indicators (particle size, texture, pH, P, K+, Ca2+, Mg2+, Al3+, and sum of bases) were also evaluated. Biological and chemical attributes were much more discriminative of study areas in the dry season. Microbial quotient (qMic) and metabolic quotient (qCO2) in the dry season showed that pasture is the most degraded land use. Conversely, nature forest and coffee with Grevillea were similar and were the best ones. In general, soil quality indicators were more sensitive to discriminate pasture and native forest from coffee systems, which, in turn, were not well discriminated among themselves.

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The rainfall regime has a significant impact on the microclimate and mass emergence of the coffee berry borer, Hypothenemus hampei (Coleoptera: Curculionidae) (CBB). Little is known, however, about the shade tree-microclimate-CBB mass emergence interaction. The objective of the present study was to compare the effect of microclimate on the mass emergence of CBB in a full sun-exposed plot with a plot shaded by trees. The experiment was conducted on a Robusta coffee farm in southern Chiapas, Mexico. In each plot, 18 traps baited with an alcohol mixture were installed to capture flying females, collecting caught individuals every hour from 8:00 to 18:00 h. A meteorological station recorded several microclimatic variables on 13 weekly sampling dates from February to May 2022. Significantly more CBB females were captured in the shaded plot. The largest number of CBB captures was recorded between 14:00 and 16:00 h for the shade plot and between 15:00 and 17:00 h for the sun-exposed plot. The mass emergence of CBB showed a positive association with precipitation, dew point, and wind speed samples and a negative association with maximum air temperature, average relative humidity, ultraviolet radiation, wind speed, and equilibrium moisture content. Our observations show that the relationship between shade trees, microclimate, and mass emergence of CBB is complex and that its study helps us to gain deeper insight into CBB bioecology and advance control techniques against this important pest.

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Coffee is one of the most consumed beverages worldwide. Espírito Santo is the largest Brazilian producer of conilon coffee, and invested in the creation of new cultivars, such as "Conquista ES8152", launched in 2019. Therefore, the present study aimed to evaluate the effects of maturation and roasting on the chemical and sensorial composition of the new conilon coffee cultivar "Conquista ES8152". The coffee was harvested containing 3 different percentages of ripe fruits: 60%, 80%, and 100%, and roasted at 3 different degrees of roasting: light, medium, and dark, to evaluate the moisture and ash content, yield of soluble extract, volatile compound profile, chlorogenic acid and caffeine content, and sensory profile. "Conquista ES8152" coffee has a moisture content between 1.38 and 2.62%; ash between 4.34 and 4.72%; and yield between 30.7 and 35.8%. Sensory scores ranged between 75 and 80 and the majority of volatile compounds belong to the pyrazine, phenol, furan, and pyrrole groups. The content of total chlorogenic acids was drastically reduced by roasting, with values between 2.40 and 9.33%, with 3-caffeoylquinic acid being the majority. Caffeine was not influenced by either maturation or roasting, with values between 2.16 and 2.41%. The volatile compounds furfural, 5-methylfurfural, and 2-ethyl-5-methylpyrazine were positively correlated with the evaluated sensory attributes and 5-methylfurfural was the only one significantly correlated with all attributes. Ethylpyrazine, furfuryl acetate, 1-furfurylpyrrole, 4-ethyl-2-methoxyphenol, and difurfuryl ether were negatively correlated. The stripping did not affect the quality and composition of this new cultivar, however, the roasting caused changes in both the chemical and sensorial profiles, appropriately indicated by the principal component analysis.

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INTRODUCTION: Many secondary metabolites isolated from plants have been described in the literature owing to their important biological properties and possible pharmacological applications. However, the identification of compounds present in complex plant extracts has remained a great scientific challenge, is often laborious, and requires a long research time with high financial cost. OBJECTIVES: The aim of this study was to develop a method that allows the identification of secondary metabolites in plant extracts with a high degree of confidence in a short period of time. MATERIAL AND METHODS: In this study, an ethanolic extract of Coffea arabica leaves was used to validate the proposed method. Countercurrent chromatography was chosen as the initial step for extraction fractionation using gradient elution. Resulting fractions presented a variation of compounds concentrations, allowing for statistical total correlation spectroscopy (STOCSY) calculations between liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-HRMS/MS) and NMR across fractions. RESULTS: The proposed method allowed the identification of 57 compounds. Of the annotated compounds, 20 were previously described in the literature for the species and 37 were reported for the first time. Among the inedited compounds, we identified flavonoids, alkaloids, phenolic acids, coumarins, and terpenes. CONCLUSION: The proposed method presents itself as a valid alternative for the study of complex extracts in an effective, fast, and reliable way that can be reproduced in the study of other extracts.

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The cryopreservation of plant germplasm at ultralow temperatures is an alternative technique for the long-term storage of seeds of the genus Coffea sp. However, for this technique to be successful, cell integrity must be maintained at all stages of the process on the basis of scientific research. The present study investigated validated cryopreservation protocols for Coffea arabica L. seeds and evaluate the effects on the physiological and biochemical characteristics of the seeds at each stage of the process. Seeds were dried on silica gel or with saturated saline solution, precooled or not in a biofreezer, immersed in nitrogen, and reheated in a water bath. After each of these steps, the physiological and biochemical quality of the seeds was determined. Pre-cooling is a step that can be dispensed with in the cryopreservation of Coffea arabica seeds, direct immersion in liquid nitrogen being more indicated. Coffea arabica L. seeds tolerate cryopreservation after rapid drying in silica gel up to water contents of 17 or 20% (wb), with greater survival at 17%. The enzyme activities of catalase, polyphenol oxidase and peroxidase are indicators of the quality of C. arabica L. seeds subjected to cryopreservation.

A criopreservação de germoplasma vegetal em temperaturas ultrabaixas é uma alternativa para o armazenamento em longo prazo de sementes do gênero Coffea sp. Entretanto, para que essa técnica apresente sucesso, a realização de pesquisas que garantam a manutenção da integridade celular em todas as etapas do processo é de fundamental importância. O objetivo com o presente trabalho foi investigar protocolos de criopreservação validados para sementes de Coffea arabica L., avaliando separadamente, os efeitos sobre as características fisiológicas e bioquímicas das sementes, em cada etapa do processo. As sementes foram secadas em sílica gel ou em solução salina saturada, submetidas ou não ao pré-resfriamento em biocongelador, em seguida imersas no nitrogênio e reaquecidas em banho-maria. Após cada uma dessas etapas, a qualidade fisiológica e bioquímica das sementes foi determinada. O pré-resfriamento é uma etapa que pode ser dispensada na criopreservação de sementes de Coffea arabica, sendo mais indicada a imersão direta em nitrogênio líquido. Sementes de Coffea arabica L. toleram a criopreservação após secagem rápida em sílica gel até teores de água de 17 ou 20% (wb), com maior sobrevivência a 17%. A atividade das enzimas catalase, polifenoloxidase e peroxidase são indicadoras da qualidade de sementes de Coffea arabica L. submetidas à criopreservação.

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