The roots growing from the java fern leaves are actually the baby plantlets (thats one of the ways they propagate). The main plant's own roots do grow out from the rhizome too (the LFS plant supplier usually just trim them off for neatness). The main plant's roots will naturally grasp around objects and dig into soil, but the rhizome itself cannot be buried, or else it may start to rot.
Marimo moss balls are actually a form of cladophora algae, but its a non-invasive algae variety so relatively okay to add to tanks. They grow super slowly... like only a few millimeters a year. So if you see particularly large ones, they have probably been around for a very long time.

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