There are a lot of excellent programs all around the country. Off the top
of my head, I would recommend Joe Suflita at the University of Oklahoma or
Jim Tiedje at Michigan State if you're interested in anaerobic degradation
of aromatics. Bollag at Penn State is also very good and they have a new
program in some sort of applied microbiology. If you want to work with
metal reduction, Derek Lovely at U. Mass is the man.
You might want to take a look at the literature (Environmental Science &
Technology, Applied and Environmental Microbiology) and see if anyone is
publishing on stuff that excites you.
Good luck,
Bill