Using deep gravel and bacteria to control nitrogen

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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

pleco_breeder wrote:I don't want to get too far away from this topic because I'm enjoying reading through the references which have been posted here. However, you should know that getting manatees for that purpose isn't as far-fetched as you would think. In the earlier part of the 20th century, there was legislation presented to congress (and it almost made it through) to import HIPPOS to the southeastern US to control the same weed. It was even being proposed as a cheap source of meat which could be harvested to curb the effects of the economic depression of the time.
Indeed, and there was also a similar initiative with capybaras a long time ago, or so I have heard. I don't mind our civic leaders proposing bad ideas in an attempt to spawn creativity, but I get scared when they follow through (like using cane toads to control flying insects in Australia, Hawaii, and elsewhere).

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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

Update: The tank has now been running since October 5th (almost 3 months) without a single water change. Although ammonia and nitrite levels are still zero and pH is stable at about 6.8 (where I wanted it), the nitrate levels are off the scale of my API water test kit (>160 ppm). Yes, I realize that this test kit is not inherently reliable, but no matter how "off" it might be, I can't imagine that a value over 160 is any kind of "good" result. I guess I haven't attained the "balance" in my tank that my LFS owner in San Francisco has in his store tanks, since his tanks showed a nitrate = 0 using the same test kit.

As I reported previously, many of my plants continue to grow poorly and more have died (by comparison, in my other "traditionally maintained" tanks, my plants are growing, despite having the same photoperiod and the same fertilizer regimen ("Flourish comprehensive supplement")). The only bright side to this is that there was virtually no algae growing in the tank (and absolutely no black beard algae, which is in all my other tanks) during this time, despite about 6-8 hr of light per day ever since I set the tank up. I suppose that if plants aren't growing well, it's no surprise that algae isn't either.

The best news is that the fish don't appear to be any worse for wear - all were healthy and thriving, although no spawning occurred in the tank (not surprising, since I never did a water change in almost 3 months). About a month ago, I started to suspect that the tank was physically too small for the large , so I took them out and added my three and some of my cichlids. These fish also seemed to thrive in the tank under these water conditions (they are still in the tank to this day).

Anyway, given that I don't have nitrate levels near zero (which was one of my goals), and also given that I want to try to breed my clown plecos, I have terminated the experiment, redecorated the tank (mainly by reducing the amount of gravel from 4 inches deep to about 1-2 inches of the same gravel, adding more driftwood, and adding PVC pipe caves for the plecos) and converted it to a traditional maintenance setup (i.e., I've resumed weekly partial water changes).

Reflections? I'd really like to know why the plants didn't do better. Also, I'm fascinated by the fact that such high nitrate levels (or whatever else is reacting with the nitrate test kit) haven't harmed the fish, especially the Apistogramma, which in my experience have been the most water quality sensitive fish I've owned (except perhaps my Oto cats - all the Otos I've ever bought have died within a month or two of purchase and I don't know why. :-\ :(( ).

Any thoughts?

Cheers, Eric
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Re: Using deep gravel and bacteria to control nitrogen

Post by 2wheelsx2 »

Did you test for phosphate? There are thought that in the absence of phosphorus that plants cannot metabolize nitrogen properly and hence the poor growth and spiking nitrate in your tank? Not saying that's what it is, but it seems it could one possibility, or maybe a contributing factor.
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

No, I didn't test for phosphate, and in hindsight I wish I had. I've never tried a phosphorus supplement either.
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

The way a deep gravel bed works is pretty reliant on the plants. If one's rooted plants are not doing well, the odds are that what is going on deeper in the gravel is not working properly either.
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

TwoTankAmin wrote:The way a deep gravel bed works is pretty reliant on the plants. If one's rooted plants are not doing well, the odds are that what is going on deeper in the gravel is not working properly either.
Yes, I agree. I wish I'd had better luck with the plants. While none of my tanks are spectacular as far as planted tanks are concerned, I've never had such bad luck with plants in my other tanks as I had in this one.
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

Reflecting on this old thread, I had an interesting conversation recently with my brother, who used to own a fish store in Washington State. I was relating the essence of this whole thread and I happened to mention that the San Francisco LFS owner described in this thread performed no water changes in his tanks - he only added water as needed to keep the levels high. My brother then noted something that to me (as a non-LFS owner) wasn't obvious at first: If the LFS in question has any good of regular business (i.e., fish sales, which this LFS does), then the LFS owner is constantly taking a lot of water out of the tanks to bag up fish that are sold. While the volume of water removed for any single fish sale may not be dramatic, the cumulative effect per week could be very significant. That, combined with the fact that almost none of this LFS's tanks have full hoods, means that water loss from the tanks can be very meaningful on a week-to-week basis. Thus, even though the LFS owner may not perform routine water changes like we might at home, he is in essence changing a lot of water regularly.

