yeah, do the water changes as much as possible. If the bacteria have already established in your filter, you should be fine.
Did this "service" add bacteria to the tank? If not, you're going to have to do water changes to get rid of all the waste. And if they did add bacteria, you won't lose it doing water changes because beneficial bacteria is not in the water column. Its attached to surfaces in the tank like filter media. So definitely do water changes.
If the sponge is really black you can throw it in the washing machine without detergent. The bacteria will be fine and the sponge will be a lot cleaner. Not sure what you mean by "base nutrients".
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