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It won't be a huge deal but I prefer to keep them separately for maximum production. Set up a new sterile culture and simply start picking the isopods out. Keep running both cultures and as the babies start to grow, they will be easier to pick out. Eventually you'll end up with a culture of giant oranges and a culture of springtails!
 

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There is going to be some competition but if you have a decent supply of isopods and not too many springtails, they don't usually get out of control. The isopods may even starve out the springs eventually. I usually wait maybe a month after seeing the first babies and then moving the adults out. The babies grow faster without the competition and the adults will breed faster without the little rugrats crawling all over the place.
 
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