After M.Sc. Applied Microbiology, one can opt for Ph.D., jobs in biotechnology and pharma companies, can be an assistant professor, a scientist or can go for government jobs like agriculture officer etc.
After B.Sc. Biotechnology, one can go for M.Sc. in Biotechnology or any allied subject like Microbiology, Biochemistry etc., can opt for jobs in biotechnology and pharma companies, can be a scientist, can join government jobs, can do a Ph.D. and be a professor and so on.