What on my shower floor and how do I permanently remove it!

[johndaly24]

Good morning all I have a new home that the builder installed this river rock style tile on my shower floor. After a few months this black stuff started coming out so my wife used bathroom bleach products to remove it. It goes away fine and then a few weeks later it comes right back and in the same places. I have thought it was mold not sure why as shower is cleaned weekly. I have tried Concrobium Mold Control Spray, but that did nothing. We are at our wits ends. Hoping to get some guidance here. Thanks in advance