Killer yeasts: expanding frontiers in the age of synthetic biology

Detection and Identification of Food-Borne Yeasts: An Overview of the Relevant Methods and Their Evolution

The presence of yeasts in food is not unexpected, as they are part of the microbiota of raw materials, employed as starter cultures in numerous fermentation processes, and also play a role in spontaneous fermentation. Nevertheless, they have the potential to induce spoilage, which can lead to significant quality issues, and certain yeasts have the ability to cause infections in humans and animals, posing a food safety risk. The detection of yeasts in food, determination of their cell number, as well as identification and typing, are therefore often tasks during the examination of certain food categories. The methods employed to achieve these objectives are diverse, encompassing both conventional culture-based techniques and more recent, genome-based studies. The objective of this study is to provide a summary article that presents the methods suitable for testing food-derived yeasts. The article will highlight the advantages, disadvantages, and potential difficulties of their applicability. Moreover, a comprehensive review of nucleic acid-based, culture-dependent and culture-independent molecular yeast identification techniques was conducted, encompassing scientific articles from the past five years (2020-2024). The search was based on the Science Direct database using the keywords "yeast and molecular identification and food".

Sustainable Approaches in Viticulture: From Wastes and Side Streams to High-Value Products

In the context of climate change, resource scarcity, and a growing global population, sustainable processes and the efficient use of raw materials are imperative. Developing best practices to guide the transition toward a circular economy with minimized waste is essential. Agricultural processes offer inspiration, as they traditionally emphasize the utilization of all parts of cultivated plants. Today, however, there is a pressing need to go beyond basic utilization and focus on the upcycling and valorization of agricultural side streams into high-value products. This chapter examines the wine and grape industry, which generates substantial volumes of side streams, including grape pomace, seeds, stems, and wine lees. In recent years, these material streams have attracted attention for their potential as raw materials rich in bioactive compounds - such as diverse polyphenols, dietary fibers, and organic acids - that can be applied across various sectors, including food, cosmetics, pharmaceuticals, and bioenergy. Key methodologies such as extraction, fermentation, and bioconversion are discussed as pathways to recover and enhance these compounds. Case studies of successful valorization initiatives are presented, demonstrating practical applications of side streams for high-value product creation. An example is the BMBF-funded project "Sustainable Beverages" focusing on the development of fermented drinks made from vine leaves that can be offered as a non-alcoholic alternative to wine. By providing an overview of the current research and technologies in wine waste valorization, this chapter serves as a valuable resource for academics, industry professionals, and policymakers seeking to advance sustainable practices within the wine sector. Ultimately, the upcycling of wine industry residues not only reduces environmental impact but also creates new revenue opportunities, driving innovation and sustainability in the industry.

Harnessing killer yeast system: from molecular insight to real world biocontrol solution

The biocontrol mechanisms of yeasts are gaining global attention as a vital response to the rising threat of antimicrobial resistance in emerging pathogens. With their diverse genetic traits, yeasts present potent antagonistic capabilities that have extensive applications across various sectors. This review examines the fundamental mechanisms and molecular bases of yeast antagonism, emphasizing innovative screening techniques for identifying effective strains. Key molecular methods, including gene identification, sequence analysis, and expression studies, reveal insights into their modes of action, such as nutrient competition, mycocin production, and volatile organic compound release. While the potential of antagonistic yeasts spans crop protection, food safety, and disease prevention, their commercial availability remains limited. To foster adoption, there is an urgent need for advanced screening methods and deeper molecular understanding. Future research should prioritize the optimization and commercialization of yeast-based biocontrol products, effectively bridging the gap between scientific discovery and practical application in combating harmful pathogens.

Wine Fermentation as a Model System for Microbial Ecology and Evolution

In vitro microbial communities have proven to be invaluable model systems for studying ecological and evolutionary processes experimentally. However, it remains unclear whether quantitative insights obtained from these laboratory systems can be applied to complex communities assembling and evolving in their natural ecological context. To bridge the gap between the lab and the 'real-world', there is a need for laboratory model systems that better approximate natural and semi-natural ecosystems. Wine fermentation presents an ideal system for this purpose, balancing experimental tractability with rich ecological and evolutionary dynamics. In this perspective piece we outline the key features that make wine fermentation a fruitful model system for ecologists and evolutionary biologists. We highlight the diversity of environmentally mediated interactions that shape community dynamics during fermentation, the complex evolutionary history of wine microbial populations, and the opportunity to study the impact of complex ecologies on evolutionary dynamics. By integrating knowledge from both wine research and microbial ecology and evolution we aim to enhance understanding and foster collaboration between these fields.