I bring this this up not to defend the premise of my OP from this thread, but simply recognize just one more reason why the deep gravel strategy might work in the tanks at that LFS whereas it wouldn't (DIDN'T) work in my own tank.
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

It is also said that the plants need to maintain ratio of phosphorus and nitrate within a certain range.

I would like to take this opportunity to correct some of my earlier statements in this thread on denitrification.

Firstly, the bacteria that do this I mistakenly called facultative aerobes, they are facultative anaerobes. This means they can also function in an aerobic environment and make use of oxygen. However, when that aerobic environment becomes anaerobic because the free oxygen is used up, it is not the bound O in nitrate that they use. I was wrong in this explanation. What the do is to use nitrate as an electron receptor and the result is the nitrate is converted to nitrogen gas and, I believe the O part then combines with H to make water. What is important is that it is not the bound O but the nitrate itself being used. So I was off in that respect.
During nitrification, alkalinity decreases by approximately 7 mg CaCO3 for each mg of ammonia-N oxidized to nitrate according to the following simplified stoichiometry:
NH4+ + 2O2 = NO3- + 2H+ + H2O
(Alkalinity loss = 2 meq of alkalinity per mole NH4+ or 7.14 mg CaCO3/mg NH4+-N)

Some of this alkalinity loss is regained when, in addition to nitrification, denitrification is used as a water treatment stage. Heterotrophic denitrification causes a release of hydroxyl ions and raises alkalinity. Each mg of nitrate-N reduced to N2 causes an alkalinity increase of 3.57 mg CaCO3 according to the following stoichiometry:
2NO3- + 12H+ + 10e- = N2 + 6H2O
(Alkalinity gain = 1 meq of alkalinity per mole NO3 or 3.57 mg CaCO3/mg NO3_ -N)
Sorry, I cannot get the site to do sub and superscripts. you can see it in proper form here on page 368 http://www.google.com/url?url=http://sc ... Xg&cad=rja

However, I got the gist of it right. The bacteria uses the nitrate which results in denitrification. If there is an anaerobic environment and there is no nitrate available, these facultative anaerobes will then use sulfates and which results in hydrogen sulfide, aka rotten egg gas. I apologize for having been off base with this.
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

Thank you TTA for that additional detail. By the way, although I've always been taught that "facultative anaerobe" was the proper term (vs. "facultative aerobe," which I've never seen used in a textbook before), functionally the two concepts would be equivalent AFAIK: The term "facultative" is used simply to connote that the aerobic (or anaerobic) condition is optional for the organism; the organism has the ability to switch between an aerobic metabolic pathway and an anaerobic one if the environmental oxygen content changes. The contrast to this is the obligate aerobe or obligate anaerobe, which must live in only an aerobic or anaerobic environment, and is killed in the other situation (i.e., the organism is "obligated" to live in a particular condition).

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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

Ha! I never thought I'd come back to this thread! :)) :)) :))

@apistomaster, @Bas Pels, @dw1305, @JamesFish, @pleco_breeder, @racoll, @Scleropages, @Shane, @TwoTankAmin (listed alphabetically; I tried to catch all who are or were regular contributors on PC and who helped me in this thread in the past)

Found this new video on YouTube which gives a tour of the LFS I spoke of earlier in this thread - the owner is a strong advocate for deep gravel, plants and NO WATER CHANGES to naturally remove nitrates.

We've all discussed the pro's, con's, and qualifiers that go into this pretty thoroughly, so I'm not posting this for sake of reopening the debate (as I've said elsewhere, I've swung the other way and now have nothing more than a thin layer of sand on bottom now). But I thought you might enjoy seeing what I was talking about before. Regardless of what you think of the owner's methods, his tanks are beautiful, especially those with the plants anchored to stands of Styrofoam against the tank walls and above tanks, creating water falls (and I imagine primitive wet-dry filters in the process).

