The myths and legends of anaerobic bacteria

[Will Billy]

I wanted to start a new thread that delved a little deeper into a previous thread i started about box filters. I not only wanted to prove the efficacy of utilizing anaerobic bacteria in conjunction with a planted tank, but to have an open discussion about the aloof denitrifying bacteria. 
 

*WARNING* This topic of conversation is HOTLY debated on other forums, i have discovered through my research. Before any of us begin to dive into this subject, I wish to remind you the rules of the C.A.R.E. Forum. Always be polite and helpful, I do not wish to start any arguments here. This is a safe place to share ideas, and information, and not a place to start a shouting match. I leave the fate of this thread for what I hope is a beneficial gain for all of us, completely up to our forum moderators and forum members who post to this thread. If you do not wish for this thread to be locked out, please, please i beg of you to be mindful of your posts. 
 

I have learned much through my googlefu of anaerobic, and anoxic bacteria. I have also learned that much like politics the subject of aerobic bacteria can be unrefuted, but the topic of anaerobic bacteria seems to be still quite a mystery filled with pseudo science and myth. Claims of deep bed substrate, sand capped soil substrate, and my recent venture into exploring products like Seachem De*Nitrate (which is pumice stones realy) and Biohome (which is splintered glass pellets). I beckon anyone with information regarding anaerobic bacteria to please share your thoughts and or experiences here. My original dive into this somewhat murky realm of anoxic and anaerobic bacteria starts with my 55 gal community tank. When i began i started with a gravel substrate. I then learned about adding plants to “assist” with my water column chemistries and management. Since i started with inert substrate, my choices of plants i could add to my tank were somewhat limited. I mostly have slow growing plants like anubias, javafern, java moss, and marimo moss balls. Fast growing plants reduce nitrates better than slow growing plants. With this in mind i came to the conclusion that what if i could assist my slow growing plants with nitrate removal by utilizing anaerobic denitrifying bacteria, to reproduce results similar to a tank with fast growing nitrate sucking, plant hogs if i could combine denitrifying bacteria with slow growing plants that i thoroughly enjoy. 
 

if anyone has  information about how anaerobic bacteria works and can share anything positive in my pursuit of truly balanced tank, please share your experience. 

[BenA]

I used to see ~ 100ppm Nitrate in my water and nothing would have helped, including X2 weekly water change (as the levels rose very quickly). Can't suggest much about the bacteria but I have read the the glass bio rings (forgot the name) can help lots as the have holes which are too small (or something like that) for O2 to enter hence anaerobic bacteria can flourish in there and 'eat' your nitrate. I have decided to add floating plants and this crashed the nitrate levels to 5ppm (API) and 12.5 (Tetra) and the fish love it.

See: Ceramic Rings: Affordable and Effective Bio Media (fishlab.com)

Edited March 26, 2021 by BenA
Added link

[Will Billy]

Hmm, floating plants crashing nitrate levels. Very interesting. I shall look into this more. 

[gardenman]

Yeah, floating plants tend to be rather prolific and are easily removed, thus taking the nitrates with them. Every Saturday I remove a large bowl of excess floating plants from my tanks. I leave enough behind so the next Saturday I'm back removing them all over again. Are they perfect? Eh, probably not, but they do suck up nitrates quite well. Duckweed grows the most prolifically in my tanks, but frogbit and salvinia are doing pretty well also. Red root floaters seem to have largely given up the fight. I also have water hyacinths floating around in three of the four tanks. Oh, and water sprite.

I've got Seachem Denitrate in both of my canister filters (though I think they called it something else when I bought it Matrix! That's it!) and frankly I don't know if it works or not. It can't hurt and might help, but I haven't noticed any huge swings in my tanks with it. I tried making a deep mud bed in a tank once using an old two liter bottle with the top cut off and filled it with top soil and capped it with some sand. As far as I could tell it just took up space. Maybe there wasn't enough of it. Maybe it needed a slow rate of water flowing through it instead of just sitting there. Who knows, but it didn't really impress me and I never repeated the experiment. The theory was if things went bad, it would be easy to remove the bottle. Things didn't go bad, but I didn't notice any real change either. My outdoor water garden has water lilies and a lotus in it and they're all planted in top soil and the water quality out there is nearly perfect year round, which is kind of amazing since there's no filtration at all. My limited experiment in the tank though showed no real change.

[DShelton]

There is a gentleman on YT that has quite a few videos about this very subject. His name is Dr Kevin Novak. He promotes what he calls a plenum, which is an undergravel filter (usually not the whole bottom of the tank) that has very very low flow, just enough to keep the bacteria alive. He does seem to have very good luck with his filters.

