Alain Mercier has been replaced as head of OC Transpo. (CBC)

Alain Mercier is out as the head of OC Transpo in a major organizational shuffle announced Wednesday.

City manager Kent Kirkpatrick said John Manconi, Ottawa's public works general manager, will take over as the general manager of transit services.

Mercier was a lightning rod for criticism during his time as head of the transit services, drawing the ire of the unionized workers after a bitter 54-day strike in December 2008 and January 2009 and the later implementation of a new scheduling system for drivers.

Transit commission head Diane Deans said the decision to replace Mercier came from Kirkpatrick, but said she fully supported the move.

Amagamated Transit Union Local 279 president Garry Queale said he doesn't like to see anybody lose their job but said he saw the move as a positive sign.

"I think personally the membership is elated that he's gone," said Queale. "Any time I'm out with the membership his name seems to surface as... the bad apple in the bushel."

Also included in the reorganization:

• Transit services and the environmental services department will now report to deputy city manager Steve Kanellakos.
• The real estate partnerships and development office — including the Lansdowne Park and Arts Court redevelopments — report to deputy city manager Nancy Schepers.
• Both the economic development branch and the corporate communications department will now report to Kirkpatrick.