Using deep gravel and bacteria to control nitrogen

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Using deep gravel and bacteria to control nitrogen

Post by bekateen » Fri Oct 03, 2014 9:36 pm

Hi All,
Do any of you rely on a deep (4"/10cm or deeper) gravel bed and denitrifying bacteria to control nitrates in your aquaria? A LFS owner recently told me that this approach can have profound positive effects on water quality in aquaria. The idea appeals to me, if it works, because my municipal water isn't that great, and from time to time I have inexplicable die-offs immediately after routine water changes (my LFS reports that other customers have experienced the same thing, leading us to believe that it is due to sudden, brief changes in tapwater quality; we wonder if our city occasionally spikes the water treatment process with chemicals to control bacterial blooms, etc). Anyway, the result is that I don't like to change the tank water any more often than necessary; because of this, while the ammonia and nitrites are zero in my tanks, nitrates get pretty high (over 40 ppm sometimes) and I have a continuous algae problem. A LFS owner says the deep gravel, combined with a bacterial mix like MicrobeLift PL would fix this. But he also says that for this to work, I need to have the deep substrate, and I should use gravel as the substrate to allow better nitrate diffusion down into the substrate to reach the anaerobic denitrifying bacteria that thrive at the bottom. But all of my tanks are filled with sand (oh, how Corys and banjo cats love sand!), and I don't want to change the substrate if I don't have to.

Does this really work with gravel? And if this can work with gravel, does anyone know if it works with sand too? Any thoughts?
Thanks, Eric

P.S., I used to use the strategy of over-filtering my tanks to keep the water clean, but the LFS owner said this might be counter-productive: He suggested that over-filtration elevates oxygen levels (that makes sense), which then promotes algae growth and at the same time inhibits the growth of the anaerobic denitrifying bacteria that I need.

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Re: Using deep gravel and bacteria to control nitrogen

Post by Shane » Fri Oct 03, 2014 10:17 pm

Let me just say that your LFS owner has some ideas that run counter to science.

Deep Gravel: What he is really talking about here is aerobic versus anaerobic filtration. Anaerobic filtration has generally fallen out of favor in the hobby, but it can work, especially in marine aquariums (Google the Berlin Method). It is just not a very convenient form of filtration for most aquarists and it precludes keeping fishes that prefer high O2 environments. Your tap water quality however has no impact on aerobic versus anaerobic filtration. If you are really interested in exploring anaerobic filtration look at buying a denitrator which will cause far less problems and is easier to maintain than an anaerobic substrate. The substrate MUST be sand. Gravel does not work as O2 can reach down in even deep gravel.

Over filtering: Algae are plants. They need CO2 NOT O2 to grow. Agitation drives out CO2 (shake a bottle of Coke) so high agitation drives off the CO2 algae needs to grow. This is why planted aquaria use minimal filtration and aeration devices. More agitation equals less algae not more.

Algae needs light and nutrients (fish waste) to grow. Any tank with an algae problem either is getting to much light, too many nutrients (dirty water), or more likely a combination of the two. A little tinkering with the intensity and/or duration of the lighting combined with regular water changes (50%ish weekly depending on stocking levels) will solve algae issues.

If your city is occasionally flushing their water system with harsh chemicals there should be list you can join to receive notifications.

Hope this helps.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 » Sat Oct 04, 2014 8:09 am

Hi all,
I used to use the strategy of over-filtering my tanks to keep the water clean, but the LFS owner said this might be counter-productive: He suggested that over-filtration elevates oxygen levels (that makes sense), which then promotes algae growth and at the same time inhibits the growth of the anaerobic denitrifying bacteria that I need.
Shane is right, I'd suggest changing your LFS.

Have a look at Shane's article "A fishkeepers guide to dissolved oxygen": http://www.planetcatfish.com/shanesworl ... ved+oxygen and this thread "achieving high oxygenation": http://www.planetcatfish.com/forum/view ... =5&t=39885.

This is an article that covers much the same ground as Shane's, but adds a little more detail "Aeration and dissolved oxygen in the aquarium" http://plecoplanet.com/?page_id=829, the background to why I wrote it is in the "achieving high oxygenation" thread.

The bottom line is that biological filtration is all about oxygen.

I only keep planted tanks because they offer a myriad of advantages including, reducing NO3. I'm also a fanatical water changer, although I ideally like small volume frequent changes.

