FLO11expression and lipid biosynthesis are required for air-liquid biofilm formation in aSaccharomyces cerevisiaeflor strain

Synthesis of acylated derivatives of chitosan oligosaccharide and evaluation of their potential antifungal agents on Fusarium oxysporum

Chitosan oligosaccharide (COS) is an important carbohydrate-based biomaterial for synthesizing candidate drugs and biological agents. This study synthesized COS derivatives by grafting acyl chlorides of different alkyl chain lengths (C8, C10, and C12) onto COS molecules and further investigated their physicochemical properties and antimicrobial activity. The COS acylated derivatives were characterized using Fourier transform infrared spectroscopy, ¹H nuclear magnetic resonance spectroscopy, X-ray diffraction, and thermogravimetric analysis. COS acylated derivatives were successfully synthesized and possessed high solubility and thermal stability. As for the evaluation of antibacterial activity, COS acylated derivatives did not significantly inhibit Escherichia coli and Staphylococcus aureus, but they significantly inhibited Fusarium oxysporum, which was superior to that of COS. Transcriptomic analysis revealed that COS acylated derivatives exerted antifungal activity mainly by downregulating the expression of efflux pumps, disrupting cell wall integrity, and impeding normal cell metabolism. Our findings provided a fundamental theory for the development of environmentally friendly antifungal agents.

Biotechnological applications of biofilms formed by osmotolerant and halotolerant yeasts

Many microorganisms are capable of developing biofilms under adverse conditions usually related to nutrient limitation. They are complex structures in which cells (in many cases of different species) are embedded in the material that they secrete, the extracellular matrix (ECM), which is composed of proteins, carbohydrates, lipids, and nucleic acids. The ECM has several functions including adhesion, cellular communication, nutrient distribution, and increased community resistance, this being the main drawback when these microorganisms are pathogenic. However, these structures have also proven useful in many biotechnological applications. Until now, the most interest shown in these regards has focused on bacterial biofilms, and the literature describing yeast biofilms is scarce, except for pathological strains. Oceans and other saline reservoirs are full of microorganisms adapted to extreme conditions, and the discovery and knowledge of their properties can be very interesting to explore new uses. Halotolerant and osmotolerant biofilm-forming yeasts have been employed for many years in the food and wine industry, with very few applications in other areas. The experience gained in bioremediation, food production and biocatalysis with bacterial biofilms can be inspiring to find new uses for halotolerant yeast biofilms. In this review, we focus on the biofilms formed by halotolerant and osmotolerant yeasts such as those belonging to Candida, Saccharomyces flor yeasts, Schwannyomyces or Debaryomyces, and their actual or potential biotechnological applications. KEY POINTS: • Biofilm formation by halotolerant and osmotolerant yeasts is reviewed. • Yeasts biofilms have been widely used in food and wine production. • The use of bacterial biofilms in bioremediation can be expanded to halotolerant yeast counterparts.

Arginine inhibits Saccharomyces cerevisiae biofilm formation by inducing endocytosis of the arginine transporter Can1

Biofilms are formed by the aggregation of microorganisms into multicellular structures that adhere to surfaces. Biofilm formation by yeast is a critical issue in clinical and industrial fields because of the strong adhesion of yeast biofilm to abiotic surfaces and tissues. Here, we clarified the arginine-mediated inhibition of biofilm formation by yeast. First, we showed that arginine inhibits biofilm formation in fungi such as Saccharomyces cerevisiae, Candida glabrata, and Cladosporium cladosporioides, but not in bacteria. In regard to the underlying mechanism, biochemical analysis indicated that arginine inhibits biofilm formation by suppressing Flo11-dependent flocculation. Intriguingly, a strain with deletion of the arginine transporter-encoding CAN1 was insensitive to arginine-mediated inhibition of biofilm formation. Finally, Can1 endocytosis appeared to be required for the inhibitory mechanism of biofilm formation by arginine. The present results could help to elucidate the molecular mechanism of yeast biofilm formation and its control.