Cheers, Eric

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Re: Using deep gravel and bacteria to control nitrogen

Post by pleco_breeder »

I'm actually glad that you dug up this one. Although the deep sand bed didn't work, there's a lot of important information in this thread that most hobbyists don't generally come across in their everyday studies. IMO, one of the better fish threads on the internet for that reason.

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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
bekateen wrote: 12 Aug 2017, 00:29Regardless of what you think of the owner's methods, his tanks are beautiful, especially those with the plants anchored to stands of Styrofoam against the tank walls and above tanks, creating water falls (and I imagine primitive wet-dry filters in the process).
Eric, thank-you for posting this.

I would have to agree, you can't fault the health of the fish and the tanks are gorgeous. I've never seen a shop like it, and I would suspect that very few other forum members have either.

Having seen the tanks I can understand why they can get away with very limited water changes (just topping up). You have heavy planting, trickle filters, emergent and floating plants, undisturbed substrates etc. and also obviously a skilled aquarist, a "fish keeper with a shop" if you like, in charge.

It is what I'd visualised when I wrote this (on page two of the thread).
dw1305 wrote: 11 Oct 2014, 22:24 I don't think it really matters whether your LFS changes much water etc. he has a set up which is pretty robust and stable in terms of water quality. Whether the deep gravel bed out-gases much N2 is pretty well irrelevant, the tank set-up will maintain water quality.
But my vision was considerably less impressive than the real thing.

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

I am curious about a couple of things re that video.

First, there is a difference between no water changes to remove nitrates and no water changes at all. I am very skeptical of claims of a healthy tank running for many years without any water changes. Imo, topping up works for only so long. So I am curious which is the case here. If you have tons of plants and only small fish in somewhat larger tanks, it will let you do much less maint. and fewer water changes. But some will still have to be done at some point. A closed environment must eventually develop imbalances. Moreover, it will also severely limit the choice of both the animals and plants which can be included.

The presence of the plants and a normal depth substrate should result in very low to no nitrates given the level of plants in those tanks. Moreover, the presences of those plants rooted in normal depth gravel should also result in a couple of anaerobic denitrifying zones naturally establishing in the substrate. I see no reason for needing a "deep bed" to achieve the results. A normal depth (2.5 - 3 inch) of substrate should do. I also believe one can achieve similar results using only plants which do not need substrate. Attached ferns and anubias plus floaters should do a pretty good job of preventing nitrate accumulation.

I really wonder how they catch fish in those tanks without making a horrible mess. It took me close to a year to nab a false SAE in well planted 45 gal. What about all the fish species we did not see in those tanks. The fish that do not live with plants? Does the store have other unplanted tanks for them?

Those fish look pretty dang healthy and I agree it is because of their environment. I would also bet that the owner feeds his stock a lot better than the average store. I love how most of those tanks look, I have had a number of jungle tanks. But I also hated working in them or having to nab fish for sale/trade or in need of treatment in an H tank.

One last observation, for whatever it is worth. There is a reason why that store is so unique relative to most stores. It is the owner. From a purely business standpoint, his methods make little sense. From the standpoint of his attitude about how he chooses to do things, they make perfect sense. If every fish store operated the same way he does, almost all would fail (because they lack the skills) plus the breadth of available species to hobbyists would be limited. I think he is the exception that proves the rule.
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Re: Using deep gravel and bacteria to control nitrogen

Post by JamesFish »

I've been running this tank a while I do a water change 50% once a month with gravel clean. Filter cleaned every 2 weeks but not same time as water change.

It has Peat plates covering most bottom with a plastic separator to keep it in. Is 2-3mm gravel rounded.

The white test result was this tank the pink one from same kit on a sand bottom tank. I did the test 4x as though the kit was faulty.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
JamesFish wrote: 14 Aug 2017, 20:32It has peat plates covering most bottom with a plastic separator to keep it in. Is 2-3mm gravel rounded.

The white test result was this tank the pink one from same kit on a sand bottom tank. I did the test 4x as though the kit was faulty.
You may be getting anaerobic denitrification in the peat layer, as you probably don't have a large enough plant mass for plant growth to account for the low nitrate NO3 level recorded.

