Yeast

• 1. Introduction

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  Yeast is a group of fungi with at least 1,500 recognized species, yet those species make up only about 1% of all the fungi scientists have described. A typical cell measures 3-4 micrometres across, and the largest reach about 40 micrometres. Most live as single cells rather than as threads or mushrooms. The word is a convenience, not a family tree, because yeasts sit in two separate phyla, the Ascomycota and the Basidiomycota. Even so, one species, Saccharomyces cerevisiae, is so familiar that many people treat its name as a synonym for the whole group. How did an organism this small end up in kitchens, breweries, laboratories and hospitals? Why did people depend on it for thousands of years before anyone agreed it was alive? And why do some yeasts feed us while others make people ill?

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• 2. Old Partners, Late Proof

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  Drawings of bakeries and breweries about 4,000 years old survive from Egypt. Archaeologists there also found early grinding stones and baking chambers built for yeast-raised bread. Nobody knows when yeast first lifted a loaf. Researchers speculate that a mixture of flour and water sat longer than usual on a warm day, and yeasts from the flour itself made it ferment. The bread that followed would have been lighter and tastier than the flat, hard cakes that came before.

  Vessels from several archaeological sites in Israel offer more direct evidence. They date to around 5,000, 3,000 and 2,500 years ago, and they were believed to have held beer and mead. Inside, scientists found yeast colonies that had survived the millennia, the first direct biological evidence of yeast use in early cultures.

  The English word comes from Old English gist and gyst, which trace back to an Indo-European root, yes-. That root meant to boil, foam or bubble, an apt picture of a fermenting vat.

  In 1680, the Dutch naturalist Anton van Leeuwenhoek became the first person to see yeast through a microscope. He judged the cells to be globular structures rather than living organisms. Researchers remained unsure whether yeasts were algae or fungi until Theodor Schwann recognized them as fungi in 1837.

  In 1857, the French microbiologist Louis Pasteur showed that bubbling oxygen into a yeast broth increased cell growth but inhibited fermentation. This observation was later named the Pasteur effect. In his paper Mémoire sur la fermentation alcoolique, Pasteur proved that living yeasts, and not a chemical catalyst, carry out alcoholic fermentation.

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• 3. From Cake to Factory

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  By 1780, the Dutch were already selling Saccharomyces cerevisiae commercially for bread-making. Around 1800, German producers began making it in the form of a cream. In 1825, a method for removing the liquid allowed yeast to be prepared as solid blocks, and the filter press of 1867 improved industrial production of those blocks. In 1872, Baron Max de Springer developed a process that made granulated yeast from beetroot molasses. Manufacturers used his technique until the First World War.

  American bakers relied almost exclusively on naturally occurring airborne yeasts until 1876. At the Centennial Exposition in Philadelphia that year, Charles L. Fleischmann exhibited commercial yeast together with a process for using it. He also served the bread it produced. Fleischmann's Yeast, introduced in 1868, was one of the earlier commercial developments in North America.

  During the Second World War, Fleischmann's developed granulated active dry yeast. It needed no refrigeration, kept longer than fresh yeast, and rose twice as fast.

  In 1920, the Fleischmann Yeast Company began a campaign called Yeast for Health, promoting yeast cakes. It first stressed vitamins and benefits for the skin and digestion. Later advertising claimed a far broader range of health benefits, and the Federal Trade Commission censured it as misleading. The fad for yeast cakes lasted until the late 1930s.

  The mechanical refrigerator, first patented in Europe in the 1850s, freed brewers and winemakers from seasonal limits. It also let them leave their cellars and other earthen spaces. Distillers had once followed the same seasons. For John Molson, who made his living in Montreal before refrigeration, the brewing season ran only from September through to May.

