Getting into a PhD program with a low gpa but good profile I am going to apply to few PhD programs in Microbiology (I'm particularly very interested in Microbial ecology) but I'm afraid my undergrad gpa (8.5/10 for the first 6 semester as I'm currently in my 7th semester) might hold me back (however I have scored 9/10 in all core biology subjects). But I have a lot of other aspects to my application. For e.g. :

I have co-authored 3 research papers which are published in peer reviewed journal.
I have co authored 6 book chapters (4 in peer reviewed journals like springer, Elsevier etc)
I have presented 4 of my papers in 3 different international conferences (2 of them I was the first author)
I received funding from ISRO-ASI scholarship (Indian Space Research Organisation- Astronautical Society of India)  to attend one of the aforementioned conferences.
One of my team projects received a funding of 38,000 USD from our college trust.
I have conducted 3 months full time research internship in a research laboratory Tsinghua University.
I have also done 2 company trainings of 10 day each.
Plus few extra curricular activities like I was in tedx team, entrepreneurship cell etc. And as part time job I also taught few high school kids.
By the way I should mention my college is well reputed  (best in the state) in my country (India) but is tier-2

I need your help! I have no idea as to which colleges I should target ( my dream College would be University of Illinois (Urbana-Champaign) because of this particular professor Bruce W Fouke. He's amazing!) But I don't know if I would be accepted. I'm also not very rich so I can only afford the application fee for 10 colleges. I need your advice! Do you guys think I should apply to M.S. first get good grades and then try out for PhD. What kind of colleges I should target? (I actually concentrate more on the laboratory and not on the affiliated University but the University would be the one screening my application).
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.