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Yes, polyatomic ions are commonplace in nature, and play a key role in life processes. There are hundreds of common polyatomic ions in nature, but among the most familiar in addition to the ammonium ion are the phosphate and nitrate ions.

 

As to the how and why of nitrogen bonding with three or four hydrogen atoms, Wikipedia has a pretty good explanation.

 

http://en.wikipedia.org/wiki/Ammonium

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