"So, what layer 2 and layer 1 protocols it generally use ?"
Often it rides on top of Ethernet.
"Also, is is true that nowadays ATM is considered obsolete ?"
Yea, probably.
"If yes, what protocols or new technics make it obsolete ?"
Ethernet, and all the technologies that ride on it. Also the Internet. (Private WAN technologies might be replaced by VPN on top of the Internet.)
"And bonus question, same as MPLS previous question, what layer 1 protocol generally use ATM?"
You mean what L1 does ATM use? If so, I believe it's various telecom L1 protocols.