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Background: The coffee crop is prominent in Brazilian agriculture, making the country a global power in this area. One of the main concerns in the coffee sector is disease, which can affect coffee productivity and quality. Thus, it is important to evaluate the factors that may affect coffee quality and thus enhance the development of strategies to reduce coffee losses and costs and optimize production. This study evaluated the influence of the type of irrigation (self-propelled, drip, and center pivot) on the time until the occurrence of phoma leaf spot on Arabica coffee plants, considering the intensity of the disease. Additionally, the association between longitudinal incidence and the time until an event of interest was assessed based on the joint modeling of longitudinal and survival data., Results: The results of this study identify the effectiveness of drip irrigation system compared with other systems; the use of such systems was associated with an ~46.5% reduction in the risk of leaf spot disease compared with the use of a self-propelled irrigation system. The use of a center pivot system increased the risk of disease progression compared with a self-propelled system. An association between the longitudinal and survival processes was also observed., Conclusion: The findings demonstrate the superior performance of the drip irrigation system in controlling phoma leaf spot disease in Arabica coffee plants compared with self-propelled and center pivot systems. This research highlights the potential of using drip irrigation to establish more effective agricultural practices in coffee cultivation, contributing to better disease management and improved crop quality. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

Coffee pulp is a by-product characterized by its richness in phenolic compounds. This study examined the catabolism of (poly)phenols in digested coffee pulp flour (CPF) and extract (CPE) during in vitro colonic fermentation. After a simulated gastrointestinal digestion, samples were fermented using human microbiota and (poly)phenol transformations were analyzed by UHPLC-ESI-MS/MS. Digested CPF and CPE contained high amounts of phenolic acids, notably 3',4'-dihydroxycinnamic (99.7-240.1 μmol 100 g -1 ) and 3,4-dihydroxybenzoic acid (174.1-491.4 μmol 100 g -1 ). During the in vitro fecal fermentation, phenylpropanoic acids (1.5- to 2.6-fold), phenyl-γ-valerolactones (1.3- to 23-fold), phenylvaleric acids (1.1- to 2-fold) and benzene derivatives (1.5-fold) increased; while benzoic and cinnamic acids, cinnamoylquinic derivatives, flavonols, benzaldehydes and diphenylpropan-2-ols decreased. The (poly)phenols in CPF were catabolized more slowly than in CPE, suggesting protection of the fibrous matrix against phenolic degradation. Coffee pulp may be a promising food ingredient rich in (poly)phenols contributing to the prevention of intestinal diseases., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: Coffee (Coffea arabica L.) is one of the most important commodities today, with a high economic value worldwide. Coffee leaf rust (Hemileia vastatrix Berk. et Br.) has been showing a high impact on Brazilian coffee trees among the various diseases that attack coffee. The climate has a great influence on the development of diseases, especially when fungi are the causal agents. This study aimed to carry out the zoning of climate favorability for coffee leaf rust in the traditional and main coffee-producing regions of Brazil. The study was conducted in 13 locations in the states of Paraná, São Paulo, Rio de Janeiro, Espírito Santo, Minas Gerais, Goiás and Bahia. Air temperature and daily precipitation data for the current scenario were collected using the WorldClim version 2.1 platform for the last climatological normal and future climate change data. The ideal climate conditions for coffee leaf rust consist of a mean air temperature ranging from 21 to 25 °C and precipitation >30 mm per month. The Coupled Model Intercomparison Projects scenarios associated with the Intergovernmental Panel on Climate Change reports consisted of the Shared Socio-Economic Pathways SSP-1 2.6, SSP-2 4.5, SSP-3 7.0 and SSP-5 8.5, the latter being considered one of the most catastrophic. All steps to carry out the suitability zoning were performed in a tool using the QGIS geographic information system software., Results: Zoning for coffee leaf rust had three classes: favorable, relatively favorable and unfavorable. Currently, the largest coffee-producing region in Brazil has 49.1% of its analyzed area classified as favorable, 39.2% as relatively favorable and 11.7% as unfavorable. In the current scenario, Patrocínio and Três Pontas are locations with high coffee production in which the favorable class is predominant. The state of Minas Gerais has an annual mean of 55.3% of its entire territory apt for the disease, with the highest occurrence between September and March., Conclusions: Climate change has a negative impact on the development of coffee leaf rust, mainly in the long term, as in the period of 2081-2100, in which the SSP-5 8.5 scenario led to a decrease in the favorable and unfavorable areas and an increase in the relatively favorable areas of 9.8%, 18.6% and 71.5% for the Brazilian territory, respectively. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

Aims: In this study, we report the use of two novel lytic polyvalent phages as a cocktail in in planta assays and their efficacy in the control of bacterial halo blight (BHB) caused by Pseudomonas coronafaciens pv. garcae (Pcg) in coffee plants., Methods and Results: Phages were isolated from samples of coffee plant leaves collected at two different locations in Brazil. Both phages belong to the class Caudoviricetes and present myovirus-like morphotypes, and both exhibited specificity to their host, Pcg strain IBSBF-158. The two phages were encapsulated in chitosan-coated Ca-alginate nanoparticles, which demonstrated promising performance, promoting reductions in disease severity ranging from 66.83% to 83.37%, depending on the timing of application relative to infection. Both phages were somewhat susceptible to the effects of abiotic factors when in free form, with solar radiation seriously negatively impacting their lytic activity. However, nanoencapsulation of both phages as a lytic cocktail within chitosan-coated Ca-alginate nanoparticles proved successful in fully stabilizing both phages from the deleterious action of UV radiation., Conclusions: Application of such lytic nanoparticles in pre- and post-inoculated coffee seedlings in in planta greenhouse assays proved successful in controlling the phytopathogen responsible for BHB of coffee, Pcg, with a significant decrease in the progression of the disease. The results suggest that lytic nanoparticles may become an effective and sustainable strategy for coffee BHB control, as an alternative to conventional approaches relying on chemical (copper hydroxide or oxychloride or kasugamycin hydrochloride) or biological agents, but more studies are needed in the field to confirm this. The phage protection system developed represents a potential alternative treatment for bacterial plant diseases with minimum damage to the environment., (© The Author(s) 2024. Published by Oxford University Press on behalf of Applied Microbiology International.)