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

I came to my understanding of the plant/substrate/nitrate relationship from a link to a paper I came across on Dr. Timothy Hovanec's site. It is a fairly old study, but it opened my eyes. You can read Dr. Hovanecs article in which I found the link, Aquatic Plants and the Nitrogen Cycle here http://www.drtimsaquatics.com/resources ... ogen-cycle

The study he discusses can be found here http://m.m.aslo.info/lo/toc/vol_42/issue_3/0529.pdf
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Re: Using deep gravel and bacteria to control nitrogen

Post by JamesFish »

Interesting read. I don't claim to know exactly what is going on in my tank just that it is working without additional media being required. I do know I see bubbles escape the gravel from time to time as the Cory's root around. I intend to add more plants before adding more fish. I also have a similar setup upstairs with much deeper gravel at 5cm with Peat underneath will try to check that tomorrow before water change is done.
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Re: Using deep gravel and bacteria to control nitrogen

Post by JamesFish »

Well having had a check before wc was clear on tank with deeper gravel. It does occur to me from reading the paper posted, using bags designed to get that bacteria, the Peat plates / gravel and plants. That perhaps it is just the conditions required for a stable amount of that bacteria I am mimicking and that is why it doesn't always work.

The bags I used were designed to drop the flow rate down and work very well even of they do stink down to about 25 where they bottom out . The media I looked at described a requirement of 50L an hour or less flow rate for the bacteria to form and function. I also remember looking at nitrate reactors that worked by exhausting O2 then being opened to allow to very drip slowly swap water with the tank.

Perhaps in the shop he is achieving this in some area of the tank. Evaporation / removing fish in bags would account for loss but how much water goes in a bag less than a L? Also a shops tank is normally heavily stocked. My condition is coming from relatively light stock levels.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
JamesFish wrote: 20 Aug 2017, 13:03 ....The media I looked at described a requirement of 50L an hour or less flow rate for the bacteria to form and function. I also remember looking at nitrate reactors that worked by exhausting O2 then being opened to allow to very drip slowly swap water with the tank. .....
You will get some anaerobic denitrification in most substrates. Because you have a layer of peat, and a relatively light planting of rooted plants, much of your substrate will be operating in the same way an anaerobic plenum (https://www.petcha.com/plenty-plenum-confusion/) would.

The advantage of the planted tanks is that the roots of plants like Cryptocoryne spp., Echinodorus spp., Nymphaea spp. etc. have morphological (aerenchyma etc) and physiological adaptions (ethanol metabolism) to allow root extension into reducing environments.

The advantage for the plant is that nutrients like iron (Fe) are reduced, from their oxidised (and plant unavailable) state, to plant available ions at negative REDOX values.

Personally I like a few more rooted plants as these create zones of fluctuating REDOX and, in my opinion, this make tanks more stable and easier to manage.

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

@dw1305

Darrel- When you say "fluctuating redox" do you mean any given zone fluctuates between aerobic and anaerobic or do you mean there are multiple zones which alternate between anaerobic and aerobic as described in the paper I referenced? That paper suggests that the zone around the roots will be aerobic and that there will be anaerobic zones above and below, i.e. alternating zones rather than alternation within a zone.

I have to admit I am chemistry challenged as I switched schools mid-way through high school which caused me to miss chemistry classes at both. Normal chemistry is hard enough but, when it happens in water, it gets a bit crazy (that is, more complex).
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
TwoTankAmin wrote: 20 Aug 2017, 22:22Darrel- When you say "fluctuating redox" do you mean any given zone fluctuates between aerobic and anaerobic or do you mean there are multiple zones which alternate between anaerobic and aerobic as described in the paper I referenced? That paper suggests that the zone around the roots will be aerobic and that there will be anaerobic zones above and below, i.e. alternating zones rather than alternation within a zone.
I think it will be a mixture of both, there will be zones that fluctuate between being oxygenated and de-oxygenated, as you suggest dependent upon a wide range of factors (http://journals.plos.org/plosone/articl ... ne.0143428), and there will also be a zonation within the substrate.

The roots are the important bit, they are "deliberately" leaky structures and will be releasing both oxygen and carbohydrates into the substrate in the rhizosphere.

Symbiosis between legumes and nitrogen fixing bacteria (https://en.wikipedia.org/wiki/Rhizobia) and Azolla and Anabaena(http://theazollafoundation.org/azolla/t ... mbiosis-2/) etc are well documentedhttps://www.ukaps.org/forum/threads/wha ... ost-430969, but nearly all plants are mycorrhizial to some degree and will alter the conditions in the substrate to favour the microbial assemblage (https://en.wikipedia.org/wiki/Root_microbiome) that offer them some evolutionary benefit.

