Organism
Monilinia fructigena
The brown rot of apples and pears, recognisable by concentric rings of buff pustules, and a major cause of fruit loss between the orchard and the mill.
Also called brown rot.
- Kind
- Mould
- Binomial
- Monilinia fructigena
- Role
- Spoilage
What it does
- Infects through wounds and through insect and bird damage, then rots the fruit from the point of entry outwards, producing a firm brown lesion rather than the watery softening of blue mould.
- Sporulates in concentric rings of buff-coloured pustules on the fruit surface, a pattern distinctive enough to identify the disease by eye at the sorting table.
- Spreads by direct contact between touching fruit, so it moves through a bin or a store rapidly once established.
- Overwinters in mummified fruit left on the tree and on the orchard floor, which makes mummy removal a direct and effective control.
- Contributes musty and earthy volatiles to juice pressed from affected fruit.
Conditions it works in
What the organism tolerates and what suppresses it. These are the levers a maker actually has: temperature, acidity, air, alcohol and sulphite.
| Condition | What is recorded |
|---|---|
| Temperature | Grows across roughly 5 °C to 30 °C, with rapid development in warm, humid conditions. |
| pH | Tolerates fruit acidity. |
| Oxygen | Aerobic; an orchard and store organism. |
What it produces
Compounds this organism makes. Which organism made a compound usually decides whether it reads as a feature or as a symptom.
Pectin lyase
The chain-cutting activity in a commercial pectinase preparation, which raises press yield and clears a juice by destroying the colloid pectin creates — and destroys the possibility of keeving in the same stroke.
Polyphenol oxidase
The copper enzyme that turns cut apple brown within seconds, and the reason a cidermaker has to decide, at the press, whether to let the juice oxidise or to stop it.
Faults it causes
Faults this organism is implicated in. Several are faults only against a particular expectation — the same activity is a signature elsewhere.
Mould taint
Musty, earthy, cellar-damp or rotten-fruit character carried in from mouldy fruit or from mouldy equipment, and a marker that the patulin question needs asking.
Excessive sediment
More deposit in the bottle or vessel than the presentation intends, ranging from a normal conditioning yeast layer to a loose sludge that clouds every pour.
Microbial haze
Cloudiness caused by a growing population of spoilage organisms, and therefore a symptom of something worse rather than a clarity problem in itself.
Gushing
Cider that erupts from the bottle on opening, either because it is over-pressurised or because something in it is nucleating the dissolved gas violently.
Patulin contamination
Contamination of juice or cider with patulin, a mycotoxin produced by *Penicillium expansum* in rotting apples — a genuine food-safety question rather than a flavour one.
Where in the process it appears
Pest and disease management
Keeping scab, canker, rots and the main insect pests to a level the orchard can carry, at a cosmetic standard well below dessert fruit but without allowing rot into the crop.
Fruit sorting
Taking rotten, mouldy and damaged fruit and foreign material out of the crop before it reaches the mill, which is the primary control on patulin in cider.
Fruit storage before milling
Holding a gathered crop between harvest and the mill, and managing what respiration, water loss and spoilage do to it while it waits.
Pruning
The recurring cut made on a cropping tree to keep light in the canopy, renew fruiting wood, hold the balance between growth and fruit, and take out disease and deadwood.
Orchard floor management
What is grown, mown, grazed or suppressed beneath and between the trees, which affects tree vigour, juice nitrogen, harvest logistics and the biological interest of the ground.
Windfall management
Deciding which fruit that has reached the orchard floor can be used, and getting the rest out of the crop before it becomes a patulin problem.
Patulin control
Managing the mycotoxin produced by rot fungi in damaged apples, which is controlled by fruit selection rather than by any treatment applied to juice.
Sweating the fruit
Deliberately heaping or storing gathered fruit so that it softens, loses water and finishes converting starch before it goes to the mill.
Hand harvesting
Taking fruit off the tree by hand into bags and bins, so that it arrives at the store undamaged and with its stalk intact.
Shaking and collecting
Bringing fruit down with a pole or letting it fall, then gathering it from the orchard floor — the traditional way most cider and perry fruit has always been harvested.
About Monilinia fructigena
Brown rot is the disease that turns an apple into a hard, brown, ringed mummy still hanging on the tree in December. Monilinia fructigena is the species principally responsible on pome fruit in Europe, and it is one of the more visible causes of loss between blossom and mill — visible because affected fruit is unmistakable, and because it does not fall cleanly with the rest of the crop.
Its epidemiology gives orchard management a direct lever. The fungus overwinters in mummified fruit and in infected spurs, so removing mummies from the tree and the orchard floor removes the inoculum for next season. Since infection needs a wound, controlling the insects and birds that puncture fruit reduces entry points, as does careful handling at harvest.
For a cider maker the point is at the sorting table. Brown-rotted fruit contributes musty volatiles and a mass of fungal material to the press, and while it is not a patulin producer on the scale of Penicillium expansum, it is not fruit that should be pressed. The rings of buff pustules make it one of the easier rots to reject by eye.
What people ask next
Questions readers ask about the things this page mentions. Each one goes to the section that answers it rather than to a page written to receive the question.
- How should a cider tree be pruned
- Why is there sediment in the bottom of my cider bottle — In a bottle-conditioned cider the sediment is yeast and is expected — pour carefully and leave the last centimetre. In a filtered cider it means something has grown since bottling.
- Can you use windfall apples for cider — Traditional cider making relies on fruit gathered from the ground, and there is nothing wrong with it if it is sound. Rotten fruit is a different matter: brown rot carries patulin into the juice and should be discarded, not pressed.
- How long can apples be kept before pressing
- Do you need to sort apples before pressing
- What is mould taint in cider
Where to go next
- All organisms — Grouped by what each does in the ferment, and by what kind of organism it is.
- Compounds — The chemistry this microbiology produces.
- Troubleshooting — Work from the symptom in the glass back to the organism.
Sources
What this page rests on. Where a source is marked as registered rather than read, CiderHQ is recording that the body is authoritative on the subject without claiming to have worked through the document itself. See our evidence policy for what each state means.
NIAB (incorporating East Malling Research)
NIAB · research institute · retrieved 2026-08-24
East Malling developed the M-series apple rootstocks that determine tree size in essentially every modern orchard, cider orchards included. The authority CiderHQ uses for rootstock behaviour.
Peer-reviewed literature on cider fermentation microbiology
Various journals · peer-reviewed literature · registered as competent for this subject
Covers the microbial succession of spontaneous cider fermentation, the role of non-Saccharomyces yeasts in the early stages, malolactic conversion by Oenococcus and Lactobacillus species, and the organisms behind the principal spoilage faults.