Using deep gravel and bacteria to control nitrogen

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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

dw1305 wrote:you might consider a "Winogradsky column" <http://archive.bio.ed.ac.uk/jdeacon/mic ... nograd.htm>. I've just set up a new one.
Yes, we've used Wingradsky columns before. They are really neat, too. I think that the aquarium setup appeals to me because of its practical application, even for the students; I've never met a student with a Winogradsky column at home, but lots of students have aquaria. :-)
dw1305 wrote: 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.

I agree. At work our tanks are barren, to make them easily sanitized freqently. But water quality is highly unstable as a result, even with filtration.
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.
Yes, I agree. And from what I've read about the gravel approach discussed in this thread, the plants are critical. Not only do they create the interactions you described, but SUPPOSEDLY (and this is something I'll wait to believe until I made it), the roots provide just a minimal amount of oxygen to the deep layers of gravel so as to inhibit the sufur reducing bacteria which require utter anoxia, but still permit the denitrifying bacteria which can tolerate minute amounts of oxygen.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
We use the tanks in the lab. a little bit, mainly as a source of Rotifers etc for microscopy practicals and to check the DO meter membranes. We don't do any experimentation on the fish, even though they are used a bit for "animal behaviour" studies.

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Not only do they create the interactions you described, but SUPPOSEDLY (and this is something I'll wait to believe until I made it), the roots provide just a minimal amount of oxygen to the deep layers of gravel so as to inhibit the sufur reducing bacteria which require utter anoxia
There is quite a lot of work on this, have a look at Perata et. al. 2011 "Plants and flooding stress" New Phytol. 190:2 pp. 269-273 <http://onlinelibrary.wiley.com/doi/10.1 ... 702.x/full>. I can get a copy if it isn't available (I'm at work).

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

Post by bekateen »

Hi Darrel,
I was able to get it successfully. Apparently my institution has access.
Thanks, Eric
P.S., I noticed that there's no thick gravel bed in those tanks of yours, but definitely well planted. :-)
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

The plants do more than provide a little bit of oxygen, they provide enough to support aerobic nitrification as . I will list a number of links to studies on this. As for the site you linked. it does have a lot of good info but also some incorrect info. I have had a few back and forth discussions with Carl on this and it takes movingg heaven and earth to make him change his stuff, and I have persuaded him to do so. I tend to double check what I read there. For example, plants take up NH4 (ammonium) not NH3 (ammonia), the bacteria prefer NH3.

Here are some links:
Betaproteobacterial ammonia oxidizers in root zones of aquatic macrophytes http://www.ingentaconnect.com/content/s ... 4/art00001

Effect of Lake Trophic Status and Rooted Macrophytes on Community Composition and Abundance of Ammonia-Oxidizing Prokaryotes in Freshwater Sediments http://aem.asm.org/content/75/10/3127.full

Long-distance transport of gases in plants: a perspective on internal aeration and radial oxygen loss from roots http://onlinelibrary.wiley.com/doi/10.1 ... 846.x/full

If you would like more, let me know.
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.
This is an interesting statement considering how many members here have bare bottom, unplanted tanks. At my peak I had 20 tanks going, 1/2 were planted and the other half had no plants and no substrate. How do folks manage to spawn and raise such healthy catfish I wonder? :d

I have a similar type of discussion on another site where the other person has never had a tanks without plants and has never done a fishless cycle. He sees no reason to do it. And I then ask him how he thinks African rift lake keepers or folks who spawn plecos in bare bottom tanks could cycle their tanks. It is still possible to have anoxic denitrifcation in such tanks, it relies on the design of the bio-media. One more interesting factoid here. In terms of the volume required for hosting nitrification vs denitrification, the latter needs less space.
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

TwoTankAmin wrote:The plants do more than provide a little bit of oxygen, they provide enough to support aerobic nitrification
Hi TwoTankAmin, Thank you for the articles; I'll take some time to digest them. As to my earlier point, I did not intend to minimize the magnitude of gas transport by the plants, or suggest that this was their only benefit to the microbiological community; I only meant to highlight the value of the plants in preventing the kind of anoxic environment that promotes sulfur reduction.
TwoTankAmin wrote:How do folks manage to spawn and raise such healthy catfish I wonder?
While my catfish experience is nowhere near as vast as that of other members at this site, it so happens that all of my cats have spawned in well-planted, sand-bottomed tanks, and I always raise my fry in sand-bottomed, slightly planted nursery tanks. I confess that I am befuddled by the bare-bottom tank; since the number of species I've spawned is small, I haven't faced a species that requires that type of arrangement. As I mentioned above, the tanks I have at work (which house aquatic frogs) are all bare-bottomed and unplanted, but they rely on strong aerobic filtration and frequent water changes; their water quality is much more whimsical than I find in my tanks at home - one dead frog can ruin water quality overnight.