I've used rain water since the 1970's, although I appreciate it isn't an option for everybody.

cheers Darrel

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Re: Using deep gravel and bacteria to control nitrogen

Post by Bas Pels » Sat Oct 04, 2014 9:20 am

Shane wrote:Agitation drives out CO2 (shake a bottle of Coke) so high agitation drives off the CO2 algae needs to grow. This is why planted aquaria use minimal filtration and aeration devices. More agitation equals less algae not more.
Although this is not exactly the topic discussed here, putting it this way is not correct

CO2 is a gas, which easily dissolves in large amounts. Further, it is everywhere

When a gas dissolves in large amounts, this actually means that very little of the gas above the water is needed in order to keep significant amounts in the water.

That is - the gas has an equilibrium between being dissolved and being free.

When it easily dissolves, the equilibrium is reached rather fast.

Oxygen does not easily dissolve, but under atmospheric circumstanses (that is 20 % oxygen in the air at 1 atmosphere) 10 mg a liter can dissolve @ 25 C. However, the equilibrium will take very long to reach - and if one would take a cup of oxygen free water, and open it to the atmosphere, it could take a day tot get 1 mg/l

CO2 dissolves much easier. The same cup would reach equilibrium within a few hours. But, due to the fact CO2 is only 0,05 % of the gasses in the air, the equilibrium is lower, some 5 mg/l

If I take a tank (A) with lots of fish, no plants and not water movement, the fish will produce CO2, which is not used and therefore the water will contain more CO2 than equlibrium

On the other hand, if I take a tank (B) without fishes, lots of planbts and no water movement, the plants will use the CO2 and the water will contain less then equilibrium

Now, I put a pump in both tanks, and the water movement will help reaching the equilibrium. Tank A, without plants, will loose CO2, while tank B will take up CO2.

Shane is right in saying that heavily planted tanks are often free of water movement in order to keep CO2 in the water, but that only applies in case CO2 is added to the water.

And in my eyes, for no good reason. After all, with water movement the tank will reach 5 mg/l without adding any, and this is the level plants will reach in nature. So this should suffice.

The bottle of coke Shane mentioned contains for more CO2 then the 5 mg/l - and therefore shaking it will repel it.

In fact, adding CO2 to the water makes it harder for the fishes to get rid of the CO2 they produced, and is therefore, in my eyes, not a good idea.

Still, I don't intent to start a discussion about whether adding CO2 is a good idea, I only intended to point out that water movement does not repel CO2, it helps reaching equilibrium.
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Re: Using deep gravel and bacteria to control nitrogen

Post by JamesFish » Sat Oct 04, 2014 11:46 am

Hi,

I'm not sure deep gravel is a good idea. That said I have seen tanks with peat (Never disturbed by gravel cleaning), gravel tidy and normal 2-3 inch deep gravel even after 2-3 months of no work measure low on the nitrate scale of below 40. Something I could never get in my shallow gravel only tanks with regular water changes. Now the comparisons between different setups are a little unfair the tank I'm measuring against is well planted with some very greedy plants and relatively low on stock. The owner feeds far less than I do as well so suffers less from over feeding issues. I feed my fish for enjoyment of watching and this leads to over feeding and more work for me.

Now the bacteria you are seeking to grow is on the market. I am experimenting with it since the 16th of August. It took 9 weeks for all packets to be added to the tank (Filter). 12 weeks before they all should have been active. It was always measuring 40-80 despite even 70-80% weekly water changes and was in the water in / out method just not working. This was enough for 120L worth of water at 1cm of fish per litre. Bigger tanks with bigger fish may require different maths. This system is supposed to last for a year and have 1 30% a month water change. I have been doing a bucket a week plus the 30% once a month. I did notice PH has dropped sligtly from an 8.2 to 7.6 and TDS was dropping. The measures on the API kit are or the last 3 weeks been 5-20 so in good area's for me.

http://www.jbl.de/en/aquatics-freshwate ... onitrat-ex

I havent noticed any side effects yet of using it. But I havent had it for long so would suggest caution if you do and I dont know if it will last its full year stated.

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Re: Using deep gravel and bacteria to control nitrogen

Post by Shane » Sat Oct 04, 2014 11:52 am

Bas,
Appreciate the finer points above and that my Coke example was a bit simplified. My point was that CO2 is driven off and O2 levels increased via surface agitation, which is counter to what his LFS is telling him. Keep in mind most planted tanks shoot for 15-35 mg/l CO2, which is substantially above 5 mg/l (and substantially below Coke's 7.48 g/l :-) ). But as you pointed out, that is another conversation.

