I think this is a good question that needs some contemplation ...
Spirit is something ethereal (without material substance) and therefore, can't scientifically be measured by any known instrument.
Spirit is a connecting force between all of life. There's no hard proof that spirit can or might -even- affect the inanimate (non living) stuff like rocks or earth or water ... but it might.
Do atheists -(at least some of them)- RECOGNIZE that there is "something" which connects humans to each other ... animals to each other ... or even, humans with animals?
I think so ... or atheists would have no desire to communicate with other life-forms!~ (After all, rocks are perfectly content to just lay in the same place for millions of years without connecting with other rocks.)