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I have a healthy calamondin tree but am unsure how to prune it etc?

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Calamondin orange do not need regular pruning to remain productive. They are usually allowed to develop on their own.

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i understand it has a shallow root system, therefore prefers wider pots rather than deep pots?

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They do have shallow roots which should be protected. I have several Calamondins growing both in half-wine barrels [5], and 13" plastic pots[4]; The ones in half-wine barrels are more productive than the ones in plastic pots, so that seems to indicate that container size/shape matters.

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also, can anyone tell me why i have a lemon growing on it????

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There is a remote posssibility that the calamondin orange was grafted to a lemon rootsock or a result of cross pollination.

I have several lime trees that were cross pollinated and the fruits are big, thick skinned and less juicy.

BTW, citrus trees need regular watering and fertilizing. In California, the citrus trees are fertilized 3x[first 2 years] to 2x[3 years to maturity]between February and September.

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Amor est vitae essentia.
Love is the essence of life.