Keller was born in Saint Petersburg in the Russian Empire, but grew up in Volsk and Saratov where his father was a physician.
He graduated from the Saratov Gymnasium in 1892 with a gold medal and joined Moscow University to study medicine.
For his role in student politics, he was expelled in December 1894 and was arrested in 1896 but released for want of evidence.
He moved to the Petrovsky district and worked as a private tutor, and later as a clerk in a book store.
He headed the Academy's soil institute [ru] from 1935 and worked at the Moscow botanical gardens from 1937 until his death.