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I would recommend spreading composted manure. This will add nitrogen and is relatively inexpensive, particularly if you compost it yourself.

Too much calcium (or too high a pH) can tie up all other nutrients, especially magnesium, potassium, boron, zinc and copper. To lower the calcium level in your soil, you'll basically have to lower its pH. The best way to do this is too add granular sulfur to the soil. About 1 pound of sulfur per fifty feet will lower the pH 1 point. This will need to be worked or tilled into the soil. Other things you can try to lower the pH levels in your soil include adding sphagnum peat or diluted vinegar.

If it is root rot related to drainage issues, you need to improve drainage. Often drainage issues are related to lack of drain holes in containers and clay or low spots if in the yard. If in a container, make sure the container has drainage holes and that those holes are open. In the ground, these articles will help you fix the possible issues:

https://www.gardeningknowhow.com/garden-how-to/soil-fertilizers/how-to-improve-clay-soil.htm

https://www.gardeningknowhow.com/garden-how-to/soil-fertilizers/yard-drainage-problems.htm

If the root rot is caused by a fungal issue, in most cases, treating the soil with a fungicide will correct the problem. There are a few forms of root rot fungus though that cannot be killed with a fungicide and the plant must be removed and destroyed.

These articles should help:
https://www.gardeningknowhow.com/garden-how-to/soil-fertilizers/improving-compacted-soil.htm
https://www.gardeningknowhow.com/garden-how-to/soil-fertilizers/how-to-improve-clay-soil.htm

What is growing in that area? You need to see if you can figure out what plant these roots might be coming from. You might also want to contact your local extension office (found under government in the phone book). They can better help you determine where the roots are coming from and how to deal with them.

No, it will not harm the plants or make them unsafe to eat.