Science

The microbiology of cider

A spontaneous cider fermentation is a succession, not an organism. What arrives from the press is a mixed population, and what finishes the job is rarely what started it.

CiderHQ holds 39 organism records. Each says what the organism does, the temperature, pH, oxygen, alcohol and sulphite conditions it works within, the compounds it produces and the faults it is responsible for.

Two limits are worth stating before you read any of them. Species-level behaviour is reasonably well described in the literature; strain-level behaviour within a species varies enormously and is not asserted here. And the claim that a named wild population is characteristic of a named orchard or valley is made far more often than it is demonstrated — house populations in a working cidery are real and well evidenced, a regional yeast signature is a much stronger claim, and these records decline to make it.

Population curves for the three groups of organisms that take turns during a cider fermentation.

Described in full

Axes: Days after pressing run left to right, from nought to thirty. Population on a logarithmic scale runs up the vertical axis. Each group is drawn with its own dash pattern and named in the key below the chart.
Apiculate yeasts: Rise fastest, peaking around day three at a level below the Saccharomyces peak, then collapse. They are killed by the alcohol the next group makes, which is why their curve falls while the ferment is still vigorous.
*Saccharomyces*: Starts as a small fraction of the population and becomes almost the entire population by the end of the first week. Holds a plateau through the main ferment and declines slowly as sugar runs out and it settles to the lees.
Lactic acid bacteria: Flat and low for the first two weeks, then rising. They need the sugar gone and the yeast quiescent before they establish, which is why malolactic fermentation is a late event or a spring one.
What the crossings mean: The point where the apiculate and Saccharomyces curves cross is the handover. Before it, aroma is being set by wild yeasts; after it, by the fermenting strain.
Why sulphite changes the picture: Sulphiting the juice suppresses the apiculate peak almost entirely and lets an inoculated Saccharomyces start from a high population. The same chart for a sulphited, inoculated ferment has one curve, not three.
The vertical scale: Logarithmic, because the populations differ by orders of magnitude rather than by percentages. A group at one hundredth of the peak is still millions of cells per millilitre.

By what it does

An organism appears under every role it holds, because most of them hold more than one and choosing between them would be inventing a distinction.

Primary fermentation (13)

Takes the sugar down. Only a few organisms can finish the job, and in practice one of them finishes almost every cider.

Secondary fermentation (6)

Works after the main ferment — refermenting in bottle or tank, or fermenting the sugars the first organism left.

Malolactic conversion (6)

Converts malic acid to lactic acid, lowering acidity and, along the way, producing the butter note of diacetyl.

Spoilage (26)

Produces something unwanted. Whether an organism belongs here depends on the style as much as the species: the same activity is a signature in one cider and a fault in another.

Surface film (6)

Grows as a film where liquid meets air, which is why headspace and topping-up discipline are the whole defence against them.

Present throughout (8)

Found in the fruit, the mill, the press cloths and the vessel as a matter of course, rather than arriving on a particular occasion.

By kind of organism

The same records sorted taxonomically, for the reader working through the microbiology rather than chasing a symptom.

Yeasts (19)

Single-celled fungi. Between them they turn the sugar into alcohol, make most of the aroma, and produce several of the notes a competition sheet would mark down.

Bacteria (13)

Lactic acid bacteria soften a cider by converting malic acid to lactic; acetic acid bacteria turn it into vinegar. The same group contains the most useful and the most destructive organisms in the cellar.

Moulds (7)

Filamentous fungi that mostly do their work before the fruit reaches the mill. They matter for what they leave behind in the juice rather than for what they do in it.

Every organism

All organism records on CiderHQ, alphabetically.

Binomials are given as the record holds them. Older writing uses superseded names for several of these organisms, and where that is so the alias is recorded on the page rather than given a page of its own.
Organism	Kind	Role
Acetobacter aceti	Bacteria	Spoilage, Present throughout
Acetobacter pasteurianus	Bacteria	Spoilage, Surface film, Present throughout
Aspergillus species	Moulds	Spoilage
Bacillus species	Bacteria	Spoilage, Present throughout
Botrytis cinerea	Moulds	Spoilage
Brettanomyces anomalus	Yeasts	Secondary fermentation, Spoilage
Candida species	Yeasts	Primary fermentation, Surface film, Spoilage, Present throughout
Clostridium species	Bacteria	Spoilage
Dekkera bruxellensis	Yeasts	Secondary fermentation, Spoilage
Film yeasts	Yeasts	Surface film, Spoilage
Gluconobacter oxydans	Bacteria	Spoilage, Present throughout
Hanseniaspora osmophila	Yeasts	Primary fermentation
Hanseniaspora uvarum	Yeasts	Primary fermentation
Hanseniaspora valbyensis	Yeasts	Primary fermentation
Kloeckera apiculata	Yeasts	Primary fermentation
Komagataeibacter species	Bacteria	Spoilage, Surface film
Lachancea thermotolerans	Yeasts	Primary fermentation
Lactiplantibacillus plantarum	Bacteria	Malolactic conversion, Spoilage
Lactobacillus brevis	Bacteria	Malolactic conversion, Spoilage
Lactobacillus collinoides	Bacteria	Malolactic conversion, Spoilage
Leuconostoc mesenteroides	Bacteria	Malolactic conversion, Spoilage
Metschnikowia pulcherrima	Yeasts	Primary fermentation
Monilinia fructigena	Moulds	Spoilage
Neonectria ditissima	Moulds	Present throughout
Oenococcus oeni	Bacteria	Malolactic conversion
Pediococcus species	Bacteria	Malolactic conversion, Spoilage
Penicillium expansum	Moulds	Spoilage
Phytophthora species	Moulds	Spoilage
Pichia membranifaciens	Yeasts	Surface film, Spoilage
Saccharomyces bayanus	Yeasts	Primary fermentation, Secondary fermentation
Saccharomyces cerevisiae	Yeasts	Primary fermentation, Secondary fermentation, Present throughout
Saccharomyces uvarum	Yeasts	Primary fermentation
Saccharomycodes ludwigii	Yeasts	Spoilage, Secondary fermentation
Schizosaccharomyces pombe	Yeasts	Primary fermentation, Spoilage
Torulaspora delbrueckii	Yeasts	Primary fermentation
Venturia inaequalis	Moulds	Present throughout
Wickerhamomyces anomalus	Yeasts	Primary fermentation, Surface film, Spoilage
Zygosaccharomyces bailii	Yeasts	Spoilage, Secondary fermentation
Zymomonas mobilis	Bacteria	Spoilage

Spoilage is a judgement, not a species

Several organisms filed under spoilage here are the defining organisms of a traditional style somewhere. Brettanomyces makes the same volatile phenols whether a drinker calls the result farmhouse character or a fault, and CiderHQ records the mechanism rather than the verdict.

Compounds — what these organisms actually make.
Troubleshooting — the faults, from the symptom rather than from the organism.
Sensory — how to tell one organism’s work from another’s in the glass.