| It depends on how robust your culture system is. You are using those 2L jars with tops which are great. The air creates positive pressure in the container and that in theory should keep contam out. Make sure that each system has dedicated parts. For instance, all parts of your system associated with nanno gets used, even after cleaning, with nanno cultures...repeatedly. Make sure that your hands are clean so that nanno cells attached to your hands do not get put into or near the Iso cultures..that kind of thing. Basically really think about what you are doing and where your hands have been. In this case they could sit fairly close to each other.
Many hatcheries have carboys on shelves above each other, each shelve will have different spp on them. They use lids/caps and blow air in which creates positive pressure. There is no dipping into the cultures but pouring out. Hands are cleaned when switching from one spp to another. They rarely get algal cross contamination. | 
