CE20 - Biologie des animaux, des organismes photosynthétiques et des microorganismes

Large-scale analysis of the adaptation of the Brettanomyces bruxellensis yeast to human fermentation processes – BrettAdapt

BrettAdapt

Large-scale analysis of the adaptation of the Brettanomyces bruxellensis yeast to human fermentation processes

B. bruxellensis shows adaptation to anthropized environments

The yeast species Brettanomyces bruxellensis is associated with various fermentation processes including wine and beer. In some of them, it is considered as a spoiler (e.g. wine) while it can have a positive contribution in beer production. Previous experiments showed a strong relationship between process isolation and genetic clusters, indicating niche adaptation.<br />The goal of the BrettAdapt proposal is to use large-scale approaches to identify genomic and phenotypic signatures of B. bruxellensis adaptation to anthropized environments.

Four aims were defined:
1- Whole genome sequencing of around 200 isolates representative of the genetic diversity of the species will be used for determining the mechanisms shaping B. bruxellensis evolution and adaptation.
2- Large-scale phenomics will be performed in beer- and wine-like media, and the impact of key environmental factors on yeast fitness and traits involved in food adaptation will be determined. Combined proteomics and metabolomics will be applied to precise the underlying molecular mechanisms.
3- The detected adaptive signatures (at the genomic or phenomic level or both) will be tested at the functional level either through competition assays or through mutant analysis, allowing the validation of the genetic and environmental factors involved in B. bruxellensis adaptation.
4- The microbial ecosystem associated with B. bruxellensis implantation will be explored using metagenomics in both beer and wine processes.

We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions, whereas aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared with S. cerevisiae. The pangenome is composed of 5,409 ORFs (open reading frames) among which 5,106 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.

Amongst the expected deliverables, large-scale datasets at the genomic and phenotypic levels will be generated, and will be available to the scientific community. The BrettAdapt project will allow deciphering the genomic, abiotic and biotic factors shaping the adaptation of B. bruxellensis to human-related environments, and more generally will improve our understanding of domesticated-like species.

Gounot, J.-S., C. Neuvéglise, K. C. Freel, H. Devillers, J. Piškur, A. Friedrich and J. Schacherer (2020). «High complexity and degree of genetic variation in Brettanomyces bruxellensis population.« Genome Biology and Evolution.
Cibrario, A., M. Avramova, M. Dimopoulou, M. Magani, C. Miot-Sertier, A. Mas, M. C. Portillo, P. Ballestra, W. Albertin, I. Masneuf-Pomarede and M. Dols-Lafargue (2019). «Brettanomyces bruxellensis wine isolates show high geographical dispersal and long persistence in cellars « Plos One.
Albertin, W., I. Masneuf-Pomarede, V. Galeote and J.-L. Legras (2019). New Insights Into Wine Yeast Diversities. Yeasts in the Production of Wine. P. Romano, M. Ciani and G. H. Fleet. New York, NY, Springer New York: 117-163.

The yeast species Brettanomyces bruxellensis is associated with various fermentation processes including wine and beer. In some of them, it is considered as a spoiler (e.g. wine) while it can have a positive contribution in beer production. Previous works showed that B. bruxellensis strains were clustered in distinct genetic groups mostly associated with either wine or beer, suggesting different niche adaptation.
The goal of the BrettAdapt proposal is to use large-scale approaches to identify genomic and phenotypic signatures of B. bruxellensis adaptation to anthropized environments. Whole genome sequencing of around 200 isolates representative of the genetic diversity of the species will be used for determining the mechanisms shaping B. bruxellensis evolution and adaptation. Large-scale phenomics will be performed in beer- and wine-like media, and the impact of key environmental factors on yeast fitness and traits involved in food adaptation will be determined. Combined proteomics and metabolomics will be applied to precise the underlying molecular mechanisms. The detected adaptive signatures (at the genomic or phenomic level or both) will be tested at the functional level either through competition assays or through mutant analysis, allowing the validation of the genetic and environmental factors involved in B. bruxellensis adaptation. Finally, the microbial ecosystem associated with B. bruxellensis implantation will be explored using metagenomics in both beer and wine processes. This will allow the identification of favorable or unfavorable biotic environments for B. bruxellensis development, opening new avenues for the understanding of direct and indirect microbial interactions in food processes. Amongst the expected deliverables, large-scale datasets at the genomic and phenotypic levels will be generated, and will be available to the scientific community. The BrettAdapt project will allow deciphering the genomic, abiotic and biotic factors shaping the adaptation of B. bruxellensis to human-related environments, and more generally will improve our understanding of domesticated-like species. From an applied viewpoint, the final goal is either to optimize its use as a starter in beer production, or to limit its development and subsequent spoilage in winemaking.

Project coordination

Warren ALBERTIN (Unité de recherche Oenologie)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

GMGM Génétique moléculaire, génomique et microbiologie (UMR 7156)
UR Oeno Unité de recherche Oenologie

Help of the ANR 541,598 euros
Beginning and duration of the scientific project: December 2018 - 48 Months

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