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• W2324366950 abstract "Yeasts associated with cocoa and coffee beans are genetically distinct. These populations have been created through the migration and mixing of populations associated with vineyards, trees in America, and the ancestral seat of this species in Far East Asia. Yeasts associated with cocoa and coffee beans are genetically distinct. These populations have been created through the migration and mixing of populations associated with vineyards, trees in America, and the ancestral seat of this species in Far East Asia. A trip to a distant continent plainly illustrates different kinds of plants and animals are found in different parts of the world: classic oak and beech woodlands in Northern Europe, and massive Kauris mixed with cabbage trees, Rimu and Nikau palms on the North Island of New Zealand, for example. Humans’ impact on species distributions is substantial: one may also see New Zealand cabbage trees happily growing in southern English gardens, and European oak trees in New Zealand parks. Microbes are key components of natural and agricultural ecosystems, but since they, by definition, are not immediately observable, the nature of their distributions is cryptic. One microbe is of particular interest as it drives the production of bread, beer, wine, spirits, and bioethanol, and is also a research super-model: the yeast Saccharomyces cerevisiae. Even for this well studied microbe, we are still unraveling the basics of its distribution and ecology [1Goddard M.R. Greig D. Saccharomyces cerevisiae: a nomadic yeast with no niche?.FEMS Yeast Res. 2015; 15: fov009Crossref PubMed Scopus (102) Google Scholar]. A new study by Ludlow et al. [2Ludlow C.L. Cromie G.A. Garmendia-Torres C. Sirr A. Hays M. Field C. Jeffery E.W. Fay J.C. Dudley A.M. Independent origins of yeast associated with coffee and cacao fermentation.Curr. Biol. 2016; 26: 965-971Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar] reported in this issue of Current Biology shows that the S. cerevisiae (herein referred to as yeast) populations associated with cocoa and coffee beans in South America and Africa are genetically distinct, and that these various populations were founded by the migration and mixing of existing yeast populations found in other habitats and areas, which was likely facilitated by humans. Humans have moved species beyond their natural ranges for thousands of years, both intentionally for agricultural purposes and unintentionally as a consequence of human migration [3Diamond J. Evolution, consequences and future of plant and animal domestication.Nature. 2002; 418: 700-707Crossref PubMed Scopus (963) Google Scholar]. Other than disease agents, whose effects are apparent once transposed, the extent to which humans have affected microbial distributions is very poorly characterized [4Litchman E. Invisible invaders: non-pathogenic invasive microbes in aquatic and terrestrial ecosystems.Ecol. Lett. 2010; 13: 1560-1572Crossref PubMed Scopus (176) Google Scholar]. Early ideas suggested microbes have virtually limitless dispersal abilities. However, while some microbes appear globally distributed, others are certainly not [5Martiny J.B.H. Bohannan B.J.M. Brown J.H. Colwell R.K. Fuhrman J.A. Green J.L. Horner-Devine M.C. Kane M. Krumins J.A. Kuske C.R. et al.Microbial biogeography: putting microorganisms on the map.Nat. Rev. Microbiol. 2006; 4: 102-112Crossref PubMed Scopus (1991) Google Scholar], and the forces which give rise to these various microbial distribution patterns are not clear [6Hanson C.A. Fuhrman J.A. Horner-Devine M.C. Martiny J.B.H. Beyond biogeographic patterns: processes shaping the microbial landscape.Nat. Rev. Microbiol. 2012; 10: 497-506PubMed Google Scholar, 7Morrison-Whittle P. Goddard M.R. Quantifying the relative roles of selective and neutral processes in defining eukaryotic microbial communities.ISME J. 2015; 9: 2003-2011Crossref PubMed Scopus (75) Google Scholar]. To help answer these types of questions Ludlow et al. [2Ludlow C.L. Cromie G.A. Garmendia-Torres C. Sirr A. Hays M. Field C. Jeffery E.W. Fay J.C. Dudley A.M. Independent origins of yeast associated with coffee and cacao fermentation.Curr. Biol. 2016; 26: 965-971Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar] focused on what has been called the world’s most important microbe. Due to its relatively small genome and experimental pliability, this species helped develop human population genomics methods. Two parallel studies revealed a global picture for this species, which sketched a few well-defined populations, but with many individuals that were chimeras (hybrids) between different groups [8Liti G. Carter D.M. Moses A.M. Warringer J. Parts L. James S.A. Davey R.P. Roberts I.N. Burt A. Koufopanou V. et al.Population genomics of domestic and wild yeasts.Nature. 2009; 458: 337-341Crossref PubMed Scopus (1050) Google Scholar, 9Schacherer J. Shapiro J.A. Ruderfer D.M. Kruglyak L. Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae.Nature. 2009; 458: 342-345Crossref PubMed Scopus (345) Google Scholar]. Yeast are sexual eukaryotes, and so mating between gametes (spores) deriving from genetically divergent populations to create such hybrids may easily occur. While some populations appeared to only reside in specific areas, one striking observation was that populations associated with winemaking were found in vineyards globally. This observation correlates with an earlier study showing the gross pattern and timing of genetic divergence within the wine population approximately matches the pattern for global dispersal of vines by humans [10Legras J.L. Merdinoglu D. Cornuet J.M. Karst F. Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history.Mol. Ecol. 2007; 16: 2091-2102Crossref PubMed Scopus (390) Google Scholar]. It was recently shown this wine group had its origins in a population residing on Mediterranean oak trees [11Almeida P. Barbosa R. Zalar P. Imanishi Y. Shimizu K. Turchetti B. Legras J.L. Serra M. Dequin S. Couloux A. et al.A population genomics insight into the Mediterranean origins of wine yeast domestication.Mol. Ecol. 2015; 24: 5412-5427Crossref PubMed Scopus (118) Google Scholar]. A separate genetically distinct yeast population has also been found on oak trees in North America [12Cromie G.A. Hyma K.E. Ludlow C.L. Garmendia-Torres C. Gilbert T.L. May P. Huang A.A. Dudley A.M. Fay J.C. Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.G3. 2013; 3: 2163-2171Crossref PubMed Scopus (104) Google Scholar]. Lastly, a further study discovered a large and genetically diverse yeast population in forests in China, and this is likely the ancestral seat of this species [13Wang Q.M. Liu W.Q. Liti G. Wang S.A. Bai F.Y. Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity.Mol. Ecol. 2012; 21: 5404-5417Crossref PubMed Scopus (192) Google Scholar]. Our knowledge of the habitat range and geographic distribution of S. cerevisiae is based on a relatively few samples taken from a few habitats in a few places [1Goddard M.R. Greig D. Saccharomyces cerevisiae: a nomadic yeast with no niche?.FEMS Yeast Res. 2015; 15: fov009Crossref PubMed Scopus (102) Google Scholar]. This yeast species is also known to be associated with the processing (fermentation) of coffee and cocoa (chocolate) beans. Like vines, humans have also moved these crops around the globe: cocoa is native to the Amazon and Orinoco basins of Colombia and Venezuela, but has been taken to Africa; coffee is native to Ethiopia, but has been reciprocally moved to South America. Ludlow et al. [2Ludlow C.L. Cromie G.A. Garmendia-Torres C. Sirr A. Hays M. Field C. Jeffery E.W. Fay J.C. Dudley A.M. Independent origins of yeast associated with coffee and cacao fermentation.Curr. Biol. 2016; 26: 965-971Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar] asked whether those yeasts associated with coffee and cocoa are part of the same populations as those associated with vines, and whether they show similar patterns of tracking crops as humans moved them. Ludlow et al. [2Ludlow C.L. Cromie G.A. Garmendia-Torres C. Sirr A. Hays M. Field C. Jeffery E.W. Fay J.C. Dudley A.M. Independent origins of yeast associated with coffee and cacao fermentation.Curr. Biol. 2016; 26: 965-971Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar] isolated 140 strains from cocoa and coffee beans originating from various locations in Africa and South America, and also included various strains representing the previously described wine, North American oak and Chinese populations. They sequenced similar parts of the genomes of each of these strains, and compared these sequences across yeast groups. The first striking observation was that strains associated with coffee and cocoa were genetically different from the wine population, and had greater diversity. This shows the yeasts associated with cocoa and coffee are not part of the vine-associated group that has been globalized by humans. Ludlow et al. [2Ludlow C.L. Cromie G.A. Garmendia-Torres C. Sirr A. Hays M. Field C. Jeffery E.W. Fay J.C. Dudley A.M. Independent origins of yeast associated with coffee and cacao fermentation.Curr. Biol. 2016; 26: 965-971Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar] went on to test the structure of these populations, which was achieved by evaluating whether there were closely related sub-groups within the data. These methods showed that the strains associated with cocoa and coffee comprised geographically distinct sub-populations. The accuracy of this genetic signal was not just at the continental scale; the genetic signatures were strong enough to discriminate between populations of yeasts residing on each crop in various regions within South America and Africa. Indeed, Ludlow et al. [2Ludlow C.L. Cromie G.A. Garmendia-Torres C. Sirr A. Hays M. Field C. Jeffery E.W. Fay J.C. Dudley A.M. Independent origins of yeast associated with coffee and cacao fermentation.Curr. Biol. 2016; 26: 965-971Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar] show that one is able to reliably predict the origin of cocoa and coffee beans given the genetic signatures of yeasts associated with these beans. While a similar pattern has been shown for yeasts associated with vines in different regions in New Zealand [14Knight S.J. Goddard M.R. Quantifying separation and similarity in a Saccharomyces cerevisiae metapopulation.ISME J. 2015; 9: 361-370Crossref PubMed Scopus (60) Google Scholar], whether such precise patterns hold for vine-associated S. cerevisiae globally has not yet been adequately tested. These observations open up the concept that microbes might be one method to authenticate the origin or provenance of crops and food produce generally. Why we find region-specific wine, coffee and cocoa