Abstract
The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. In research, next generation sequencing allows accurate mapping of the microbiomes that characterise ecosystems of biotechnological and/or medical relevance. But the gap between mapping and understanding, to be filled by “functional microbiomics”, requires the collection and integration of many different layers of complex data sets, from molecular multi-omics to spatial imaging technologies to online ecosystem monitoring tools. Holistically, studying the complexity of most microbial ecosystems, consisting of hundreds of species in specific spatial arrangements, is beyond our current technical capabilities, and simpler model systems with fewer species and reduced spatial complexity are required to establish the fundamental rules of ecosystem functioning. One such ecosystem, the ecosystem responsible for natural alcoholic fermentation, can provide an excellent tool to study evolutionarily relevant interactions between multiple species within a relatively easily controlled environment. This review will critically evaluate the approaches that are currently implemented to dissect the cellular and molecular networks that govern this ecosystem.
Key points
• Evolutionarily isolated fermentation ecosystem can be used as an ecological model.
• Experimental toolbox is gearing towards mechanistic understanding of this ecosystem.
• Integration of multidisciplinary datasets is key to predictive understanding.
Graphical abstract
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References
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The authors would like to thank the following funders for supporting this research: the National Research Foundation of South Africa through Grant numbers 83471 (SA Research Chair in Integrated Wine Science) to FFB and Grant number 118505 (Competitive Programme for Rated Researchers) to MES, and the Royal Society Future Leaders—Independent African Researchers (FLAIR) grant to DR.
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The manuscript was conceptualised by FFB, and all authors contributed to the initial draft. The draft was revised and collated into a manuscript by CGC. Figures were drawn by CGC, tables were drawn by NAL. All authors approved the final version of the manuscript.
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Conacher, C., Luyt, N., Naidoo-Blassoples, R. et al. The ecology of wine fermentation: a model for the study of complex microbial ecosystems. Appl Microbiol Biotechnol 105, 3027–3043 (2021). https://doi.org/10.1007/s00253-021-11270-6
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DOI: https://doi.org/10.1007/s00253-021-11270-6