Our objective was to monitor the main enzymes of coffee germinal metabolism and chemical composition during Self-Induced Anaerobiosis Fermentation (SIAF) with yeasts (Saccharomyces cerevisiae (CCMA0543), Candida parapsilosis (CCMA0544) and Torulospora delbrueckii (CCMA0684)) evaluating their relationship with seed germination. The starter cultures were assessed by qPCR. The organic acids were analyzed by liquid chromatography. Catalase (CAT), Esterase (EST), Alcohol dehydrogenase (ADH), and Isocitrate Lyase (ICL) enzyme activity was confirmed by the presence of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-Page) gel bands. The formation of a white halo confirmed the activity of the enzyme endo-β-mannanase, and its quantification was performed using the diameter of the halo of both the samples and the standard curve. At the end of the fermentation process, S. cerevisiae and T. delbrueckii presented the highest populations (>7 log 10 cells/g). Succinic acids (average -1.11 g/kg) were consumed during SIAF. Lactic acid increased after 180 h in coffees fermented by the SIAF method (average 3.57 g/kg). CAT and EST showed high activity in the conventional process. ADH activity was detected in both processes after 180 h of the SIAF method. Yeast inoculation during the SIAF method increased the activity of ICL andshowed more intense activity in the first 96 h of fermentation, especially the pulped coffee. Endo-β-mannanase activity was intense during conventional coffee processing (9.89-10.99 pmol/min/g). Natural processing tends to preserve a higher percentage of viable seeds. Therefore, the processing and fermentation methods impact seed quality differently., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Global warming and extreme climate conditions caused by unsuitable temperature and humidity lead to coffee leaf rust ( Hemileia vastatrix ) diseases in coffee plantations. Coffee leaf rust is a severe problem that reduces productivity. Currently, pesticide spraying is considered the most effective solution for mitigating coffee leaf rust. However, the application of pesticide spray is still not efficient for most farmers worldwide. In these cases, pruning the most infected leaves with leaf rust at coffee plantations is important to help pesticide spraying to be more efficient by creating a more targeted, accessible treatment. Therefore, detecting coffee leaf rust is important to support the decision on pruning infected leaves. The dataset was acquired from a coffee farm in Majalengka Regency, Indonesia. Only images with clearly visible spots of coffee leaf rust were selected. Data collection was performed via two devices, a digital mirrorless camera and a phone camera, to diversify the dataset and test it with different datasets. The dataset, comprising a total of 2024 images, was divided into three sets with a ratio of 70% for training (1417 images), 20% for validation (405 images), and 10% for testing (202 images). Images with leaves infected by coffee leaf rust were labeled via LabelImg ® with the label "CLR". All labeled images were used to train the YOLOv5 and YOLOv8 algorithms through the convolutional neural network (CNN). The trained model was tested with a test dataset, a digital mirrorless camera image dataset (100 images), a phone camera dataset (100 images), and real-time detection with a coffee leaf rust image dataset. After the model was trained, coffee leaf rust was detected in each frame. The mean average precision (mAP) and recall for the trained YOLOv5 model were 69% and 63.4%, respectively. For YOLOv8, the mAP and recall were approximately 70.2% and 65.9%, respectively. To evaluate the performance of the two trained models in detecting coffee leaf rust on trees, 202 original images were used for testing with the best-trained weight from each model. Compared to YOLOv5, YOLOv8 demonstrated superior accuracy in detecting coffee leaf rust. With a mAP of 73.2%, YOLOv8 outperformed YOLOv5, which achieved a mAP of 70.5%. An edge device was utilized to deploy real-time detection of CLR with the best-trained model. The detection was successfully executed with high confidence in detecting CLR. The system was further integrated into pruning solutions for Arabica coffee farms. A pruning device was designed using Autodesk Fusion 360 ® and fabricated for testing on a coffee plantation in Indonesia.

Two outbreaks of coffee wilt disease have devastated African coffee production. A PLOS Biology study suggests that horizontal gene transfer via large Starship transposons between 2 fungal species played a key role in the repeated emergence of the disease., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Wingfield, Wingfield. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Outbreaks of fungal diseases have devastated plants and animals throughout history. Over the past century, the repeated emergence of coffee wilt disease caused by the fungal pathogen Fusarium xylarioides severely impacted coffee production across sub-Saharan Africa. To improve the disease management of such pathogens, it is crucial to understand their genetic structure and evolutionary potential. We compared the genomes of 13 historic strains spanning 6 decades and multiple disease outbreaks to investigate population structure and host specialisation. We found that F. xylarioides comprised at least 4 distinct lineages: 1 host-specific to Coffea arabica, 1 to C. canephora var. robusta, and 2 historic lineages isolated from various Coffea species. The presence/absence of large genomic regions across populations, the higher genetic similarities of these regions between species than expected based on genome-wide divergence and their locations in different loci in genomes across populations showed that horizontal transfers of effector genes from members of the F. oxysporum species complex contributed to host specificity. Multiple transfers into F. xylarioides populations matched different parts of the F. oxysporum mobile pathogenicity chromosome and were enriched in effector genes and transposons. Effector genes in this region and other carbohydrate-active enzymes important in the breakdown of plant cell walls were shown by transcriptomics to be highly expressed during infection of C. arabica by the fungal arabica strains. Widespread sharing of specific transposons between F. xylarioides and F. oxysporum, and the correspondence of a putative horizontally transferred regions to a Starship (large mobile element involved in horizontal gene transfers in fungi), reinforce the inference of horizontal transfers and suggest that mobile elements were involved. Our results support the hypothesis that horizontal gene transfers contributed to the repeated emergence of coffee wilt disease., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Peck et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Saccharomyces cerevisiae CCMA 0159 is reported as a promising biocontrol agent against ochratoxin A (OTA)-producing fungi in coffee. Coffea arabica and Coffea canephora (var. Conilon or Robusta) are the most widely consumed coffee species around the world, cultivated in tropical and subtropical regions, each exhibiting distinct physicochemical and sensory characteristics. The objective of this study was to compare the growth and OTA production by Aspergillus carbonarius, A. ochraceus, and A. westerdijkiae in C. arabica and C. canephora, along with assessing the efficiency of S. cerevisiae CCMA 0159 in biocontrolling ochratoxigenic fungi in both coffee varieties. A. carbonarius exhibited a higher growth rate and OTA production in both coffee varieties, with C. canephora showing particular susceptibility. Conversely, A. ochraceus and A. westerdijkiae demonstrated lower growth and OTA production. S. cerevisiae was effective in biocontrolling the fungal isolates, inhibiting over 80 % of A. carbonarius growth in both coffee varieties. Among the mechanisms of action of the biological control agent, the production of volatile organic compounds stands out. The results of this study confirm the significant potential of S. cerevisiae CCMA 0159 as a biocontrol agent against Aspergillus for application in coffee-producing areas., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: Yeast and lactic acid bacteria (LAB) play an important part in the post-harvest fermentation of coffee. This study applied lab-scale fermentation to commercial green coffee beans using dry coffee pulp as the substrate, with the aim of modifying coffee-bean flavor. In addition to spontaneous fermentation, yeast and LAB isolated from coffee beans and dried coffee pulp were added during fermentation., Results: Co-inoculation of yeast and LAB showed a significant effect on the chlorogenic acid content after between 24 and 72 h of fermentation. Acetic, citric, malic, lactic, and quinic acids were shown to be affected significantly (P < 0.05) by fermentation and inoculation. Gas chromatography detected that esters, alcohols, aldehydes, furans, and pyrazines were the primary compounds in the coffee beans. Certain volatile groups were present in greater concentrations and broader varieties within the inoculated beans. The highest cupping scores were given to beans that had been co-inoculated with yeast and LAB., Conclusion: Overall, the use of yeasts and LAB starters showed potential to create coffee beverages with desirable characteristics by standardized fermentation. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

Peru is the ninth-largest coffee producer and the largest organic coffee exporter worldwide. Specific modifications in the microbial consortia during fermentation control the flavor of coffee. It is still unclear how fermentation duration affects microbial communities. This study aimed to provide insights into the diversity and functional behavior of the bacterial microbiome during coffee fermentation in northern Peru using shotgun metagenomics. Accordingly, metagenomic DNA was extracted and sequenced from samples of the liquid fraction during the short fermentation process (SFP) in Amazonas (6 and 12 h) and long fermentation process (LFP) in Cajamarca (6, 12, 18, 24, and 36 h). Our findings indicate that common (e.g., Acetobacter, Lactobacillus, Leuconostoc, and Weissella) and unique (e.g., Acidiphilium and Methylobacterium) acid-tolerant bacteria from the SFP and LFP play crucial roles and have a positive impact on the sensory qualities of coffee. Specifically, the LFP from San Ignacio might be associated with the high sensory quality of coffee based on the release of catalytic, hydrolase, oxidoreductase, transferase, and transporter enzymes in the InterPro and KEGG profiles. Additionally, these bacterial microorganisms metabolize several compounds (e.g., isoleucine, betaine, galactose, tryptophan, arginine, and cobalamin) into volatile compounds, mainly in the LFP, enhancing the flavor and aroma of coffees. This characteristic suggests that the LFP has a stronger effect on coffee quality than does the SFP on the basis of bacterial diversity and functional prediction. These findings provide new perspectives on the potential biotechnological uses of autochthonous microorganisms to produce superior-quality coffee beans from northern Peru., (© 2024 Institute of Food Technologists.)

