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Do you bleach the roots?

Are you supposed to submerse the whole plant in the bleach solution
including the roots or just the part above the root.  I put a whole java
fern in for the recommended time and all the small fine root hairs
dissolved leaving only limp brown roots.  The plant seems to be surviving
though and all the algae is gone. But does this harm the roots. What
about other plants like swords?  I have seen algae in  the area around
the crown of these plants.  Should I bleach this area.  And my anubias
are attached to driftwood so the entire root is exposed to algae spores. 
Thanks in advance.


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