Brettanomyces bruxellensis population survey reveals a diploid-triploid complex structured according to substrate of isolation and geographical distribution

Abstract

Brettanomyces bruxellensis is a unicellular fungus of increasing industrial and scientific interest over the past 15 years. Previous studies revealed high genotypic diversity amongst B. bruxellensis strains as well as strain-dependent phenotypic characteristics. Genomic assemblies revealed that some strains harbour triploid genomes and based upon prior genotyping it was inferred that a triploid population was widely dispersed across Australian wine regions. We performed an intraspecific diversity genotypic survey of 1488 B. bruxellensis isolates from 29 countries, 5 continents and 9 different fermentation niches. Using microsatellite analysis in combination with different statistical approaches, we demonstrate that the studied population is structured according to ploidy level, substrate of isolation and geographical origin of the strains, underlying the relative importance of each factor. We found that geographical origin has a different contribution to the population structure according to the substrate of origin, suggesting an anthropic influence on the spatial biodiversity of this microorganism of industrial interest. The observed clustering was correlated to variable stress response, as strains from different groups displayed variation in tolerance to the wine preservative sulfur dioxide (SO2). The potential contribution of the triploid state for adaptation to industrial fermentations and dissemination of the species B. bruxellensis is discussed.

High complexity and degree of genetic variation inBrettanomyces bruxellensispopulation

“…These clusters are mostly in accordance with the five major clusters recently described using microsatellites on a very large population (Avramova, et al 2018). For example, the two triploid clusters, G3N1 and G3N2, correspond respectively to the so-called triploid beer AWRI1608-like cluster and the triploid wine AWRI1499-like cluster.…”

“…The level of ploidy is supposed to be linked to the substrate of isolation and geographical distribution (Albertin, et al 2014). Traditionnally, genomic variability has essentially been restricted to the exploration of small regions of the genomes (Conterno, et al 2006;Crauwels, et al 2014;Avramova, et al 2018;Agnolucci, et al 2009;Curtin, et al 2007;Vigentini, et al 2012). More recently, the complete genomes of a limited number of strains have been sequenced and assembled (Borneman, et al 2014;Crauwels, et al 2014;Curtin, et al 2012;Piskur, et al 2012;Olsen, et al 2015).…”

“…Comparison of these genomes suggested that polyploid and hybridization events might play a significant role in the evolution of this species (Borneman, et al 2014). The most recent population survey was performed on a large collection of almost 1,500 isolates based on 12 microsatellite regions and showed that the population is structured according to ploidy level, substrate of isolation, and geographical origin of the strain (Avramova, et al 2018).…”

New genome assemblies reveal patterns of domestication and adaptation acrossBrettanomyces(Dekkera) species

“…Brettanomyces [17,[35][36][37][38][39]. This genome plasticity is thought to be a mechanism in yeast for adaptation…”

“…Brettanomyces (Landry et al, 2006, Hellborg and Piskur, 2009, Vigentini et al, 2012, Borneman et al, 2014, Ishchuk et al, 2016, Avramova et al, 2018. This genome plasticity is thought to be a mechanism in yeast for adaptation to new environments and niches, and in response to new stressors (see Marsit et al (2017)…”