Anyway, thanks for the extra info; the more the better.
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Re: Using deep gravel and bacteria to control nitrogen

Post by JamesFish »

Nobody knows everything. Most keepers learn from others, experience or reading than trying it out.

Measuring success is something I'm sure depends on what you set out to do. For instance if you set out to make X tank and you got P its not a success. But if you set out to make a great home for your catfish they like it and live long happy lives than that's probably what I would call a success.

I hope you keep this thread up to date and see where it goes. Let me know if you get bubbles from the gravel please.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
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........This is an interesting statement considering how many members here have bare bottom, unplanted tanks. At my peak I had 20 tanks going, 1/2 were planted and the other half had no plants and no substrate. How do folks manage to spawn and raise such healthy catfish I wonder?

This is back to where we started, experienced aquarists like yourself are usually pretty good at water management, they can see things a lot earlier than the average fish keeper and respond to signals that most of us wouldn't see. The bottom line is that they can work with bare tanks etc in ways that the average aquarist can't in the long term.

I'm not making any claims for myself, I know I'm a fairly average fish keeper and I need all the help I can get. I adapted and developed KISS solutions like the planted trickle filters and the duckweed index partially because I'm not a very conscientious fish keeper. It gives me a lot more wriggle room and when things go wrong, they go wrong pretty slowly. This gives me more chance to respond.

It was really when I got to know the late Bob Marklew (Macvsog23 on this forum) that I began to appreciate how little I really knew about fish keeping.

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

Post by Juiceyfish »

Shane wrote: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.
-Shane
this is a good fact !! How about I have no alegae in the tank that's submersed in the water but on the glass where my light sits that isn't submersed in water is full I've algae every week when I do water changes.... Is this from too much light in the tank my tank is clean and clear as a whistle but the glass on the Canopy is where it grows.....I usually have my lights on for 12 hours sometimes less is this too much?


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Re: Using deep gravel and bacteria to control nitrogen

Post by Shane »

Unless you are growing medium to high light plants a 12 hour photoperiod is probably too long. Most lower light plants (Java fern and moss, Anubias) will be fine on 6-8 hours of light. In tanks without plants you really only need enough light to enjoy the fishes and ensure they are healthy. My fish only tanks get 4 hours (6pm-10pm) which is the time period when I am home most to watch them.

BTW I love it when algae grows on the tank cover. I just slide the glass in a rearing tank and let the Ancistrus fry clean it. This is how they are fed by commerial breeders who use big sheets of clear plastic over ponds to grow algae in the same way.

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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

What most of this boils down to, in terms of understanding the bacteria is understanding bio-films. None of these bacteria is water borne, they live attached to surfaces encapsulated in a bio-film they create. This is where the nitrifiers live. But they are far from alone. In the end it is neither the filter nor the media which do the work in our tanks, it is the microorganisms ensconced inside the bio-flims attached to such hard surfaces that are doing the work.

What I find interesting about all this is how the various bacteria etc. in the bio-film are located at specific depths and juxtapositions. They are arrayed in such a fashion that they get what they need. And the work together, the same bacteria that would break down organic waste will break down the dead bacteria in the bio-film turning to something other bacteria can use and vice versa. Moreover, the bio-film also affords them protection from all sorts of "bad" things including drying out.

