I never worked with anything else than Protozoa, but I would pour several
sterile dishes with the appropriate nutrient agar, make a diluted suspension
of cells with sterilized culture medium (wash cells several times?) and
plate them in the form of a "snailhouse" line. (Principle: Cells become more
and more diluted to the end of the line.) At the end of the line you should
have single cells growing on the agar that - hopefully - don't have any
bacteria with them.
I'm always sceptic about antibiotica usage since various fungi survive this
treatment. And if Cyanobacteria survice antibiotics - I'm not shure?