 

I have been poking around the scientific literature, but with my local university libraries closed due to SARS-COV2 I have been limited to the the abstracts available through google scholar so I do not have the full papers of each. In my limited research, I have found several papers that suggest plants prefer NH3, as well as several others that suggest plants have a preference for NO3.

 

My curiosity along this line started when I found Dr Novak, and was curious about whether or not I should put a plenum in my new 145l tank. (i.e. is removal of NO3 by methods other than plant uptake desirable?). As of now, the jury is still out, but I am starting to lean the "no it is not" way.

[BenA]

15 hours ago, Will Billy said:

Hmm, floating plants crashing nitrate levels. Very interesting. I shall look into this more. 

Just a word of caution. Some plants such as Duck Weed are nearly impossible to get rid off so think twice which plant you introduce. 

[CalmedByFish]

15 hours ago, Will Billy said:

Hmm, floating plants crashing nitrate levels. Very interesting. I shall look into this more. 

I also just learned this a couple weeks ago and started researching. The result is that I've added hornwort, watersprite, and pennywort. One thing I didn't consider was the hilarious aesthetics. Hornwort looks like I chopped up a Christmas tree and threw it in an aquarium, and watersprite looks like I bought too much parsley and didn't know what else to do with it. Pennywort, on the other hand, looks like lily pads. 

[Biotope Biologist]

I can discuss this point a bit as I have done a lot of research of "water treatment" both in marine and freshwater systems.

 

So anaerobic bacteria as you know is bacteria that exists in the absence of oxygen. In fact oxygen is toxic to most species of anaerobic bacteria and will kill them. The benefits of anaerobic bacteria is that they produce some pretty awesome organic compounds as waste that especially plants love. Commonly they produce phosphorous, carbon dioxide, and sulfates. In a wastewater treatment faculty anaerobic in combination with aerobic bacteria are used to breakdown complex waste and turn it into, basically fertilizer. Both populations are considered a must for proper waste water recycling especially in combination with planted detention ponds.

 

Now in a home aquaria you have a closed system. Which makes utilizing the advantages of anaerobic bacteria, rather difficult. I have tried many times to incorporate anaerobic bacteria in both large industrial fish ponds and aquarium to limited success. Usually I try to separate anaerobic bacteria in their own sump or filter because disturbing the bed leads to oxygen and oxygen leads to mass die offs. The other concern is methane and carbon dioxide, if the gas exchange in the water is not monitored you can cause toxic stress to the gills of your fish.

 

When people have typically had issues with anaerobic bacteria in the aquarium, the scenario usually follows having deep unaerated substrate. Either you or your fish decide to disturb this bed releasing trapped CO2 and CH4 and killing the anaerobic bacteria causing a die off. This causes basically ammonia spikes.

 

EPA and department of Ecology are wonderful free resources for wastewater treatment here is a brief one:

https://www3.epa.gov/npdes/pubs/alagoons.pdf

[BenA]

2 hours ago, Biotope Biologist said:

When people have typically had issues with anaerobic bacteria in the aquarium, the scenario usually follows having deep unaerated substrate. Either you or your fish decide to disturb this bed releasing trapped CO2 and CH4 and killing the anaerobic bacteria causing a die off. This causes basically ammonia spikes.

So if I may ask a question.

My sand depth is between 2" (5cm) to 3" (7.5cm). Would you recommend to shift or stir the sand, say, once a month or not to worry as it is not deep enough?

Thanks

[Biotope Biologist]

I wouldn't worry it's not deep enough. It'll still get some water movement through it depending on the grain. 

If Cory still sells his sand that stuff is the best! It's coarse enough to allow good circulation but fine enough that sand rooting fish don't injure themselves

[BenA]

Thank you.

I wish I could get some of the co-op stuff. I tried but they don't ship overseas, especially the medication that I wanted to include.

[gardenman]

If you decide to try a refugium or separate sump to lower nitrates, and you've got money to burn, there's a product out there called Miracle Mud that supposedly is great. (If you believe the marketing.) It's mostly used in marine tanks as reef hobbyists typically are more willing to spend money on stuff that may or may not work, but they also sell a freshwater version. It's been around since 1989 but has never really taken off. (Largely due to the cost and the need to replace 50% of it each year.) The marketing for it makes it sound like the answer to everyone's prayers, but how much of that is marketing and how much is reality? If you're giving it a try, you'll need ten pounds for a 40-65 gallon tank's sump/refugium and it retails at around $70 for ten pounds. (It's expensive mud as mud goes.) Then you need to replace 50% each year. Kudos to the Miracle Mud's maker as they've stuck with the product for decades now, but it's kind of pricey mud and has never really caught on in the hobby. Still, if you want to try and wipe out nitrates i your tank, it's not the most expensive option out there.

