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<p>Coffee is a globally significant socio-economic commodity in international agriculture due to its export potential and its role in generating income for farmers. However, the potato taste defect (PTD) in coffee varieties, characterized by a raw potato-like odor, affects the flavor quality of brewed coffee and reduces its commercial value, particularly in the East African region. Although volatile compounds, <i>Antestiopsis orbitalis</i>, and bacteria have been implicated in PTD in coffee beans, little is known about the diversity, composition, and metabolic functions of fungal communities associated with PTD in Arabica coffee beans on a larger scale. In this study, we investigated the fungal diversity, composition, and metabolic functions in Arabica coffee beans exhibiting visual and taste defects, as well as those in normal conditions, across six districts in Rwanda. We used metabarcoding of the fungal ITS1 region of the rRNA gene cluster to analyze these differences. High-throughput sequencing data revealed that all fungal alpha diversity indices (except evenness) and beta diversity indices were significantly higher in broken/low-taste (BLT)-score Arabica coffee beans compared to normal/high-taste (NHT)-score beans. Ascomycota, Basidiomycota, and Chytridiomycota were the only fungal phyla detected in Arabica coffee samples associated with a potato-like odor. Furthermore, the number of operational taxonomic units was higher in BLT-score Arabica coffee beans than in NHT-score beans. The BLT-score <i>Arabica</i> coffee beans showed a higher relative abundance of the fungal genera <i>Fusarium</i>, <i>Penicillium</i>, <i>Aspergillus</i>, <i>Talaromyces</i>, <i>Thermomyces</i>, <i>Kazachstania</i>, and <i>Clavispora</i> compared to NHT-score beans. Redundancy analysis (RDA) revealed relationships between dominant fungal species and both coffee taste scores and bean appearance. Six fungal species, <i>Talaromyces pinophilus</i>, <i>Thermomyces lanuginosus</i>, <i>Aspergillus spp</i>., <i>Penicillium cinnamopurpureum</i>, <i>Kazachstania humilis</i>, and <i>Pichia norvegensis</i>, exhibited significant negative correlations with taste scores of BLT-score Arabica coffee beans, suggesting their potential involvement in the development of PTD. In contrast, two fungal species, <i>Clavispora lusitaniae</i> and <i>Candida quercitrusa</i>, showed positive correlations with these characteristics. Functional annotation using FUNGuild indicated that the fungal metabolic functions in BLT-score samples were predominantly associated with plant pathogens, epiphytic-plant pathogens, endophytic-plant pathogens, and saprotroph guilds. This study identifies potential fungal taxa associated with PTD, opening new avenues for exploring specific fungal phylotypes linked to this off-flavor.</p>

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Metabarcoding analysis of fungal communities associated with potato-like odor in Rwandan Coffea arabica from key coffee washing stations

  • 期刊论文

  • 发表日期：

    2026年5月18日

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  • Jane Mukamugema,
  • Benjamin Manirakiza,
  • Janvier Uwayezu,
  • Antoine Nsabimana

摘要

Coffee is a globally significant socio-economic commodity in international agriculture due to its export potential and its role in generating income for farmers. However, the potato taste defect (PTD) in coffee varieties, characterized by a raw potato-like odor, affects the flavor quality of brewed coffee and reduces its commercial value, particularly in the East African region. Although volatile compounds, Antestiopsis orbitalis, and bacteria have been implicated in PTD in coffee beans, little is known about the diversity, composition, and metabolic functions of fungal communities associated with PTD in Arabica coffee beans on a larger scale. In this study, we investigated the fungal diversity, composition, and metabolic functions in Arabica coffee beans exhibiting visual and taste defects, as well as those in normal conditions, across six districts in Rwanda. We used metabarcoding of the fungal ITS1 region of the rRNA gene cluster to analyze these differences. High-throughput sequencing data revealed that all fungal alpha diversity indices (except evenness) and beta diversity indices were significantly higher in broken/low-taste (BLT)-score Arabica coffee beans compared to normal/high-taste (NHT)-score beans. Ascomycota, Basidiomycota, and Chytridiomycota were the only fungal phyla detected in Arabica coffee samples associated with a potato-like odor. Furthermore, the number of operational taxonomic units was higher in BLT-score Arabica coffee beans than in NHT-score beans. The BLT-score Arabica coffee beans showed a higher relative abundance of the fungal genera Fusarium, Penicillium, Aspergillus, Talaromyces, Thermomyces, Kazachstania, and Clavispora compared to NHT-score beans. Redundancy analysis (RDA) revealed relationships between dominant fungal species and both coffee taste scores and bean appearance. Six fungal species, Talaromyces pinophilus, Thermomyces lanuginosus, Aspergillus spp., Penicillium cinnamopurpureum, Kazachstania humilis, and Pichia norvegensis, exhibited significant negative correlations with taste scores of BLT-score Arabica coffee beans, suggesting their potential involvement in the development of PTD. In contrast, two fungal species, Clavispora lusitaniae and Candida quercitrusa, showed positive correlations with these characteristics. Functional annotation using FUNGuild indicated that the fungal metabolic functions in BLT-score samples were predominantly associated with plant pathogens, epiphytic-plant pathogens, endophytic-plant pathogens, and saprotroph guilds. This study identifies potential fungal taxa associated with PTD, opening new avenues for exploring specific fungal phylotypes linked to this off-flavor.