Coffee fermentation is a complex process, mainly involving bacteria and yeasts, whose interaction influences beverage quality. The way this process is conducted affects the interactions between these microorganisms. To identify microbial diversity in fermenting coffee, samples were collected from 20 farms in the Department of Quindío, Colombia. Metataxonomic analyses using high-throughput sequencing and volatile organic compound identification in green coffee beans were performed with HS-SPME and GC-MS. Potential relationships between some families and genera with different fermentation types and coffee quality were evaluated. In our results, samples presented with high richness and diversity were greater for bacteria than for yeast/fungi. The Enterobacteriaceae family dominated at the beginning of fermentation, while Leuconostoc, Lactobacillus, Gluconobacter, and Acetobacter genera dominated at the end, a finding related to pH reduction and final coffee quality. Overall, 167 fungal families were identified, but Saccharomyceaceae dominated from the beginning. Alcohols and esters were the main chemical classes identified in green coffee bean samples from these fermentations. These results will facilitate the identification process conditions that influence the presence and abundance of microorganisms related to quality as well as contributing to the design of strategies to conduct fermentations to improve the final quality of coffee.

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. [ ] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

El manejo de plagas y enfermedades del café debe ser preventivo e integral. La broca del café produce pérdidas, debido a que disminuye el peso de la producción, deteriora la calidad del grano lo cual disminuye el precio de venta, y aumenta los costos de producción por las acciones de control que deben adelantarse.

Coffee leaf rust, caused by the fungusHemileia vastatrix(Basidiomycota; Pucciniomycota),is a devastating disease spread worldwide. To improve the available genomes, we use PacBio HiFi sequencing enhanced by Dovetail Omni-C chromatin conformation capture to assemble a highly contiguous 747.98 Mb genome of an isolate collected fromCoffea arabica.

La gotera u ojo de gallo es una enfermedad de épocas húmedas o con lluvias frecuentes; sin embargo, su manejo preventivo se inicia desde la época seca o con lluvias scasas y se continua durante todo el ciclo de producción y de cosecha.