Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology

Plant-related Philistine ritual practices at biblical Gath

The Philistine culture (Iron Age, ca. 1200-604 BCE) profoundly impacted the southern Levant's cultural history, agronomy, and dietary customs. Nevertheless, our knowledge of the Philistines' cultic praxis and deities, is limited and uncertain. Here, we combine archaeological data with a meticulous study of plant use at two successive temples at Tell eṣ-Ṣâfī/Gath. We provide a list of the plants used, their time of harvest, mode of offering, and possible symbolism. Analysis of the temples' macrobotanical (seed and fruits) plant assemblage reveals the offerings; that the inception date for rites was early spring; and sheds light on the date of the final utilization of the temples (late summer/early fall). Besides food crops, we note the earliest cultic use of chaste tree (Vitex agnus-castus), crown daisy (Glebionis coronaria), and scabious (Lomelosia argentea). These wide-spread Mediterranean plants were known so far only in later cults-of early Greek deities, such as Hera, Artemis, Demeter, and Asclepios. We discuss the data as reflecting that the Philistine religion relied on the magic and power of nature, such as fresh water and seasonality, which influence human life, health, and activity. In sum, our results offer novel insights into the culture of the Philistines.

Yeasts Inhabiting Extreme Environments and Their Biotechnological Applications

Yeasts are microscopic fungi inhabiting all Earth environments, including those inhospitable for most life forms, considered extreme environments. According to their habitats, yeasts could be extremotolerant or extremophiles. Some are polyextremophiles, depending on their growth capacity, tolerance, and survival in the face of their habitat's physical and chemical constitution. The extreme yeasts are relevant for the industrial production of value-added compounds, such as biofuels, lipids, carotenoids, recombinant proteins, enzymes, among others. This review calls attention to the importance of yeasts inhabiting extreme environments, including metabolic and adaptive aspects to tolerate conditions of cold, heat, water availability, pH, salinity, osmolarity, UV radiation, and metal toxicity, which are relevant for biotechnological applications. We explore the habitats of extreme yeasts, highlighting key species, physiology, adaptations, and molecular identification. Finally, we summarize several findings related to the industrially-important extremophilic yeasts and describe current trends in biotechnological applications that will impact the bioeconomy.

Water is a preservative of microbes

Water is the cellular milieu, drives all biochemistry within Earth's biosphere and facilitates microbe-mediated decay processes. Instead of reviewing these topics, the current article focuses on the activities of water as a preservative-its capacity to maintain the long-term integrity and viability of microbial cells-and identifies the mechanisms by which this occurs. Water provides for, and maintains, cellular structures; buffers against thermodynamic extremes, at various scales; can mitigate events that are traumatic to the cell membrane, such as desiccation-rehydration, freeze-thawing and thermal shock; prevents microbial dehydration that can otherwise exacerbate oxidative damage; mitigates against biocidal factors (in some circumstances reducing ultraviolet radiation and diluting solute stressors or toxic substances); and is effective at electrostatic screening so prevents damage to the cell by the intense electrostatic fields of some ions. In addition, the water retained in desiccated cells (historically referred to as 'bound' water) plays key roles in biomacromolecular structures and their interactions even for fully hydrated cells. Assuming that the components of the cell membrane are chemically stable or at least repairable, and the environment is fairly constant, water molecules can apparently maintain membrane geometries over very long periods provided these configurations represent thermodynamically stable states. The spores and vegetative cells of many microbes survive longer in the presence of vapour-phase water (at moderate-to-high relative humidities) than under more-arid conditions. There are several mechanisms by which large bodies of water, when cooled during subzero weather conditions remain in a liquid state thus preventing potentially dangerous (freeze-thaw) transitions for their microbiome. Microbial life can be preserved in pure water, freshwater systems, seawater, brines, ice/permafrost, sugar-rich aqueous milieux and vapour-phase water according to laboratory-based studies carried out over periods of years to decades and some natural environments that have yielded cells that are apparently thousands, or even (for hypersaline fluid inclusions of mineralized NaCl) hundreds of millions, of years old. The term preservative has often been restricted to those substances used to extend the shelf life of foods (e.g. sodium benzoate, nitrites and sulphites) or those used to conserve dead organisms, such as ethanol or formaldehyde. For living microorganisms however, the ultimate preservative may actually be water. Implications of this role are discussed with reference to the ecology of halophiles, human pathogens and other microbes; food science; biotechnology; biosignatures for life and other aspects of astrobiology; and the large-scale release/reactivation of preserved microbes caused by global climate change.

