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With my rooted plants, I usually poke around the area, stirring things up and gently touching the vacuum to plant/substrate. I've never had a plant sucked up by doing this. When I'm having a diatom outbreak in a new tank, I've even vacuumed the plants themselves. As long as the input can't get completely covered by a plant's leaf, there shouldn't be a problem (an entirely covered siphon creates enough suction to lift a sizable piece of slate, I have found)
With my java ferns and java moss, I generally avoid the area (they're on driftwood) and let the bottom feeders/shrimp deal with that mess.
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