Yeast biofilm in food realms: occurrence and control

In natural environments, microorganisms form microbial aggregates called biofilms able to adhere to a multitude of different surfaces. Yeasts make no exception to this rule, being able to form biofilms in a plethora of environmental niches. In food realms, yeast biofilms may cause major problems due to their alterative activities. In addition, yeast biofilms are tenacious structures difficult to eradicate or treat with the current arsenal of antifungal agents. Thus, much effort is being made to develop novel approaches to prevent and disrupt yeast biofilms, for example through the use of natural antimicrobials or small molecules with both inhibiting and dispersing properties. The aim of this review is to provide a synopsis of the most recent literature on yeast biofilms regarding: (i) biofilm formation mechanisms; (ii) occurrence in food and in food-related environments; and (iii) inhibition and dispersal using natural compounds, in particular.

The microbial challenge of winemaking: yeast-bacteria compatibility

The diversity and complexity of wine environments present challenges for predicting success of fermentation. In particular, compatibility between yeast and lactic acid bacteria is affected by chemical and physical parameters that are strain and cultivar specific. This review focuses on the impact of compound production by microbes and physical interactions between microbes that ultimately influence how yeast and bacteria may work together during fermentation. This review also highlights the importance of understanding microbial interactions for yeast-bacteria compatibility in the wine context.

Biofilm architecture: An emerging synthetic biology target

Synthetic biologists are exploiting biofilms as an effective mechanism for producing various outputs. Metabolic optimization has become commonplace as a method of maximizing system output. In addition to production pathways, the biofilm itself contributes to the efficacy of production. The purpose of this review is to highlight opportunities that might be leveraged to further enhance production in preexisting biofilm production systems. These opportunities may be used with previously established production systems as a method of improving system efficiency further. This may be accomplished through the reduction in the cost of establishing and maintaining biofilms, and maintenance of the enhancement of product yield per unit of time, per unit of area, or per unit of required input.

The administration of L-cysteine and L-arginine inhibits biofilm formation in wild-type biofilm-forming yeast by modulating FLO11 gene expression

Microbial biofilms are undesired in food manufacturing, drinking water distribution systems, and clinical realms. Yeast biofilms are particularly problematic because of the strong capacity of yeast cells to adhere to abiotic surfaces, cells, and tissues. Novel approaches have been developed over recent years to prevent the establishment of microbial biofilms, such as through the use of small molecules with inhibiting and dispersing properties. Here, we studied the inhibitory activity of 11 different amino acids on the biofilm formation ability of three wild-type Saccharomyces cerevisiae strains and the reference strain ∑1278b. Subsequent evaluation of different concentrations of the two most effective amino acids, namely, arginine and cysteine, revealed that they acted in different ways. Arginine prevented biofilm formation by reducing FLO11 gene expression; its addition did not affect cell viability and was even found to enhance cell metabolism (vitality marker) as determined by phenotype microarray (PM) analysis. On the contrary, the addition of cysteine reduced both cell viability and vitality as well as FLO11 expression. Thus, the use of cysteine and arginine as agents against biofilm formation can be diversified depending on the most desired action towards yeast growth.

The veil of flor's structure, composition and interactions in biological ageing wines

Biological ageing occurs after fermentation of the grape must and it is due to the appearance of a biofilm on the surface of the wine called “veil of flor”. Yeast involved in veil formation are mainly Saccharomyces cerevisiae and they have traditionally been divided into four races according to their ability to metabolize different sugars. The growth of flor yeasts depends on different factors, such as the aerobic assimilation of the wine ethanol, since the medium is deficient in both sugars and nitrogen. Actually, flor yeast metabolism is different from wine S. cerevisiaeyeast, but it hasn't been analysed yet. Thus, the aim of this work is to study the diversity of flor yeast strains and to analyse the composition and the structure of the veil of flor in Jerez-Xérés-Sherry D.O. The results of this work revealed 14 different genotypes of S. cerevisiaestrains using multiplex-microsatellite PCR and these strains showed 8 different biochemical profiles using a similar procedure than traditionally. In addition, mannose and glucose were found in veil of flor complex using UHPLC-MS.

Comparative analysis of intracellular metabolites, proteins and their molecular functions in a flor yeast strain under two enological conditions

Flor yeasts confer a wide range of organoleptic properties to Sherry-type wines during a process called "biological aging" that takes place after alcoholic fermentation. These kinds of yeasts adapt to a biological aging condition by forming a biofilm known as "flor velum" and by changing from fermentative to oxidative metabolism. It has been reported that some functions such as increase of cell surface hydrophobicity or changes to lipid metabolism are enhanced when yeasts switch to biofilm lifestyle. Here, we attempt to reveal intracellular metabolites and protein molecular functions not documented before that are relevant in biofilm formation and in fermentation by an endometabolome and proteome screening. We report that at early stages of biofilm formation, flor yeasts accumulate mannose, trehalose, glycerol, oleic and stearic acids and synthesize high amounts of GTPases, glycosylases and lipoproteins. On the other hand, in early fermentation, flor yeasts rapidly consume glucose and phosphoric acid; and produce abundant proteins related to chromatin binding, transcription factors and methyl transferases.