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period

We subjected human paleofeces dating from the Bronze Age to the Baroque period (18th century AD) to in-depth microscopic, metagenomic, and proteomic analyses. The paleofeces were preserved in the underground salt mines of the UNESCO World Heritage site of Hallstatt in Austria. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as some of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products. Due to these traditional dietary habits, all ancient miners up to the Baroque period have gut microbiome structures akin to modern non-Westernized individuals whose diets are also mainly composed of unprocessed foods and fresh fruits and vegetables. This may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, in one of the Iron Age samples, we observed a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provides the first molecular evidence for blue cheese and beer consumption in Iron Age Europe.

Alcohol-Related Liver Disease

Content available: Author Interview and Audio Recording.

The Venusian Lower Atmosphere Haze as a Depot for Desiccated Microbial Life: A Proposed Life Cycle for Persistence of the Venusian Aerial Biosphere

We revisit the hypothesis that there is life in the venusian clouds to propose a life cycle that resolves the conundrum of how life can persist aloft for hundreds of millions to billions of years. Most discussions of an aerial biosphere in the venusian atmosphere temperate layers never address whether the life-small microbial-type particles-is free floating or confined to the liquid environment inside cloud droplets. We argue that life must reside inside liquid droplets such that it will be protected from a fatal net loss of liquid to the atmosphere, an unavoidable problem for any free-floating microbial life forms. However, the droplet habitat poses a lifetime limitation: Droplets inexorably grow (over a few months) to large enough sizes that are forced by gravity to settle downward to hotter, uninhabitable layers of the venusian atmosphere. (Droplet fragmentation-which would reduce particle size-does not occur in venusian atmosphere conditions.) We propose for the first time that the only way life can survive indefinitely is with a life cycle that involves microbial life drying out as liquid droplets evaporate during settling, with the small desiccated "spores" halting at, and partially populating, the venusian atmosphere stagnant lower haze layer (33-48 km altitude). We, thus, call the venusian lower haze layer a "depot" for desiccated microbial life. The spores eventually return to the cloud layer by upward diffusion caused by mixing induced by gravity waves, act as cloud condensation nuclei, and rehydrate for a continued life cycle. We also review the challenges for life in the extremely harsh conditions of the venusian atmosphere, refuting the notion that the "habitable" cloud layer has an analogy in any terrestrial environment.

Endurance of extremely prolonged nutrient prevention across kingdoms of life

Numerous observations demonstrate that microorganisms can survive very long periods of nutrient deprivation and starvation. Moreover, it is evident that prolonged periods of starvation are a feature of many habitats, and many cells in all kingdoms of life are found in prolonged starvation conditions. Bacteria exhibit a range of responses to long-term starvation. These include genetic adaptations such as the long-term stationary phase and the growth advantage in stationary phase phenotypes characterized by mutations in stress-signaling genes and elevated mutation rates. Here, we suggest using the term "endurance of prolonged nutrient prevention" (EPNP phase), to describe this phase, which was also recently described in eukaryotes. Here, we review this literature and describe the current knowledge about the adaptations to very long-term starvation conditions in bacteria and eukaryotes, its conceptual and structural conservation across all kingdoms of life, and point out possible directions that merit further research.

Comparison of Two Aspergillus oryzae Genomes From Different Clades Reveals Independent Evolution of Alpha-Amylase Duplication, Variation in Secondary Metabolism Genes, and Differences in Primary Metabolism