Interesting reads on this can be found:

The biofilm matrix
http://www.researchgate.net/publication ... 170c50.pdf

Bacterial Adhesion: Seen Any Good Biofilms Lately?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC118072/

Ecophysiological Interaction between Nitrifying Bacteria and Heterotrophic Bacteria in Autotrophic Nitrifying Biofilms as Determined by Microautoradiography-Fluorescence In Situ Hybridization
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC368389/

Microenvironments and distribution of nitrifying bacteria in a membrane-bound biofilm (Abstract)
http://onlinelibrary.wiley.com/doi/10.1 ... ated=false
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
What I find interesting about all this is how the various bacteria etc. in the bio-film are located at specific depths and juxtapositions. They are arrayed in such a fashion that they get what they need. And the work together, the same bacteria that would break down organic waste will break down the dead bacteria in the bio-film turning to something other bacteria can use and vice versa. Moreover, the bio-film also affords them protection from all sorts of "bad" things including drying out.
Thank you very much for the links, I've downloaded them and I'll be very interested in having a proper look through them. I'm still hoping that we will do more "waste water" work in the future.

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

Post by David R »

I'll start with a little disclaimer that I have only very lightly skim-read the rather lengthy and detailed replies in this thread, but here's my 2c...

I wouldn't even consider the idea of using a deep substrate bed for this purpose in a FW aquarium for many reasons, but mainly because it wastes valuable swimming space and almost certainly won't be as effective as using terrestrial plants with submerged roots, such as Pothos (Epipremnum aureum), to keep nitrates in check. I have two plants growing in the sump of my 2000L tank, and with my moderate stocking even feeding 2-3 times daily I rarely hit 10ppm a week after a water change. I could get away with changing <10% weekly based on nitrate readings alone (or much longer intervals between changes), but I still usually change 20-30% weekly for all the other factors not tested for. It is nice to know I have the capacity to go away for a couple of weeks without having to worry about someone else doing a water change on the tank though.

If you are trying to extend the period between water changes I'd say Pothos are a must, they don't need much light (mine are under an 8W compact fluorescent bulb in a desk lamp) and they don't require CO2 during the day, or release it back into the water at night, like submerged plants. They're easy to find almost anywhere house plants are sold, often called 'Devils Ivy' or 'Golden Pothos'.

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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

Hi David,
Thanks for the suggestions.
David R wrote:I wouldn't even consider the idea of using a deep substrate bed for this purpose in a FW aquarium for many reasons, but mainly because it wastes valuable swimming space
Very true - As I mentioned above, I set up an experimental tank, a standard 15 Gallon, with 4" gravel and dang it looks silly - the gravel occupies approximately 40% of the depth of the tank. LOL - Definitely not desirable in shallower tanks, although I would think not so significant in taller tanks (my 36 Gallon bowfront already has almost 3" of sand in the bottom, and I think it looks pretty good; one more inch wouldn't be too severe in that tank). And your concern about depth and swimming space is something I ponder - One of the resources sited in an earlier post in this thread stated that the anaerobic denitrifying bacteria exist in the 3-4" depth range; if so, then maybe I can get away with slightly less substrate than a full 4".
David R wrote:... Pothos (Epipremnum aureum)... I have two plants growing in the sump of my 2000L tank... If you are trying to extend the period between water changes I'd say Pothos are a must.
Compared to how you described your tank, I think I have a heavier nitrogen-load (per gallon) in my main tank, between the number of fish and the amount of food I give them (plus, since I maintain a live colony of Tubifex worms in the sandy substrate for the cats to graze on ad libidum, these worms are not only excess food for fish but they are simultaneously animals contributing to the nitrogen waste in the tank).

My tank is planted, but I've never tried what you're suggesting. On this point, I have to be honest about my naïveté: I have no experience with sumps. I have used Golden Pothos before in semi-aquatic terraria set up for my frogs (at home, not work), but can it be used in a fully aquatic setting? Doesn't it have to be at least partially aerial? If so, that would be a challenge for me because my tanks have only a very small air space above the water (a couple of inches between the water level and the standard manufacturer's hood. All the plants-on-top aquaria I've ever seen are open-topped, but my tanks aren't. If I can work around that limitation, your idea is very appealing to me; I'd enjoy having plants grow above the water line.

I'll try and tinker around with this some.
Cheers, Eric
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
I have used Golden Pothos before in semi-aquatic terraria set up for my frogs (at home, not work), but can it be used in a fully aquatic setting? Doesn't it have to be at least partially aerial?
The Pothos (Epipremnum aureum) just has the lower end of the stem in the water, the leaves are all emersed.