One thing that you have to bear in mind with Lobelia dortmanna is that it is a small plant, with very slow growth, that occurs in cold oligotrophic lakes (http://www.plant-identification.co.uk/s ... tmanna.htm).

If you looked at a plant with a higher potential growth rate (like a Spartina x anglica, Rhizophora mangle, Cyperus papyrus or Phragmites australis) etc. they would have a much larger zone of influence around the root (https://www.srs.fs.usda.gov/pubs/20165/).

There is quite a lot of work on Phragmites etc. for use in constructed wetlands.

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

TY Darrel
@dw1305

You made me read a whole lot :-B

I am not sure when was the last time I tested for nitrate in any of my tanks. I think it was several years ago because I was doing a dry season on a zebra pleco tank (unlit and no plants) which meant fewer and smaller water changes. I wanted the TDS to rise but not due to nitrate which I wanted to keep low. So I tested once or twice for nitrate levels which were not a problem.

The one thing I know about denitrification, besides it needs an anaerobic environment, is that it requires a slow flow to be effective. A deep bed would definitely be very slow flow, but one's filter can also be slow. This means any need for additional circulation, aeration or current has to be provided by other devices than the filter. Nitrification also works best with lower flow rates than many filters have. To encourage denitrification via a filter requires using large amounts of media which makes it similar to a deep bed in some respects.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
TwoTankAmin wrote: 22 Aug 2017, 22:16 I am not sure when was the last time I tested for nitrate in any of my tanks. I think it was several years ago because I was doing a dry season on a zebra pleco tank (unlit and no plants) which meant fewer and smaller water changes. I wanted the TDS to rise but not due to nitrate which I wanted to keep low. So I tested once or twice for nitrate levels which were not a problem.
I don't test for nitrates either, we have the capability (we use the NO3 Ion Selective Electrodes a lot), but even with ISE there are still issues, and heavy planting removes nitrate accumulation as an issue. I'm still a regular water changer, and if I was forced to forgo plants I would increase the volume of the water changes.
TwoTankAmin wrote: 22 Aug 2017, 22:16The one thing I know about denitrification, besides it needs an anaerobic environment, is that it requires a slow flow to be effective. A deep bed would definitely be very slow flow, but one's filter can also be slow. This means any need for additional circulation, aeration or current has to be provided by other devices than the filter. Nitrification also works best with lower flow rates than many filters have. To encourage denitrification via a filter requires using large amounts of media which makes it similar to a deep bed in some respects.
The slow flow in denitrification coils etc. is really just to ensure that the water is de-oxygenated.
TwoTankAmin wrote: 22 Aug 2017, 22:16Nitrification also works best with lower flow rates than many filters have.
I'm not sure about that, I think it would depend upon the nature of the biofilm. I like high flow rates because they ensure oxygenation. In activated sludge sewage treatment (https://en.wikipedia.org/wiki/Activated_sludge) you have a huge amount of churn (to get enough oxygen into the system to deal with the large bio-load), and the microbes are aggregated into free floating flocs in the filtration system.

Potential oxygen issues are why I don't like de-nitrication in a canister filter, you are always balanced on a knife edge between aerobic nitrification and anaerobic de-nitrification. This is because there is a finite amount of oxygen that enter the filter and that oxygen can't be replenished while the water is inside the filter.

If you ensure that all your filter media is aerobic the potential for ammonia levels to build up (where there is insufficient oxygen for nitrification) isn't an issue.

If you have a substrate (or an HMF), these have access to oxygenated water and there will always be areas (near the interface with the tank water) where nitrification will occur.

Having rooted (ideally emergent) plants offers belt and braces, because you have the increased (synergistic) nitrification capacity of plant/microbe bio-filtration.

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by Bas Pels »

Potential oxygen issues are why I don't like de-nitrication in a canister filter, you are always balanced on a knife edge between aerobic nitrification and anaerobic de-nitrification. This is because there is a finite amount of oxygen that enter the filter and that oxygen can't be replenished while the water is inside the filter.
this is precisely why I don´t like canister filters: the amount of oxytgen entering is finite, and therefore you risk flushing in water with nitrite or ammonium. Water which, further, is virtually free of oxygen.

This can be, partially, compensated by flushing the water along the surface, enabling it to take up oxygen, but still - this is not what one wants.