populations for this species is not clear. It might be due to chance — that certain types randomly seeded different populations in certain areas, and that subsequent microbial movement has not been rampant enough to fully-mix these populations. Or, it might be due to the actions of selection: that these various populations have adaptively diverged to the prevailing conditions in each of these areas. It is more realistically some mix of these two [7Morrison-Whittle P. Goddard M.R. Quantifying the relative roles of selective and neutral processes in defining eukaryotic microbial communities.ISME J. 2015; 9: 2003-2011Crossref PubMed Scopus (75) Google Scholar]. Next Ludlow et al. [2Ludlow C.L. Cromie G.A. Garmendia-Torres C. Sirr A. Hays M. Field C. Jeffery E.W. Fay J.C. Dudley A.M. Independent origins of yeast associated with coffee and cacao fermentation.Curr. Biol. 2016; 26: 965-971Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar] asked how the coffee and cocoa bean populations were different. Their fascinating finding was that these populations did not harbour novel types of genes (alleles), but rather different combinations of alleles already present in the North American oak, wine and Chinese populations. This implies that various components of these other populations have become combined to create the separate coffee and cocoa populations currently observed. Given that neither coffee nor cocoa are grown close to these other yeast populations, this requires inferring the migration of members of the wine, North American Oak and Chinese populations. Ludlow et al. [2Ludlow C.L. Cromie G.A. Garmendia-Torres C. Sirr A. Hays M. Field C. Jeffery E.W. Fay J.C. Dudley A.M. Independent origins of yeast associated with coffee and cacao fermentation.Curr. Biol. 2016; 26: 965-971Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar] conduct some nice analyses and estimate these migration events, and this is shown in Figure 1. While the picture is not completely clear, there are some clear signals, for example 30% of the South American cocoa population migrated from the North American oak population. It is not directly demonstrated that humans are the agent of transfer, but we seem the most likely vectors given our association with these crops and the distances involved. Why S. cerevisiae is associated with these various crops in the first place is rather perplexing; in fact this species has been isolated from a range of habitats, including humans. It has been asserted that S. cerevisiae is adapted to inhabit fruits, but these and other observations make this an increasingly unattractive thesis. It has recently been suggested that S. cerevisiae is not specifically adapted to any habitat, but is a generalist [1Goddard M.R. Greig D. Saccharomyces cerevisiae: a nomadic yeast with no niche?.FEMS Yeast Res. 2015; 15: fov009Crossref PubMed Scopus (102) Google Scholar]. The more places we look, the more we may discover novel S. cerevisiae populations. This study more generally illustrates the extent to which human activities may alter and manipulate the range and variability of microbial species, and create novel biodiversity through the fusion of genetically disparate populations. There is another level to consider; a microbe such as S. cerevisiae is involved in the post-harvest processing of crops it is associated with: grapes and grain into wine, bread and beer; cocoa into chocolate; and coffee beans into products suitable for drinking. The appeal and popularity of these products is in part due to their aroma and flavour, which is significantly influenced by yeasts during fermentation. For wine, coffee and chocolate, further appeal and value derives from the different aroma and flavour profiles sourced from different regions of the world, encapsulated by the concept of terroir. It has recently been shown that some small but significant fraction of region-specific wine aroma and flavour signatures may be driven by yeasts [15Knight S. Klaere S. Fedrizzi B. Goddard M.R. Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir.Sci. Rep. 2015; 5: 14233Crossref PubMed Scopus (160) Google Scholar]. Ludlow et al.’s [2Ludlow C.L. Cromie G.A. Garmendia-Torres C. Sirr A. Hays M. Field C. Jeffery E.W. Fay J.C. Dudley A.M. Independent origins of yeast associated with coffee and cacao fermentation.Curr. Biol. 2016; 26: 965-971Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar] study shows that since different yeast populations are also associated with coffee and cocoa grown in different regions, this concept might hold for other crops and their transformed produce too. Independent Origins of Yeast Associated with Coffee and Cacao FermentationLudlow et al.Current BiologyMarch 24, 2016In BriefHuman activity has driven the migration and mingling of previously isolated populations of plants, animals, and insects. Is the same true for microorganisms? Ludlow et al. find that yeasts associated with coffee and cacao form distinct populations with independent origins through admixtures of previously known populations, including wine yeasts. Full-Text PDF Open Archive" @default.
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• W2324366950 date "2016-04-01" @default.
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• W2324366950 title "Microbiology: Mixing Wine, Chocolate, and Coffee" @default.
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