Why has the base of my plant's stem gone black and soft?

The signature symptom is a plant wilting in wet soil. Everything above is dying of thirst while standing in water, because the pipework at the bottom of the stem has been destroyed. It looks like a disease and it is usually the result of an arrangement — a few centimetres of soil, mulch or water in the wrong place.

Step by step

1. Scrape the soil away and look at the collar.The collar is the point where stem meets root, and it should sit at or very slightly above the finished soil level. Clear the soil and mulch back a hand's width and look. Soft, dark, sunken bark at that point, sometimes smelling sour, is basal rot.
2. Check how deep it was planted.A plant set with its collar below soil level has bark permanently in damp ground, and bark is not adapted to that. This is the single commonest cause and it applies to shrubs, trees, tomatoes, brassicas and clematis alike — though clematis is deliberately planted deep for a different reason.
3. Look for a mulch volcano.Mulch heaped up the stem, common around newly planted trees, holds moisture directly against the bark and kills the plant slowly. Mulch should be a doughnut with a clear ring of bare soil round the stem, not a cone.
4. Look at where water goes.If the soil surface dishes inwards toward the plant, rain collects in a saucer around the stem after every downpour. It should slope gently away. A downpipe, a path fall or a gutter drip aimed at the base does the same thing.
5. Look for a wound.Strimmer and mower damage around the base of a tree or shrub is extremely common and often unnoticed, because it is under the grass line. Any wound is an entry point, and repeated damage girdles the plant on its own.
6. Identify which organism is exploiting it, if you need to.Water moulds such as phytophthora in wet ground produce a dark, wet rot with a distinct margin, often with a reddish-brown stain in the tissue just under the bark. Sclerotinia produces dense white cottony growth with hard black grains embedded in it, and is common on beans, lettuce, dahlias and sunflowers. Simple wound infection produces a rot around the injury. The practical response is the same for all three.
7. Test whether it has gone all the way round.Feel and scratch the whole circumference at the base. If firm, living tissue remains on one side, the plant has a route for water and food and may survive. If it is soft right round, the plant is girdled and everything above it will die however green it looks today.
8. Act on the answer honestly.Girdled: remove the plant, bag it, and do not replant the same family there. Partially affected: clear the soil and mulch back to expose the collar to air, improve drainage, stop watering near the stem, and see whether it holds. There is no treatment that repairs rotted tissue.
9. Correct the site before anything new goes in.Raise the planting position, break up compaction, improve drainage or build a raised bed, and plant at the correct depth with the collar visible. A replacement planted the same way will do the same thing.
10. Treat seedling collapse as a separate problem.Seedlings that keel over at soil level with a pinched, thread-like stem are damping off, a different set of organisms with a different response — clean trays, fresh compost, less water, more air.

Tips

• On a newly planted tree, you should be able to see the flare where the trunk widens into the roots. If the trunk goes into the ground like a telegraph pole, it is too deep.
• Keep grass and planting away from the base of a young tree with a mulched circle. It removes competition and it removes the strimmer.
• Tomatoes and brassicas can be planted deeper than they grew, because they root from the buried stem. Most woody plants cannot.
• Basal rot in pots is nearly always a saucer left full of water, or a drainage hole blocked against a hard surface.

Common mistakes

• Piling mulch against the stem to protect it — It is the mechanism of the damage. Mulch conserves water, and water held against bark rots it.
• Watering directly at the base of a plant with a rotting collar — Water at the drip line instead. Concentrating water at the stem is what caused it.
• Cutting the rot out and hoping — Unlike a canker on a branch, there is nowhere to cut back to at the collar. Removing tissue there removes the plant's only connection to its roots.
• Replanting the same thing in the same hole — The cause was the site, the depth or the drainage. All three are still there.

Questions people ask