The LFS owner's advice to Bekateen that high O2 levels from "over filtration" cause algae is patently ridiculous.

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Re: Using deep gravel and bacteria to control nitrogen

Post by Scleropages » Sat Oct 04, 2014 6:49 pm

bekateen, you wrote that your local tap water may suffer from variations in quality from time to time. Rather than doing something to try to improve your tap water, is there any chance that you can collect rain water? A large rubbermaid garbage can placed under a gutter pipe can collect water quite quickly. I have used this method for several years and have had no problems with using the water in my planted and riverine aquariums. I see that you're in California and know fully well there is a severe drought there. However, it does rain in Stockton in the winter, no?

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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen » Sat Oct 04, 2014 8:18 pm

Scleropages wrote:bekateen, you wrote that your local tap water may suffer from variations in quality from time to time. Rather than doing something to try to improve your tap water, is there any chance that you can collect rain water? A large rubbermaid garbage can placed under a gutter pipe can collect water quite quickly. I have used this method for several years and have had no problems with using the water in my planted and riverine aquariums. I see that you're in California and know fully well there is a severe drought there. However, it does rain in Stockton in the winter, no?
I'll keep this brief because I'm away from my computer. :-)
Scleropages, I haven't tried rain water and that could be a partial solution, but yes you're right, California is experiencing record drought, and it's particularly bad in some areas, including mine. But for sure, in the winter I could use rainwater for some of my changes. I'd need to careful to keep the container covered, because my region is also plagued by mosquitoes and West Nile virus; mosquito abatement is another priority in my area. But definitely rainwater is an option some months of the year.

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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen » Sat Oct 04, 2014 8:51 pm

Shane wrote:The LFS owner's advice to Bekateen that high O2 levels from "over filtration" cause algae is patently ridiculous.
Shane,
I will be honest and state that I may not have represented my LFS owner's position completely right. I mean that I might be putting words in his mouth on this point: He may have meant simply that higher oxygenation hurts the anaerobic denitrification process, which would lead to higher nitrate levels, which would promote algae growth. I don't know if he meant more than this.

I think the reason why i am so intrigued with his proposal, besides my concern with local water quality, is that his tanks look amazing, and all of his tanks in his store have deep small-gravel (not sand) substrates, heavily planted, gently filtered, and no algae.

Again, I'm away from my computer so I don't want to write a longer post to expand on this; I'll expand more later.
Cheers, Eric.

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Re: Using deep gravel and bacteria to control nitrogen

Post by racoll » Sat Oct 04, 2014 10:40 pm

Some thoughts for you Eric. Hope they are helpful.

(1) If you suffer fluctuating tapwater quality, I would do regular, smaller water changes rather than larger, irregular ones. Two 5-10% changes per week, perhaps? That way your parameters stay more stable, and if there are problems with the tapwater one day, little harm should come.

(2) Nitrates often get the blame for algae problems, but I think lighting is more important. Algae can get out of control with even a small amount of nitrate in the water (they don't need a lot), and nitrate reduction often has little effect. Light, however, has a bigger impact I found, and simply by reducing the intensity and duration of light, algae can disappear quickly. Fast growing floating plants such as hornwort (Ceratophyllum) are perfect to shade the tank, as well as adding driftwood to slightly stain the water. Try reducing the photoperiod by a few hours too.

(3) The LFS owner's tanks are heavily planted, and this explains why he has no algae problems. When plants thrive, they outcompete and actually retard algal growth. I doubt that he is experiencing anaerobic denitrification in his fine gravel bed. Rather, the plants are just using up the nitrates, as they need a lot more of it than algae do. His tanks are obviously well balanced in terms of light, nutrient input, and plant growth, and these tanks rarely have algae problems.

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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 » Sun Oct 05, 2014 12:41 am

Hi all,
I'm in agreement with "Racoll", it is the plants that make the difference, not the substrate. Having said that in a planted substrate which has been undisturbed for some times you will get zones where you have low REDOX values and reduction reactions will occur. Have a look at <http://www.skepticalaquarist.com/nitrog ... rification>

"Bas Pel" is also correct if you don't add CO2 (in planted tanks) greater water circulation leads to greater gas exchange. The best filters for any tank are wet and dry trickle filters, because they have a huge gas exchange capacity, and the Rolls-Royce of trickle filters is a planted one.

