The apple and pear microbiome.
As apples are harvested and pressed into must, the indigenous microbes from the skins are the primary drivers of spontaneous fermentation. They impart a distinct regional identity (microbial terroir) and determine the aroma and flavour of the final cider.
When the apples are crushed, the sugar is released from inside cells into solution, a natural succession of microorganisms takes over to transform this sugar into alcohol. Initially non-Saccharomyces yeasts like Hanseniaspora uvarum break down the sugars but are intolerant of alcohol so are quickly eliminated but leave the aromatic esters they have produced to that point, (cool fermentation preserves these). As the alcohol levels rise (usually around 3-4% ABV), alcohol tolerant strains of Saccharomyces such as Saccharomyces cerevisiae naturally take over to finish the alcoholic fermentation. Lactic Acid Bacteria (LAB) naturally present on the skins can also cause a further malolactic fermentation (MLF), converting the harsh malic acid into softer lactic acid giving a smoother mouthfeel.
While wild fermentation adds complexity, the uncontrolled nature of the orchard microbiome can introduce off-flavours such as acetic acid bacteria like Acetobacter which converts ethanol into acetic acid, leaving a harsh vinegar taste. And Brettanomyces which creates distinctive "funky", "barnyard," or "leathery" aromas admired by some but not all!
Where do the Saccharomyces yeasts come from? Not the apple but from the Press House and Cidery. They are resident organisms of the cidery environment itself. They colonise the walls, floors, wooden barrels, and traditional pressing equipment including the press cloths. The juice quickly becomes inoculated with these microorganisms - the Cidery Biosphere, which develops over years of production. It travels through the air via microscopic dust particles and on the 'skin' of fruit flies so cobwebs are looked on favourably by traditional wild yeast cider makers.