Going with the Flo: The Role of Flo11-Dependent and Independent Interactions in Yeast Mat Formation

Strains of the bakers’ yeast Saccharomyces cerevisiae that are able to generate a multicellular structure called a mat on low percentage (0.3%) agar plates are given a selective advantage over strains that cannot exhibit this phenotype. This environment may exhibit some similarities to the rotting fruit on which S. cerevisiae often grows in nature. Mat formation occurs when the cells spread over the plate as they grow, and cells in the center of the biofilm aggregate to form multicellular structures that resemble a floral pattern. This multicellular behavior is dependent on the cell surface flocculin Flo11. This review covers recent information on the structure of Flo11 and how this likely impacts mat formation as well as how variegated expression of Flo11 influences mat formation. Finally, it also discusses several Flo11-independent genetic factors that control mat formation, such as vacuolar protein sorting (VPS) genes, cell wall signaling components, and heat shock proteins.

Flor Yeast Diversity and Dynamics in Biologically Aged Wines

Wine biological aging is characterized by the development of yeast strains that form a biofilm on the wine surface after alcoholic fermentation. These yeasts, known as flor yeasts, form a velum that protects the wine from oxidation during aging. Thirty-nine velums aged from 1 to 6 years were sampled from “Vin jaune” from two different cellars. We show for the first time that these velums possess various aspects in term of color and surface aspects. Surprisingly, the heterogeneous velums are mostly composed of one species, S. cerevisiae. Scanning electron microscope observations of these velums revealed unprecedented biofilm structures and various yeast morphologies formed by the sole S. cerevisiae species. Our results highlight that different strains of Saccharomyces are present in these velums. Unexpectedly, in the same velum, flor yeast strain succession occurred during aging, supporting the assumption that environmental changes are responsible for these shifts. Despite numerous sample wine analyses, very few flor yeasts could be isolated from wine following alcoholic fermentation, suggesting that flor yeast development results from the colonization of yeast present in the aging cellar. We analyzed the FLO11 and ICR1 sequence of different S. cerevisiae strains in order to understand how the same strain of S. cerevisiae could form various types of biofilm. Among the strains analyzed, some were heterozygote at the FLO11 locus, while others presented two different alleles of ICR1 (wild type and a 111 bp deletion). We could not find a strong link between strain genotypes and velum characteristics. The same strain in different wines could form a velum having very different characteristics, highlighting a matrix effect.

Differential Proteome Analysis of a Flor Yeast Strain under Biofilm Formation

Several Saccharomyces cerevisiae strains (flor yeasts) form a biofilm (flor velum) on the surface of Sherry wines after fermentation, when glucose is depleted. This flor velum is fundamental to biological aging of these particular wines. In this study, we identify abundant proteins in the formation of the biofilm of an industrial flor yeast strain. A database search to enrich flor yeast “biological process” and “cellular component” according to Gene Ontology Terminology (GO Terms) and, “pathways” was carried out. The most abundant proteins detected were largely involved in respiration, translation, stress damage prevention and repair, amino acid metabolism (glycine, isoleucine, leucine and arginine), glycolysis/gluconeogenesis and biosynthesis of vitamin B9 (folate). These proteins were located in cellular components as in the peroxisome, mitochondria, vacuole, cell wall and extracellular region; being these two last directly related with the flor formation. Proteins like Bgl2p, Gcv3p, Hyp2p, Mdh1p, Suc2p and Ygp1p were quantified in very high levels. This study reveals some expected processes and provides new and important information for the design of conditions and genetic constructions of flor yeasts for improving the cellular survival and, thus, to optimize biological aging of Sherry wine production.

Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping

Candida albicans biofilm formation is an important virulence factor in the pathogenesis of disease, a characteristic which has been shown to be heterogeneous in clinical isolates. Using an unbiased computational approach we investigated the central metabolic pathways driving biofilm heterogeneity. Transcripts from high (HBF) and low (LBF) biofilm forming isolates were analysed by RNA sequencing, with 6312 genes identified to be expressed in these two phenotypes. With a dedicated computational approach we identified and validated a significantly differentially expressed subnetwork of genes associated with these biofilm phenotypes. Our analysis revealed amino acid metabolism, such as arginine, proline, aspartate and glutamate metabolism, were predominantly upregulated in the HBF phenotype. On the contrary, purine, starch and sucrose metabolism was generally upregulated in the LBF phenotype. The aspartate aminotransferase gene AAT1 was found to be a common member of these amino acid pathways and significantly upregulated in the HBF phenotype. Pharmacological inhibition of AAT1 enzyme activity significantly reduced biofilm formation in a dose-dependent manner. Collectively, these findings provide evidence that biofilm phenotype is associated with differential regulation of metabolic pathways. Understanding and targeting such pathways, such as amino acid metabolism, is potentially useful for developing diagnostics and new antifungals to treat biofilm-based infections.

Flor Yeast: New Perspectives Beyond Wine Aging

The most important dogma in white-wine production is the preservation of the wine aroma and the limitation of the oxidative action of oxygen. In contrast, the aging of Sherry and Sherry-like wines is an aerobic process that depends on the oxidative activity of flor strains of Saccharomyces cerevisiae. Under depletion of nitrogen and fermentable carbon sources, these yeast produce aggregates of floating cells and form an air–liquid biofilm on the wine surface, which is also known as velum or flor. This behavior is due to genetic and metabolic peculiarities that differentiate flor yeast from other wine yeast. This review will focus first on the most updated data obtained through the analysis of flor yeast with -omic tools. Comparative genomics, proteomics, and metabolomics of flor and wine yeast strains are shedding new light on several features of these special yeast, and in particular, they have revealed the extent of proteome remodeling imposed by the biofilm life-style. Finally, new insights in terms of promotion and inhibition of biofilm formation through small molecules, amino acids, and di/tri-peptides, and novel possibilities for the exploitation of biofilm immobilization within a fungal hyphae framework, will be discussed.

Involvement of glycolysis/gluconeogenesis and signaling regulatory pathways in Saccharomyces cerevisiae biofilms during fermentation

Compared to free (free-living) cells, biofilm cells show increased resistance and stability to high-pressure fermentation conditions, although the reasons underlying these phenomena remain unclear. Here, we investigated biofilm formation with immobilized Saccharomyces cerevisiae cells grown on fiber surfaces during the process of ethanol fermentation. The development of biofilm colonies was visualized by fluorescent labeling and confocal microscopy. RNA from yeast cells at three different biofilm development periods was extracted and sequenced by high-throughput sequencing. We quantitated gene expression differences between biofilm cells and free cells and found that 2098, 1556, and 927 genes were significantly differentially expressed, respectively. We also validated the expression of previously reported genes and identified novel genes and pathways under the control of this system. Statistical analysis revealed that biofilm genes show significant gene expression changes principally in the initial period of biofilm formation compared to later periods. Carbohydrate metabolism, amino acid metabolism, signal transduction, and oxidoreductase activity were needed for biofilm formation. In contrast to previous findings, we observed some differential expression performances of FLO family genes, indicating that cell aggregation in our immobilized fermentation system was possibly independent of flocculation. Cyclic AMP-protein kinase A and mitogen-activated protein kinase pathways regulated signal transduction pathways during yeast biofilm formation. We found that carbohydrate metabolism, especially glycolysis/gluconeogenesis, played a key role in the development of S. cerevisiae biofilms. This work provides an important dataset for future studies aimed at gaining insight into the regulatory mechanisms of immobilized cells in biofilms, as well as for optimizing bioprocessing applications with S. cerevisiae.

Two-dimensionality of yeast colony expansion accompanied by pattern formation

Yeasts can form multicellular patterns as they expand on agar plates, a phenotype that requires a functional copy of the FLO11 gene. Although the biochemical and molecular requirements for such patterns have been examined, the mechanisms underlying their formation are not entirely clear. Here we develop quantitative methods to accurately characterize the size, shape, and surface patterns of yeast colonies for various combinations of agar and sugar concentrations. We combine these measurements with mathematical and physical models and find that FLO11 gene constrains cells to grow near the agar surface, causing the formation of larger and more irregular colonies that undergo hierarchical wrinkling. Head-to-head competition assays on agar plates indicate that two-dimensional constraint on the expansion of FLO11 wild type (FLO11) cells confers a fitness advantage over FLO11 knockout (flo11Δ) cells on the agar surface.

