Differences between the Leaf Mycobiome of Coffea arabica and Wild Coffee Species and Their Modulation by Caffeine/Chlorogenic Acid Content

The study of microbes associated with the coffee tree has been gaining strength in recent years. In this work, we compared the leaf mycobiome of the traditional crop Coffea arabica with wild species Coffea racemosa and Coffea stenophylla using ITS sequencing for qualitative information and real-time PCR for quantitative information, seeking to relate the mycobiomes with the content of caffeine and chlorogenic acid in leaves. Dothideomycetes, Wallemiomycetes, and Tremellomycetes are the dominant classes of fungi. The core leaf mycobiome among the three Coffea species is formed by Hannaella, Cladosporium, Cryptococcus, Erythrobasidium, and Alternaria. A network analysis showed that Phoma, an important C. arabica pathogen, is negatively related to six fungal species present in C. racemosa and C. stenophylla and absent in C. arabica. Finally, C. arabica have more than 35 times the concentration of caffeine and 2.5 times the concentration of chlorogenic acid than C. stenophylla and C. racemosa. The relationship between caffeine/chlorogenic acid content, the leaf mycobiome, and genotype pathogen resistance is discussed.

Author Correction: New species and records of Trichoderma isolated as mycoparasites and endophytes from cultivated and wild coffee in Africa

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

New species and records of Trichoderma isolated as mycoparasites and endophytes from cultivated and wild coffee in Africa

A survey for species of the genus Trichoderma occurring as endophytes of Coffea, and as mycoparasites of coffee rusts (Hemileia), was undertaken in Africa; concentrating on Cameroon and Ethiopia. Ninety-four isolates of Trichoderma were obtained during this study: 76 as endophytes of healthy leaves, stems and berries and, 18 directly from colonized rust pustules. A phylogenetic analysis of all isolates used a combination of three genes: translation elongation factor-1α (tef1), rpb2 and cal for selected isolates. GCPSR criteria were used for the recognition of species; supported by morphological and cultural characters. The results reveal a previously unrecorded diversity of Trichoderma species endophytic in both wild and cultivated Coffea, and mycoparasitic on Hemileia rusts. Sixteen species were delimited, including four novel taxa which are described herein: T. botryosum, T. caeruloviride, T. lentissimum and T. pseudopyramidale. Two of these new species, T. botryosum and T. pseudopyramidale, constituted over 60% of the total isolations, predominantly from wild C. arabica in Ethiopian cloud forest. In sharp contrast, not a single isolate of Trichoderma was obtained using the same isolation protocol during a survey of coffee in four Brazilian states, suggesting the existence of a ‘Trichoderma void’ in the endophyte mycobiota of coffee outside of Africa. The potential use of these African Trichoderma isolates in classical biological control, either as endophytic bodyguards—to protect coffee plants from Hemileia vastatrix, the fungus causing coffee leaf rust (CLR)—or to reduce its impact through mycoparasitism, is discussed, with reference to the on-going CLR crisis in Central America.

Monitoring Wild Coffee Using Ground Survey and Satellite Observation in Community-Managed Forest in Sheko, South-West Ethiopia

Preserving wild coffee in the natural forest, especially in southwest Ethiopia, is important for maintaining the genetic diversity of Arabica coffee and sustaining coffee production. To monitor the changes in wild coffee in the natural forest, we conducted an in situ baseline survey in 2015, and 30 of those survey sites were re-visited in 2019. Those surveys involved counting the number of mature mother trees, saplings and seedlings, as well as recording details of the sites, including disturbance, accessibility and forest conditions. Satellite imagery was combined with the site-specific in situ survey data to provide evidence of the forest condition around the study sites and therefore help more fully explore the causes for the changes in the wild coffee stock. The results show that, overall, the population of mother coffee trees was maintained during the 4-year period, and a slight increase in saplings occurred. Closer examination reveals considerable variations between sites, with some equally accessible sites showing a sharp decline in the number of mother trees while others show consistent increases. This study demonstrates the importance of systematic surveys, especially for the areas where forest cover and wild coffee plants are highly variable, and this may help explore community-specific approaches in managing wild coffee in the forest.