All other filters have acces to new oxygen, and are, therefore, better.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
Bas Pels wrote: 24 Aug 2017, 14:49 this is precisely why I don´t like canister filters: the amount of oxygen entering is finite, and therefore you risk flushing in water with nitrite or ammonium. Water which, further, is virtually free of oxygen.

This can be, partially, compensated by flushing the water along the surface, enabling it to take up oxygen, but still - this is not what one wants.

All other filters have access to new oxygen, and are, therefore, better.
That is it.

I use canister filters, partially for ease of use, and because they are quiet, but I'm definitely a fan of trickle filters, HOBs and HMFs.

The one point I'd really like to make for people is please, please don't use your filter as a syphon. You want oxygen and ammonia in the filter, you don't want anything else.

There is a good web-site, aimed at aquaculturists, on bio-filtration at (http://biofilters.com).

It hasn't been updated recently, but it contains a lot of useful information that can be scaled down for the aquarist.

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by Lycosid »

I hate to play necromancer and raise this thread from the dead but I recently discovered that I had (accidentally) replicated some of the conditions that spawned this thread in the first place. I present this tale for your edification.

First, what did I replicate?
A heavily planted tank with deep substrate, a decent number of (small) fish, no water changes (only top-offs) for about a nine months, and a final reading of 0 across all nitrogenous waste products.
planted tank.jpg
This happened through a series of bizarre accidents. Several years ago when I took my current job there were a number of fish tanks in a teaching lab that were, frankly, filthy cesspools. I drained these and slowly set them up as teaching display tanks. A 55-gallon at one end of the room became my largest attempt at an ecosystem tank ever. I've done these before in 2-liter soda bottles. The basic idea is to create a self-sustaining ecosystem in a closed system (normally literally sealed) by adding water and mud from a local still-water ecosystem and letting things sprout and hatch. (Current record: eight years. Largest animal: copepods.) So I took this tank, stripped everything down, and then split the substrate into a rocky side and a muddy side. The substrate included some potting soil that was in lab and a lot of mud from a local wetland and the water ended up being multiple samples from every natural body of water I stuck my containers into for a span of two years. Fast forward a few years. At this point I've dumped dozens of plant and invertebrate species into this tank and it's green with plants and the water seethes with tiny animals. It's also got a tank light, sits in front off a window, and has a bubble wall and an overflow-spray bar water circulation system through a small sump. No technical filtration, though, and since it's an ecosystem tank no maintenance beyond replacing evaporated water.

At this point I begin to need a ready supply of feeder fish for some of my research on predatory strategies in larger fish. My guppy breeding experiment needs to be scaled up and the fry are being eaten, so I throw the guppies into the ecosystem tank without changing anything. It works brilliantly, and I soon have guppies everywhere. Which creates a problem, because every time I try to siphon water out I siphon guppy fry out. I promise myself I'll work out a way to siphon out water without siphoning out guppies "soon". Nine months later I realize that it's been a while since I moved guppies into the tank without a single actual water change and make sure my RA tests the guppy tank along with a test on another tank that we are concerned about. The test shows nitrates in that tank, so it works, but everything reads zero in the guppy tank.

So, do I believe that deep substrate is magical? No. (Although I did use a lot of powdered unicorn horn in the original tank layout.) I think this is what happened (and what may be happening in the original LFS).

1. The plants, obviously.
2. The deep substrate....as a support for so many plants. Not only does it hold a lot of roots but it also started with a lot of nutrients and once I started feeding a breeding colony of guppies it would trap extra nutrients. It's totally impossible to vacuum this substrate.
3. Algae. Not surprisingly, with this much light there's a problem with green hair algae growing, sometimes in big tangles, on the back of the tank. I occasionally just pull it out because it's unsightly (as I suspect an LFS owner would), but it also tears loose in tangles and sticks to the overflow teeth, which can cause issues if I let too much of it sit there, so I pull that out. As it happens, I also keep telling myself that I'm going to use the biomass of the algae for something and so I've been dumping it all into a bucket next to the tank, and so I know that in the past nine month I've removed enough algae that when dried it takes up about as much room as five of my own closed fists would. I suspect that this is the missing nitrate right here.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
Lycosid wrote: 04 Jan 2018, 03:11 ........1. The plants, obviously.
2. The deep substrate....as a support for so many plants. Not only does it hold a lot of roots but it also started with a lot of nutrients and once I started feeding a breeding colony of guppies it would trap extra nutrients. It's totally impossible to vacuum this substrate.
3. Algae. Not surprisingly, with this much light there's a problem with green hair algae growing, sometimes in big tangles, on the back of the tank. I occasionally just pull it out because it's unsightly (as I suspect an LFS owner would), but it also tears loose in tangles and sticks to the overflow teeth, which can cause issues if I let too much of it sit there, so I pull that out. As it happens, I also keep telling myself that I'm going to use the biomass of the algae for something and so I've been dumping it all into a bucket next to the tank, and so I know that in the past nine month I've removed enough algae that when dried it takes up about as much room as five of my own closed fists would. I suspect that this is the missing nitrate right here.
I'm sure you are right, it doesn't matter what the plant is, when you remove it, you remove fixed nitrogen.