Microbial biofilms are commonly found in nature and are highly relevant to public health. Biofilms can impose high risks to drinking water distribution by stable adherence to the interior of water pipes, and to food industry by contamination of food processing systems. Biofilm adherence to indwelling medical devices causes high rates of clinical infections that are difficult to eliminate as biofilm microbes resist treatment with antibiotics and biocides. These microbial abilities are related to the spatial composition and overall morphology of the biofilm. While the mechanisms underlying biofilm structure and morphology have been examined for bacteria, much less is known about eukaryotic biofilms. Here we find that the size, shape and patterning of budding yeast colonies can arise from constraining colony expansion to the surface of agar plates. Through computational analysis and mathematical modeling, we find that rapid colony expansion, colony shape irregularity and hierarchical wrinkling of the yeast colony surface can result from two-dimensionality of expansion imposed by the adhesin FLO11. Finally, we find that two-dimensional expansion conveys competitive advantage during head-to-head competition with the mutant cells lacking FLO11.

Proteins involved in flor yeast carbon metabolism under biofilm formation conditions

A lack of sugars during the production of biologically aged wines after fermentation of grape must causes flor yeasts to metabolize other carbon molecules formed during fermentation (ethanol and glycerol, mainly). In this work, a proteome analysis involving OFFGEL fractionation prior to LC/MS detection was used to elucidate the carbon metabolism of a flor yeast strain under biofilm formation conditions (BFC). The results were compared with those obtained under non-biofilm formation conditions (NBFC). Proteins associated to processes such as non-fermentable carbon uptake, the glyoxylate and TCA cycles, cellular respiration and inositol metabolism were detected at higher concentrations under BFC than under the reference conditions (NBFC). This study constitutes the first attempt at identifying the flor yeast proteins responsible for the peculiar sensory profile of biologically aged wines. A better metabolic knowledge of flor yeasts might facilitate the development of effective strategies for improved production of these special wines.

Flor yeasts of Saccharomyces cerevisiae--their ecology, genetics and metabolism

The aging of certain white wines is dependent on the presence of yeast strains that develop a biofilm on the wine surface after the alcoholic fermentation. These strains belong to the genus Saccharomyces and are called flor yeasts. These strains possess distinctive characteristics compared with Saccharomyces cerevisiae fermenting strain. The most important one is their capacity to form a biofilm on the air-liquid interface of the wine. The major gene involved in this phenotype is FLO11, however other genes are also involved in velum formation by these yeast and will be detailed. Other striking features presented in this review are their aneuploidy, and their mitochondrial DNA polymorphism which seems to reflect adaptive evolution of the yeast to a stressful environment where acetaldehyde and ethanol are present at elevated concentration. The biofilm assures access to oxygen and therefore permits continued growth on non-fermentable ethanol. This specific metabolism explains the peculiar organoleptic profile of these wines, especially their content in acetaldehyde and sotolon. This review deals with these different specificities of flor yeasts and will also underline the existing gaps regarding these astonishing yeasts.

Cell aggregations in yeasts and their applications

Yeasts can display four types of cellular aggregation: sexual, flocculation, biofilm formation, and filamentous growth. These cell aggregations arise, in some yeast strains, as a response to environmental or physiological changes. Sexual aggregation is part of the yeast mating process, representing the first step of meiotic recombination. The flocculation phenomenon is a calcium-dependent asexual reversible cellular aggregation that allows the yeast to withstand adverse conditions. Biofilm formation consists of multicellular aggregates that adhere to solid surfaces and are embedded in a protein matrix; this gives the yeast strain either the ability to colonize new environments or to survive harsh environmental conditions. Finally, the filamentous growth is the ability of some yeast strains to grow in filament forms. Filamentous growth can be attained by two different means, with the formation of either hyphae or pseudohyphae. Both hyphae and pseudohyphae arise when the yeast strain is under nutrient starvation conditions and they represent a means for the microbial strain to spread over a wide area to survey for food sources, without increasing its biomass. Additionally, this filamentous growth is also responsible for the invasive growth of some yeast.