The biggest threat to nursery trees is deer browsing. In the winter when most food sources are gone, Deer enjoy browsing young tree bark to get at the cambium layer where sugars are transported. Even small amounts of damage to a sapling’s bark may be too much for a young tree. Deer will jump over a six foot tall fence, so keeping them out of an area is very difficult. At the nursery we use second hand wire fencing to create a cage around our larger beds. For individual trees, wrapping a tight cylinder of material around the trunk works well. We use fencing, hardware cloth, old window screens, and sometimes plastic pipe to protect our trees. We also plant some trees and shrubs that are specifically designed to attract and feed deer. These include the fast growing Red Osier Dogwood, a native species with vibrant purple bark, and Beech trees. Keeping trees and shrubs like this on the outskirts of your more valuable plants will do a good job at deterring any curious nibbles.
If you don't have any extra wire laying around, or don't want to buy new materials (we don't blame you) a free, zero-waste alternative is to use invasive rose and barberry. These thorny invasives, which you can learn about here, grow quickly and abundantly. To use these, cut two or three large branches and gently lay them around your tree of interest making sure to cover the entire height of your sapling. We've found this to be an extremely effective deterrent, and once winter is over you can burn the branches for biochar, or simply chop it up and leave it as mulch around your tree.