I've been looking at Dr Kevin Novak's blog on anoxic filters. I don't think he is right about how his filters work, but they use a similar combination of plants and and substrate with fluctuating REDOX values (biocensosis bucket) to maintain water quality.

This is from <http://anoxicfiltrationsystem.blogspot. ... -tony.html>.

Image

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
I thought that reviving this thread might be the most suitable place to put this reference in.

I recently, serendipitously, found an interesting open source paper: "Myriophyllum aquaticum Constructed Wetland Effectively Removes Nitrogen in Swine Wastewater" (https://www.frontiersin.org/articles/10 ... 01932/full).

Although it is dealing with, somewhat, more polluted water than we are it quantifies a lot of the variables mentioned in this thread.

This is from the abstract, but the whole paper is worth reading.
.....stands of Myriophyllum aquaticum to treat swine wastewater. Steady-state conditions were achieved throughout the 600-day operating period, and a high (98.3%) average ammonia removal efficiency under a N loading rate of 9 kg ha-1 d-1 was observed. To determine whether this high efficiency was associated with the performance of active microbes, the abundance, structure, and interactions of microbial community were compared in the un-vegetated and vegetated samples. Real-time quantitative polymerase chain reactions showed the abundances of nitrifying genes (archaeal and bacterial amoA) and denitrifying genes (nirS, nirK, and nosZ) were increased significantly by M. aquaticum in the sediments, and the strongest effects were observed for the archaeal amoA (218-fold) and nirS genes (4620-fold). High-throughput sequencing of microbial 16S rRNA gene amplicons showed that M. aquaticum greatly changed the microbial community, and ammonium oxidizers (Nitrosospira and Nitrososphaera), nitrite-oxidizing bacteria (Nitrospira), and abundant denitrifiers including Rhodoplanes, Bradyrhizobium, and Hyphomicrobium, were enriched significantly in the sediments.
cheers Darrel
Last edited by dw1305 on 14 May 2019, 16:38, edited 3 times in total.
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

I think this thread is a pretty good one to keep going over time. I am not sure if I posted it here, but there is an old paper which first appeared in Limnology and Oceanography, 1997. I found it via the site of Dr. Timothy A. Hovanec in his article, "Aquatic Plants and the Nitrogen Cycle."
http://www.drtimsaquatics.com/resources ... ogen-cycle

Here is the info on the paper.

"Nitrification and denitrification in the rhizosphere of the aquatic macrophyte Lobelia dortmanna L."
Nils Risgaard‐ Petersen, Kim Jensen
https://aslopubs.onlinelibrary.wiley.co ... .42.3.0529
Abstract

Nitrogen and O2 transformations were studied in sediments covered by Lobelia dortmanna L.; a combination of 15N isotope pairing and microsensor (O2, NO3−, and NH4+) techniques were used. Transformation rates and microprofiles were compared with data obtained in bare sediments. The two types of sediment were incubated in doublecompartment chambers connected to a continuous flow‐through system.

