# Microbiology question--substrate turning black and spreading



## javalee (May 8, 2006)

Hello,

I've been so pleased with my 29g planted tank, however, some nasty bacteria/fungus/algae? that was in a previous tank that killed all my crypts has made it into this tank. It was growing as a fuzzy white mat over my gravel and low plants. It had a bluish cast to it. Very much looked like fungus. I kept vacuuming it out and it would come right back.

Here's the kicker: it turns everything beneath it anaerobic. In fact, the gravel it covers becomes stained black. The substrate below is anearobic and releasing smelly gas.

Here's another interesting point. I feed this tank a lot. One day I didn't feed at all, and all the snails, and oto catfish ate all the nasty stuff off the substrate. I watched them clean it all up in one day!

So what's the problem? It remains where the snails can't reach it, about one inch below the surface there is a blackish-blue tint to the gravel and tons of bubbles of that nasty smelling gas. Now my crypts in that area are melting. The stuff is spreading around the tank, and only one corner remains normal looking, with no blackish-blue tint to the substrate and gas.

What is this stuff? My guess is fungus, but it could be bacteria too, I guess. Now I know it's not algae if it's growing below the substrate on a side not exposed to sunlight. How can I get rid of it? It killed my 2.5 gallon tank. I took one healthy plant from that tank and soaked it in a H202 solution before adding it to this tank. Now the nasty anearobic stuff has spread out from the base of this very plant in the new tank. In the 2.5g tank, with no snails or otos to eat it, it coated the entire surface of the gravel and low lying plants in a whitish blue mat, and again, turned everything black beneath it.

HELP! I love this new tank and I think this gas may be harming my fish. They seem to be going downhill, slowed down and hanging at the bottom. I am running a powerhead. This is what the tank looks like now...









pH=8.3
GH=4d
Nitrate=5ppm

Thanks for reading my long post, and for any advice you can provide!
Javalee


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## mistergreen (Mar 3, 2007)

What's your substrate?

When it goes anarobic, lots of bad chemicals can kill you fish. It's probably the cause for the fungus. It could be yeast too..


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## deepdiver (May 30, 2006)

Blue-Green algae (cyanobacteria) ?????


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## Ownager2004 (Apr 18, 2006)

Sounds like bacteria to me. Most bacteria that produce the smelly gasses(like H2S) aren't that tolerant to oxygen. How deep is your substrate? If its possible I would give the gravel a good stir and add an airstone to your tank. That should help combat the problem.


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## Edward (May 25, 2004)

Water aeration will help.


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## ed seeley (Dec 1, 2006)

I had what sounds like a very similar problem with my nano tank. A piece of bogwood was the source, but the fungus/bacteria spread onto the substrate and turned it very smelly and black. It also killied a number of plants by attacking the bottom of stems, especially Rotala wallichi.

I had to remove the wood and then did a lot of water changes removing the black sand and any sign of fungus. I removed some of the plants and washed them in tap water. I had to do this a few times. My cardinal tetras seemed unaffected by it though, but they stayed well clear of it.

I would really up the water changes for a while and try to syphon off any sign of this when you do. I'd cut back on the feeding for a while too to try and ease the load on the tank.


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## dwalstad (Apr 14, 2006)

Javalee,

It sounds like your substrate is too rich and/or too deep and going anaerobic. 

If the gas truly smells (hydrogen sulfide), your fish are in danger.

I would do water changes, gravel cleaning, add an airstone, and poke the substrate (introduces oxygenated water). Don't worry so much about killing this stuff as counteracting the conditions that are causing it. The black stuff is probably bacteria and algae coated with precipitated iron sulfide, which is turning the goop black. It's annoying but probably just part of the substrate chaos I discussed in my book.

If this substrate is less than 6 months old, I'd try to keep it aerobic as much as possible until it settles down. Eventually, as the organic matter gets digested and starts to "age", the problem will go away. If the snails are eating it and not dying, that's a good sign! 

Diana


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## essabee (Oct 11, 2006)

Javalee you have given all details except what substrate you have used and how; and as your problem is substrate based it would help if you would post details.

