Those atoms are covalently bonded, but one has one more lone pair than it usually would, based on Lewis structures. So they are, in essence, ions.
For example, HO- indicates that the O atom has 3 lone pairs and only one bond.
Oxygen has no charge with two bonds, nitrogen with 3 bonds, and carbon with 4 bonds.
Note that the number of bonds these atoms must have to have no charge is the group number of the Noble gases (Group 8A) minus that atom's group number.
For example, oxygen's group number is 6, so it will not have a charge if it has 8 - 6 bonds.
Remember that the O atom is still covalently bonded to the hydrogen.