With a view to modulating the flavour profiles of Australian coffee, this investigation focused on three estates in New South Wales. Coffee cherries were processed into beans with wet fermented and non-fermented methods to evaluate the effects of fermentation and terroir on microbial population dynamics, volatile composition, and sensory properties. Thirty-three volatiles were quantified in green and roasted coffee beans - 12 esters, 9 alcohols, 6 acids, 3 monoterpenes, 2 norisoprenoids, 1 aldehyde - and 5 thiols were quantified in roasted coffee brews. Sensory descriptive analysis defined appearance, aroma, and flavour attributes to describe the coffee brews. Fermented coffees were characterised by increased intensity of 'black tea leaves' and 'dark chocolate' aromas and 'burnt toast' flavour. Results suggested that wet fermentation of Australian coffee cherries could enhance the content of some volatile compounds known to convey "floral" and "fruity" aromas commonly ascribed to premium coffees from traditional producing regions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Traditionally, control of coffee plant bacterial halo blight (BHB) caused by the phytopathogen Pseudomonas coronafaciens pv. garcae (Pcg) involves frequent spraying of coffee plantations with non-environmentally friendly and potentially bacterial resistance-promoting copper products or with kasugamycin hydrochloride. In this study we report a leap forward in the quest for a new ecofriendly approach, characterizing (both physicochemically and biologically) and testing both in vitro and ex vivo a new lytic phage for Pcg. An in-depth molecular (genomic and DNA structural features) characterization of the phage was also undertaken. Phage PcgS01F belongs to the class Caudoviricetes, Drexlerviridae family and genus Guelphvirus, and presents a siphovirus-like morphotype. Phage PcgS01F showed a latency period of 40 min and a burst size of 46 PFU/host cell, allowing to conclude that it replicates well in Pcg IBSBF-158. At Multiplicity Of Infection (MOI, or the ratio of phage to bacteria) 1000, the performance of phage PcgS01F was much better than at MOI 10, promoting increasing bacterial reductions until the end of the in vitro inactivation assays, stabilizing at a significant 82 % bacterial load reduction. Phage PcgS01F infected and killed Pcg cells ex vivo in coffee plant leaves artificially contaminated, with a maximum of Pcg inactivation of 7.66 log CFU/mL at MOI 1000 after 36 h of incubation. This study provides evidence that the isolated phage is a promising candidate against the causative agent of BHB in coffee plants., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results., (Copyright © 2024 Elsevier Inc. All rights reserved.)

In recent years, the role of microbial communities in agricultural systems has received increasing attention, particularly concerning their impact on plant health and productivity. However, the influence of host plant genetic factors on the microbial composition of coffee plants remains largely unexplored. This study provides the first comprehensive investigation into how genotype affects the microbial communities present in the rhizosphere and fruits of Coffea canephora. Conducted on a commercial coffee farm in Brazil, we analyzed six genotypes of C. canephora var. Conilon. Soil and fruit samples were collected from which microbial DNA was extracted and sequenced, targeting the V3-V4 region of the 16 S rDNA and the ITS1 region for fungi. A total of 12,239,769 reads were generated from the 16 S rDNA and ITS1 regions. The PCoA revealed distinct patterns of beta diversity, with genotype 153 exhibiting significant isolation in soil bacterial communities. The dominant bacterial orders included Rhizobiales and Rhodobacterales, while the fungal community comprised diverse taxa from Saccharomycetales and Hypocreales. LEfSe analysis identified key metagenomic biomarkers, highlighting genotype Baiano 4 for its richness in fruit-associated taxa, whereas genotype 153 exhibited lower diversity in both soil and fruit samples. This work enhances our understanding of the microbiomes associated with different coffee genotypes, providing evidence of how host genetic variation influences microbial community composition. Our findings indicate that specific microbial taxa are enriched in the fruits and soil of various genotypes. Future research should focus on identifying these microorganisms and elucidating their specific functions within the rhizosphere and coffee fruits., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Plant U-box genes play an important role in the regulation of plant hormone signal transduction, stress tolerance, and pathogen resistance; however, their functions in coffee (Coffea canephora L.) remain largely unexplored. In this study, we identified 47 CcPUB genes in the C. canephora L. genome, clustering them into nine groups via phylogenetic tree. The CcPUB genes were unevenly distributed across the 11 chromosomes of C. canephora L., with the majority (11) on chromosome 2 and none on chromosome 8. The cis-acting elements analysis showed that CcPUB genes were involved in abiotic and biotic stresses, phytohormone responsive, and plant growth and development. RNA-seq data revealed diverse expression patterns of CcPUB genes across leaves, stems, and fruits tissues. qRT-PCR analyses under dehydration, low temperature, SA, and Colletotrichum stresses showed significant up-regulation of CcPUB2, CcPUB24, CcPUB34, and CcPUB40 in leaves. Furthermore, subcellular localization showed CcPUB2 and CcPUB34 were located in the plasma membrane and nucleus, and CcPUB24 and CcPUB40 were located in the nucleus. This study provides valuable insights into the roles of PUB genes in stress responses and phytohormone signaling in C. canephora L., and provided basis for functional characterization of PUB genes in C. canephora L., (© 2024. The Author(s).)

Coffee leaf rust (CLR), caused by Hemileia vastatrix , is considered a highly important phytosanitary problem in Mexico. Currently, there are few microorganisms used as biocontrol alternatives to chemical control of CLR in organic coffee fields in Mexico. This study evaluates the use of Paenibacillus sp. NMA1017 as a biocontrol agent to inhibit the development of H. vastatrix in in vitro and in vivo (greenhouse) experiments. Hemileia vastatrix urediniospores were placed on water agar plates, and then Paenibacillus sp. NMA1017 was inoculated simultaneously or 8 h later. Urediniospores germination rate was reduced by 94% when the NMA1017 strain was inoculated simultaneously with the urediniospores and reduced by 38% when NMA1017 was inoculated 8 h later. Experiments with 8-month-old Bourbon coffee plants that were infected with H. vastatrix showed that disease incidence was reduced by 38, 90, and 50% when NMA1017 was applied 8 days before, simultaneously, or 8 days after the application of H. vastatrix , respectively. Paenibacillus sp. NMA1017 also reduced the severity of CLR on the leaves by up to 62%. The germination urediniospores of other rust pathogens such as Puccinia sorghi (maize leaf rust), Puccinia triticina (wheat leaf rust), Puccinia graminis f. sp. tritici (black stem rust of wheat), Uromyces striatus (alfalfa leaf rust), and Phragmidium sp. (rosebush leaf rust) were also inhibited. Use of the potential biocontrol agent Paenibacillus sp. NMA1017 might help reduce the application of chemical fungicides for the control of CLR, making coffee a more sustainable crop and providing management options for organic coffee growers., Competing Interests: The author(s) declare no conflict of interest.

