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      Saccharomyces cerevisiae: a nomadic yeast with no niche?

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          Abstract

          Different species are usually thought to have specific adaptations, which allow them to occupy different ecological niches. But recent neutral ecology theory suggests that species diversity can simply be the result of random sampling, due to finite population sizes and limited dispersal. Neutral models predict that species are not necessarily adapted to specific niches, but are functionally equivalent across a range of habitats. Here, we evaluate the ecology of Saccharomyces cerevisiae, one of the most important microbial species in human history. The artificial collection, concentration and fermentation of large volumes of fruit for alcohol production produce an environment in which S. cerevisiae thrives, and therefore it is assumed that fruit is the ecological niche that S. cerevisiae inhabits and has adapted to. We find very little direct evidence that S. cerevisiae is adapted to fruit, or indeed to any other specific niche. We propose instead a neutral nomad model for S. cerevisiae, which we believe should be used as the starting hypothesis in attempting to unravel the ecology of this important microbe.

          Abstract

          It is assumed that Saccharomyces cerevisiae is adapted to inhabit fruits; however, we find very little evidence for adaptation to any niche. Instead, we propose a neutral nomad model for S. cerevisiae.

          Abstract

          Graphical Abstract Figure.

          It is assumed that Saccharomyces cerevisiae is adapted to inhabit fruits; however, we find very little evidence for adaptation to any niche. Instead, we propose a neutral nomad model for S. cerevisiae.

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          Population genomics of domestic and wild yeasts

          Since the completion of the genome sequence of Saccharomyces cerevisiae in 19961,2, there has been an exponential increase in complete genome sequences accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions3,4, population structure5-8, and sexual versus asexual reproduction9,10. Less well understood at the whole genome level are the evolutionary processes acting within populations and species leading to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to four-fold or more coverage of the genome sequences of over seventy isolates of the baker's yeast, S. cerevisiae, and its closest relative, S. paradoxus. We examine variation in gene content, SNPs, indels, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. Interestingly, S. paradoxus populations are well delineated along geographic boundaries while the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variation.
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            The tragedy of the commons. The population problem has no technical solution; it requires a fundamental extension in morality.

            G. Hardin (1968)
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              Relative roles of niche and neutral processes in structuring a soil microbial community.

              Most attempts to identify the processes that structure natural communities have focused on conspicuous macroorganisms whereas the processes responsible for structuring microbial communities remain relatively unknown. Two main theories explaining these processes have emerged; niche theory, which highlights the importance of deterministic processes, and neutral theory, which focuses on stochastic processes. We examined whether neutral or niche-based mechanisms best explain the composition and structure of communities of a functionally important soil microbe, the arbuscular mycorrhizal (AM) fungi. Using molecular techniques, we surveyed AM fungi from 425 individual plants of 28 plant species along a soil pH gradient. There was evidence that both niche and neutral processes structured this community. Species abundances fitted the zero-sum multinomial distribution and there was evidence of dispersal limitation, both indicators of neutral processes. However, we found stronger support that niche differentiation based on abiotic soil factors, primarily pH, was structuring the AM fungal community. Host plant species affected AM fungal community composition negligibly compared to soil pH. We conclude that although niche partitioning was the primary mechanism regulating the composition and diversity of natural AM fungal communities, these communities are also influenced by stochastic-neutral processes. This study represents one of the most comprehensive investigations of community-level processes acting on soil microbes; revealing a community that although influenced by stochastic processes, still responded in a predictable manner to a major abiotic niche axis, soil pH. The strong response to environmental factors of this community highlights the susceptibility of soil microbes to environmental change.
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                Author and article information

                Journal
                FEMS Yeast Res
                FEMS Yeast Res
                femsyr
                FEMSYR
                FEMS Yeast Research
                Oxford University Press
                1567-1356
                1567-1364
                27 February 2015
                May 2015
                27 February 2015
                : 15
                : 3
                : fov009
                Affiliations
                [1 ]The School of Biological Sciences, the University of Auckland, Auckland 1142, New Zealand
                [2 ]The School of Life Sciences, the University of Lincoln, Lincoln LN6 7DL, UK
                [3 ]Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
                [4 ]Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
                Author notes
                [* ] Corresponding author: The School of Biological Sciences, the University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand. Tel: +00-64-9-3737599; E-mail: m.goddard@ 123456auckland.ac.nz
                Article
                10.1093/femsyr/fov009
                4444983
                25725024
                69d848b6-13b6-4d5b-a62c-d4d501a9438d
                © FEMS 2015.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 21 February 2015
                : 20 January 2015
                Page count
                Pages: 6
                Categories
                Commentary
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                Custom metadata
                May 2015

                Molecular biology
                crabtree effect,fermentation,fruit,adaptation,niche,neutral ecology,natural history
                Molecular biology
                crabtree effect, fermentation, fruit, adaptation, niche, neutral ecology, natural history

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