Independent Origins of Yeast Associated with Coffee and Cacao Fermentation

Abstract

SUMMARY Modern transportation networks have facilitated the migration and mingling of previously isolated populations of plants, animals, and insects. Human activities can also influence the global distribution of microorganisms. The best understood example is yeasts associated with winemaking. Humans began making wine in the Middle East over 9,000 years ago [1, 2]. Selecting favorable fermentation products created specialized strains of Saccharomyces cerevisiae [3, 4] that were transported along with the grapevines. Today, S. cerevisiae strains residing in vineyards around the world are genetically similar, and their population structure suggests a common origin that followed the path of human migration [3–7]. Like wine, coffee and cacao depend on microbial fermentation [8, 9] and have been globally dispersed by humans. Theobroma cacao originated in the Amazon and Orinoco Basins of Colombia and Venezuela [10], was cultivated in Central America by the Mesoamerican peoples, and introduced to Europeans by Cortés in 1530 [11]. Coffea, native to Ethiopia, was disseminated by Arab traders throughout the Middle East and North Africa in the 6th century and was introduced to European consumers in the 17th century [12]. Here, we test whether the yeasts associated with coffee and cacao are genetically similar, crop-specific populations or genetically diverse, geography-specific populations. Our results uncovered populations that, while defined by niche and geography, also bear signatures of admixture between major populations in events independent of the transport of the plants. Thus, human-associated fermentations and migration may have affected the distribution of yeast involved in the production of coffee and chocolate.

European derivedSaccharomyces cerevisiaecolonisation of New Zealand vineyards aided by humans

“…2016; Ludlow et al . 2016). The degree to which phylogenomic methods are able to recover any signal when there is diffuse population structure is not clear, i.e.…”

“…Ludlow et al . (2016) reasonably suggest that the movement of these strains, and thus creation of these populations, was facilitated by humans. Similarly, the recently discovery of a novel lineage in Brazil shows it was formed in part by hybridisation of migrants from the European/wine group with endemic S. paradoxus , which presumably then facilitated the colonisation of native Brazilian trees (Barbosa et al .…”

“…2016; Ludlow et al . 2016). The Saccharomyces genus is composed of seven species and originated 10–20 million years ago (Hittinger 2013).…”

“…2015), the discovery of hybrid populations associated with coffee and coca (Ludlow et al . 2016) and novel linages in Brazil (Barbosa et al . 2016).…”

“…A very recent study described genetically distinct populations of S. cerevisiae associated with coffee and cocoa in Africa and South America (Ludlow et al . 2016); intriguingly, these do not contain novel alleles, but are inferred to have been created by the mixing of existing populations associated with European vineyards, American oak trees and the ancestral seat of this species in Far East Asia. Ludlow et al .…”