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I have heard this mentioned many times that at the base of a tree or plant you need to leave the surface uncovered so that air can get into the soil. How true is this?

The idea is that if you are laying down decorative pebbles or a thick ground cover you need to leave a reasonable space around the base of the tree.

I was looking at the picture below in this question and thought about telling the person, but I'm not sure that what I understand is fact or just something many people assume is true.

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I believe this is more true with trees. The idea is you do not want mulch piled up against the trunk of the tree. If mulch is covering tree bark, the bark will stay moist and provide good conditions for fungi and bacteria which could cause disease in the tree. Also, the nitrogen in the rain that is responsible for "composting" the mulch, could also compost the tree bark as if it were mulch. You could actually compost an entire, small live tree if you pile enough compostable material on top of it and add nitrogen. All that is necessary is the right conditions of moisture, fuel (carbon), and nitrogen.

So to prevent things like this from happening, its standard practice to rake-back the mulch a number of inches from the trunks of trees. With pebbles, plastic, or rubber mulches, composting may not be an issue, but moisure and fungal growth would be.

Some plants, like tomatoes, you can pile dirt around the stems to initiate new roots to grow from the stems. Most trees won't behave this way and what you'd actually accomplish is to bury to roots under more soil and could harm the tree. But even with tomatoes, if you pile mulch too thickly around the stems, you still may compost (maybe digest is a better word... or rot) the stem. The green tomato stem is a good source of nitrogen. Lay a pile of wet dead leaves against it and there is a possibility of composting. So, its particularly important to keep dead, carbon material away from the living parts of plants.

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Hmm, well I've never heard that one before, keeping the ground clear so air can get into it. That is not the reason clear space should be left round some plants. There is a reason you keep clear space, particularly around some trees when they are first planted, which is to reduce competition for water and nutrients in the immediate area, until the tree has settled in and put out larger roots and is therefore capable of finding its own sources of both. This is not really an issue with smaller plants, such as new shrubs or perennials, though, but primarily with trees. Some trees (such as dwarf or small fruit trees) are grafted onto a dwarfing rootstock - this means the roots will never get huge, so keeping a space of about 3 feet clear all round the trunk is a good idea. That, though, does not mean you cannot put a mulch in that spot, in fact, if the ground is already damp, adding mulch to the top helps to retain moisture, and if the mulch is organic, will break down gradually over time and add humus to the soil above the roots, which is also a good thing. The important thing with mulch is that it should not be sitting against the main stem or trunk of a plant, so reducing the layer at that central point is important, or leaving an inch or three clear of mulch all round so that the level is not higher around the base of the stem.

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