I rooted a few hardwood cuttings in pure vermiculite in a ~1 gal. pvc container. I can see the roots developed behind the transparent wall of the container. Now, I am thinking of transplanting them into individual containers. I can separate them in water without damaging the roots and likewise replace in a loose substrate. Do you think it is a good idea or should I wait till Autumn? I suspect that they will survive during the summer all in one container without any organic potting soil. I am based in the northern part of Turkey and our climate similar to that of Eugene/Oregon.

I'd vote for separating. They will need a humid environment after repotting until the roots re-establish a molecular connection with the new soil.

Alternatively, you could start watering with a compost tea, and introduce some organics into the current potting mix.