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On of my tomato is rotten at the bottom. At the same time I observe that the connection between the plant and fruit is broken. Not sure what happened first though. Is this just a physical damage that caused rotting? Am I missing calcium?

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That doesn't look like calcium deficiency. I think your fruit is simply dying from being cut from the plant. It must've been knocked or jostled, but not enough to knock it loose. The connected fruit looks healthy, as do the leaves. You can pick it off if you want, it doesn't matter.

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