If the OP reads the links (in my earlier post in this thread) it covers all the areas, in the posts in this thread, much more thoroughly.

cheers Darrel

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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin » Sun Oct 05, 2014 3:39 am

Hopefully I will explain this properly. (I got it a bit wrong and need to correct this.)

In a tank which has no plants growing in the substrate, there is no oxygen below about the top 1/2 inch or a bit less. However, in a planted tank things change. The plants want to help the bacteria because the bacteria do good things for the plants in terms of ammonia and nitrate. So plants will transport oxygen down to their roots and let it out. This creates a way for the nitrifiers and other aerobes to function deeper in the substrate. What results in the substrate is an upper aerobic layer and a deeper aerobic layer. In between there will be another layer where denitrification can occur. Hold onto to this thought while we look at denitrification itself.

Rather than put it in my own words, here is a quick explanation of the bacteria and processes that can be involved:
Biological denitrification is an anaerobic respiration reaction in which nitrate (NO3) is reduced. Denitrifying bacteria are aerobic autotrophs or heterotrophs that can switch to anaerobic growth when nitrate is used as an electron acceptor (Bitton 1994). Denitrification can occur by two pathways. The dissimilative nitrate reduction pathway requires anoxic conditions and results in the liberation of nitrogen gas from the water column (Reed et al. 1988; Madigan et al. 1997). Under aerobic conditions denitrification results in the assimilative pathway or accumulation of nitrogen into biomass (Bitton 1994; Madigan et al. 1997). It is desirable to encourage the dissimilative pathway of denitrification so that nitrogen may be completely removed from the system in gaseous form rather than simply recycled through the system in biomass. In order for this to occur, there must be insufficient molecular or dissolved oxygen present so that the bacteria use the nitrate rather than the oxygen. The rate of the denitrification reaction is relatively fast when there is no free oxygen present (< 0.5 mg/l is ideal). The denitrification rate drops to zero when the dissolved oxygen level reaches 2.0 mg/l.
from http://www.selba.org/EngTaster/Ecologic ... ation.html

There are three basic environmental levels of oxygen. Aerobic in which there is plenty of free oxygen to be used or breathed, Anaerobic which has no free, but does have bound oxygen, and the third is Anoxic which has no free or bound oxygen . Bound oxygen is "bound" up with something else. This thread is about one such a compound, Nitrate, which is one Nitrogen and three oxygen. The oxygen is bound to the nitrogen. In an anaerobic environment the facultative aerobic bacteria mentioned above are able to strip and use the bound oxygen from the Nitrate and that leaves the nitrogen. The nitrogen will be in the form of a harmless gas which will leave the water and return to the atmosphere. However, when these bacteria can not find bound oxygen, i.e. the environment becomes anoxic, they will switch to using sulfates. When they do this what they produce is the nasty rotten egg smelling gas, hydrogen sulfide, which is not wanted in a tank.

In an aquarium there are two basic means for having denitrifying bacteria colonizing and functioning. One is the planted tank because that above example of two levels of aerobic nitrification have that middle layer between them which will be anaerobic, being fed nitrate from above and below. But what if one has no plants or has a bare bottom tank? There are still ways to develop denitrifying bacteria. This is done via ones filter or in the selection of what sort of filter media on uses. One way is to use a Hamburg matten filter and another is to use special media in one's filter.

The use of this sort of media builds up the various oxygen using bacteria in the media and, as the water moves through the media, these aerobes use up all the free oxygen. At this point the facultative bacteria have nothing available but the bound oxygen in the nitrate created by the aerobic nitrifiers. So where the denitrifying bacteria are has become an anaerobic environment.

No matter how one develops the denitrifying bacteria- in the planted substrate, in a Matten filter or in media designed to foster their growth- they will be the last nitrifying/denitrifying bacteria to become well established in a tank. It does take some time.

I hope this all made sense.

Edit comments: I mixed up the terms aerobic and anoxic- I had them reversed. I also misspelled facultative as facultive. I apologize for the errors.
Last edited by TwoTankAmin on Tue Oct 21, 2014 7:37 pm, edited 1 time in total.
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Re: Using deep gravel and bacteria to control nitrogen

Post by apistomaster » Sun Oct 05, 2014 4:31 am

Hi bekateen,
You have been given very good advice and explanations here from some very skilled aquarists and more than a few scientists.

