A Symphony Beneath the Canopy: How Soil and Cherry Bacteria Orchestrate the Taste of Colombian Coffee

by Dr. Steffen Schwarz, Coffee Consulate

In the rugged hills of Cundinamarca, Colombia, the future of coffee flavour may rest in the invisible hands—or rather, microbial communities—thriving beneath our feet and on the surface of coffee cherries. A new study by Kutos et al. (2025) dives deep into the unexplored world of plant-associated bacteria and their pivotal role in shaping the sensory qualities of one of the world’s most prized beverages: Arabica coffee.

Coffee has long been celebrated as an agricultural product where “terroir”—the synergy between plant, place, and people—imbues each bean with a unique signature. Traditionally, connoisseurs attributed distinctive flavours to altitude, climate, and farm management. Now, thanks to advances in microbiome research, scientists are uncovering how local bacterial communities act as yet another dimension in the story of terroir, influencing not only plant health but taste itself.

Kutos and colleagues set out to understand this relationship by sampling 320 soils and 320 coffee cherries from 22 farms in the San Francisco area of Cundinamarca. These farms differed in management style—open sun and shaded agroforestry systems—and in whether they regularly produced a “specialty flavour profile” (notably, brown-sugar notes coveted by specialty buyers).

All plants in the study were of the Castillo variety and sampled across two harvest periods to ensure robust results. Crucially, all were farmed by growers within the same technical support network, minimising confounding variables.

By using next-generation DNA sequencing techniques, the researchers resolved over 31,000 bacterial variants (or “ASVs”) in soil samples and nearly 9,000 in cherry samples. The difference between these two habitats was striking: while soils hosted a rich variety of bacterial phyla—such as Proteobacteria, Actinobacteriota, and Acidobacteriota—cherries had more than double the proportion of Proteobacteria and were comparatively less diverse.

Despite this diversity gap, some families (for instance, Sphingomonadaceae and Pseudomonadaceae) managed to bridge the divide, appearing across both environments—a hint of microbial continuity from root to fruit.

The most tantalising finding was the clear distinction between the bacterial communities in soils and cherries based both on farming system (sun vs shade) and flavour profile (specialty vs non-specialty). Shade-grown, flavour-producing farms not only boasted distinctive bacterial communities but also the most unique ones among all subgroups.

The study found several bacterial taxa strongly associated with the presence or absence of the specialty flavour profile. For example:

• In shade farms, Acidothermus, Jatrophihabitans, and Chujaibacter were more abundant when quality flavour was present.

• In cherries, two Nocardioides and two Pseudonocardia ASVs stood out in flavourful shade-farm cherries, while some Sphingomonas taxa were linked specifically to the absence of such flavour.

• Non-flavour farms, regardless of sun or shade, saw higher abundances of acetic acid bacteria (Acetobacteraceae)—a group that may negatively impact coffee taste.

Contrary to expectation, no significant differences emerged in the abundance patterns of lactic acid bacteria, which have often been associated with improved fermentation and flavour in prior research.

This microbial distinction is more than an academic curiosity. As the industry faces intensifying agricultural pressures, understanding these bacterial signatures could help develop farm-specific biofertilisers or microbial “inoculants” that boost both crop quality and environmental resilience.

Nevertheless, the study cautions that biofertiliser impact will depend profoundly on the local farm context. What works in shaded agroforestry may fail on an exposed sun farm due to different environmental constraints that shape microbiome assembly.

The results offer a glimpse into a microbial terroir for coffee—echoing patterns long recognised in wine and now scientifically validated in coffee using a single plant variety across a defined landscape. These discoveries set the stage for further research, raising pivotal questions: Can these bacterial communities be consistently manipulated to improve taste? Will future cup scores hinge on the subtle interplay of soil, cherry, and bacterium?

What is clear is that the journey from soil to cup is more intricate, more mysterious, and more interconnected than previously imagined. The unseen orchestra of bacteria beneath the Colombian canopy may well be crafting the next revolution in coffee quality.

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References:

• Kutos, S., Bennett, R. E., Santos, D., Botero-Delgadillo, E., & Muletz-Wolz, C. R. "Soil and cherry bacterial communities predict flavour on coffee farms." Scientific Reports 15, 19387 (2025). https://doi.org/10.1038/s41598-025-03665-6

For supplementary materials and data, see: https://doi.org/10.1038/s41598-025-03665-6