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There are all kinds of bugs that go after roots especially trying to grow trees in pots and even more if your trying to start something is indoors. It's like the natural predators and bio are out of whack and the bad can get multiplied quick if the manipulated environment hits right. Had those stupid little gnats go crazy on some nuts I was starting indoors a couple years ago, have had same but not as bad in pots outside. A little to much or not enough water sets that stuff off sometimes too.
I dont believe they were nematodes. I believe nematodes are impossible to see without magnification. I dont believe nematodes that affect apple tree roots are found at concentrations high enough in soil that has not previously had apple trees in it to cause that quick of a die off. Likely the overly wet dirt was the cause of your root stock demise.
I assumed you meant apple or pear root stock cuttings? Maybe you were referring to some other type of cuttings? I have never seen apple or pear root stock grow roots in a bucket of water. If you did then I would patent the process immediately!!
You said root stock cuttings in the 1st post. That is where the confusion lies I believe. Apple and pear root stock already has roots when you receive it. A cutting would not have roots. Cuttings from root stocks are not propagated by placing them in water.