About all I feel I can contribute here is to advise you to buy an reverse osmosis water purification unit since collecting rain water isn't a viable option for you.
I know the water supplies are way below normal and unfortunately most of these units only produce 1 or 3 gallons for every 10 gallons that run through them. Variables affecting the pure water yield include but are not limited to water temperatures, water pressure, water TDS and the quality of the equipment. The so called waste water is actually only slightly more mineral rich than the source water so it is perfectly suitable for fish native to mineral rich waters. This waste water may be used for nearly any typical need other than keeping soft water fishes. It can be drunk, cooking and watering outdoor plants.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 » Sun Oct 05, 2014 11:00 am

Hi all,
That is a really good summary post by "TwoTankAmin", who I know has spent a long term looking at the fate of fixed nitrogen in the aquarium.

From my point of view, with the exception of a matten filter, I think that the concept of having both aerobic and anaerobic filtration occurring simultaneously in the filter media is a flawed concept. This is especially true of canister filters.

The problem is that to achieve aerobic and anaerobic filtration in the filter, you are dependent upon the balance between flow through the filter and how often you clean the filter media.

The idea with a very micro-porous media is that the inner pores are anaerobic and within these de-nitrification of NO3 to N2 gas occurs, in the larger macro-pores aerobic bacteria convert NH3 - NO2 - NO3 (which is an oxygen intensive process)

But, how are you meant to get the flow at a level where you get the mix of aerobic/anaerobic? if all your filter material becomes anaerobic, you lose all your biological filtration and toxic ammonia levels build up.

You also have the problem that you don't have any rapid response to increased NH3 load. If a fish dies, or you inadvertently add chloramine treated water during a water change, you are into a positive feedback loop where the tank water becomes increasingly de-oxygenated, leading to further fish death, more ammonia, greater de-oxygenation, further fish death etc.

If you aim to keep all your filter media aerobic you have a situation where you have more resilience against increases in NH3, and if you have plants as well, particularly those with access to aerial CO2, you have a negative feedback loop where increased amounts of fixed nitrogen lead to more plant growth. When you thin the plants the nitrogen is exported.

cheers Darrel

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Re: Using deep gravel and bacteria to control nitrogen

Post by anteatergoanna » Sun Oct 05, 2014 1:43 pm

Question....I have a thin layer of gravel (easier to keep clean), and all of my plants are in pots. I have a lot of plants, and most grow up and spread across the surface. My plants are really healthy. Is it as beneficial having them in pots or is it better for them to be planted into the substrate?
Thanks


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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin » Sun Oct 05, 2014 2:49 pm

It is important to understand that denitrification in an aquarium happens under anoxic rather than anaerobic conditions. If the later predominates, you will end up with poison gas not nitrogen gas. Denitrification works fine in filters with the proper media as explained above. This media is a good host for bacteria, has a good flow through rate and this is what permits the outer layers of bacteria to remove the free O and to create the bound O in nitrate which the facultive bacteria will then remove the bound oxygen from. For this reason one can easily have nitrification and denitrification in almost any filter. Bear in mind that all of the free oxygen is not being removed from the water, only that water which asctually goes through the media rather than around it. And then bear in mind that surface agitation in a tank restores oxygen to the water.

Next, in a well planted tank nitrate should rarely be an issue since plants consume nitrate. The reason the aquatic plants are transporting oxygen deeper into the substrate is to allow the bacteria which break down organics into ammonia to function and then for the aerobic nitrifying bacteria to further process it. The plants will take up some of that ammonia (as ammmonium) and the nitrate as well. What nitrate they don't use, the denitrifiers will. For people who have tap water with nitrate that is sufficient to cause issues in a tank, or heavy stocking which does the same, there is a natural method for handling it- a veggie filter. This is basically a well planted sump. These would be used in situations where one cannot put plants into the main tank yet still needs to deal with excess nitrate. The plants in the filter will use it. They will also use up other things which otherwise would need to be removed by other means.

