Something growing in tank

Question
We have a 46 gallon aquarium.  We have serpe tetra's, neon, and anglefish.  WE had the pleco's(spelling)(algea eater), but they last a week then die.  The algea eaters are the only dying like that. We have several tanks and never had problems.  This tank has fake plants and the brown gravel that we bought in the pet store that is aquarium gravel.  The gravel starts getting this dark brown(almost black) spots growing on it, and within a week it has covered the entire bottom of the tank and has grown inside the filter.  I am at my wits end on what this is.  Algea killer will not touch this stuff.  I have to completely drain the tank, wash the gravel and it still comes back!!!!  ALl the levels are correct in the tank, i just can't figure out what this is growing in the tank!!  PLEASE HELP!!!  I don't want to have to drain my tank and get rid of it due to this problem!

Answer
Hi Jennifer
First thing, you don't ever want to completely break down your tank and clean everything, as tempting as it is sometimes.  That just kills off all the beneficial bacteria that's growing in the tank, which in turn will cause your tank to go through a mini or full cycle process again while the bacteria grows back.  It lives on the gravel/substrate, decorations, glass, filter, filter media.  If you do need to scrub any decorations or such, first try to do it in a bucket of the used tank water, and use a new toothbrush if needed.

Now, my first question, what exactly are your ammonia, nitrites, and nitrates reading?  Some test kits will show that a small amount of ammonia or nitrites is fine, but really there should be none.  Nitrates should be reading ideally under 20 ppm.  If anything other then these levels are showing, that could be what's killing off the plecos so quickly.  Another possibility, there may not be any food/algae for them(I'll get into the algae in the next paragraph).  Plecos are great algae cleaners, I let one of my tanks go with the algae for a few months, then I brought in my pleco from the pond.  He had it completely cleaned within 24 hours.  You usually need to substitute their diet with algae wafers, shrimp pellets, romaine lettuce, spinach leaves, zucchini, cucumbers, etc.  

Now for the algae....usually brown algae is called diatoms.  It's my understanding, plecos don't usually like this type, but oto cats love it.  Usually it starts out with little brown spots on the glass or gravel, then goes from there.  They're also pretty common when you first set up a tank.  They can be caused by high nitrates, silicates in the water-possibly from the gravel or your water source.  Here's a link, you'll need to copy/paste to your browser.  Describes it a little more detailed, and if it is this type, it tells how to get rid of it:
 http://freshaquarium.about.com/cs/maintenance1/p/algaebrown.htm

Now another type that it may be, is blue green algae.  It can be blue, green, brown, or black.  This type of algae isn't an algae, it's a cynobacteria, thus requires an antibiotic to help get rid of it, as well as a few other things like frequent water changes and hand removal.  This stuff is really slimy too.  Here's a link that describes that better as well.  I'd say you're dealing with one of these two, which are both treatable.

http://freshaquarium.about.com/cs/maintenance1/p/algaebluegreen.htm

That site used to have pictures on there of the different algaes, can't seem to find it though.  Hope that helps, and good luck.  If you have more questions, please ask.

Christy