Wine fermentation microbiome: a landscape from different Portuguese wine appellations

Abstract

Grapes and wine musts harbor a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. In this work, we tackle this using a metagenomics approach to describe the natural microbial communities, both fungal and bacterial microorganisms, associated with spontaneous wine fermentations. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation – Initial Musts (IM), and Start and End of alcoholic fermentations (SF and EF, respectively). The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the IM, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida, and Schizosaccharomyces). Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected. Interestingly, a biogeographical correlation for both fungal and bacterial communities was identified between wine appellations at IM suggesting that each wine region contains specific and embedded microbial communities which may contribute to the uniqueness of regional wines.

Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

“…These authors even predicted the metabolome of the wine from the microbial composition by using machine learnig techniques [54]. Similar results have also been generated from other studies [55,56].…”

“…Even though there is no clear answer to this debate, studies from Suárez et al [64] and Pinto et al [56] seem to support the latter hypothesis.…”

“…The most frequent fungi described by NGS analysis are Saccharomyces, Hanseniaspora, Issatchenkia, Rhodotorula, Penicillium, Cladosporium, Botrytis, Sporobolomyces, Aspergillus, Cryptococcus and Pichia [56][57][58], with most studies reporting high abundance of Hanseniaspora and Saccharomyces during the mid and end of the fermentation respectively. Stefanini et al [32] in a Vino Santo study, found that fungal species composition undergoes a dynamic change with a declining tendency overtime, and that small changes in fermentation procedures may result in significant differences in microbial communities.…”

Is microbial terroir related to geographic distance between vineyards?

“…Taxonomical assignments showed that most OTUs found in the Chilean vineyard samples corresponded to the fungal and bacterial species commonly found in grapes or grape must in various world wine regions (Bokulich et al ., ; Taylor et al ., ; Piao et al ., ; Pinto et al ., ; Portillo et al ., ). Relative abundance analysis of the fungal OTUs showed that Dothideomycetes was the most abundant taxonomical class, which made up 78%–96% of the total sequences of each sample (Fig.…”

“…For example, indigenous yeasts and lactic and acetic bacteria living in grapes greatly affect the aroma of wine (Knight et al, 2015;Vigentini et al, 2016), and the epiphyte fungal and bacterial diversity of leaves are closely related to the health status of grapevines (Pinto et al, 2014). Recently, several studies have shown that regional differences in grape microbial community compositions, so called 'microbial terroir' (Bokulich et al, 2014;Gilbert et al, 2014;Taylor et al, 2014;Morrison-Whittle and Goddard, 2015;Pinto et al, 2015) are significantly correlated with the regional characteristics of wine flavour (Knight et al, 2015;Bokulich et al, 2016). However, there is little discussion as to why the microbial community composition of wine grapes is differentiated at regional or broad spatial scales (but see Morrison-Whittle and Goddard, 2015).…”