When you buy the trees and dirt to plant the trees, are you selling them the trees?  I assume so.  Then your cost of the trees you sell this customer would be COGS for the trees you sell.  If you are also have a line item for the dirt, then I think the dirt too could be considered COGS.  But you can only have a COGS for the dirt volume you actually sold them.  If you have dirt in inventory at $2 per cu ft and a tree took 3 cu ft and if you had a line item on the invoice of 3 cu ft of dirt at $3 per cu ft.  Then your Sales Revenue on this item would be $9 and the COGS would be $6.  However if you are not selling the dirt and it is an expense for the installation of the trees then it would be an expense of doing business.  The other items you mention unless they are sold with the trees are NOT COGS they are business expenses.

Also any COGS would only apply when you are SELLING the trees.  When you are doing you other services you mentioned (pruning or tree removal) you are not selling anything.  So you are providing a service.  In that case there is not Sales Revenue and not COGS, it is all Service Revenue and Business Expense.  You could categorize the expenses are Repair Expense, Equipment (Which you may need to depreciate to spread out the expense over several periods) or Supplies Expense etc.