Fermentation using starter cultures has been considered an alternative and economically viable technology for the production of specialty coffees. This type of technology promotes several benefits, such as increased sensory quality, control over the fermentation process, predictability of the final product and added value. Coffee (Coffea arabica L.) samples for this study were collected in Presidente Olegário - MG (2018/19 crop year) in the Cerrado region of Minas Gerais. The effects of natural fermentation and inoculation of the yeast Torulaspora delbrueckii and duration of fermentation (0, 24, 48, 72 and 96 hours) on the sensory and chemical quality (analysis of bioactive, volatile, and organic compounds and fatty acids) of coffee were evaluated. The objective of this study was to determine the effect of fermentation time and starter culture inoculation on the chemical composition of fermented coffees. Fermentation time significantly influenced the sensory description of the coffee beverage, with notes of honey, brown sugar and almond predominating up to 48 hours, for coffees fermented for 72 and 96 hours the notes described were and fruity, winey notes. The chemical composition was primarily influenced by fermentation time.

Coffee berry disease is caused by Colletotrichum kahawae , a quarantine fungus still absent from most coffee-producing countries. Given the potential adverse effects on coffee berry production, it is a severe worldwide threat to farmers and industry. Current biosecurity management focuses on exclusion by applying quarantine measures, including the certification of coffee plants and their products. However, methods for detecting C. kahawae by National Plant Protection Organization (NPPO) laboratories still need approval. This research aims to functionally demonstrate, standardize, and validate a method for detecting and discriminating C. kahawae from other Colletotrichum species that may be present in coffee plant samples. The method proposes to use an end-point PCR marker for the mating type gene ( MAT1-2-1 ) and a confirmatory test with a real-time quantitative PCR (qPCR) marker developed on the glutamine synthetase gene. The C. kahawae amplicons for the Cen-CkM10 qPCR marker exhibited specific melting temperature values and high-resolution melt profiles that could be readily differentiated from other tested species, including their relatives. Given the fungus's quarantine status, specificity was tested using artificial mixtures of DNA of C. kahawae with other Colletotrichum species and coffee plant DNA. The described method will enable NPPOs in coffee-producing and exporting countries, especially Colombia, to prevent this pathogen's entry, establishment, and spread.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license., Competing Interests: The author(s) declare no conflict of interest.

Hemileia vastatrix, causal agent of coffee leaf rust (CLR), is an aggressive pathogen of coffee plants worldwide. Conventional fungicides play a major role in the suppression of this disease, but a recent shift toward eco-friendly farming practices has occurred and additional novel, effective, and sustainable strategies for CLR control are needed. Naturally occurring fungal antagonists could be well-positioned to meet this demand, but these fungi need to be isolated and tested for efficacy to identify organisms with potential. In this study, a survey of fungi associated with CLR lesions in four districts of Hawai'i Island, HI, USA (Kona, Ka'ū, Hāmākua, and Hilo) was conducted. Coffee leaves infected with CLR were collected from 22 locations and over 600 lesions were plated on ½ APDA and CTC 4T media. DNA was extracted from purified isolates and the internal transcribed spacer region (ITS) was sequenced and analyzed by BLASTn. In total, 194 isolates comprising 50 taxa were recovered. Several of the genera are known antagonists of CLR or other plant pathogens, including Simplicillium, Akanthomyces, Cladosporium, Fusarium, and Clonostachys. The wide diversity of fungi associated with CLR lesions provide a wealth of possibilities for identifying potential CLR antagonists that could serve as a valuable tool for coffee farmers as part of an integrated pest management plan., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Studies have shown that a diverse and metabolically active microbiota exists throughout different stages of coffee processing, from pre- to post-harvest. This microbiota originates from both the cultivation and processing environments. Additionally, microorganisms from the soil can be found on the fruit due to the transfer between them. This study reviews the microbiota present in Arabica coffee fruits and the soils where the plants are grown. It examines how microbial profiles are related to coffee variety, altitude, cultivation region, and processing method, and establishes a connection between the microbiota in soil and fruit. A diverse microbiota was observed in both coffee fruits and soils, with similar microorganisms identified across different growing regions, processing methods, and coffee varieties. However, exclusive detections of some microorganisms were also observed. These differences highlight the influence of terroir on coffee's microbial composition, confirming that environmental conditions, genetic factors, and processing methods shape coffee microbiota. Since microbial development during coffee fermentation can affect the beverage's quality, the data presented in this review offer valuable insights for researchers and producers. Understanding the influence of processing methods, coffee varieties, and cultivation regions on coffee microbiota enables the selection of specific fermentation conditions or starter cultures to enhance terroir characteristics or adjust microbial populations to favor or introduce microorganisms beneficial for coffee quality., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Coffee, the second most traded commodity globally after petroleum and is the most exported cash crop of Ethiopia. However, coffee cultivation faces challenges due to fungal diseases, resulting in significant yield losses. The primary fungal diseases affecting coffee production include coffee berry disease, wilt disease (caused by Gibberella xylarioides), and coffee leaf rust. In this study, we aimed to isolate potentially antagonistic actinomycetes from the root rhizosphere of wild Coffea arabica plants in the Yayo coffee forest biosphere in southwestern Ethiopia. Soil samples were collected from the rhizosphere, and actinomycetes were selectively isolated and identified to the genus level by morphological, physiological, and biochemical characterization. These pure isolates were screened for their antagonistic activity against Gibberella xylarioides in vitro using a dual culturing method. Promising isolates demonstrating strong inhibition of fungal mycelial growth were further investigated through in vivo experiments using coffee seedlings. A total of 82 rhizobacteria were isolated. These isolates' inhibition of fungal mycelial growth varied from 0% to 83.3%. Among them, four isolates MUA26, MUA13, MUA52, and MUA14 demonstrated the highest percentage inhibition of fungal mycelial growth: 83.3%, 80%, 76.67%, and 73.3%, respectively. Seedlings inoculated with MUA13, MUA14, and MUA26 during the challenge inoculations (Rhizobacteria + Gibberella xylarioides) exhibited the lowest disease incidence compared to the infected fungi (P < 0.05). Notably, the seedlings inoculated with MUA26 demonstrated the highest disease control efficiency, reaching 83% (P < 0.05). MUA26 was found to produce extracellular enzymes, including chitinase, protease, and lipase, which acted as inhibitors. In summary, this study highlights that MUA26, among the actinomycete isolates, exhibited significant antagonistic activity against Gibberella xylarioides f.sp. coffea. Its efficacy in controlling coffee wilt disease, both in vitro and in vivo, positions it as a potential bioinoculant for managing coffee wilt disease., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Nuguse, Kejela. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Here, we report on a Cordyceps species entering into a multi-trophic, multi-kingdom association. Cordyceps cateniannulata, isolated from the stem of wild Coffea arabica in Ethiopia, is shown to function as an endophyte, a mycoparasite and an entomopathogen. A detailed polyphasic taxonomic study, including a multilocus phylogenetic analysis, confirmed its identity. An emended description of C. cateniannulata is provided herein. Previously, this species was known as a pathogen of various insect hosts in both the Old and New World. The endophytic status of C. cateniannulata was confirmed by re-isolating it from inoculated coffee plants. Inoculation studies have further shown that C. cateniannulata is a mycoparasite of Hemileia vastatrix, as well as an entomopathogen of major coffee pests; infecting and killing Hypothenemus hampei and Leucoptera coffeella. This is the first record of C. cateniannulata from Africa, as well as an endophyte and a mycoparasite. The implications for its use as a biocontrol agent are discussed., (Copyright © 2024 British Mycological Society. Published by Elsevier Ltd. All rights reserved.)

