Using Atomic Force Microscopy.

This great stuff is what Grad Students can do on the web:

Studying Bacteria with Atomic Force Microscopy (AFM)
Posted 17 April 2006 by André under André’s Research

AFM has been widely used in the life sciences since the application of optical lever detection by Hansma and co workers in the late ‘80s so it was no surprise that when I searched the literature I found a bunch of papers describing experiments on bacteria using AFM. In case you’re interested in doing something similar here’s an annotated bibliography with most of the papers I found [pdf]. As always, the list is incomplete—especially the section on bacterial adhesion since that’s not my primary interest right now even though it forms the bulk of the literature. Never the less, you’ll get a good survey of the field if you have a look at the papers in the list and dive into the web of citations...continues at link in more detail.