Microbes (bacteria, yeasts, molds), in addition to plants and animals, were domesticated for their roles in food preservation, nutrition and flavor. Aspergillus oryzae is a domesticated filamentous fungal species traditionally used during fermentation of Asian foods and beverage, such as sake, soy sauce, and miso. To date, little is known about the extent of genome and phenotypic variation of A. oryzae isolates from different clades. Here, we used long-read Oxford Nanopore and short-read Illumina sequencing to produce a highly accurate and contiguous genome assemble of A. oryzae 14160, an industrial strain from China. To understand the relationship of this isolate, we performed phylogenetic analysis with 90 A. oryzae isolates and 1 isolate of the A. oryzae progenitor, Aspergillus flavus. This analysis showed that A. oryzae 14160 is a member of clade A, in comparison to the RIB 40 type strain, which is a member of clade F. To explore genome variation between isolates from distinct A. oryzae clades, we compared the A. oryzae 14160 genome with the complete RIB 40 genome. Our results provide evidence of independent evolution of the alpha-amylase gene duplication, which is one of the major adaptive mutations resulting from domestication. Synteny analysis revealed that both genomes have three copies of the alpha-amylase gene, but only one copy on chromosome 2 was conserved. While the RIB 40 genome had additional copies of the alpha-amylase gene on chromosomes III, and V, 14160 had a second copy on chromosome II and an third copy on chromosome VI. Additionally, we identified hundreds of lineage specific genes, and putative high impact mutations in genes involved in secondary metabolism, including several of the core biosynthetic genes. Finally, to examine the functional effects of genome variation between strains, we measured amylase activity, proteolytic activity, and growth rate on several different substrates. RIB 40 produced significantly higher levels of amylase compared to 14160 when grown on rice and starch. Accordingly, RIB 40 grew faster on rice, while 14160 grew faster on soy. Taken together, our analyses reveal substantial genome and phenotypic variation within A. oryzae.

Proteomics Answers Which Yeast Genes Are Specific for Baking, Brewing, and Ethanol Production

Yeast strains are convenient models for studying domestication processes. The ability of yeast to ferment carbon sources from various substrates and to produce ethanol and carbon dioxide is the core of brewing, winemaking, and ethanol production technologies. The present study reveals the differences among yeast strains used in various industries. To understand this, we performed a proteomic study of industrial Saccharomyces cerevisiae strains followed by a comparative analysis of available yeast genetic data. Individual protein expression levels in domesticated strains from different industries indicated modulation resulting from response to technological environments. The innovative nature of this research was the discovery of genes overexpressed in yeast strains adapted to brewing, baking, and ethanol production, typical genes for specific domestication were found. We discovered a gene set typical for brewer's yeast strains. Baker's yeast had a specific gene adapted to osmotic stress. Toxic stress was typical for yeast used for ethanol production. The data obtained can be applied for targeted improvement of industrial strains.

Never Change a Brewing Yeast? Why Not, There Are Plenty to Choose From

Fermented foods and particularly beer have accompanied the development of human civilization for thousands of years. Saccharomyces cerevisiae, the dominant yeast in the production of alcoholic beverages, probably co-evolved with human activity. Considering that alcoholic fermentations emerged worldwide, the number of strains used in beer production nowadays is surprisingly low. Thus, the genetic diversity is often limited. This is among others related to the switch from a household brewing style to a more artisan brewing regime during the sixteenth century and latterly the development of single yeast isolation techniques at the Carlsberg Research Laboratory in 1883, resulting in process optimizations in the brewing industry. However, due to fierce competition within the beer market and the increasing demand for novel beer styles, diversification is becoming increasingly important. Moreover, the emergence of craft brewing has influenced big breweries to rediscover yeast as a significant contributor to a beer's aroma profile and realize that there is still room for innovation in the fermentation process. Here, we aim at giving a brief overview on how currently used S. cerevisiae brewing yeasts emerged and comment on the rationale behind replacing them with novel strains. We will present potential sources of yeasts that have not only been used in beer brewing before, including natural sources and sources linked to human activity but also an overlooked source, such as yeast culture collections. We will briefly comment on common yeast isolation techniques and finally touch on additional challenges for the brewing industry in replacing their current brewer's yeasts.

Archaeology of Cuisine and Cooking

This review demonstrates that recent contributions by archaeologists to the study of cuisine and cooking present a new addition to the field of anthropology. Archaeologists situate their work historically and contextually by examining cuisines that are culturally constructed. Studying cooking and food preparation helps elucidate relationships among material practices, understandings of taste, identity, power, and meaning in a society. Archaeologists can not only discover specific ingredients in food, but also reconstruct recipes, decipher regional cuisines, ascertain sensory experiences, recover the tools in spatial context, recreate techniques used to prepare food in the past, and overall learn more about the social and cultural contexts of the human experience. This type of investigation is possible because archaeological work uses complementary data to explain social practices and because advances in archaeological methods make accessible previously undetectable data. Experimental archaeology focused on cooking in the past has not only revealed important social information but also captured the imagination of the public. Archaeological research on cooking and cuisine reveals social, political, religious, and economic practices in the past, and it has a unique ability to engage the present with the past through public outreach and solutions to food-related problems.

