Hi there,
I work in a multidisciplinary project, so I ll say what I 've noticed (maybe not representative).... so, it came to my attention that one study on infectious disease costed so much money (they were doing DNA sequencing).
However, microbiology is definitely not dead, especially when you work with other disciplines like environmental health/ building science investigations. It is actually cutting edge (qPCR and ELISA for fungi and bacteria, allergens, fatty acids, plasticizes, MVOCs).
Anyway, what is important now is to see what you CAN do with the money and the lab you have.