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• 4. Rising and Brewing

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  In bread dough, Saccharomyces cerevisiae turns fermentable sugars into carbon dioxide, and the gas forms pockets that make the dough rise. Baking kills the yeast and sets those pockets, which leaves a soft, spongy texture. At first the yeast respires with oxygen, producing carbon dioxide and water. Once the oxygen is gone, fermentation begins and ethanol appears as a waste product, which evaporates in the oven.

  Bakers can test whether yeast is still alive by dropping it into a weak solution of water and sugar. Live yeast foams and bubbles. Recipes call this step proofing. With a sourdough starter, flour and water replace the sugar, and the step is called proofing the sponge. A long rise improves flavor, but if the dough is left too long at the start, the yeast can fail to lift the bread in the final stages.

  By the late 18th century, brewers had identified two yeast strains. Saccharomyces cerevisiae is a top-cropping yeast that forms a foam on the surface of the wort. Saccharomyces pastorianus is a bottom-cropping yeast, typically used for lagers, and it ferments well at low temperatures. The line between them is thinner than the names suggest. Decades ago, taxonomists reclassified S. carlsbergensis, also called uvarum, as a member of S. cerevisiae, because the only clear difference is metabolic. Lager strains secrete an enzyme called melibiase, which splits the sugar melibiose into more fermentable simple sugars.

  The common top-cropping brewer's yeast and the common baking yeast are the same species, but they are different strains. Baking strains are aggressive and make dough rise in the shortest possible time. Brewing strains work more slowly, leave fewer off-flavours and, in some cases, tolerate alcohol concentrations up to 22%.

  The genus Dekkera, also known as Brettanomyces, plays an important part in making lambic and specialty sour ales. It also conditions one particular Belgian Trappist beer. In recent years, craft brewers have experimented with it, and a handful of breweries have made beers fermented mainly with pure Brettanomyces cultures.

  On grape skins, wine yeast is already waiting. Fermenting with this wild yeast gives unpredictable results, because the outcome depends on which species happen to be present. Most winemakers therefore add a pure culture, which quickly dominates and suppresses the wild yeasts. Most added strains are Saccharomyces cerevisiae, though not every strain suits winemaking, and the strain chosen has a direct effect on the finished wine.

  Brettanomyces can also spoil wine. It produces volatile phenolic compounds, grouped under the name Brettanomyces character, with aromas described as antiseptic or barnyard. Researchers at the University of British Columbia found a strain that reduces amines, which cause off-flavors in red wine and Chardonnay. In some people those amines also trigger headaches and hypertension, and about 30% of people are sensitive to biogenic amines such as histamines.

  Yeast also flavors food directly, with an umami taste much like monosodium glutamate. To make yeast extract, producers add salt to a yeast suspension, and the cells shrivel and begin digesting their own proteins. Extracts of this kind go into Vegemite and Promite in Australia, Marmite in the United Kingdom, Vitam-R in Germany and Cenovis in Switzerland.

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• 5. Budding and Rare Sex

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  Most growth in Saccharomyces cerevisiae happens by budding. A small bud, sometimes called a bleb or daughter cell, forms on the parent, and the parent's nucleus splits so that one daughter nucleus moves into the bud. The bud grows until it separates, and it is usually smaller than its mother. Schizosaccharomyces pombe divides by fission instead, producing two daughter cells of equal size. Some species link budding cells into strings called pseudohyphae. Fungi that can switch between a yeast form and a mold form, depending on temperature or other conditions, are called dimorphic.

  Hard times change the plan. When nutrients run out, haploid cells die, but diploid cells can undergo sporulation, in which meiosis produces haploid spores that may later mate and restore the diploid state. Schizosaccharomyces pombe mates when nutrients are limited. Hydrogen peroxide, which causes oxidative DNA damage, strongly induces its mating and spore formation.

  Katz Ezov and colleagues presented evidence that natural populations of Saccharomyces cerevisiae reproduce mostly by cloning and selfing. Mating usually happens between members of the same clonal population. Analysis of the ancestry of natural strains suggests that out-crossing occurs only about once every 50,000 cell divisions. That rate is too low for the long-term benefit of diversity to explain why sex persists. A short-term benefit, such as recombinational repair during meiosis, may be the real reason.

