Bacteria and archaea have developed multiple antiviral mechanisms, and genomic evidence indicates that several of these antiviral systems co-occur in the same strain. Here, we introduce DefenseFinder, a tool that automatically detects known antiviral systems in prokaryotic genomes. We use DefenseFinder to analyse 21000 fully sequenced prokaryotic genomes, and find that antiviral strategies vary drastically between phyla, species and strains. Variations in composition of antiviral systems correlate with genome size, viral threat, and lifestyle traits. DefenseFinder will facilitate large-scale genomic analysis of antiviral defense systems and the study of host-virus interactions in prokaryotes.

The winemaking process involves the alcoholic fermentation of must, often followed by malolactic fermentation (MLF). The latter, mainly carried out by the lactic acid bacterium Oenococcus oeni, is used to improve wine quality when acidity reduction is required. Moreover, it prevents microbial spoilage and improves the wine’s organoleptic profile. Prior observations showed that O. oeni is able to resist several months in harsh wine conditions when adhered on oak barrels. Since biofilm is a prevailing microbial lifestyle in natural environments, the capacity of O. oeni to form biofilms was investigated on winemaking material such as stainless steel and oak chips. Scanning Electron Microscopy and Confocal Laser Scanning Microscopy showed that O. oeni was able to adhere to these surfaces and form spatially organized microcolonies embedded in extracellular substances. To assess the competitive advantage of this mode of life in wine, the properties of biofilm and planktonic cells were compared after inoculation in a fermented must (pH 3.5 or 3.2 and 12% ethanol) The results indicated that the biofilm culture of O. oeni conferred (i) increased tolerance to wine stress, and (ii) functional performance with effective malolactic activities. Relative gene expression focusing on stress genes and genes involved in EPS synthesis was investigated in a mature biofilm and emphasized the role of the matrix in increased biofilm resistance. As oak is commonly used in wine aging, we focused on the O. oeni biofilm on this material and its contribution to the development of wine color and the release of aromatic compounds. Analytical chromatography was used to target the main oak aging compounds such as vanillin, gaiacol, eugenol, whisky-lactones, and furfural. The results reveal that O. oeni biofilm developed on oak can modulate the wood-wine transfer of volatile aromatic compounds during MLF and aging by decreasing furfural, gaiacol, and eugenol in particular. This work showed that O. oeni forms biofilms consisting of stress-tolerant cells capable of efficient MLF under winemaking conditions. Therefore surface-associated behaviors should be considered in the development of improved strategies for the control of MLF in wine.

Facing the abundance and diversity of phages, bacteria have developed multiple anti-phage mechanisms. In the past three years, the number of known anti-phage mechanisms has been expanded by at least 5-fold rendering our view of prokaryotic immunity obsolete. Most anti-phage systems have been studied as standalone mechanisms, however many examples demonstrate strains encode not one but several anti-viral mechanisms. How these different systems integrate into an anti-viral arsenal at the strain level remains to be elucidated. Much could be learned from establishing fundamental description of features such as the number and diversity of anti-phage systems encoded in a given genome. To address this question, we developed DefenseFinder, a tool that automatically detects known anti-phage systems in prokaryotic genomes. We applied DefenseFinder to >20 000 fully sequenced genomes, generating a systematic and quantitative view of the anti-viral arsenal of prokaryotes. We show prokaryotic genomes encode on average five anti-phage systems from three different families of systems. This number varies drastically from one strain to another and is influenced by the genome size and the number of prophages encoded. Distributions of different systems are also very heterogenous with some systems being enriched in prophages and in specific clades. Finally, we provide a detailed comparison of the anti-viral arsenal of 15 common bacterial species, revealing drastic differences in anti-viral strategies. Overall, our work provides a free and open-source software, available as a command line tool or, on webserver. It allows the rapid detection of anti-phage systems, enables a comprehensive description of the anti-viral arsenal of prokaryotes and paves the way for large scale genomics study in the field of anti-phage defense.

Although differences in yeast biodiversity have often been found between vineyards subjected to organic protection or conventional protection, little is known about the effect of copper and sulfur fungicides (the only fungicides allowed in organic farming) on yeast populations. The sensitivity to copper and sulfur of 158 yeast isolates of seven different species (Aureobasidium pullulans, Hanseniaspora guilliermondii, H. uvarum, Metschnikowia sp., Pichia membranifaciens, Saccharomyces cerevisiae and Starmerella bacillaris) was evaluated. The species A. pullulans and St. bacillaris appeared to be more resistant to copper than the other species tested. The species A. pullulans, H. guilliermondii and Metschnikowia sp. had the highest sulfur resistance. Thus, only isolates of the species A. pullulans exhibited high resistance to both antifungal agents. These results may explain the lower diversity of yeasts present on berries and the strong dominance of the species A. pullulans for vineyards protected by copper or sulfur-based fungicides compared to other vineyards reported by several studies.