Mobilome of Oenococcus oeni: a role for the supremacy of the strains in wine?

Oenococcus oeni is the key lactic acid bacterium involved in malolactic fermentation (MLF), a secondary fermentation that improve the quality of wine. Strains belonging to this species are capable to survive, proliferate and dominate in this complex ecosystem, despite the harsh winemaking conditions (e.g., low pH, high level of ethanol, presence of sulfites, nutrient restriction) and the strong competition among several microorganisms. This adaptability could be linked to the genome plasticity of O. oeni, due to the lack of the mismatch repair system which leads to a high level of mutation frequency and horizontal gene transfer (HGT) (Marcobal et al., 2008; Bon et al., 2009). A recent study of Favier et al. (2012) has reported the presence of two large plasmids (18.3 and 21.9 kb) in some O. oeni strains, most of them used as starter cultures to promote MLF. Sequence analysis of these plasmids has revealed the presence of several hypothetical proteins, and also of transposases, besides genes with a predicted function. In addition, one of the two plasmids, pOENI-1v2, had been previously reported by Piffanelli et al. (2010) in the strain KM383 from Amarone, a wine characterized by a very high ethanol content (15% v/v). The results shown by these authors give an indication that these plasmids could enhance the genetic flexibility of the strains, thus contributing to their fitness and supremacy in wine. However, studies on the possible relationships among fitness, dominance and mobilome, represented by plasmids and mobile elements, are very scanty, especially for oenological bacteria. Therefore, in this study, we investigated the distribution of the two described plasmids and some genes present therein in a collection of 27 O. oeni strains, including a subcollection of 13 strains isolated during a single spontaneous MLF of Amarone wine (Zapparoli et al., 2012). The PCR screening for the nickase revealed that such gene was present in the 42% of strains isolated from Amarone wine, whereas it was not found in the strains isolated from other wines. This observation represents a further evidence that some plasmids could effectively contribute to bacterial fitness, especially in a hostile environment such as Amarone wine. As regards the analysis of other plasmid-related genes, particular attention was paid to transposases. Indeed, in literature, a genomic island of O. oeni PSU-1 has been described as almost identical to a genomic region of Lactobacillus plantarum WCFS1 (Bon et al., 2009); in the flanking regions we observed the presence of a transposase highly related to sequences present in Lactobacillus helveticus, Pediococcus claussenii, both in genome and plasmid, and partially in plasmid pNP40 of Lactococcus lactis. These findings indicate an important role of transposases as target for recombination and integration of plasmids in O. oeni genome. Therefore, the mobilome could be a major driving force in HGT among bacterial strains, made possible by microbial interactions in the shared ecological niche. Further studies regarding the expression and translation of plasmid-related genes are needed, to understand their physiological role in the adaptation, activity and dominance of strains in wine ecosystem.