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Black spots are commonly seen with potassium deficiency.
The spots themselves will not get better, but the new growth will grow without black spots.

Black spots could also be any of several algae. Some dark algae are closer to brown or blue-green, but could look black or almost black.
 

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That looks more like an algae, not potassium deficiency.

Ditto windelov: Java fern grows tied to things, not planted in the substrate, though if the substrate is very open (gravel, coarse sand) it can do OK.

The leaves grow upward from a stem, and the roots grow downward from the same stem. This stem should not be planted below the substrate.
 
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