Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau

Abstract

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.

Physical–Chemical and Metataxonomic Characterization of the Microbial Communities Present during the Fermentation of Three Varieties of Coffee from Colombia and Their Sensory Qualities

“…of coffee [62], importantly, the geographical conditions and agronomic management of the coffee crops evaluated were the same, and the results of this study suggest that the microbial communities during fermentation may be different according to the variety; similar results were found by other authors [60,63]. However, the differences between the microbial communities in fermentation also allowed us to establish that there is no single way to obtain high-quality washed coffee; rather, the biochemical changes caused by microorganisms during fermentation and the coffee beans can enhance the intrinsic quality of each variety.…”

“…al. [60] reported the microorganisms found in the rhizosphere of two coffee varieties, Bourbon and Castillo, grown in Popayán-Cauca (Colombia), and they were compared with respect to the organoleptic properties of the coffee cup, demonstrating that each variety of coffee has a distinct microbial profile, which may be related to the plants' physiological, nutritional, and sanitary needs.…”

Microorganismos de suelo y su relación con la calidad de la bebida de café: Una revisión

“…Investigadores han relacionado el microbioma bacteriano de la rizosfera y del proceso de fermentación de café (Pino et al, 2023). Estos autores encontraron que los filos Proteobacteria, Bacteroidetes, Firmicutes y Acidobacteria fueron los taxones bacterianos dominantes y comunes tanto en suelo como en frutos.…”

Imputation of missing microclimate data of coffee-pine agroforestry with machine learning

“…The gaps in climate change policies, particularly concerning water-related aspects, as emphasized in the AR6 WG1 report, underscore the challenges associated with acquiring comprehensive and accurate microclimate data [6]. Moreover, the need for further research to understand the biodiversity of bacteria in the coffee rhizosphere and their resulting effects highlights the current gaps in knowledge regarding the complex ecological factors that affect microclimatic conditions within agroforestry systems [7]. Moreover, the research focused on methods for completing datasets to detect contamination in groundwater reserves underscores the importance of data imputation techniques in filling voids in microclimatic information.…”