If you are interested in this approach, there are some excellent articles on the net. One is by one of the expert people who very early on put up with a very rank newbie. http://badmanstropicalfish.com/articles/article69.html
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 » Sun Oct 05, 2014 9:29 pm

Hi all,
Denitrification works fine in filters with the proper media as explained above. This media is a good host for bacteria, has a good flow through rate and this is what permits the outer layers of bacteria to remove the free O and to create the bound O in nitrate which the facultive bacteria will then remove the bound oxygen from. For this reason one can easily have nitrification and denitrification in almost any filter. Bear in mind that all of the free oxygen is not being removed from the water, only that water which asctually goes through the media rather than around it. And then bear in mind that surface agitation in a tank restores oxygen to the water.
I like lots if flow and plants, but we are going to have to differ on whether having anoxic areas in your filter is a good idea. The vegetable filter article at Badman's Tropicals is another good one.

If people are interested in this area in more detail I recommend the posting by "Greg's Peas" (a microbiologist) in this post on UKAPs,
When I was running the lab we would always come up against the same problems. We would build a biochamber on site to grow and utilise Nitrobacter & Nitrosomonas for waste water cleaning. These bacteria will grow like mad under a wide range of conditions.

The problem though was always 'contact time' and 'oxygenation levels'. Hitting that sweet spot of slow enough flow to allow the bacteria to do their 'job' with enough airation was hard. We would mostly resort to a huge airstone in one of the sumps. The amount of times I've wondered how this could be incorporated into a canister filter.....

We also used to sell pure cultures to 'pond folk'. Their NH3/NO3 problems would be instantly resolved upon addition of the bacteria but over time their levels would fall again and the problems would arise once more.
Post here:<http://www.ukaps.org/forum/threads/alfa ... tes.19636/>

cheers Darrel

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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin » Mon Oct 06, 2014 4:36 am

I like lots if flow and plants, but we are going to have to differ on whether having anoxic areas in your filter is a good idea.
Thats fine. but what about those tanks with no plants and those with no subtrate?

And I guess I failed to explain how denitrification works in fliters with special media. Think of them as microfilters. Besides. whether you like the idea or not, it is still happening in your tank. First, in your substrate:
Abstract
Nitrogen and 0, transformations were studied in sediments covered by Lobelia dortmanna L.; a combination of lsN isotope pairing and microsensor (0,, NO,-, and NH,+) 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 02, NO,-, and NH,+ within the sediment. The rate of coupled nitrification-denitrification was greater than sixfold higher in L. dortmanna-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 0, was released from the L. dortmanna roots to the surrounding sediment both during illumination and in darkness. This release of 0, expanded the oxic sediment volume and stimulated nitrification, shown by the high concentrations of NO,- (-30 FM) that accumulated within the rhizosphere. Both lsN, 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.
from http://m.m.aslo.info/lo/toc/vol_42/issue_3/0529.pdf

And in your filter and other places in your tank where there is a biofilm (including on your plants):
Denitrification occurs in anoxic environments in the presence of oxidized carbon and inorganic nitrogen compounds. Given these requirements, it might be assumed that such conditions, confined to specific microsites, exist in most recirculating aquaculture
systems. In a study on trickling filter biofilms, denitrification activity was observed in distinct zones of the biofilm (Dalsgaard and Revsbech, 1992). By means of microsensors, denitrification activity was measured at a depth of 0.2–0.3 mm below the biofilm surface. Oxygen levels and organic matter availability dictated the depth of the denitrifying zone. Ammonia lowered nitrate assimilation rates and increased nitrate availability for denitrification. Few studies have quantified passive denitrifying activity
in recirculating systems. Passive denitrification, estimated by mass and isotopic balances of major nitrogen pools (Thoman et al., 2001), accounted for a nitrogen loss of 9–21% in a closed recirculating mariculture system for culture of red drum (Sciaenops
ocellatus). These findings were supported by a study on a marine recirculating shrimp production system (McCarthy and Gardner, 2003) where, using membrane inlet mass spectrometry, significant nitrate removal was detected in media from a nitrifying filter and sediment derived from the system. Additional evidence for the denitrification potential of nitrifying media was recently provided in a study on a moving bed bioreactor in a recirculating facility for culture of gilthead seabream (Sparus aurata) by Tal et al. (2003).............

Also, no distinct differences are found between denitrification reactors operated in freshwater and marine systems. It should
be noted, however, that due to differences in operational parameters of these systems, such comparisons are extremely difficult.
from http://www.google.com/url?url=http://sc ... Xg&cad=rja
“Everyone is entitled to his own opinion, but not to his own facts.” Daniel Patrick Moynihan

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bekateen
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen » Mon Oct 06, 2014 5:07 am

Dang it - Do you ever spend a good long time... almost an hour, literally... crafting what you want to say next, and then your browser freezes and you lose it all?!? Oh well, all I can do is start over:

Thank you all for your comments. A lot of you have responded, so I won't attempt to quote from individual posts. I've read all of your comments carefully, and I followed all of your links to other articles and sources.