  Yeasts need no sunlight. As chemoorganotrophs, they take energy from organic compounds, mostly hexose sugars such as glucose and fructose, or disaccharides such as sucrose and maltose. Some species can also use pentose sugars such as ribose, alcohols and organic acids. Some require oxygen, while others are facultative anaerobes, and no known yeast species grows only without oxygen. Most grow best in a neutral or slightly acidic environment.

  Temperature preferences differ widely. Leucosporidium frigidum grows between minus 2 and 20 degrees Celsius, Saccharomyces telluris between 5 and 35, and Candida slooffi between 28 and 45. Cells can survive freezing under certain conditions, though their viability declines over time. Some pucciniomycete yeasts, in the genera Sporidiobolus and Sporobolomyces, release asexual ballistoconidia that disperse through the air.

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• 6. Wild Yeasts

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  Apple and peach skins carry naturally occurring yeasts, as do plant saps and the exudates of cacti. Yeasts turn up wherever sugar is plentiful, and some live in soil and on insects. Yeasts from soil and fruit skins have been shown to dominate the fungal succession as fruit decays. Their ecology and biodiversity remain poorly understood compared with those of other microorganisms.

  Candida albicans, Rhodotorula rubra, Torulopsis and Trichosporon cutaneum have all been found between people's toes as part of the skin flora. Yeasts also live in the gut flora of mammals and some insects, and deep-sea environments host a range of them.

  In 1894, Bernhard Fischer isolated the first marine yeasts from the Atlantic Ocean and identified them as Torula and Mycoderma species. Later isolates came from seawater, seaweeds, fish and marine mammals. Some are land yeasts that survived being carried to sea, while obligate marine yeasts are confined to marine habitats. Marine yeasts grow better on a medium made with seawater than on one made with freshwater. One marine yeast has produced bioethanol in seawater-based media, which could reduce the water footprint of that fuel.

  An Indian study of seven bee species and nine plant species found 45 yeast species from 16 genera living in flower nectaries and bee honey stomachs. Most belonged to the genus Candida. Dekkera intermedia was the most common species in honey stomachs, and Candida blankii the most common in nectaries. Flowers of A. indica bloom more when Candida blankii is present, although the mechanism is not fully understood.

  Yeast in the nectaries of the stinking hellebore raises the temperature of the flower. That warmth may help attract pollinators by increasing the evaporation of volatile compounds. Yeast can also produce a pheromone resembling that of the honeybee, and it attracts the small hive beetle in the same way. A hive that contains yeast may therefore be easier for the beetle to infest.

  A black yeast has been recorded in a complex relationship among ants, their mutualistic fungus, a parasite of that fungus, and a bacterium that kills the parasite. The yeast harms the antibiotic-producing bacteria, so it may let the parasite spread and affect the ants' health. Ants of the genus Cyphomyrmex grow a different yeast species. In the digestive tract of bess beetles, Spathaspora passalidarum ferments xylose and helps the beetles digest plant cells.

  Many fruits make sugars that attract yeasts, which ferment them into alcohol. Fruit-eating mammals find the scent of alcohol attractive, because it signals ripe, sugary fruit. In return, the mammals help disperse both the seeds and the yeast spores.

  Certain strains of some species make proteins called killer toxins, which eliminate competing strains. This can cause problems in winemaking, but toxin-producing strains could also be used to advantage in making wine.

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• 7. The Lab Workhorse

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  On the 24th of April 1996, Saccharomyces cerevisiae was announced as the first eukaryote to have its genome fully sequenced. The genome consists of 12 million base pairs. At the time, it was the most complex organism ever sequenced, and the work took seven years and more than 100 laboratories. Schizosaccharomyces pombe followed in 2002 as the sixth eukaryotic genome, with 13.8 million base pairs. By 2014, over 50 yeast species had been sequenced and published. Gene annotations for the two main models are kept in the databases SGD and PomBase.

