You may have to take it down and start over. Pretty much you let your wood dry out one year for every inch of wood. you could take the pieces to a lumber yard and have them kiln dried. You don't want you diners exposed to mold and fungi. The carpenter helping you should have said something.

Fungus? Like mold? If so, perhaps try bleach, or taking out the wood and using something else. Fungus/mold in a restaurant is definitely not a good thing.

You already posted the photo. Get rid of it all before the health department closes you down.

The wood has to reach what's called Equilibrium Moisture Content (EMC), which is different for various areas of the country/world. I don't know about end grain slabs, which is what you have, but the rule of thumb for lumber air drying (vs. kiln drying) is 1 year for each inch of thickness. Moisture leaves the end grain faster than the side and/or edge of the boards, so in your case the drying time will probably be shorter. If it is not dried in a controlled environment your slabs are going to split radially, due to drying too fast.