If you haven't got much space between the lid and the water you can use floaters, or let an Anubias grow out above the water level. These are Hygrophila corymbosa and Anubias barteri that have "escaped".

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

Post by bekateen »

Yes, I can definitely do that! It's always been my understanding that terrestrial plants can be more photosynthetic because of the direct light exposure (no light being absorbed by water). Does this small portion of plant above the waterline really have a bigger impact on nitrate levels than a proportional amount of submerged plant?

And as for floaters, I used to have duckweed on the surface of one of my tanks, but it was all tussled about by my overactive external power filter, eventually getting sucked in and clogging the filter, and ultimately getting destroyed by the filter. What about the various pond lilies sold in pet shops: Do they grow too large for aquaria?

As an aside, the LFS owner advocating deep gravel also uses duckweed and floating plants; bases on my problem with my duckweed, I suspect that's one reason why he advocates weaker filtration rather than overfiltration. He also uses a really neat trick tying mosses and other small rootless plants to vertical styrofoam sheets partially submerged at the back of the tank. This creates a wall of greenery, some of the blocks sticking out of the water an inch or two. And for these he creates a gentle water return above the plants to keep them wet. When the plants overgrow the foam, it looks really cool, and I'm sure it helps a lot with nitrates too. :-)
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
It's always been my understanding that terrestrial plants can be more photosynthetic because of the direct light exposure (no light being absorbed by water). Does this small portion of plant above the waterline really have a bigger impact on nitrate levels than a proportional amount of submerged plant?

That would be true in lakes etc. but I think in the shallow, relatively transparent, water we have in out tanks that CO2 availability is a much bigger issue. Emergent plants have access to ~400ppm CO2 as against ~2ppm in submerged conditions. Light drives photosynthesis, but carbon availability is often the limiting factor. I haven't got any figures but emergent plants definitely help with nutrient removal.

This is why aquascapers aim for ~30ppm CO2, even higher levels would be optimal for plants, but you asphyxiate your live stock via the Bohr Root effect. They also add unlimited nutrients via "Estimative Index" and achieve startling plant growth.

I'm not interested in optimal plant growth, I'm interested in the plants maintaining high water quality.
And as for floaters, I used to have duckweed on the surface of one of my tanks, but it was all tussled about by my overactive external power filter, eventually getting sucked in and clogging the filter, and ultimately getting destroyed by the filter. What about the various pond lilies sold in pet shops: Do they grow too large for aquaria?
I have Frogbit, Nile Cabbage and Salvinia, and as you can see from the picture I have reasonable surface flow, but a big sponge on the filter. You can get Lilies for the aquarium, they grow a bit big generally, but you can control them by removing some of the floating pads. I have had Nymphaea lotus 'Red' in a 2' tank for the last ~5 years, and I only let it have 3 floating leaves. If I go away for a couple of weeks it will have covered the surface by the time I'm back.
As an aside, the LFS owner advocating deep gravel also uses duckweed and floating plants; bases on my problem with my duckweed, I suspect that's one reason why he advocates weaker filtration rather than overfiltration. He also uses a really neat trick tying mosses and other small rootless plants to vertical styrofoam sheets partially submerged at the back of the tank. This creates a wall of greenery, some of the blocks sticking out of the water an inch or two. And for these he creates a gentle water return above the plants to keep them wet. When the plants overgrow the foam, it looks really cool, and I'm sure it helps a lot with nitrates too.
I'd recommend this approach. 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.

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

Post by bekateen »

Just a quick reply, because I'm on my mobile phone. Of course, the CO2, duh! Don't know why I didn't think that in first place.

Don't find many floating plants at LFS in Stockton (IDK why not). Yesterday I drove 1 hour to LFS in Sacramento to get some frogbit and a few other rooted plants. IMHO, that's a long way to drive for plants - I think I just crossed the line into "aquarium freak." :-D

By the way, what is "floating Anubius?" Is it just normal Anubius that isn't planted in the substrate, or is it a special type of Anubius?

