NEW YORK (GenomeWeb) – Sequencing analysis has found that yeasts associated with cacao and coffee beans are highly diverse, harboring evidence of admixtures that coincide with human migrations.
Coffee and cacao spread from Ethiopia and the Amazon, respectively, and are now grown at various sites near the equator. After both beans are harvested, they are fermented for a few days to break up their pulp, a process that influences their character and flavor.
Researchers from the Pacific Northwest Diabetes Research Institute and elsewhere performed restriction site-associated DNA sequencing (RAD-seq) on yeast strains isolated from cacao and coffee beans from around the world. As they reported today in Current Biology, they found that the yeast genetic sequences cluster strongly by geography, though hold hints of admixture.
"Our study suggests a complex interplay between human activity and microbes involved in the production of coffee and chocolate," senior author Aimée Dudley from PNDRI said in a statement. "Humans have transported and cultivated the plants, but at least for one important species, their associated microbes have arisen from transport and mingling in events that are independent of the transport of the plants themselves."
She and her colleagues focused in particular on Saccharomyces cerevisiae, and cultured live yeast from cacao and coffee beans from around the world. They were able to obtain 78 yeast strains from cacao from 13 countries, such as Colombia, Ghana, and Madagascar, as well as from 67 yeast strains from coffee from 14 countries, including Colombia, Ethiopia, and Uganda.
Using RAD-seq, the researchers sequenced the same 3 percent of each strain's genome and compared those stretches to previously published data from 35 wine-associated yeast strains. But while those wine yeast strains exhibited limited genetic diversity, the strains isolated from cacao and coffee showed significantly greater genetic diversity, the researchers reported, suggesting independent origins.
Even though the beans were obtained from multiple suppliers from different places and at different times, both the cacao- and coffee-associated yeast strains clustered strongly at the country level. Based on just those genetic signatures, the researchers could predict the country of origin for these yeast strains 86 percent of the time for cacao and 79 percent of the time for coffee.
Using the Markov chain Monte Carlo algorithm InStruct, Dudley and her colleagues further analyzed the yeast population structure. Based on the RAD-seq data they generated along with a set of 262 previously analyzed S. cerevisiae strains, they uncovered 12 likely populations, up from previous estimates of eight. The cacao and coffee yeast strains largely fall into clusters based on their niche and geographical origin, and most of the cacao and coffee strains fell into four new populations where they were the majority or even the only members.
However, two of the major populations include strains from samples from other continents, suggesting a complex migration pattern. Alternatively, the researchers noted that the mislabeling of samples was also a possible explanation.
These new cacao and coffee bean yeast populations, the researchers reported, are not made up of strains with novel alleles, but instead are admixtures of three known yeast populations. In addition, they noted that these admixtures largely reflected the geographic proximity of the samples' origins and human migration patterns.
For instance, the South American cacao and coffee yeast populations share alleles with the North American oak population, while the African cacao and coffee yeast populations reflect a mixture of European and Asian alleles.
Based on a phylogenetic tree analysis, the researchers confirmed three of their five suspected migration events, some of which reflected what is known about the movements of cacao and coffee beans.
"Human activities may have fostered the establishment of these hybrid groups," Dudley and her colleagues wrote in their paper. "In several cases, the combinations of alleles present in these groups coincide with known paths of transportation, organized cultivation, and fermentation of the crops."
These alleles, they added, could further represent a source of phenotypic diversity that could be use to improve both cacao and coffee.