Any coating that oxidizes black, or any dark earth tone, is possible. Manganese oxides are common as nugget coatings and are found in SW Oregon. Silver that has leached to the surface of gold nuggets over time can oxidize black before eroding off. This can be found in areas where silver percentage in native gold is relatively high. Copper, also found in native gold nuggets, will act in much the same manner as silver, but will oxidize in green, blue, and red earth tone shades, depending on local conditions.
I am certain there are other completely natural conditions that can cause a dark layer, of varying thickness, on gold nuggets, but my notes are in the attic, I think.
Time for more coffee.