  Both species are simple eukaryotic cells, and they serve as models for all eukaryotes, humans included. Researchers use them to study the cell cycle, DNA replication, recombination, cell division and metabolism. Yeasts are easy to culture and manipulate, which led to standard techniques such as yeast two-hybrid, synthetic genetic array analysis and tetrad analysis. Many proteins important in human biology were first discovered through their yeast counterparts, including cell cycle proteins, signaling proteins and protein-processing enzymes.

  About 20% of biopharmaceuticals are made in Saccharomyces cerevisiae, including insulin, hepatitis vaccines and human serum albumin. The species is easy to engineer, its physiology and genetics are well known, and it copes with harsh industrial conditions. Engineered yeasts can also make phenolics, isoprenoids, alkaloids and polyketides, a technique called metabolic engineering.

  Ethanol fuel begins with milling a feedstock such as sugar cane or field corn. Dilute sulfuric acid or fungal alpha amylase enzymes then break the starches into complex sugars, and a glucoamylase reduces those to simple sugars. Yeasts convert the simple sugars to ethanol, which distillation purifies to as much as 96%. Saccharomyces strains have been engineered to ferment xylose from agricultural residues, paper wastes and wood chips. That lets cellulosic ethanol be made from cheaper feedstocks. Yeasts have also been used recently to generate electricity in microbial fuel cells.

  Yarrowia lipolytica degrades palm oil mill effluent, the explosive TNT, and hydrocarbons such as alkanes, fatty acids, fats and oils. It tolerates high concentrations of salt and heavy metals, and researchers are investigating it as a heavy metal biosorbent. Saccharomyces cerevisiae may help clean arsenic from industrial effluent, and yeasts from Brazilian gold mines accumulate silver ions. The same appetite has a downside, because certain yeasts are known to degrade bronze statues.

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• 8. Unwelcome Guests

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  Cryptococcus neoformans and Cryptococcus gattii are the main causes of cryptococcosis, a fungal infection found in about one million HIV/AIDS patients. It causes over 600,000 deaths annually. These opportunistic pathogens threaten people with compromised immune systems. A rigid polysaccharide capsule around their cells helps them avoid being recognized and engulfed by white blood cells.

  Yeasts of the genus Candida cause oral and vaginal infections known as candidiasis. They normally live as commensals on the mucous membranes of humans and other warm-blooded animals. Sometimes the same strains turn pathogenic, sprouting a hyphal outgrowth that penetrates the mucosal membrane and causes irritation and shedding of tissue. Candida glabrata is the second most common Candida pathogen after C. albicans, infecting the urogenital tract and the bloodstream, a condition called candidemia. Candida auris was identified more recently.

  Not every yeast in the gut is an enemy. Some probiotic supplements use Saccharomyces boulardii to maintain and restore the natural flora of the digestive tract. It has been shown to reduce the symptoms of acute diarrhea and the chance of infection by Clostridium difficile.

  In food, yeasts grow wherever the pH is 5.0 or lower and sugars, organic acids or other easy carbon sources are present. As they grow, they alter the food's physical, chemical and sensory properties, and the food spoils. Spoilage shows on the surfaces of cheeses and meats, or as fermentation in juices, syrups and jams. Zygosaccharomyces has a long history as a spoilage yeast, because it grows despite high levels of sucrose, ethanol, acetic acid, sorbic acid, benzoic acid and sulfur dioxide. Those are some of the most common food preservation methods. Candida blankii has even been detected in Iberian ham and meat. Methylene blue is used to test for live yeast cells.

  On pickled vegetables, a white, thready growth called kahm yeast often appears after exposure to air. It is harmless but gives the pickles a bad flavor, so it must be removed regularly during fermentation. Yeast killer toxins, meanwhile, may have medical uses in treating yeast infections.

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