The presence of L. dortmanna profoundly influenced both the nitrification‐denitrification activity and porewater profiles of O2, NO3−, and NH4+ within the sediment. The rate of coupled nitrification‐denitrification was greater than sixfold higher in L. dortmnanna‐vegetated sediment than in bare sediment throughout the light–dark cycle. Illumination of the Lobelia sediment reduced denitrification activity by ∼30%. In contrast, this process was unaffected by light–dark shifts in the bare sediment. Oxygen microprofiles showed that O2 was released from the L. dortmanna roots to the surrounding sediment both during illumination and in darkness. This release of O2 expanded the oxic sediment volume and stimulated nitrification, shown by the high concentrations of NO3− (∼30 µM) that accumulated within the rhizosphere. Both 15N2 isotope and microsensor data showed that the root‐associated nitrification site was surrounded by two sites of denitrification above and below, and this led to a more efficient coupling between nitrification and denitrification in the Lobelia sediment than in the bare sediment.
Also, to clarify my statement that nitrification (and denitrification) work best with slower flow rates. I should have made it clearer. Slower is relative in that there are two considerations. One is contact time. The organisms in the biofilm can only extract what they need from the water when they are in contact with it. But more important is the potential effect of shearing which is caused by an excessive flow rate. This refers to causing parts or all of the biofilm being "ripped" off of the surface to which it is attached.

When I set up my first 3 inch thick, 20 ppi Mattenfilter on a 33 long using a pump, I was advised by Dr. Tanner to shoot for flow rate between 150 and 200 gph. Considering the oft stated rule of needing a 10 times/hour turnover, that 33 would have used closer to a 330 gph flow. Since I began using Mattens and the Poret cubes, I have not tested nitrate levels in any tanks where I use these filters as i have seen no reason for doing so.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
TwoTankAmin wrote: 14 May 2019, 16:27 I think this thread is a pretty good one to keep going over time. I am not sure if I posted it here, but there is an old paper which first appeared in Limnology and Oceanography, 1997. I found it via the site of Dr. Timothy A. Hovanec in his article, "Aquatic Plants and the Nitrogen Cycle."
http://www.drtimsaquatics.com/resources ... ogen-cycle
I'd like to think the thread is of some interest to people, other than you and me, as well.

Anything that helps people have healthy vibrant aquariums, that they can enjoy, rather than staggering from disaster to disaster must be a good thing.

You linked in the Petersen & Jensen Lobelia dortmanna paper on page 3. It is also referenced in the Sun et al M. aquaticum paper.

I haven't been all the way through them yet, but I have some other papers looking at intermittent aeration of constructed wetlands. The aim is to increase total nitrogen removal by extending the zones of fluctuating REDOX, where both aerobic nitrification and anaerobic denitrification will occur.
TwoTankAmin wrote: 14 May 2019, 16:27 Also, to clarify my statement that nitrification (and denitrification) work best with slower flow rates. I should have made it clearer. Slower is relative in that there are two considerations. One is contact time. The organisms in the biofilm can only extract what they need from the water when they are in contact with it. But more important is the potential effect of shearing which is caused by an excessive flow rate. This refers to causing parts or all of the biofilm being "ripped" off of the surface to which it is attached.
There is an optimal depth of biofilm, the Kaldnes "K" type floating cell media were actually designed to be self-cleaning, but to retain this optimal depth of biofilm. I think they were developed for commercial Salmon Aquaculture, but have found a wider application in waste water treatment (http://www.veoliawatertech.com/news-res ... /46021.htm).
TwoTankAmin wrote: 14 May 2019, 16:27When I set up my first 3 inch thick, 20 ppi Mattenfilter on a 33 long using a pump, I was advised by Dr. Tanner to shoot for flow rate between 150 and 200 gph. Considering the oft stated rule of needing a 10 times/hour turnover, that 33 would have used closer to a 330 gph flow.
The 10x rule only really applies to Hi-tech planted tanks where aquascapers have added CO2, it is to distribute the dissolved CO2, it isn't really anything to do with biological filtration. Often the filter will be augmented with a Koralia type powerhead to increase the flow. If you don't add CO2 (I don't and I never will) you only need much lower turn-over rates.
TwoTankAmin wrote: 14 May 2019, 16:27 Since I began using Mattens and the Poret cubes.
I look on HMF filters as a special case, they combine the role of filter and substrate. I'm a great advocate of using them.

I think it is linked in earlier in the thread, but for any-one who hasn't read it I'd recommend Dr Stephan Tanner's article on "aquarium biofiltration" (http://www.swisstropicals.com/library/a ... iltration/).
TwoTankAmin wrote: 14 May 2019, 16:27I have not tested nitrate levels in any tanks where I use these filters as i have seen no reason for doing so
I very occasionally use a lab. ISE to measure NO3 from the tanks, but usually I just use plant health (via the Duckweed Index (http://www.planetcatfish.com/forum/view ... hp?t=36231)) and an even more occasional conductivity measurement.

cheers Darrel
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