Background: Climate influences the interaction between pathogens and their hosts significantly. This is particularly evident in the coffee industry, where fungal diseases like Cercospora coffeicola, causing brown-eye spot, can reduce yields drastically. This study focuses on forecasting coffee brown-eye spot using various models that incorporate agrometeorological data, allowing for predictions at least 1 week prior to the occurrence of disease. Data were gathered from eight locations across São Paulo and Minas Gerais, encompassing the South and Cerrado regions of Minas Gerais state. In the initial phase, various machine learning (ML) models and topologies were calibrated to forecast brown-eye spot, identifying one with potential for advanced decision-making. The top-performing models were then employed in the next stage to forecast and spatially project the severity of brown-eye spot across 2681 key Brazilian coffee-producing municipalities. Meteorological data were sourced from NASA's Prediction of Worldwide Energy Resources platform, and the Penman-Monteith method was used to estimate reference evapotranspiration, leading to a Thornthwaite and Mather water-balance calculation. Six ML models - K-nearest neighbors (KNN), artificial neural network multilayer perceptron (MLP), support vector machine (SVM), random forests (RF), extreme gradient boosting (XGBoost), and gradient boosting regression (GradBOOSTING) - were employed, considering disease latency to time define input variables., Results: These models utilized climatic elements such as average air temperature, relative humidity, leaf wetness duration, rainfall, evapotranspiration, water deficit, and surplus. The XGBoost model proved most effective in high-yielding conditions, demonstrating high precision and accuracy. Conversely, the SVM model excelled in low-yielding scenarios. The incidence of brown-eye spot varied noticeably between high- and low-yield conditions, with significant regional differences observed. The accuracy of predicting brown-eye spot severity in coffee plantations depended on the biennial production cycle. High-yielding trees showed superior results with the XGBoost model (R 2  = 0.77, root mean squared error, RMSE = 10.53), whereas the SVM model performed better under low-yielding conditions (precision 0.76, RMSE = 12.82)., Conclusion: The study's application of agrometeorological variables and ML models successfully predicted the incidence of brown-eye spot in coffee plantations with a 7 day lead time, illustrating that they were valuable tools for managing this significant agricultural challenge. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

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., Competing Interests: The author(s) declare no conflict of interest.

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 (qCO 2 ), microbial quotient (qMic), enzyme activities (urease, acid phosphatase and fluorescein diacetate hydrolysis (FDA)). Physical and chemical indicators (particle size, texture, pH, P, K + , Ca 2+ , Mg 2+ , Al 3+ , 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 (qCO 2 ) 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., (© 2024. The Author(s) under exclusive licence to Sociedade Brasileira de Microbiologia.)

Yeast, which plays a pivotal role in the brewing, food, and medical industries, exhibits a close relationship with human beings. In this study, we isolated and purified 60 yeast strains from the natural fermentation broth of Sidamo coffee beans to screen for indigenous beneficial yeasts. Among them, 25 strains were obtained through morphological characterization on nutritional agar medium from Wallerstein Laboratory (WL), with molecular biology identifying Saccharomyces cerevisiae strain YBB-47 and the remaining 24 yeast strains identified as Pichia kudriavzevii. We investigated the fermentation performance, alcohol tolerance, SO 2 tolerance, pH tolerance, sugar tolerance, temperature tolerance, ester production capacity, ethanol production capacity, H 2 S production capacity, and other brewing characteristics of YBB-33 and YBB-47. The results demonstrated that both strains could tolerate up to 3% alcohol by volume at a high sucrose mass concentration (400 g/L) under elevated temperature conditions (40 ℃), while also exhibiting a remarkable ability to withstand an SO 2 mass concentration of 300 g/L at pH 3.2. Moreover, S. cerevisiae YBB-47 displayed a rapid gas production rate and strong ethanol productivity. whereas P. kudriavzevii YBB-33 exhibited excellent alcohol tolerance. Furthermore, this systematic classification and characterization of coffee bean yeast strains from the Sidamo region can potentially uncover additional yeasts that offer high-quality resources for industrial-scale coffee bean production., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

The plant-parasitic root-knot nematode Meloidogyne exigua causes significant damage and is an important threat in Coffea arabica plantations. The utilization of plant-beneficial microbes as biological control agents against sedentary endoparasitic nematodes has been a longstanding strategy. However, their application in field conditions to control root-knot nematodes and their interaction with the rhizospheric microbiota of coffee plants remain largely unexplored. This study aimed to investigate the effects of biological control agent-based bioproducts and a chemical nematicide, used in various combinations, on the control of root-knot nematodes and the profiling of the coffee plant rhizomicrobiome in a field trial. The commercially available biological products, including Trichoderma asperellum URM 5911 (Quality), Bacillus subtilis UFPEDA 764 (Rizos), Bacillus methylotrophicus UFPEDA 20 (Onix), and nematicide Cadusafos (Rugby), were applied to adult coffee plants. The population of second-stage juveniles (J 2 ) and eggs, as well as plant yield, were evaluated over three consecutive years. However, no significant differences were observed between the control group and the groups treated with bioproducts and the nematicide. Furthermore, the diversity and community composition of bacteria, fungi, and eukaryotes in the rhizosphere soil of bioproduct-treated plants were evaluated. The dominant phyla identified in the 16 S, ITS2, and 18 S communities included Proteobacteria, Acidobacteria, Actinobacteria, Ascomycota, Mortierellomycota, and Cercozoa in both consecutive years. There were no significant differences detected in the Shannon diversity of 16 S, ITS2, and 18 S communities between the years of data. The application of a combination of T. asperellum, B. subtilis, and B. methylotrophicus, as well as the use of Cadusafos alone and in combination with T. asperellum, B. subtilis, and B. methylotrophicus, resulted in a significant reduction (26.08%, 39.13%, and 21.73%, respectively) in the relative abundance of Fusarium spp. Moreover, the relative abundance of Trichoderma spp. significantly increased by 500%, 200%, and 100% at the genus level, respectively, compared to the control treatment. By constructing a co-occurrence network, we discovered a complex network structure among the species in all the bioproduct-treated groups. However, our findings indicate that the introduction of exogenous beneficial microbes into field conditions was unable to modulate the existing microbiota significantly. These findings suggest that the applied bioproducts had no significant impact on the reshaping of the overall microbial diversity in the rhizosphere microbiome but rather recruited selected microrganisms and assured net return to the grower. The results underscore the intricate nature of the rhizosphere microbiome and suggest the necessity for alternate biocontrol strategies and a re-evaluation of agricultural practices to improve nematode control by aligning with the complex ecological interactions in the rhizosphere., Competing Interests: Declaration of Competing Interest The authors declare no competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Biocontrol Agents (BCAs) can be an eco-friendly alternative to fungicides to reduce the contamination with mycotoxigenic fungi on coffee. In the present study, different strains of bacteria and yeasts were isolated from Ivorian Robusta coffee. Their ability to reduce fungal growth and Ochratoxin A (OTA) production during their confrontation against Aspergillus carbonarius was screened on solid media. Some strains were able to reduce growth and OTA production by 85 % and 90 % and were molecularly identified as two yeasts, Rhodosporidiobolus ruineniae and Meyerozyma caribbica. Subsequent tests on liquid media with A. carbonarius or solely with OTA revealed adhesion of R. ruineniae to the mycelium of A. carbonarius through Scanning Electron Microscopy, and an OTA adsorption efficiency of 50 %. For M. caribbica potential degradation of OTA after 24 h incubation was observed. Both yeasts could be potential BCAs good candidates for Ivorian Robusta coffee protection against A. carbonarius and OTA contamination., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Ontogenic resistance has been described for many plant-pathogen systems. Conversely, coffee leaf rust, a major fungal disease that drastically reduces coffee production, exhibits a form of ontogenic susceptibility, with a higher infection risk for mature leaves. To take into account stage-dependent crop response to phytopathogenic fungi, we developed an SEIR-U epidemiological model, where U stands for spores, which differentiates between young and mature leaves. Based on this model, we also explored the impact of ontogenic resistance on the sporulation rate. We computed the basic reproduction number [Formula: see text], which classically determines the stability of the disease-free equilibrium. We identified forward and backward bifurcation cases. The backward bifurcation is generated by the high sporulation of young leaves compared to mature ones. In this case, when the basic reproduction number is less than one, the disease can persist. These results provide useful insights on the disease dynamics and its control. In particular, ontogenic resistance may require higher control efforts to eradicate the disease., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Microbial contamination of coffee beans arises from various factors such as harvesting, handling, and storage practices, during which ochratoxin A (OTA)-producing fungi develop and proliferate. The presence of elevated concentrations of OTA poses a serious health risk to coffee consumers. Therefore, the implementation of a post-harvest treatment involving the use of bacteria known to antagonize OTA-producing fungi constitutes a safe alternative for reducing or eliminating the toxin's concentration in coffee beans. In this study, coffee beans (Coffea arabica L.) were inoculated with Bacillus licheniformis M2-7, after which we monitored fungal growth, in vitro antagonism, and OTA concentration. Our findings demonstrated that coffee beans inoculated with this bacterial strain exhibited a significant decrease in fungal populations belonging to the genera Aspergillus and Penicillium, which are known to produce OTA. Moreover, strain M2-7 decreased the growth rates of these fungi from 67.8% to 95.5% (P < 0.05). Similarly, inoculation with B. licheniformis strain M2-7 effectively reduced the OTA concentration from 24.35 ± 1.61 to 5.52 ± 1.69 µg/kg (P < 0.05) in stored coffee beans. These findings suggest that B. licheniformis M2-7 holds promise as a potential post-harvest treatment for coffee beans in storage, as it effectively inhibits the proliferation of OTA-producing fungi and lowers the toxin's concentration., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Coffea spp. is the source of one of the most widely consumed beverages in the world. However, the cultivation of this crop is threatened by Hemileia vastatrix Berk & Broome, a fungal disease, which reduces the productivity and can cause significant economic losses. In this protocol, coffee leaf segment derived from a chemical mutagenesis process are inoculated with uredospores of the pathogen. Subsequently, the gene expression changes are analyzed over the time (0, 5, 24, 48, and 120 h) using quantitative real-time polymerase chain reaction (RT-qPCR). The procedures and example data are presented for expression analysis in the CaWRKY1 gene. This procedure can be applied for quantitative analysis of other genes of interest to coffee breeders and scientists for elucidating the molecular mechanisms involved in the interaction between the plant and pathogen, potentially leading to the development of more efficient approaches for managing this disease., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Endophytic fungi produce a range of known metabolites and several others, not yet explored, which present important biological activities from the pharmaceutical and industrial perspective. Several studies have reported the diversity of endophytes in Coffea arabica plants, although few have been described in organic cultures. In the current paper, we describe the chemical profile of specialized metabolites in the ethyl acetate phase in a strain of the endophytic fungus Colletotrichum siamense associated with coffee (Coffea arabica L.) (Rubiaceae) and its potential against tumor cells and bacteria of medical and food importance. Cytotoxicity assays in tumor cells MCF-7 and HepG2/C3A were performed by MTT and microdilution in broth to evaluate the antibacterial action of metabolic extract. The antiproliferative assay showed promising results after 24 h of treatment, with 50% injunction concentrations for the two cell types. UHPLC-MS/MS analyses with an electrospray ionization source were used to analyze the extracts and identify compounds of species Colletotrichum siamense, which is still little explored as a source of active metabolites. Many of these compounds observed in the endophytic need to be chemically synthesized in industry, at high costs, while production by the fungus becomes a chemically and economically more viable alternative. Pyrocatechol, gentisyl alcohol, and alpha-linolenic acid, associated with different mechanisms of action against tumor cells, were detected among the main compounds. The extract of the endophytic fungus Colletotrichum siamense presented several compounds with pharmacological potential and antibacterial activity, corroborating its potential in biotechnological applications., (© 2023. The Author(s) under exclusive licence to Sociedade Brasileira de Microbiologia.)