First let me state that I do get what you're saying about nitrogen and the aerobic/anaerobic bacteria. I am well versed in the biology/theory of it, but what I lack is any PRACTICAL experience with its applicability to real aquaria. And that's why I turned to you folks - I knew that together, you guys have decades of experience to offer, and for that I'm grateful.

I will take your advice about more frequent and smaller water changes, and I'll try the shorter photoperiod (although will this affect how often my Corys and banjos spawn?); I'll also try the rainwater idea in the winter - assuming we get some good rain this year (the drought in California really is THAT bad; it's been going on for a couple of years now, and is forcast to repeat again this year; if any of you are religious, prayers are appreciated; if any of you aren't, good thoughts are appreciated too. Sorry, off topic).

The other take away that I get from your comments is that as a group, none of you rely on a natural anaerobic biological denitrification system INSIDE your tanks (not counting various external filters). That said, some of you have met people who manage to achieve what might be called a zen balance in planted aquaria, and at least one of you have used or are trying to use bacterial supplements.

Given your feedback, I am not going to try this strategy in my main tanks. However, I am still really curious as to what does go on in the gravel, and I love my planted tanks (although I'm not going to attempt CO2 supplementation), so I am establishing a new experimental tank, a 15G which I will treat exactly as described by the LFS guy (as an aside, a website, albeit a commercial one, that describes this same strategy can be found here: http://www.americanaquariumproducts.com ... cycle.html; I'm not promoting its merits, but just providing it as a source).

I will use 4" of the small-size gravel (~1-3mm; see pic), maintain pH at 6.8, and add the bacterial supplement daily for two weeks, then continue to monitor the tank for another couple of months (my LFS guy said it can take weeks or months to establish), monitoring and logging ammonia, nitrites, and nitrates the whole time. (I can also check DO/BOD, so I'll follow that too).
gravel.jpg
If I can get it to work, I will report back in the future. If this seems like an exercise in futility, please know that I have another motive too - I teach college freshman biology, and I'm looking for a new long-term lab experiment for my students to run in class, whereby they can study a little microbiology and learn some ecology (about biogeochemical cycles) at the same time.

Thanks again. If you want to post more to this thread, be my guest - I am eager to read what you have to say. Or, if you think your comments are more relevant just to me and my experiment, and would not be of interest to the general population here, feel free to PM me.

Good night (or day, depending on what part of the world you're in),
Eric

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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 » Mon Oct 06, 2014 11:06 am

Hi all,
I teach college freshman biology, and I'm looking for a new long-term lab experiment for my students to run in class, whereby they can study a little microbiology and learn some ecology (about biogeochemical cycles) at the same time.
Great idea, as well as the tanks you might consider a "Winogradsky column" <http://archive.bio.ed.ac.uk/jdeacon/mic ... nograd.htm>. I've just set up a new one.
DW1305 wrote:"I like lots if flow and plants, but we are going to have to differ on whether having anoxic areas in your filter is a good idea." ........Thats fine. but what about those tanks with no plants and those with no subtrate?
I've never had a tank without plants and a substrate, for me it would be like playing poker where every-one else had a full pack, but I'm playing without the picture cards.
Both lsN, 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.
That is very much where I'm coming from as well, all sorts of symbiotic & mutual relationships and complex biochemistry is occurring in the rhizosphere, in fact all of ecology is "shades of grey".

I'd make a real distinction between what happens in the substrate and what happens in the filter. I want a an undisturbed mature substrate with plant roots and a complex range of organisms and REDOX reactions.

Conversely I want a filter where all the media is aerobic, with a pre-filter on the intake to remove organic debris. I only want the ammonia and oxygenated water entering the filter, and then I want to ensure that the oxygen supply always comfortably exceeds the BOD. It is a KISS solution.

The only case where I would make an exception from the separate filter and substrate recommendations is for a Hamburg Matten Filter (HMF), where you can combine the 2 functions. I've had planted matten filters set up and left for extended time periods in high BOD situations, and they offer great filtration.

cheers Darrel

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