Your problem is that your substrate has gone anaerobic and is populated with the entirely different organisms which thrive in anaerobic conditions producing chemicals by reduction most of which is not well tolerated (and some are toxic too) by aerobic organisms which include your plants and fishes.

For immediate relief you require to vacuum your substrate, aerate your water, and do some water changes. You may consider removing your fishes to temporary tubs and also removing your plants before giving a thorough vacuum of substrate, then replanting and putting your fishes back.

For long time relief you require to rectify the conditions which caused the anaerobic condition, and for that you need to post the details about your substrate if you seek help.


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## javalee (May 8, 2006)

Thank you everyone for your replies.

Ed Seeley, you seem to know just what I'm talking about! It isn't BGA. Look at the photo below. It is some kind of organism that grows above and creates the conditions below it, and it's like once it gets it there I can't get rid of it. I have vacuumed the organism and black stuff that accompanies it several times and it just comes back slowly but surely. 

I have had several natural planted tanks now over several years and understand that they can go anearobic if the depth is too thick or there isn't enough root penetration; however, believe me, this is not the issue in this tank. I should have posted the photo first to clarify that this is not a problem with my soil, but the soil is experience problems from an organism introduced to it by a plant from another tank with the same organism and problems---fuzzy whitish, bluish,gray growth above, and anearobic conditions below.

My substrate is potting soil, but is not involved in this problem as this organism (bacterial or fungal) created the same condtitions in my last tank with topsoil from my property.

I'll show you a photo of the carpeting it can do and how it makes everything beneath it look. It's entirely possible that a fungus or bacteria could do this, and I'm wondering if Diana could expound upon this. Note the fuzzy growth above the substrate, and the blackish coloring of the gravel below along the glass. Also, note the oto who came to eat it










The problem is that the constant water changes and vacuuming required to keep it away (about once per week or two weeks) are too many water changes for a natural planted tank and my plants end up with nutrient deficiencies. I did all the disinfecting I could do when I set up this tank because this stuff meant the end of my 2.5g. I should never have "disinfected' a plant from that tank and put it in this one. Shouldn't have taken the chance. I don't wanna lose this tank---I love it! Too bad the MTS won't dig any deeper than about an inch.

thanks and beware of this stuff!

Javalee


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## mistergreen (Mar 3, 2007)

Maybe the gravel layer is too thick.. I had the same problem. I took out half the gravel and added aeration.. It's looking tons better.


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## dwalstad (Apr 14, 2006)

thanks for photo. Very helpful. It looks like a fungus or filamentous bacteria (Actinomycetes). They're both strictly aerobic. Nothing too alarming.

How old is this substrate?


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## furballi (Feb 2, 2007)

500 mg of tetracycline added to each 10 gal of water in the tank will fix the problem. Repeat dosage for five consecutive days. You need to change 50% of the water everyday BEFORE you add another dose of tetracycline. Note that tetracycline will turn the water RED. The "cycle" bacteria will be MINIMALLY affected by this treatment (very safe). You'll probably see clumps of white milky slime developing in the tank after the 2nd day of treatment. Just siphon it out during the water change.

Continue to change 50% of the water everyday *after* the treatment. Note that the water will remain pink/red for at least one week, even with the water change. Tetracycline is harmless to fish, but I don't have any experience with shrimp.

Aquarium pharmaceutical sells tetracyline in a box of ten packages (available at many pet stores).


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## kimo (Apr 21, 2006)

From the photo is looks more like regular dark green algae... that is getting light because it is right next to the glass. Nothing to worry about.


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## javalee (May 8, 2006)

Diana,

Thanks for checking back with me. Sorry for the delay; lightening took out my modem and I was off for about a week! Anyway, the substrate is about 2 months old. I levelled it and measured throughout with a measuring stick and got a depth of 1.5" of soil and the same of gravel. Truly, this stuff came out of my other tank and it did the exact same thing:crypts began dying as the white fuzzy carpet spread, and everything below turned black and smelly.

Furballi, why do you suggest antibiotic treatment? I'm not sure I want to put my fish through that without knowing for certain what the organism is and that it is causing the problem.