Yes it's all about finding that balance. Hopefully I find it sooner than later.
Thanks, Eric
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
By the way, what is "floating Anubius?" Is it just normal Anubius that isn't planted in the substrate
Yes it is just a normal Anubias. I used to have them all fixed to pieces of bog-wood etc., but now I just chunk a bit off and put it in the tank and ignore it. If I have a new tank I would re-attach them to some wood, but most of my tanks are pretty full of plants so I don't really need to, I can just put them in.
Don't find many floating plants at LFS in Stockton
No they aren't off for sale in UK ones either. I'm not sure why this is. Possibly because Tropica etc grew most of their plants emersed? or possibly because they don't sell?

I give as many of my spares away as possible to hobbiests and a local LFS, but I always have spare.

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

Post by Raul-7 »

As far as floating plants, the best for nitrates are Eichornia sp.; they are commonly used in waste water treatment. http://article.sapub.org/10.5923.j.re.2 ... tml#Sec3.1

As far as emerged, I'd say Pothos works really well.


Or you can setup a reactor using a media like Sachem deNitrate and run a low flow pump [less than 50gph] through it to cultivate anaerobic bacteria to convert that NO3 into N2.
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

Raul-7 wrote:As far as floating plants, the best for nitrates are Eichornia sp.; they are commonly used in waste water treatment. http://article.sapub.org/10.5923.j.re.2 ... tml#Sec3.1

As far as emerged, I'd say Pothos works really well.


Or you can setup a reactor using a media like Sachem deNitrate and run a low flow pump [less than 50gph] through it to cultivate anaerobic bacteria to convert that NO3 into N2.
Thanks Raul-7. Hyacinth are beautiful plants, too. I'll see what's available in my area.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
"Raul7" you are right, but I'd only recommend Eichornia if you have a lot of light. I've tried it a few times, but it always dwindles away in the winter. You may have more joy in California, we are a long way N. in the UK, and our winters are pretty gloomy.

Pistia is almost as good, and is more tolerant of lower light. If you look at the posted link (by Raul7) the details for Pistia are immediately after those for Eichornia.

An alternative route, using anoxic denitrification of NO3 and out gassing as N2, is described in "twotankamin's" very informative posts and links earlier in the thread.

cheers Darrel
Last edited by dw1305 on 13 Oct 2014, 16:52, edited 1 time in total.
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Re: Using deep gravel and bacteria to control nitrogen

Post by pleco_breeder »

Just a quick note. Water hyacinth are considered invasive, and illegal to sell, purchase, or transport in California. This holds true for most states within the US as well. I don't know the disposal method used in California, but know having one found in your tanks or ponds in Arizona results in the water being "bombed" with a strong herbicide to remove any risk of seeds within the system. It's probably not worth the risk when other methods can work.

EDIT: I hadn't reviewed the page fully before posting, but feel I would be remiss if I didn't mention that Pistia is also controlled in a lot of areas. I don't think this currently includes California, but definitely check on it before taking the risk.

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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
Water hyacinth are considered invasive, and illegal to sell, purchase, or transport in California
That is a good point, it is one of the world's worst weeds. I'm not knowledgeable about US laws, but I should probably have thought of that: Eichornia crassipes via UF/IFAS Center for Aquatic and Invasive Plants <http://plants.ifas.ufl.edu/node/141>.

From the same site Pistia may, or may not, be native to the USA, and isn't on the list of Federal noxious weeds <http://plants.ifas.ufl.edu/node/328>.

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

Post by bekateen »

pleco_breeder wrote:Just a quick note. Water hyacinth are considered invasive, and illegal to sell, purchase, or transport in California. This holds true for most states within the US as well. I don't know the disposal method used in California, but know having one found in your tanks or ponds in Arizona results in the water being "bombed" with a strong herbicide to remove any risk of seeds within the system. It's probably not worth the risk when other methods can work.

EDIT: I hadn't reviewed the page fully before posting, but feel I would be remiss if I didn't mention that Pistia is also controlled in a lot of areas. I don't think this currently includes California, but definitely check on it before taking the risk.

Larry
Definitely, thank you Larry.
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

I forgot about this study, it shows how a planted substrate with roots differs from those not planted. here is a link to the full paper:

Nitrification and denitrification in the rhizosphere of the aquatic macrophyte
Lobelia dortmanna L.

