Having a Biotechnology degree opens up many more doors, in various fields like industrial processes, management jobs while microbiology jobs are more research oriented. You also have an option of doing an MBA in Biotechnology, which a new and emerging field of work. The job market while not absolutely lucrative is growing with the Biotechnology sector on the increase in India. There are jobs in the agricultural, pharmaceuticals, medical and various other fields, making it a very flexible subject. Also, there are many independent Biotechnology start up companies that promise a good future. After a few years experience, the salary does increase, as does your market value. What I have found is that in most jobs the requirements is for either Biotechnology or Microbiology graduates, though the latter tends to go for Quality Control in various industries. When it comes to salary, the starting pay packages are usually in the same range, though managerial positions always pay more than research ones. It is important to mention that while PhDs are available without Fellowships, it would be most prudent to try and gain one, due to low funding in most Ph.D. programmes. In relation to this, it must be mentioned that there are many Fellowship programs, like the DBT-JRF and CSIR-NET that provide Fellowships to scholars in Biotechnology. This aspect is much more developed for Biotechnology than Microbiology. While concluding it must be mentioned that while regarding jobs both fields seem at par, for PhDs in India Biotechnology does seem to have an edge. However, it is up to you which field you would like to follow. Follow what you have the most interest in because that is inadvertently the field you will succeed at the most, no matter of the numbers and trends. You can do biotechnology related courses from:
University of Hyderabad-School of Life Sciences, University of Mumbai-Institute of Chemical Technology, National Dairy Research Institute
Rajiv Gandhi Center for Biotechnology
Lovely Professional University
Delhi Technological University-Department of Biotechnology, Indian Institute of Technology-Department of Biochemical Engineering & Biotechnology, Delhi University
Banaras Hindu University
Jawaharlal Nehru University
Aligarh Muslim University of Mumbai

Both the courses are good and have different values and scope. You should choose the course according to your passion and interest.

If we compare both the courses then B.Sc Biotechnology i s more diverse field compared to B.Sc microbiology. If we talk about the scope then B.Sc Biotechnology have more scope in terms of career and research and it is fastest growing field.

Good luck!!