I don't know about any proven method. However, I can think about a method that I used to measure the microbial activity in the soil that I was using in potting trials. I was collecting subsamples of each of the pots and putting them into hermetic flasks. On the cap of the flasks I was putting a rubber seal, that was keeping it hermetic, but allowed us to inject a needle to take samples from the air of the flask. We analyzed with an IRGA the difference in CO2 content and consumption for each of the soils, that gives you an estimate of the microbial activity of it.
If you are able to kill all microorganisms except the algae that are of your interest, I think it could be a suitable method for you.
I attach the article where I describe the M+M of this microbial activity.