[Daniel]

8 hours ago, Biotope Biologist said:

If Cory still sells his sand that stuff is the best! It's coarse enough to allow good circulation but fine enough that sand rooting fish don't injure themselves

I think this is the sand in question, CEMEX's Lapis Lustre #60:

[L.W. Wetarm]

https://aquariumscience.org/index.php/7-5-denitrifying-media/

Here is an interesting read on the subject of anaerobic bacteria and denitrifying filter media. It made enough sense to me for me to pull my media reactor filled with DeNitrate. I will probably phase out Matrix and Biohome over time in favor of Poret foam. 

[BenA]

Very interesting and informative site. Thanks.

[anewbie]

I've gotten a bit of the stuff in my 2 1/2 inch substrate. My nitrate in a fish density tank stayed around 2ppm for 8 months (i changed the 20L for a 40B). Another common area is on sponges in a sump - if you have such an arragement.

-

I was unaware that slight disturbance can caused an ammonia spike.

[L.W. Wetarm]

1 hour ago, BenA said:

Very interesting and informative site. Thanks.

I have been studying the information on this site for a couple of weeks now and I have to say that it has really adjusted my thinking on filtration and the whole subject of beneficial bacteria and the ammonia oxidation process. It took me a couple of reads to really buy into what he’s preaching but he does back it with science instead of anecdotal evidence.  

[Biotope Biologist]

11 hours ago, gardenman said:

If you decide to try a refugium or separate sump to lower nitrates, and you've got money to burn, there's a product out there called Miracle Mud that supposedly is great. (If you believe the marketing.) 

Thanks for this I actually got started down a rabbit hole and now have red mangroves and anoxic live sand from two little fishies on the way. I guess I will be building a red mangrove swamp biotope in the next year now using the mangroves and anoxic soil as a filter. I almost wonder if I will need a true filtration system or if they can handle the bioload on their own as a sort of "display refugium." I plan on also instating the help of macro algaes.

[gardenman]

13 minutes ago, Biotope Biologist said:

Thanks for this I actually got started down a rabbit hole and now have red mangroves and anoxic live sand from two little fishies on the way. I guess I will be building a red mangrove swamp biotope in the next year now using the mangroves and anoxic soil as a filter. I almost wonder if I will need a true filtration system or if they can handle the bioload on their own as a sort of "display refugium." I plan on also instating the help of macro algaes.

A pet shop (somewhere in the Midwest I think?) made a YouTube video that I saw a long time ago that had a large discus display tank and used the freshwater Miracle Mud in a sump as a refugium and claimed to have undetectable levels of nitrates without ever doing a water change. This was a very heavily stocked tank also. I can't find that video now, but there are dozens, if not hundreds of YouTube videos on Miracle Mud being used in refugiums. You can spend hours/days watching all of them.

[OnlyGenusCaps]

This is a great and interesting topic!  I am an ecologist, and have colleagues who study nitrogen fluxes in aquatic systems.  It's very cool stuff whether you are talking about the reasons for the dead zone in the Gulf of Mexico or the processes in a home aquarium.

In terms of the anoxic, denitrification process, my suspicion is at the scale of the home aquarium it would simply be easier to do water changes or grow plants to reduce nitrates.  Indeed, I'm not certain it is possible to have denitrifying bacteria perform the function to any degree that would be beneficial (depending on stocking rates, of course). 

I'm trying to think of the best way to explain this, so please excuse me if I am fumbling a bit here.  For the most part, we try to keep O2 fairly high in aquarium water.  This is true not just in the display, but as we run it through filters.  Unless that oxygen is utilized by something, it doesn't tend to decrease dramatically (stays in equilibrium with normal solubility with the air).  Yes, loads of aerobic processes are going on in our tanks.  But to favor denitrification, it takes pretty low oxygen.  Denitrification is the least energetically efficient process in the aquarium "nitrogen cycle".  That means that the flow of oxygenated water to any given surface must be fairly low, or the O2 is too high and the process is no longer favored.  That can be achieved; however, think about if you had to achieve this with your typical biofiltration.  Think of the area you would need for beneficial bacterial growth if the flow had to remain low to every surface to achieve conversion of ammonium to nitrate.  So, while I think denitrification occurs in all aquaria, the area necessary to deplete the influx of nitrates would be massive, given the low flow rates that would be required to first deplete the oxygen.  After running through an effective denitrification reactor, the water would then need to be rapidly re-oxygenated or it would be lethal to the animals in the aquarium.

