Biotechnology

Since you are asking this question to us to give our preference, first of all I will say that you must check the job availability in both the courses, then think of taking the course. But, for me, I will say that it will be better to take Industrial Microbiology, because you know day by day technology is developing and, thus there will be high requirement of researchers based on industrial microbiology, though both the fields are based on research studies and they generally give emphasis on that only. So, there is a need of microbiologists in almost every nation. I don't think it will harm you, if you pursue M.Sc. programme in Industrial Microbiology.

Both the fields are good and have importance (as inter-related).
Considering job prospects I would say biotechnology comes first to bioinformatics:
Biotechnology is related to laboratory(both dry and wet lab) works which include from sample extraction, preparation and further processes and the work includes (biochemistry, molecular biology, genetics, microbiology, immunology, etc.) whereas Bioinformatics is related to dry laboratory work where you use the biotechnology samples and analyse them using the software.
Both are inter related, and the process would be biotechnological work followed by bioinformatics and also many times certain samples directly used in bioinformatic analysis.