Nils Risgaard-Petersen and Kim Jensen
Institute of Biological Science, Department of Microbial Ecology, University of Aarhus, Ny Munkegade Bldg. 540,
DK-8000 Aarhus C, Denmark
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.
fromhttp://m.m.aslo.info/lo/toc/vol_42/issue_3/0529.pdf

The paper was investigating why a plant would transport oxygen via its roots such that the result would be to foster nitrifying and denitrifying bacteria which would be in competition for nitrogen with the plant- ammonia (as NH4) and nitrate. For this discussion the relevant thing to take from this paper here are that nitrification coupled with denitrification is natures way. And it seems to me this would be perfectly fine in a tank. After all aren't filters basically intended to do as much of the job nature does as is possible?

I do not see how having both nitrifying and denitrifying bacteria coexisting in an established fw tank or that their presence in the same filter in such a tank is anything but beneficial from the research I have read. Nor can one really argue that the removal of some free O from the water going through the media in a filter by bacteria, especially in a planted tank, is a danger. Considering how much oxygen fish breath and that plants use at night, this would surely deplete DO levels a lot more than anything bacteria might do. If this were an issue, there would be a whole lot more suffocated dead fish in tanks all over the world.

However, I am open minded and am willing to consider any science which shows the above to be incorrect. I welcome reading any links to the science which shows having both nitrifying and denitrifying bacteria at work in a tank, be it in the substrate or in the the filter, is a bad or unnatural thing. (I specifically mean having them living in close proximity as in the same media, bio-film or planted substrate.) I learn as much by being shown I am wrong as I do from being shown what is right.
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

TwoTankAmin, thanks for the reference. I'm swamped at work for the next few days, but I'll read the full article as soon as I can. The more perspective, the better!
Cheers,
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
The paper was investigating why a plant would transport oxygen via its roots such that the result would be to foster nitrifying and denitrifying bacteria which would be in competition for nitrogen with the plant- ammonia (as NH4) and nitrate. For this discussion the relevant thing to take from this paper here are that nitrification coupled with denitrification is natures way. And it seems to me this would be perfectly fine in a tank. After all aren't filters basically intended to do as much of the job nature does as is possible? I do not see how having both nitrifying and denitrifying bacteria coexisting in an established fw tank or that their presence in the same filter in such a tank is anything but beneficial from the research I have read.
I don't think any-one is arguing that de-nitrification isn't a good thing in the substrate, but I'm convinced it can rapidly become a problem in the filter media.

This is because you have both aerobic and anaerobic processes occurring with little spatial separation. You need to obtain a balance where have a steep oxygen gradient from aerobic to anaerobic over a very short distance

The conversion of NH3 to NO2 to NO3 is an oxygen intensive process (we've gone from 3 hydrogen atoms to 3 oxygen), and we are much more concerned with NH3 & NO2 than we are with NO3.

Ammonia and nitrite are toxic at very low levels, whilst NO3 has very low toxicity. I don't care if NO3 levels rise, the plants in the tank will respond with extra growth, but if NO2 or NH3 levels rise I'd have dead fish long before the plants have depleted the extra nitrogen.

The problem with de-nitrification occurring in the filter media
If the bio-load increases (extra ammonia from a decaying fish, emergency chloramine dosing in the tap water, etc.) or the supply of oxygen falls (partially blocked filter, very low atmospheric pressure, very warm water etc) you have a situation where the water in the filter will rapidly become de-oxygenated and ammonia will build up, starting a positive feed-back loop of lower oxygen, more ammonia, fish death, leading to more ammonia, lower oxygen levels etc.

Why aerobic filter media has built in stability
If you keep all the filter media aerobic you have much more capacity to deal with the scenarios above, as long as we can keep a flow of oxygenated water across the filter media it has an enormous capacity to deal with increased bio-load. This is why sewage works use "wet and dry" trickle filter beds, the large gas exchange surface allows the beds to deal with "water" with a huge bio-load.

Why having a relatively undisturbed substrate and plants will improve water quality
I keep planted tanks, with a substrate and emergent plants, for exactly the reasons set out in the Lobelia dortmanna study. I don't vacuum my substrate, or re-plant the plants, and fairly quickly after planting the substrate will have zones of positive and negative REDOX activity.

Within the upper substrate you will get aerobic nitrification, but only a few centimetres below the substrates’ surface as oxygen levels you get a zone of "facultative anaerobes" they utilise oxygen when it is available, but if O2 levels are low, they use NO3, stripping the oxygen and out-gassing (N2) gas.

