I am glad I found this topic tonight for I have been wondering about plants and our chickens come spring for we plan on doing some raise beds. But this has have me some new idea for their new run I am building them. Right now it's completely bare and my question is what about their digging up the plants or should I put rocks or something around the bottom of the plants??
(Note: I am in the northern hemisphere, so the primary sun comes from the south in my garden, shade is created on the north side of objects during the hottest hours of the day)
I have a lot of small fruit shrubs (blueberry, gooseberry, Saskatoonberry etc) they are planted along the north side of a raised bed and thus naturally create cool and shade during the hot days. The hens (and ducks) have decided to make sleeping spots under the shrubs along the fence and they do dig a little. The digging stops weeds from growing, but has never damaged the trees.
If I were planting in your garden (new trees that have not yet established deep roots) I would dig deeper than normal, make a wider than usual ring of fresh dirt, and bury them deeper than normal. The goal being that the roots spread quickly outward and downward.
But,at least my girls, in my soil, don't dig very deep. The "dust bath" is at most the "thickness" of a very spread out little hen. My bantams dig down about 5", in order to swirl around in the heaven that is a bath.
This little hole they make then gathers water when it rains, the hole absorbs water easily and creates a benefit to the trees of an aerated soil.
The trees they favor tend to do better than those they don't like.
(All that to say) I don't put rocks at the foot of trees, but I will throw lots of fresh straw with poo in it at the foot of shrubs and smaller trees in the fall (just before snow) in order to protect from freezing.
Since the hens carry out lots of bits of straw and pine shavings into the run, the level of soil there tends to rise, so that adds a thickness to the soil. (Eventually)
They downside? Last year I had a mouse eat the bark off a tree where I had lots of straw, so I think I made a great winter home for this mouse. It was my error, normally (even pre-chickens) I would put little metal mouse trap boxes at the foot of fruit trees in the winter. Otherwise they kill those trees.
(Apologies to mouse lovers, I live in the woods, they are many here, in no danger of any suffering. I even protect them from many predators by not allowing many predator birds to come in the area while protecting my chickens, and not allowing feral cats hunting here)