Biocatalysis - Key enabling tools from biocatalytic one-step and multi-step reactions to biocatalytic total synthesis

In the area of human-made innovations to improve the quality of life, biocatalysis has already had a great impact and contributed enormously to a growing number of catalytic transformations aimed at the detection and analysis of compounds, the bioconversion of starting materials and the preparation of target compounds at any scale, from laboratory small scale to industrial large scale. The key enabling tools which have been developed in biocatalysis over the last decades also provide great opportunities for further development and numerous applications in various sectors of the global bioeconomy. Systems biocatalysis is a modular, bottom-up approach to designing the architecture of enzyme-catalyzed reaction steps in a synthetic route from starting materials to target molecules. The integration of biocatalysis and sustainable chemistry in vitro aims at ideal conversions with high molecular economy and their intensification. Retrosynthetic analysis in the chemical and biological domain has been a valuable tool for target-oriented synthesis while, on the other hand, diversity-oriented synthesis builds on forward-looking analysis. Bioinformatic tools for rapid identification of the required enzyme functions, efficient enzyme production systems, as well as generalized bioprocess design tools, are important for rapid prototyping of the biocatalytic reactions. The tools for enzyme engineering and the reaction engineering of each enzyme-catalyzed one-step reaction are also valuable for coupling reactions. The tools to overcome interaction issues with other components or enzymes are of great interest in designing multi-step reactions as well as in biocatalytic total synthesis.

Bioarchaeology: a profitable dialogue between microbiology and archaeology

The cultivation of yeasts from up to 5000‐year‐old beer vessels in Israel allows insights into early domestication of microbes for food production, but also raises questions about long‐term survival of microbes under dormancy or slow growth.

Isolation and Characterization of Live Yeast Cells from Ancient Clay Vessels

Ancient fermented food has been studied mainly based on residue analysis and recipes and reconstruction attempts were performed using modern domesticated yeast. Furthermore, microorganisms which participated in fermentation were studied using ancient-DNA techniques. In a recent paper, we presented a novel approach based on the hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. Here we present a pipeline for isolation of yeast from clay vessels uncovered in archeological sites and transferred to the microbiology lab where they can be isolated and characterized. This method opens new avenues for experimental archeology and enables attempts to recreate ancient food and beverages using the original microorganisms.

How to Train Your Fungus

Domestication led to profound changes in human culture. During this period, humans used breeding strategies to select for desirable traits in crops and livestock. These practices led to genetic and phenotypic changes that are trackable through archaeological and genomic records. Bacteria, yeasts, and molds also experienced domestication during the agricultural revolution, but the effects of domestication on microbes are poorly understood in comparison to plants and animals. Bodinaku et al. used experimental evolution to track the phenotypic changes that occur when wild Penicillium molds specialize and adapt to the cheese environment (I. Bodinaku, J. Shaffer, A. B. Connors, J. L. Steenwyk, et al., mBio 10:e02445-19, 2019, https://mbio.asm.org/content/10/5/e02445-19.long). Amazingly, after only eight generations of growth in a laboratory cheese environment, mutants emerged whose traits resembled those of the Brie and Camembert cheese mold Penicillium camemberti This study demonstrated that the early stages of microbial domestication can occur rapidly and suggested that experimental evolution may be a viable strategy to exploit the metabolic diversity of wild microbes for food fermentation.

Eukaryotic Adaptation to Years-Long Starvation Resembles that of Bacteria

The Growth Advantage in Stationary Phase (GASP) phenomenon, described in bacteria, reflects the genetic adaptation of bacteria to stress, including starvation, for a long time. Unlike in stationary phase where no cell division occurs, GASP harbors active cell division, concurrent with genetic adaptation.

Here we show that GASP occurs also in eukaryotes.

Two strains of Saccharomyces cerevisiae (Sc404 and Sc424) have been isolated from 2-year-old sealed bottles of beer. These strains presented advantage in survival and growth over the parent during stress. The differences between the strains are irreversible and therefore genetic in origin rather than epigenetic. Direct competition assays show that Sc404 and Sc424 outcompete the parent in direct competition. DNA sequencing shows changes of the genome: the TOR complexes are mutated, and DNA repair gene mutations confer a mutator phenotype. The differences between the strains are reflected in a difference in taste between beers brewed from them.

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Yeast genetically adapts to long-term starvation in a similar way to bacteria

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Adaptation to long-term starvation in yeast includes multi-stress tolerance

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Adaptation to long-term starvation in yeast includes mutations in TORC

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Adaptation to long-term starvation in yeast includes a mutator phenotype