In the substrate you are in system like you are suggesting for the filter, with the aerobic nitrifying bacteria providing the nitrate, and their high oxygen demand using the limited supply of oxygen.

The real difference is that the very upper zone of the substrate, and the immediate plant rhizosphere, will always being oxygenated. At the tank water substrate boundary you have a much more extensive gas exchange surface, which is immediately below a water column which is in contact with atmospheric oxygen levels.

I'm always go to have plants and a substrate and I'm going to leave the substrate relatively undisturbed.

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

Post by dw1305 »

Hi all,
I should also have said the closest analogy to keeping tanks for Loricariids would be from commercial aquaculture of Salmonids, using re-circulating systems. The advantage that examples from Salmonid culture over waste water treatment, or aquaculture systems for Channel Catfish or Tilapia, is that Salmonids are a lot less forgiving of lapses in water quality and require high levels of oxygenation at all times.

This is: Neil et al. (2013) "Freshwater Culture Of Salmonids In Recirculating Aquaculture Systems (RAS) With Emphasis On The Monitoring And Control Of Key Environmental Parameters." University of Glasgow <http://eprints.gla.ac.uk/85116/1/85116.pdf>.

This is a review of of "Hybrid constructed wetlands for wastewater treatment" <http://www.iaees.org/publications/journ ... atment.pdf>. In these systems there would be both aerobic nitrification and anaerobic de-nitrification, but with a spatial separation between them.

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

Post by TwoTankAmin »

I guess I am failing to explain the processes and bacteria involved clearly. So I will lean on SeaCgem to do it. They have a nedia called Matrix which is specifically designed to foster and support nitrification and denitrification in a single filter in the same media.
Matrix™ is a high porosity biomedia that provides efficient biofiltration for the removal of nitrogenous waste. Matrix™ is a porous inorganic solid about 10 mm in diameter. Each liter of Matrix™ provides as much surface (>~700 m2) as 170 liters of plastic balls! Plastic bio-materials provide only external surface area, whereas Matrix™ provides both external and internal macroporous surface area. These macropores are ideally sized for the support of nitrifying and denitrifying bacteria. This allows Matrix™, unlike other forms of biomedia, to remove nitrate along with ammonia and nitrite, simultaneously and in the same filter.

Matrix™ is completely inert and will not breakdown. It need not be replaced. Since the majority of the bacteria are internal, Matrix™ may be rinsed when needed without damaging the filter. Matrix™ is compatible with all types of wet or wet-dry filters.........

For biological filter media, specific surface area (measured as surface area per gram of material, or surface area per some specified volume of material) is very important. These products provide surface sites for bacteria to attach and do their work. The greater the surface area per gram of medium, the greater the number of bacteria that can attach. Thus a high specific surface area is desirable.

There is a second consideration, and that is the size of the pores in the medium. Generally, with very large pore diameters, we have smaller specific surface area, so that is not good. This generally rules out pores above 10 microns in diameter. But we can go too far in the other direction. If we have a very large number of very, very small pores, then our specific surface area number will be phenomenal, but the medium will not work very well as a biological medium. This is due to physical limitations, specifically too small a volume to support bacterial growth, and the decreasing efficiency of fluid transport (necessary to carry nutrients to the bacteria and waste away from the bacteria) with very small pore sizes. (Small pores still play important roles in physical and chemical processes, such as adsorption.)
from http://www.seachem.com/Products/product ... atrix.html

But let me come at this from another angle, Oxygen. The bacteria that do the denitrification are the facultative aerobes. Moreover, they get there originally because there is oxygen for them in the tank water. As long as they are not "forced" into denitrification, they are using up oxygen. Over time as a biofilm matures, it becomes possible for the autotrophic and heterotrophic aerobes to use all the O that comes their way and the result is that there is now nitrate but no free O left at that given depth of the biofim. And this will be the case whether or not there are any denitrifiers present. So inside the biofilm deeper in the media, the facultative bacteria living there will not get any free O. But instead of dying off to be in balance with the available O for them, they are able to switch over to using nitrate. When they do this they are no longer using free O. since it has been used up by the other bacteria. However, now they are denitrifying the tank, which is a benefit. So, bacteria that were using free O stop doing so and nitrate which was accumulating is now being reduced.

