HERE'S TO THEE | HUMAN AND MICROBIAL SOCIALITIES | Simon Pope

“In spring, when the warmer weather arrives, we’re given safe-harbour by the leaves of the apple trees; and some of us are fed by nutrients that ooze from diseased or injured plant tissue. Those of us that also take part in fermentation become common in flower nectar and bacterial wetwood.”

“We're also abundant in the soil at this time of year. We're more common at its surface, our population decreasing in its lower layers. Those of us that can contribute to ‘cider-spoilage’ thrive here. In general, we're more abundant around the roots of the apple trees, with some of us only found in these rhizopshere soils. Some of us are only found on decaying fruit and fresh bird droppings in the grass during spring.”

“You can find us, along with other microbial flora on both the exterior and interior of apple tree buds, where we live there, along with mould. The bud is full of microbial life, and we are especially numerous in the stamens and stigmas.”

“In the early-summer, as the buds open into flowers, our populations change. Yeast flora becomes more widespread as the spring turns to summer. Apple blossom hosts those of us that are associated with flowers more generally. The sugars, amino acids, and organic acids that are exuded from leaves provide nutrients for our populations that live on the blossoms. We form ‘microcolonies’ at the base of the petioles of some of the tree's spur leaves, but not on the extension leaves. We're also found on the stigma and hypanthium of apple blossoms, in numbers equal to or greater than those for bacteria. Bacteria also live with us there.”

“You can find us in many areas around the farm: our populations increase on the grasses and plants in the orchard, and in early summer clover, buttercups, dandelions, act as our hosts. We also live on small slugs and in worms. Sometimes we transfer in the air, along with mould spores, from the orchard floor to the apples.”

“Many insects, including caterpillars, summer-fruit tortrix and mites are ‘microbiologically sterile’ but might still carry us. The apple-blossom weevil carry only moulds, but a wide variety and number of us are carried by other insects including spiders, St. Mark fever flies, bees, crane flies, aphids, manure flies, red and black frog hoppers, ants, wasps, and fruit flies. Even those carrying low numbers of us, like the frog-hopper will carry at least three species. Bumble bees work synergistically with honey bees to pollinate flowers in the orchard, and they carry us on their legs and in their honey sacs; those of us who are sugar-tolerant are found in nectar in their beehives – as well as in nectar on apple blossom.”

“We're introduced onto apple tree leaves by bird-droppings, especially those of us that produce carotenoids – a compound that protects us against the effects of reactive forms of oxygen and radiation. We form diverse populations from fresh bird-droppings falling on the grass in the orchard. We're less abundant on tree bark, and are sometimes found there in insect excreta. As the fruits mature, we continue to thrive both inside and on the surface of the apple. Our populations become more complex, and vary in composition and scale in the different sections of the fruit. The greatest numbers of us live on the skin and in the flesh under the stalk and the eye of the apple, but we live in all fleshy parts of the apple too. Some of us increase considerably, at the expense of the others. The phenolic compounds associated with the apple variety also influences how prevalent we are on the fruit’s skin at this stage their maturity. They’re a reservoir for other fungi too, some of whom make themselves known to you as blemishes on the apple skin.”

“When the apples are ripe and begin to fall to the orchard floor, our populations become modified once more, and additional species begin to colonize the fruit. Some of us continue to live on the grass beneath the trees. Some of us no longer live on the fruit. Once you’ve picked up the apples from the orchard floor and placed them into sacks, our populations increase. Some of us live only on fallen leaves, and on slugs at this time.”

“Washing the fruit before pressing reduces the number of our species on their exterior. Once the juice is expressed from the mature fruit, some of us who live in pressing equipment, hoses and juice tanks, as well as walls, floors, and surfaces, soon cause active fermentation. Some of us, along with acetic acid bacteria, are found in the pound-house during pressing, during late autumn and early winter. We adapt to the favourable conditions in cider-making equipment, and may grow in pressure gauges or filters, or in lubricating oils.”

“Fermentation begins in the ‘fruit yeast’ phase with those of us who are apiculate – whose shape is truncated to a point. Some of our species begin to dominate, and microbial succession is a general phenomenon of spontaneous fermentation. From the beginning of fermentation, Saccharomyces species are dominant, especially cerevisiae (and sometimes C. bayanus). At 14 days, Candida lucitaniae is likely to be present also, to be replaced by Saccharomyces species between days 30 and 100 of this fermentation phase. Following this, until the 150th day, Kloeckera and Candida populations begin to thrive, along with Saccharomyces species. Saccharomyces ludwigii is often present, and Zygosaccharomyces species and Torula forms are also common. Saccharomyces uvarum might dominate at this stage, and haploid or circulare mutations may be found, especially at the end of fermentation when thiamin and nitrogenous components are less available to us.”

“Sometimes sulphur dioxide is used to control the growth of our populations. Aerobic organisms are more sensitive than fermenting organisms, and sulphur can kill some of us, as well as acetic acid bacteria. Non-sulphured apple juice usually contains those of us that produce a “film”, but also acetic acid bacteria, which live in the barn and on wooden vessels. Fermentation is more rapid in sulphured juice, when Saccharomyces species lack competition from other micro-organisms. Different strains of Saccharomyces cerevisiae are found in each farm and Hansenula species, Brettanomyces species, S’codes ludwigii, or its bisporus variety may also be found in the fermenting juice. We initiate fermentation spontaneously when the temperature is above 10ºC. Any fermentation of mixed microflora is dominated by Saccharomyces cerevisiae var. uvarum, and takes between one and one and a half months, with malolactic fermentation occurring during the yeast fermentation process. Anaerobic organisms such as Saccharomyces species, and some lactic acid bacteria, (albeit lower in number) survive the addition of sulphur dioxide. These continue to live in cider and may continue the process of fermentation, or produce a haze or deposit.”

“In next stage of fermentation we are involved in malolactic conversion – the transformation of malic to lactic acid. This results from a diversity of lactic acid bacteria and contributes to the cider’s microbial stability. Lactic acid bacteria compete with us for nutrients in the apple juice, and our populations decrease after approximately 125 days of fermentation – coinciding with an increase in the population of lactic acid bacteria. The proportion of various micro-organisms fluctuates over time, depending on the number of ‘transitory mycoflora’ that add to those of us that are resident on the farm.”

“During fermentation, Saccharomyces species can produce acetaldehyde, and pyruvic and 2-oxoglutaric acids. They also convert pectic acid to galacturonic acid by secreting a polygalacturonase. The distribution of lactic acid bacteria is highly variable from one ecosystem to the next. Malic acid increases in concentration during fermentation of sulphited apple juice. Some of us produce small amounts of acetic acid, and film-forming yeasts living on the surface of the cider convert ethanol and malate to carbon dioxide, water and acetaldehyde when exposed to air during storage. Some of us – particularly Candida ethanolica – may establish resident communities in wooden casks.”

“We are digested by larval and adult stages of Dropsophila species, and in the post-harvest season, these fruit flies carry some of us to the orchard. We contribute to the decay of fruit, and any fallen fruit left to rot on the ground host more of us than on the mature fruit.” “Some of us are still active within the cider and, as you ingest it, within your digestive tract. A diverse population of us are found in ‘wild-type’ ciders, as well as bacteria. Once ingested, and in the gut, those of us present in cider face immense competition from these bacteria. The molecular mechanisms that we use to establish ourselves in your digestive system give us the appearance of a harmless commensal. This is done through the interplay between our cell walls and your own immune response. Some of our Saccharomcyes kin survive alongside some bacteria, and may enrich their populations.”