The coming wave of confluent biosynthetic, bioinformational and bioengineering technologies

Information and energy flows form the basis of all economic activity, with advanced technologies underpinning both. Profound uncertainties caused by geostrategic forces have accelerated a trillion-dollar race for technological superiority. The result is an onrush of "technovation" at the nexus of synthetic biotechnologies, information technologies, nanotechnologies and engineering technologies. This article explores recent breakthroughs in integrating chip technologies and synthetic bioinformational engineering. It investigates prospects of biomolecules as carriers of stored digital data, synthetic cells-on-a-chip, and hybrid semiconductors and next-generation artificial intelligence processors. Consilience-unity of knowledge-redefines possibilities emerging from the living interface of biologically-inspired engineering and engineering-enabled biology.

Profiles of Killer Systems and Volatile Organic Compounds of Rowanberry and Rosehip-Inhabiting Yeasts Substantiate Implications for Biocontrol

Yeasts produce numerous antimicrobial agents such as killer toxins, volatile organic compounds (VOCs), and other secondary metabolites, establishing themselves in developing natural and sustainable biocontrol strategies for agriculture and food preservation. This study addressed the biocontrol potential of yeasts, isolated from spontaneous fermentations of rosehips (Rosa canina L.) and rowanberries (Sorbus aucuparia L.), focusing on their killer phenotypes and VOCs production. Yeasts were isolated using spontaneous fermentations with Hanseniaspora uvarum and Metschnikowia pulcherrima identified as the dominant species, comprising approximately 70% of the yeast population. Among 163 isolated strains, 20% demonstrated killing activity, with Saccharomyces cerevisiae exhibiting the strongest killing efficiency, as well as Pichia anomala and M. pulcherrima showing broad-spectrum antagonistic activity. This study identified dsRNA-encoded killer phenotypes in S. cerevisiae, S. paradoxus, and Torulaspora delbrueckii, revealing multiple distinct killer toxin types. The biocontrol potential of wild berry-inhabiting yeasts was demonstrated in a real food system, grape juice, where the S. cerevisiae K2-type killer strain significantly reduced fungal contaminants. The selected H. uvarum, M. pulcherrima, S. cerevisiae, and S. paradoxus yeast strains representing both berries were applied for VOC analysis and identification by gas chromatography-linked mass spectrometry. It was revealed that the patterns of emitted volatiles are yeast species-specific. Statistically significant differences between the individual VOCs were observed among killing phenotype-possessing vs. non-killer S. paradoxus yeasts, thus revealing the involvement of killer systems in multi-level biocontrol enablement. The performed studies deepen our understanding of potential yeast biocontrol mechanisms, highlight the importance of produced antimicrobials and volatiles in ensuring antagonistic efficacy, and prove the relevance of isolated biocontrol yeasts for improving food safety.

The Viral K1 Killer Yeast System: Toxicity, Immunity, and Resistance

Killer yeasts, such as the K1 killer strain of S. cerevisiae, express a secreted anti-competitive toxin whose production and propagation require the presence of two vertically-transmitted dsRNA viruses. In sensitive cells lacking killer virus infection, toxin binding to the cell wall results in ion pore formation, disruption of osmotic homeostasis, and cell death. However, the exact mechanism(s) of K1 toxin killing activity, how killer yeasts are immune to their own toxin, and which factors could influence adaptation and resistance to K1 toxin within formerly sensitive populations are still unknown. Here, we describe the state of knowledge about K1 killer toxin, including current models of toxin processing and killing activity, and a summary of known modifiers of K1 toxin immunity and resistance. In addition, we discuss two key signaling pathways, HOG (high osmolarity glycerol) and CWI (cell wall integrity), whose involvement in an adaptive response to K1 killer toxin in sensitive cells has been previously documented but requires further study. As both host-virus and sensitive-killer competition have been documented in killer systems like K1, further characterization of K1 killer yeasts may provide a useful model system for study of both intracellular genetic conflict and counter-adaptation between competing sensitive and killer populations.