I am not saying that this is entirely impossible.  And as a scientist, I am always eager to be disproved by good data.  That said, I remain highly skeptical of the efficacy of such systems (even after watching videos made by certain doctors).  Additionally, I am not certain that an effective denitrification reactor would be a better option than simply changing your water regularly, or growing plants (even if only in a refugium).  Yes, plants will largely have an affinity for ammonium over nitrates, but they will scavenge nitrates quite effectively (which plants are best for this purpose in a freshwater system, remains an open question for me). 

[Biotope Biologist]

Hello fellow scientist in a related field. I too struggle with translating what we see commonly in our trade into layman so anybody can read my posts and feel like a scientist. It is very hard to come across as sincere especially in the field of science. Thus why I think we should be able to use emojis in research papers (kidding). I tried in my initial post to make it succinct but I was trying to touch on the points that you, I think, put into words better than I did. 

 

I have been reading about mangroves as stated above and they seem to do well only in brackish and saltwater aquariums where they don't get out competed for resources by other plants. The fact that they grow in anoxic soil, while also exchanging oxygen and nitrates in the aquarium had me intrigued. Again in my studies anoxic or anaerobic bacteria alone are not sufficient in converting free nitrates into byproducts. It only seems to do well in conjunction with aerobic bacteria. The mangrove in these cases seems to be a key structure in these environments. In my case I would be using macro algaes as homes for this aerobic bacteria.

[Will Billy]

I hate to admit it bu the results my test is showing, is starting to fall in line with the article @L.W. Wetarm posted. The 5 gallon buckets had a bit of initial improvement but have since leveled off. The 55 gallon tank however did show a significant initial improvement (likely due to larger filtration media volume), but it is beginning to level off too. I always knew plant would absorb nitrates, i was just hoping to assist them with bacteria and sorta of meet them in the middle. So far my experiment isnt producing the results i had hoped for. Its still early in the experiment, and im not giving up just yet, but its looking like adding more plants is the only way to go to reduce water changes and or water change volume. Again it was never my wish to remove water changes entirely, i was hoping to find a mechanism to reduce frequency and volume. Not looking good folks, but ima hang in there and continue to report my findings. 

[Biotope Biologist]

This is one of the wonderful things about science. We may state things as matter of fact, but we never are truly certain and hope to be proven wrong. This is why we constantly test eachother's hypothesis. Even if it has been proven 200 times or 200,000 times all it takes is one experiment with good controls to throw a wrench into what we assumed was true from the initial experiment.

 

I wish you luck in your endeavors.

[OnlyGenusCaps]

8 hours ago, Will Billy said:

I hate to admit it bu the results my test is showing, is starting to fall in line with the article @L.W. Wetarm posted.

Dave has put together a good site there, and it's one of the best sources for well supported information in a hobby that is so often rife with half-truths, common knowledge, and personal anecdote.  It does come with the one caveat that he is focused on highly stocked tanks - when you put in loads of plants, it changes some the outcomes and there is also less available data out there to reference.

[gardenman]

9 hours ago, Biotope Biologist said:

This is one of the wonderful things about science. We may state things as matter of fact, but we never are truly certain and hope to be proven wrong. This is why we constantly test eachother's hypothesis. Even if it has been proven 200 times or 200,000 times all it takes is one experiment with good controls to throw a wrench into what we assumed was true from the initial experiment.

 

I wish you luck in your endeavors.

Yeah. Astronomers knew all about the rings of Saturn until Voyager flew by and got some close up photos that proved nearly all of the "known" stuff wrong. When I hear people saying we all must do something because there's a scientific agreement on it, I cringe. As a general rule, the more scientists agree on something, the more likely it is they're wrong.

Things like aquariums have so many variables that it's hard to come to a firm conclusion on just about anything. Even something simple like "How much ammonia is toxic to a fish?" has a lot of "it depends" involved. Water temperature, pH, and more can all affect it and not just a little, but a lot. A low pH tank kept cold can have an insanely high amount of ammonia with no harm to the fish. A higher pH tank at a warmer temp can kill a fish at a tenth of that level.

My 50 gallon tank is horrifically overcrowded by any objective measure, but it's doing fine. Why? It's been set up and running for about forty years with the same substrate and many of the same decorations/plants. It's housed an Oscar, a very large Midas Cichlid, some large goldfish, and now a vast school of Neon swordtails and super red bristlenose plecos. All lived long and happy lives in that tank. Is it a magic tank? Probably not. It's likely that the substrate and tank decor have built up such a massive load of bacteria over the years that it can handle anything. I don't disturb it and just leave it be and everyone's happy.