This all becomes much more relevant in those millions of tanks which have no plants and/or no substrate. It is fine to say "I do only planted tanks." unfortunately that is of little help to all those tanks with no or minimal plants. "Help, I have 40 ppm nitrate in my tap water and I keep an overstocked African rift lake tank for Tangs. How can I deal with high nitrate?"

I still see no logical nor scientific reason for not having nitrification and denitrification inside the same media and filter on a freshwater tank. Now if somebody has a greater than normal nitrate problem, I can see setting up a second filter with even better media for denitrification such as biodegrading polymer beads. But even this method requires the initial colonization of the biofilm by aerobes which will deplete the O for the denitrifiers to work.

Finally, at its heart the purpose of filtration in an aquarium is to do the work nature would in the wild. The ideal tank would be one in which we never changed the water and the filter and/or planting took care of the water quality. The ideal tank would be a self sustaining ecosystem. Now we all know this is impossible. However, I think it makes sense to get as close to this ideal state as we can, biologically speaking. Denitrifying bacteria should potentially be a better way to deal with excess nitrate than water changes or chemicals just as ammonia oxidizing microorganisms are a better way to deal with ammonia than water changes or chemicals.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
So inside the biofilm deeper in the media, the facultative bacteria living there will not get any free O. But instead of dying off to be in balance with the available O for them, they are able to switch over to using nitrate. When they do this they are no longer using free O. since it has been used up by the other bacteria. However, now they are denitrifying the tank, which is a benefit. So, bacteria that were using free O stop doing so and nitrate which was accumulating is now being reduced.
I think we will just have to differ on whether denitrification in the filter material is a good idea. I'm not saying it isn't possible, because it obviously is, but I'm really interested in the probable, rather than the possible.

Risk management, negative feedback and single point of failure

I'm going to talk about "single point of failure", resilience and risk assessment. They are fairly prosaic titles, and it isn't going to be a very exciting, but I would recommend it as an approach to everybody.

Single point of failure
This all becomes much more relevant in those millions of tanks which have no plants and/or no substrate. It is fine to say "I do only planted tanks." unfortunately that is of little help to all those tanks with no or minimal plants. "Help, I have 40 ppm nitrate in my tap water and I keep an overstocked African rift lake tank for Tangs. How can I deal with high nitrate?"
Problems with this is the filter has now become a "single point of failure".

It is also a severe risk and has a reasonable likelihood of happening.

If I was in this position, I would want the "no substrate, no plants" scenario to occur for as short a time as possible. As soon as I could I would add a substrate, even a thin layer of sand. I've now added resilience (I'm still dependent upon the filter, but I have a secondary site for nitrification in the substrate). If I add plants (they can be planted in a separate tank, or in planting basket with their stems emergent, or in an over-tank trickle filter) I've added more resilience, and also a negative feedback loop and an indication of the nutrient status of the tank (via the Duckweed Index <http://www.planetcatfish.com/forum/view ... weed+index>).

Tank design and management based upon risk assessment
It's not a "sexy" subject, but I'll cover it anyway.

My primary concern, and the primary requirement of all fish is that the water has enough dissolved oxygen at all times. If we have even a very limited period where the water doesn't have enough oxygen for the fishes requirement, the fish will die. Oxygen requirement will differ between fish, but large rheophilic fish are particularly at risk, which is partially why I wrote "Aeration and dissolved oxygen in the aquarium" <http://plecoplanet.com/?page_id=829>, this covers the mechanisms that deplete, and replenish, oxygen in the aquarium. As well as tank dimensions, and methods of adding oxygen to the water and removing CO2 etc., it has quite a lot on biological filtration because that is one of the major users of dissolved oxygen.

Because low oxygen levels are a severe risk I need to minimise the chances of them occurring, which is why I don't want potential single points of failure, or systems which require continual maintenance to keep them functioning. High NO3 levels are a low risk to the fish, but high NH3 levels will kill them by both direct toxicity and by depleting the available dissolved oxygen.

I want stable resilient systems, where if things go wrong I have secondary systems (an additional filter etc.) and negative feedback loops ("belt and braces") to keep the fish alive, and buy me enough time to make the necessary changes.

cheers Darrel
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