Advice for the Home Gardener from the Help Desk of the
UC Master Gardener Program of Contra Costa County
UC does not have any recommendations for the home gardener to deal with this. It will likely not damage the tree, but the lemons can look pretty bad and will not keep well. The infection does not penetrate beyond the rind. As you've seen, the inside of the lemon is still good.
The best advice is to remove all the fruit once the weather has dried and to remove and dispose (i.e., green can) of any fallen leaves and fruit from around the tree. This is to remove as much of the fungal material as you can. The spores were probably on the ground and were splashed up into the tree when it rained. Add fresh mulch in that area which will help to cover up existing spores. Do this after the weather becomes dry (be sure to leave the trunk area clear of mulch by 4”). You can also thin out some of the canopy to let in more light and air, but don't prune while it is wet. Dispose of the tree pruning into the green can too. With the recommended effort hopefully, you can stop this pest and have lemons next year.
Please don't hesitate to contact us again if you have more questions.
Help Desk of the UC Master Gardener Program of Contra Costa County (SEH)
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Note: UC Master Gardeners Program of Contra Costa's Help Desk is available almost year-round to answer your gardening questions. Except for a few holidays (e.g., last 2 weeks December), we're open every week, Monday through Thursday for walk-ins from 9:00 am to Noon at 2380 Bisso Lane, Concord, CA 94520. We can also be reached via telephone: (925) 608-6683, email: firstname.lastname@example.org, or on the web at http://ccmg.ucanr.edu/Ask_Us/. MGCC Blogs can be found at http://ccmg.ucanr.edu/HortCoCo/ You can also subscribe to the Blog.