Kimo, there's nothing "regular" about this stuff:-D , trust me. It's not dark green. It's white with a blue tinge and very fungus-like, cottony. It grows in a matt, like BGA, but cottony, not slimy.

To update all, I did vacuum the substrate, just the gravel part. A huge amount of gas was sucked up and the water that was in the bucket was inky black, utterly opaque, and not from soil because I didn't go that deep. It was the black gunk from the gravel and it SMELLED up my entire apartment. I had to open all the windows as I was worried it would kill my bird!

The fish looked noticeably better by the end of the day. But, as I mentioned in the previous posts, well, it's already turning black again . The water changes weren't great for the plants as I get nutrient deficiency signs shortly after each one because I have to do them. 

Not sure how to resolve this, but i guess I have to somehow balance the health of my fish and my plants. The fish will come first if it comes down to it.

Thanks for y'all's continued interest and suggestions.

Javalee


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## furballi (Feb 2, 2007)

The Tetracycline with NOT kill the fish, plants, or beneficial bacteria. My only concern is that it will kill whatever that's in your substrate, which will quickly foul up the water column if you don't change at least 50% of the water each day.

If you are super paranoid, then temporarily move the fish to a large bucket along with the filter. DO NOT feed the fish. Treat the tank for five days (include water changes) and return the fish to their old home.


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## Ownager2004 (Apr 18, 2006)

I think its clear that you have 2 different infections in your tank. 

One is causing the black precipitate(probably FeS), as I believe dwalstad mentioned is a classic sign of H2S production. The smell is also another giveaway. This is almost certainly an anaerobic bacteria. It has probably colonized the soil underneath of your gravel and will likely keep reinfecting the gravel. Im not to familiar with the 'el natural' tanks so I cant really suggest any good way to stop it without making a mess. Your going to have to aerate that soil somehow. Its hard to say how well the tetracycline will penetrate the soil as well or wether your particular organism will be sensitive.

That white fuzzy stuff... as dwalstad mentioned, is probably a fungus or actinomycete. I wouldn't worry about it. Clear it away manually as you see it and it will probably go away for good sooner than later.


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## essabee (Oct 11, 2006)

javalee said:


> SNIP
> To update all, I did vacuum the substrate, just the gravel part. A huge amount of gas was sucked up and the water that was in the bucket was inky black, utterly opaque, and not from soil because I didn't go that deep. It was the black gunk from the gravel and it SMELLED up my entire apartment. I had to open all the windows as I was worried it would kill my bird!
> 
> The fish looked noticeably better by the end of the day. But, as I mentioned in the previous posts, well, it's already turning black again . The water changes weren't great for the plants as I get nutrient deficiency signs shortly after each one because I have to do them.
> ...


I have posted once before in this thread, where I told you that although you need to vacuum your gravel it is not going to solve your problem and I asked you for your substrate details.

So you have 1.5" of soil. No details of the type.

Now the actual organism which is troubling you is in your soil. The gass (H2S, PH3, CH4, etc.) is being produced in the soil and escaping upwards carrying along with the flow caused by the escaping gasses, are several chemicals, both soluble and insoluble solids, this includes the black precipate you observe in your gravel just above the affected area. The fungus/algae/bacteria is feeding on these minerals, and is not the problem. Treating the aquarium with antibiotic is not going to be a great help unless the antibiotic penetrates 1.5-3" depth of the soil where your problem lies.

When I first started using soil in my aquarium some 20-25 years ago, this happened to me using rich soils, rich in organic not fully degraded substances, like raw manure. I did what you had once done before, throw away the substrate and start again. I have not ever successfully used any treatment which solved that problem.

I know what I would like to try in your aquarium, but I would do so only after removing your fishes to a safe temporary home. I would treat the affected area a margin beyond injecting hot concentrated caustic soda/potash (NaOH/KOH) solution. This would degrade the organic matter and kill the causing agent in the soil, inject to the bottom and the hot solution will rise upwards to cover the entire soil portion. Inject small amounts and spread your application like saturation bombing. Check your aquarium Ph both before and after your application and if necessary correct the same with a little vinegar or CO2.

I am sorry that I cannot certify the treatment as safe, but I think it can work safely.


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