We may add viruses in the feature, but I think at this scale they'd mostly appear as clouds. I'll find you some good concept images to work off of.
These have a sort of spherical/rounded cube/rounded rectangular prism shape to them, but from top view they should mostly appear as rounded squares or ovals. They are typically more rounded than square, but when in chains the squishing causes them to take a more squared shape. Compare this:
And I'm pretty sure we're having cyanobacteria only appear as chains, so go for a shape based off that. Would you be able to make the cyanobacteria cells partially transparent, and then have darker green circles inside of them (As is visible in the pictures I posted)?
Bacillus Shaped Bacteria
Another common shape for bacteria is the bacillus. This one is more like the typical bacterial cell we imagine when we think bacteria. These ones look like pills; they're small rounded cylindrically shaped cells. There's two kinds you could make models for here. A simple kind, like this:
And then another kind with attached and animated flagella and cilia.
Coccus Shaped Bacteria
The last kind is pretty simple, they'd just be coccus shaped except not in chains like the cyanobacteria.