Rust and Moss

So I was waiting for my wife to pick me up at work and, bored, I wandered over to look at a tree. Looked at all the moss and lichens and began to wonder: How many living organisms are on this tree! How does one count the number of moss? And how about stuff sharing the same root structure? Are they one or a bunch? Or just a living glob? Now surely any decent biologists could answer these questions—and of course are welcome to do so--but the deeper question of how we distinguish between closely connected things is a real one, not so easily answered.