Dear Ann,

Thank you for reaching out to the UVM Extension Master Gardener Program with your question.

It looks like you had some beautiful ripe tomatoes. There are a variety of problems that can cause black spots on tomatoes. You did not mention any problem with the foliage of the plants. I think the sunken black areas on the stem end are post harvest fruit rot. This can be caused by a variety of fungi or bacteria. The pattern suggests entry into the fruit through cracks at the stem end. Cracks are common on tomatoes especially some of the larger varieties. Cracking can be caused by excessive nitrogen or uneven moisture. Unfortunately the cracks can act as a point of entry for fungi and/or bacteria that can cause fruit rot. It is difficult to determine the extent of the fruit involvement in the photos. For fruits that have extensive areas of rot it is probably better to compost them. For fruits that have more isolated areas of rot you could try to cut off the involved area with an inch of surrounding tissue. If the remaining tissue looks uninvolved you should be able to eat the remaining fruit.

Practices that will help minimize the risk for post harvest fruit rot include harvesting the tomatoes before they reach peak ripeness on the vine, avoiding harvesting when the plants and fruits are wet, only harvesting fruit that appears free of decay. Tomatoes should be dry when stored and positioned to allow air circulation between the fruits. In the photo the fruits are in a bowl with some stacking of the fruit. Placing a single layer of fruit in a vessel such as a wire basket would allow better air circulation. Alternately you can place the tomatoes on an open surface ensuring that there is no skin contact between the fruits. They should be stored at room temperature. Microorganisms will be present on harvested fruit. Any damage to the skin will allow the organisms to enter the fruit and cause rot. The stem scar that is left after removing the stem is another common point of entry for microorganisms that can cause fruit rot. It takes time for the rot to develop so use your tomatoes promptly after harvesting. Prioritize use of fruit that has cracking, no intact stem or any other skin damage first. If you are unable to use them quickly you might consider using one of a variety of methods to preserve them for future use.

https://nchfp.uga.edu/#gsc.tab=0

https://extension.umn.edu/plant-diseases/insects-and-diseases-tomatoes

https://edis.ifas.ufl.edu/publication/HS131

https://extension.umd.edu/resource/key-common-problems-tomatoes/

https://hgic.clemson.edu/factsheet/tomato-diseases-disorders/

https://extension.umn.edu/preserving-and-preparing/are-molds-foods-dangerous