Getting into a PhD program with a low gpa but good profile
Given your other accomplishments I don't think the GPA will be disqualifying, and normally I would say don't worry about it, but in your case it's more of an issue. Your accomplishments are exceptionally strong for a rising senior in microbiology and are out of line with your weaker GPA, which will raise the obvious red flag that either your CV or your application are fraudulent.
You should address this in your applications. Specifically detailing your role in your major accomplishments and when you did the work would be a good way to head off any concerns from an admissions committee. You should also try to have your letters of recommendation be as specific as possible about exactly what you have contributed to the respective publications, which is another good way of keeping admissions from worrying too much.
I would also discourage you from applying to MS programs - most in microbiology are unfunded now and applying to a program you cant afford is pointless.