Fungi are essential players in the maintenance of global coffee productivity, but their taxonomic and functional diversity in tropical and subtropical soils of Latin America remains largely unexplored. To address this concern, soil fungi were surveyed in six farms in three traditional coffee-growing regions of Colombia (Cauca, Magdalena, and Risaralda). Five farms were organic and newly established (30 years old) with higher shade cover. We used amplicon sequencing and functional prediction based on the FUNGuild annotation tool. Fungal community composition diverged among farms, with Mortierella (Mortierellomycota) and Saitozyma (Basidiomycota) among the most prevalent genera. Functional prediction revealed the predominance of saprotroph-symbiotroph and pathotroph fungi. The endophyte and litter decomposer Mortierella genus was dominant within the saprotrophs and symbiotrophs. The pathotroph community was characterized by insect pathogen species belonging to the Metarhizium (Ascomycota) genus. Indeed, M. anisopliae and M. marquandii were identified as indicator species in the conventional long-term shaded farm. This study revealed that coffee plantations studied sustain a diverse fungal community and nurture potentially beneficial species. Further studies are needed to elucidate how particular management practices can nourish beneficial fungi, suppress detrimental species, and promote more sustainable coffee production.

Introduction: Coffee is one of the leading tropical crops produced worldwide. Colombia ranks third in coffee production in the world. Microorganisms associated with coffee plants can have many biotechnological applications, such as plant growth promotion and biological control. Objective: To describe the bacteria present in the soil associated with coffee cultivation. This was done using a bulk sequencing or 16S rRNA metabarcoding approach. Methodology: Soil samples were collected to analyze their microbiome from three different departments of Colombia (Cauca, Risaralda and Magdalena). The plants were of different ages, and the crop management was different (conventional and organic). Subsequently, an analysis was carried out using Qiime2 to describe the communities associated with coffee cultivation and soil chemical properties. Results: Some important genera were identified, such as Janthinobacterium, Bacillus, Actinomadura and Actinoallomurus. These genera can be used as plant growth promoters, organic matter transformers, producers of antibiotics and metabolites with potential biotechnological applications. Implications: The study presented in this manuscript describes the communities associated with the soil in coffee cultivation. However, a much more complex approach could be through metagenomics, where the bacterial communities and the functions of; however, this vision is up to ten times higher in cost. Conclusion: Through the results obtained, it is concluded that the studies carried out through metabarcoding help to understand the composition of the microorganisms associated with coffee and, with this, try to elucidate the functions of the associated microorganisms.

Introduction: The ecosystem services provided by soil microbial communities are critical for the resilience of agroecosystems, ensuring environmental conservation and food security. Long-term experiments comparing contrasting crop rotations are valuable tools for monitoring microbial responses, but they rarely include all crop phases within a single year. Therefore, the long-term agronomic impact may be masked by the immediate effect of the crop evaluated. In this study, we compared different crop rotations based on the Intensification Sequence Index (ISI), which considers the soil occupation time, and analyzed the impact of cover crops and two nitrogen fertilization strategies.Material and methods: We used an experiment initiated in 2006 with the following crop rotations: Soybean-Soybean, Maize-Wheat/Soybean, and Maize-Soybean-Wheat/Soybean. Soil samples were taken after the harvest of each summer crop phase (i.e., Soybean, Maize, Wheat/Soybean), and the soil prokaryotic community was monitored using 16S rRNA gene sequencing.Results and discussion: We observed that ISI and crop phase were the main predictors of microbial community composition, explaining 14.7% and 13.0% of the variation, respectively. Nitrogen fertilization had a minor effect (3.12%) and was detected only after maize sampling; cover crops had no significant effect. However, the presence of cover crops showed higher alpha diversity and an increased abundance of Proteobacteria. Maize enriched the abundance of certain taxa of Planctomycetes and Verrucomicrobia, while Soybean increased the abundance of Bacteroidetes and Proteobacteria. Comparatively, Soybean enriched Mucilaginibacter and Geobacter, while Wheat/Soybean enriched Brevundimonas and Roseimicrobium.Conclusion: Our results demonstrate that crop phase is as important as the long-term legacy of crop rotations in shaping the microbial community and that specific taxa responses are highly dependent on the crop phase surveyed.