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How does one vacuum

The owner of my LFS has told me to vacuum while siphoning for my water
changes.  I am used to doing this with fish tanks.  I am not sure how to
do this with a planted tank.

My tank has no open areas.  Every square inch of the bottom has pants
&/or roots.  When I attempt to siphon the top level of the gravel I
start pulling up plants.

Is vacuuming really required?  Is there an easy way without stressing
the entire system?

Gerry Beathard