Java fern just has ugly roots, really. They always look brown and dead.
I thought some diagrams might help (really, I was just bored and wanted to draw something).
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You can bury them in the substrate, you just need to bury them like this:
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And NOT like this:
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Most people just prefer to tie them to rocks/driftwood because it makes it a bit easier to keep them anchored, but in my experience, they do grow a bit better when they have their roots in the substrate.