During wet fermentation, mucilage layers in coffee cherries must be removed completely. To explain mucilage degradation, several controversial hypotheses have been proposed. The aim of this work was to improve our understanding of the kinetics of mucilage breakdown. Pulped coffee beans were wet fermented with seven different treatments for 36 h. Endogenous bacteria and yeasts are selectively suppressed, and pectinases or lactic acid are added. They also involve maintaining the beans at pH 7 throughout fermentation and using spontaneous fermentation without additives as a control. During spontaneous fermentation, yeast and lactic acid bacteria were detected and significantly increased to 5.5 log colony-forming units (CFU)/mL and 5.2 log CFU/mL, respectively. In the first 12 h of fermentation, there was a significant degree of endogenous pectinolytic activity, which resulted in partly destroyed beans in the absence of microorganisms. By adding pectinase and lactic acid to the fermentation mass, the breakdown process was accelerated in less than 8 h. When yeast was present throughout the fermentation, complete degradation was achieved. Bacteria played no critical role in the degradation. Klebsiella pneumoniae and Erwinia soli were found in a lower population and showed weaker pectinolytic activities compared to Hanseniaspora uvarum and Pichia kudriavzevii. During wet fermentation, mucilage degradation appears to be mediated by endogenous enzymes at the early stage, whereas microbial contributions, mainly yeasts, occur subsequently. H. uvarum and P. kudriavzevii may be promising candidates to be tested in future studies as coffee starter cultures to better control the mucilage degradation process., (© 2023 The Authors. Yeast published by John Wiley & Sons Ltd.)

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., (© The Author(s) 2023. Published by Oxford University Press on behalf of Applied Microbiology International.)

Aims: The American leaf spot, caused by Mycena citricolor, is an important disease of coffee (Coffea arabica), mostly in Central America. Currently, there are limited pathogen control alternatives that are environment friendly and economically accessible. The use of fungi isolated from the plant endomycobiota in their native habitats is on the rise because studies show their great potential for biological control. To begin to generate a green alternative to control M. citricolor, the objectives of the present study were to (i) collect, identify, screen (in vitro and in planta), and select endophytic fungi from wild Rubiaceae collected in old-growth forests of Costa Rica; (ii) confirm endophytic colonization in coffee plantlets; (iii) evaluate the effects of the endophytes on plantlet development; and (iv) corroborate the antagonistic ability in planta., Methods and Results: Through in vitro and in planta antagonism assays, we found that out of the selected isolates (i.e. Daldinia eschscholzii GU11N, Nectria pseudotrichia GUHN1, Purpureocillium aff. lilacinum CT24, Sarocladium aff. kiliense CT25, Trichoderma rifaii CT5, T. aff. crassum G1C, T. aff. atroviride G7T, T. aff. strigosellum GU12, and Xylaria multiplex GU14T), Trichoderma spp. produced the highest growth inhibition percentages in vitro. Trichoderma isolates CT5 and G1C were then tested in planta using Coffea arabica cv. caturra plantlets. Endophytic colonization was verified, followed by in planta growth promotion and antagonism assays., Conclusions: Results show that Trichoderma isolates CT5 and G1C have potential for plant growth promotion and antagonism against Mycena citricolor, reducing incidence and severity, and preventing plant mortality., (© The Author(s) 2023. Published by Oxford University Press on behalf of Applied Microbiology International.)

