Influence of the farming system on the epiphytic yeasts and yeast-like fungi colonizing grape berries during the ripening process.

Grape berries are colonized by a wide array of epiphytic microorganisms such as yeast and filamentous fungi. This microbiota plays a major role in crop health and also interferes with the winemaking process. In this study, culture-dependent and -independent methods were used to investigate the dynamics and diversity of the yeast and yeast-like microorganisms on the grape berry surface during maturation and the influence of cropping systems in this microflora. The results showed a significant impact of both the farming system and the maturity stage on the epiphytic yeast and yeast-like community. A quantitative approach based on counting cultivable populations indicated an increase in the yeast and yeast-like population during the grape ripening process, reaching a maximum when the berries became overripe. The cultivable yeast and yeast-like population also varied significantly depending on the farming system. Microorganism counts were significantly higher for organically- than conventionally-farmed grapes. The yeast and yeast-like community structures were analysed by culture independent methods, using CE-SSCP. The results revealed changes in the genetic structure of the yeast and yeast-like community throughout the ripening process, as well as the impact of the farming system. Copper-based fungicide treatments were revealed as the main factor responsible for the differences in microbial population densities between samples of different farming systems. The results showed a negative correlation between copper levels and yeast and yeast-like populations, providing evidence that copper inhibited this epiphytic community. Taken together, our results showed that shifts in the microbial community were related to changes in the composition of the grape-berry surface, particularly sugar exudation and the occurrence of copper residues from pesticide treatments.

Characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations.

Despite its importance in plant health and crop quality, the diversity of epiphytic bacteria on grape berries and other plant parts, like leaves and bark, remains poorly described, as does the role of telluric bacteria in plant colonization. In this study, we compare the bacterial community size and structure in vineyard soils, as well as on grapevine bark, leaves and berries. Analyses of culturable bacteria revealed differences in the size and structure of the populations in each ecosystem. The highest bacteria population counts and the greatest diversity of genera were found in soil samples, followed by bark, grapes and leaves. The identification of isolates revealed that some genera - Pseudomonas, Curtobacterium, and Bacillus - were present in all ecosystems, but in different amounts, while others were ecosystem-specific. About 50% of the genera were common to soil and bark, but absent from leaves and grapes. The opposite was also observed: grape and leaf samples presented 50% of genera in common that were absent from trunk and soil. The bacterial community structure analyzed by T-RFLP indicated similarities between the profiles of leaves and grapes, on the one hand, and bark and soil, on the other, reflecting the number of shared T-RFs. The results suggest an interaction between telluric bacterial communities and the epiphytic bacteria present on the different grapevine parts.

IS30 elements are mediators of genetic diversity in Oenococcus oeni.

Oenococcus oeni is responsible for the malolactic fermentation of wines. Genomic diversity has been recently established in the species and extensive attention is now being given to the genomic bases of strain-specific differences. We explored the role of insertion sequences (IS), which are considered as driving forces for novel genotypic and phenotypic variants in prokaryotes. The present study focuses on members of the IS30 family, which are widespread among lactic acid bacteria. An in silico analysis of the three available genomes of O. oeni in combination with the use of an inverse PCR strategy targeting conserved IS30-related sequences indicated the presence of seven IS30 copies in the pangenome of O. oeni. A primer designed to anneal to the conserved 3' end of the IS30 element was paired with each of the seven primers selected to bind to unique sequences upstream of each of the seven mobile elements identified. The study presents an overview of the abundance, and the genomic environment of IS30 elements in the O. oeni pangenome and shows that the two existing genetic sub-populations previously described in the species through multilocus sequence typing analysis (MLST) differ in their IS30 content. Possible IS30 impacts on bacterial adaptation are discussed.