Background: The microbial biodiversity and the role of microorganisms in the fermentation of washed coffee in Colombia were investigated using the Bourbon and Castillo coffee varieties. DNA sequencing was used to evaluate the soil microbial biota and their contribution to fermentation. The potential benefits of these microorganisms were analyzed, including increased productivity and the need to understand the rhizospheric bacterial species to optimize these benefits., Methods: This study used coffee beans for DNA extraction and 16 S rRNA sequencing. The beans were pulped, samples were stored at 4ºC, and the fermentation process was at 19.5ºC and 24ºC. The fermented mucilage and root-soil samples were collected in duplicate at 0, 12, and 24 h. DNA was extracted from the samples at a concentration of 20 ng/µl per sample, and the data obtained were analyzed using the Mothur platform., Results: The study demonstrates that the coffee rhizosphere is a diverse ecosystem composed primarily of microorganisms that cannot be cultured in the laboratory. This suggests that the microbial community may vary depending on the coffee variety and play an essential role in fermentation and overall coffee quality., Conclusions: The study highlights the importance of understanding and optimizing the microbial diversity in coffee production, which could have implications for the sustainability and success of coffee production. DNA sequencing techniques can help characterize the structure of the soil microbial biota and evaluate its contribution to coffee fermentation. Finally, further research is needed to fully understand the biodiversity of coffee rhizospheric bacteria and their role., (© 2023. The Author(s).)

Research has demonstrated that intraspecific functional trait variation underpins plant responses to environmental variability. However, few studies have evaluated how trait variation shifts in response to plant pathogens, even though pathogens are a major driver of plant demography and diversity, and despite evidence of plants expressing distinct strategies in response to pathogen pressures. Understanding trait-pathogen relationships can provide a more realistic understanding of global patterns of functional trait variation. We examined leaf intraspecific trait variability (ITV) in response to foliar disease severity, using Coffea arabica cv. Caturra as a model species. We quantified coffee leaf rust (CLR) severity-a fungal disease prominent in coffee systems-and measured key coffee leaf functional traits under contrasting, but widespread, management conditions in an agroforestry system. We found that coffee plants express significant ITV, which is largely related to shade tree treatment and leaf position within coffee canopy strata. Yet within a single plant canopy stratum, CLR severity increased with increasing resource conserving trait values. However, coffee leaves with visible signs of disease expressed overall greater resource acquiring trait values, as compared to plants without visible signs of disease. We provide among the first evidence that leaf traits are correlated with foliar disease severity in coffee, and that functional trait relationships and syndromes shift in response to increased disease prevalence in this plant-pathogen system. In doing so, we address a vital gap in our understanding of global patterns of functional trait variation and highlight the need to further explore the potential role of pathogens within established global trait relationships and spectra., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Gagliardi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Fungal diseases cause serious damages in crop worldwide. In particular, coffee leaf rust (CLR), caused by fungus Hemileia vastatrix attacks coffee leaves and reduces coffee yield. This paper presents a multi-seasonal model of the CLR development in the coffee plantation with continuous dynamics during the rainy season and a discrete event to represent the simpler dynamics during the dry season. Biological control using predators through one or more discrete introduction events over the year is then added. Analytical and semi-numerical studies are performed to identify how much and how frequently predators need to be introduced through the definition of a threshold value, as a function of various parameters. We show that the best strategy to efficiently control the disease depends on the predator mortality: low mortality parasites need be released only once a year, while high mortality parasites should be released more frequently to ensure their persistence in the plantation. This work hence provides qualitative and quantitative bases for the deployment of predator-based biocontrol, a promising alternative to fungicides for rust control., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Clotilde Djuikem reports financial support was provided by National Research Institute for Computing and Automation., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Arabica and robusta are the two major coffee beans being sold worldwide. It is well recognized that coffee quality is influenced by their origin and the microbiological activities that drive their fermentation. However, in many coffee plantations, information about the natural diversity of bacteria that inhabit the arabica and robusta coffee cherries is limited. Here, we sampled arabica and robusta coffee cherries from Malang, East Java, Indonesia, then sequenced and analysed their bacterial composition. We found that: (a) arabica cherries contained bacteria with less diversity and abundance compared with robusta; (b) both coffee cherries were heavily populated by extremophiles, presumably dispersed from volcanic activities; (c) groups known to be involved in coffee fermentation such as lactic acid bacteria, acetic acid bacteria, Enterobacteria, and soil-associated bacteria were present in both arabica and robusta coffee cherries, and (d) arabica cherries were dominated by Leuconostoc pseudomesenteroides. These findings highlight that coffee cherry bacteria are highly diverse, the majority of which might come from the environment, with some potentially beneficial or detrimental to coffee quality. Knowledge of the natural microbial diversity of coffee cherries may be useful for the development of coffee fermentation technologies to yield coffee beans with consistent quality., (© The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.)

Background: Pseudomonas spp. promotes plant growth and colonizes a wide range of environments. During the annotation of a Coffea arabica ESTs database, we detected a considerable number of contaminant Pseudomonas sequences, specially associated with leaves. The genome of a Pseudomonas isolated from coffee leaves was sequenced to investigate in silico information that could offer insights about bacterial adaptation to coffee phyllosphere. In parallel, several experiments were performed to confirm certain physiological characteristics that could be associated with phyllospheric behavior. Finally, in vivo and in vitro experiments were carried out to verify whether this isolate could serve as a biocontrol agent against coffee rust and how the isolate could act against the infection.  RESULTS: The isolate showed several genes that are associated with resistance to environmental stresses, such as genes encoding heat/cold shock proteins, antioxidant enzymes, carbon starvation proteins, proteins that control osmotic balance and biofilm formation. There was an increase of exopolysaccharides synthesis in response to osmotic stress, which may protect cells from dessication on phyllosphere. Metabolic pathways for degradation and incorporation into citrate cycle of phenolic compounds present in coffee were found, and experimentally confirmed. In addition, MN1F was found to be highly tolerant to caffeine. The experiments of biocontrol against coffee leaf rust showed that the isolate can control the progress of the disease, most likely through competition for resources., Conclusion: Genomic analysis and experimental data suggest that there are adaptations of this Pseudomonas to live in association with coffee leaves and to act as a biocontrol agent., (© 2022. The Author(s).)

The devastating disease coffee leaf rust, caused by Hemileia vastatrix , has been a major constraint to worldwide coffee production. Recently, H. vastatrix populations were shown to be structured into three divergent genetic lineages with marked host specialization (C1, C2, and C3). However, there is yet no overall understanding of the population dynamics and adaptation of the most widespread and epidemiological relevant H. vastatrix group (C3). We used restriction site-associated DNA sequencing to generate 13,804 single nucleotide polymorphisms (SNPs) across a worldwide collection of 99 H. vastatrix isolates. Phylogenetic analyses uncovered a well-supported structuring within C3, with three main subgroups (SGs; SGI, SGII, and SGIII), which seem to reflect the historical distribution, breeding, and exchange of coffee cultivars. SGI shows a ladder-like diversification pattern and occurs across all four continents sampled, SGII is mainly restricted to Africa, and SGIII is observed only in Timor, revealing a higher genetic differentiation. Outlier and association tests globally identified 112 SNPs under putative positive selection, which impacted population structure. In particular, 29 overlapping SNPs per se seemed to have an extremely strong effect on H. vastatrix population divergence. We also found exclusive and fixed alleles associated with the SGs supporting local adaptation. Functional annotation revealed that transposable elements may play a role in host adaptation. Our study provides a higher-resolution perspective on the evolutionary history of H. vastatrix on cultivated coffee, showing its strong ability to adapt and the strength of the selective force imposed by coffee hosts, which should be taken into account when designing strategies for pathogen dissemination control and selective breeding.

Wet coffee fermentation is widely used in coffee-producing regions such as Colombia and Hawaii, but it is not widespread in Brazil. This study aimed to evaluate inoculating the lactic acid bacteria Leuconostoc mesenteroides CCMA1105 and Lactiplantibacillus plantarum CCMA 1065 and the yeasts Saccharomyces cerevisiae CCMA0543 and Torulaspora delbrueckii CCMA0684 as starter cultures on wet coffee fermentation using the SIAF method (self-induced anaerobiosis fermentation). The microbial activity resulted in high consumption of the carbohydrates glucose (98.6%), fructose (97.6%), and sucrose (100%), in addition to the production of lactic and acetic acids, impacting the final quality of the beverage. A total of 108 volatile compounds belonging to 17 classes were identified in the green and roasted coffee samples, including 2,3-butanediol produced by lactic acid bacteria, contributing to coffee's aromatic profile. The final scores for the coffees from the different fermentations ranged from 79.0 to 83.25. The inoculated fermentations were classified as specialty according to the Specialty Coffee Association. Therefore, whole coffee fruit processed via wet using SIAF method and yeast and lactic acid bacteria starter is an alternative for improving wet fermented coffee quality and obtaining coffee beverages with a different sensory profile., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Hemileia vastatrix is the most important fungal pathogen of coffee and the causal agent of recurrent disease epidemics that have invaded nearly every coffee growing region in the world. The development of coffee varieties resistant to H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown, and conflicting studies and interpretations exist as to whether the fungus is undergoing sexual reproduction. Here we used population genetics of H. vastatrix to infer the reproductive mode of the fungus across most of its geographic range, including Central Africa, Southeast Asia, the Caribbean, and South and Central America. The population structure of H. vastatrix was determined via eight simple sequence repeat markers developed for this study. The analyses of the standardized index of association, Hardy-Weinberg equilibrium, and clonal richness all strongly support asexual reproduction of H. vastatrix in all sampled areas. Similarly, a minimum spanning network tree reinforces the interpretation of clonal reproduction in the sampled H. vastatrix populations. These findings may have profound implications for resistance breeding and management programs against H. vastatrix .

Pathogen-associated molecular patterns (PAMPs) are recognized by pattern recognition receptors (PRRs) localized on the host plasma membrane. These receptors activate a broad-spectrum and durable defense, which are desired characteristics for disease resistance in plant breeding programs. In this study, candidate sequences for PRRs with lysin motifs (LysM) were investigated in the Coffea arabica genome. For this, approaches based on the principle of sequence similarity, conservation of motifs and domains, phylogenetic analysis, and modulation of gene expression in response to Hemileia vastatrix were used. The candidate sequences for PRRs in C. arabica (Ca1-LYP, Ca2-LYP, Ca1-CERK1, Ca2-CERK1, Ca-LYK4, Ca1-LYK5 and Ca2-LYK5) showed high similarity with the reference PRRs used: Os-CEBiP, At-CERK1, At-LYK4 and At-LYK5. Moreover, the ectodomains of these sequences showed high identity or similarity with the reference sequences, indicating structural and functional conservation. The studied sequences are also phylogenetically related to the reference PRRs described in Arabidopsis, rice, and other plant species. All candidates for receptors had their expression induced after the inoculation with H. vastatrix, since the first time of sampling at 6 hours post-inoculation (hpi). At 24 hpi, there was a significant increase in expression, for most of the receptors evaluated, and at 48 hpi, a suppression. The results showed that the candidate sequences for PRRs in the C. arabica genome display high homology with fungal PRRs already described in the literature. Besides, they respond to pathogen inoculation and seem to be involved in the perception or signaling of fungal chitin, acting as receptors or co-receptors of this molecule. These findings represent an advance in the understanding of the basal immunity of this species., Competing Interests: The authors have declared that no competing interests exist. Therefore, this does not alter our adherence to PLOS ONE policies on sharing data and materials.

Plant cells use different structural mechanisms, either constitutive or inducible, to defend themselves from fungal infection. Encapsulation is an efficient inducible mechanism to isolate the fungal haustoria from the plant cell protoplast. Conversely, pectin, one of the polymeric components of the cell wall, is a target of several pectolytic enzymes in necrotrophic interactions. Here, a protocol to detect pectin and fungal hyphae through optical microscopy is presented. The pectin-rich encapsulation in the cells of coffee leaves infected by the rust fungus Hemileia vastatrix and the mesophyll cell wall modification induced by Cercospora coffeicola are investigated. Lesioned leaf samples were fixed with the Karnovsky solution, dehydrated, and embedded in glycol methacrylate for 2-4 days. All steps were followed by vacuum-pumping to remove air in the intercellular spaces and improve the embedding process. The embedded blocks were sectioned into 5-7 µm thick sections, which were deposited on a glass slide covered with water and subsequently heated at 40 °C for 30 min. Next, the slides were double-stained with 5% cotton blue in lactophenol to detect the fungus and 0.05% ruthenium red in water to detect pectin (acidic groups of polyuronic acids of pectin). Fungal haustoria of Hemileia vastatrix were found to be encapsulated by pectin. In coffee cercosporiosis, mesophyll cells exhibited dissolution of cell walls, and intercellular hyphae and conidiophores were observed. The method presented here is effective to detect a pectin-associated response in the plant-fungi interaction.

A coccus-shaped organism, designated ALS3 T , was isolated from fresh coffee cherries collected at a farm located in the Ali Mountain region of Taiwan. Sequence analysis of its 16S rRNA gene indicated that strain ALS3 T belongs to the genus Enterococcus and has more than 98.5 % sequence similarity to Enterococcus pallens and Enterococcus hermanniensis . When comparing the ALS3 T genome with these two type strains, the average nucleotide identity values and digital DNA-DNA hybridization values were 72.6-73.3 and 19.2 %, respectively. The G+C content of the genomic DNA from strain ALS3 T was 35.6 mol%. Results of sequence analysis, together with enzymatic activities and characteristics of carbohydrate metabolism, indicated that strain ALS3 T is distinct and represents a novel species, for which the name Enterococcus alishanensis sp. nov. is proposed. The type strain is ALS3 T (=NBRC 109593 T =BCRC 80605 T ).

Critical transitions, sudden responses to slow changes in environmental drivers, are inherent in many dynamic processes, prompting a search for early warning signals. We apply this framework to understanding the coffee rust disease, which experienced an unprecedented outbreak in Mesoamerica in 2012-2013, likely a critical transition. Based on monthly infection data from 128 study quadrats in a 45-ha plot in southern Mexico from 2014 to 2020, we find that the persistent seasonal epidemic following the initial outbreak collapses in an evident subsequent critical transition. Characteristic signals of "critical slowing down" precede this collapse and are correlated with reduced rainfall, as expected from climate change, and planting of rust-resistant varieties, an ongoing management intervention. Recoveries from catastrophes may themselves be experienced as a critical transition and managers should consider the larger dynamical landscape for the possibility of subsequent transitions. Early warning signals could therefore be useful when evaluating mitigation effectiveness., (© 2022. The Author(s).)

The polyphasic taxonomic study of a novel endophytic actinobacterium strain (CA2R105 T ) was carried out. The strain formed fragmented substrate mycelium and showed chemotaxonomic properties typical of members of the genus Nocardia, i.e. the presence of mycolic acid and MK-8 (H 4ω-cycl ) in its cells. Strain CA2R105 T exhibited the highest 16S rRNA gene sequence similarity to Nocardia jiangxiensis NBRC 101359 T (99.2%). The genome-based taxonomic analysis revealed low average nucleotide identity-blast and digital DNA-DNA hybridization values (<93.7, and <65.2%, respectively) to its closest relative. Moreover, many different phenotypic characteristics were observed between strain CA2R105 T and all related Nocardia -type strains. This taxonomic evidence suggested that strain CA2R105 T should be judged as representing a novel species of the genus Nocardia and the name, Nocardia coffeae sp. nov. is proposed. The type strain is CA2R105 T (=TBRC 11247 T =NBRC 114292 T ).