I think I was never born I'm just glad to still be here If I was it was so long ago I can't remember anyway.
On topic a couple of thoughts:
I think it's useful to look at the forces(physical and biological) in play in denitrification. Once understood I think it becomes clear that a wide range of approaches to managing denitrification are availabe to suit the needs of a particular aquarium and the tastes and prefernces of the individual aquarist.
It's not just about nitrate . Heterotrophic bacteria that use nitrate need organic carbon. Getting it to them in a deep sand bed requires that the bed be live for bio agitation or some other force such as advection moves it to them. ideally both. In addition to the diffusion(molecular movement toward equilibrium in water) that would occur but is very weak. So getting a balance of water flow high enough to deliver the nitrate laden water and organic carbon without making it so high that too much oxygen is available is the trick.
At first glance the RUGF may look like a nitrifier with a high degree of fluidization and high oxygen content negating the need for heterotrophs to use nitrate. In fact I think that's how it might turn out for many who attempted it. However, Paul has been running his successfully for a long time with a reasonably high biolaod and I respect that. With the proper flow rate and some ofthe supports he uses , I don't see why it wouldn't work.
The existence of a chemotrophic nitrogen fixing anaerobic heterotroph is suspect. If it does exist, I believe it would have to survive on organic carbon left over if any after the denitrifyig and sulfate using bacteria.It would be oligotrophic ( surviving on very low amounts of carbon ) and as such would be low in energy , density and activity. So I just dont think nitrogen fixing in a deep bed is a real concern.It requires energy and there isn't likely enough of an energy source in the depths.
BTW Whys I never heard the word hyperhypoxic before. What does it mean? Hyper usually means high and hypo usually means low.
The following is from another post of mine on a different thread. it goes over some of the forces in play and some of the alternative designs for denitrifying substrata. I thought it would serve as a useful summary:
Tom,
I don't think the are that many facts and they aren't terribly arcane. I'll attempt to summarize and get back on the track :
Terminology:
Advection: predominantly horizontal current and the wave action it produces as it encounters(an) obstruction(s)in it's path as well as the resulting "endo upwelling" under the obstruction. The upwelling occurs directly under the obstruction in a mirror image of it's footprint and height. At a horizontal flow rate of 10cm per second the endo upwelling will occur at a rate of 1cm per hour in the model presented by Sprung and Delbeek. The upwelling also results in water being pulled down .
Sprung and Delbbek use the term advection to describe this phenomenon as do Heutel and Rausch in their research(2). . Esoteric interpretations of discipline specific claims to specific terminology wether they be from engineering, meteorology ,chemistry etc . notwithstanding, I'll stick with them since they represent fields more closely related to reef keeping.
Diffusion: for the purposes of this discussion is the movement of molecules in water toward equilibrium. Some might call this convection but again , I'll use the terminology most commonly used in reef keeping literature.
Nitrification: the aerobic activity of autotrophic bacteria(those that can use inorganic carbon such as bi carbonate and CO2/carbonic acid)in oxic and hypoxic areas to convert decaying material to ammonia and nitrite and coenzymes such as adenosine triphosphate which they uses for energy transfer to enable life functions including cell division.
Denitrification: the anerobic activity of of heterotrphic bacteria(those that need organic carbon for energy) in hypoxic and near anoxic areas to convert nitrate to free nitrogen gas and coenzymes.
Faculative bacteria (those that can use either organic or non organic carbon for energy ) likely also play a role in both nitrification and denitrification.
Applications:
Trickle filters or towers : support high oxygen ,oxic areas and thus produce nitrate as an end product since they do not support heterotrophic bacteria which perish in the presence of oxygen.
Deep sand beds,generally over 4 inches deep as well as live rock can include : oxic , hypoxic and anoxic areas. Both autotrophic and heterotrophic bacteria can flourish in and on them. However, the heterotrophs need a source of organic carbon for energy and coenzme production. The autotrophs do fine with non organic carbon sources. So the deep sand bed needs a supply of organic material(dissolved or undisolved ) to keep the heterotrophs that use the nitrate viable. Obviously, it also needs a supply of nitrate. The bed (or rock) is fed by the water that moves through it via advection and/or the channeling and transport activity of benthic fuana. Diffusion supports the equilibriation of organic carbon molecules and nitrates throughout the water.
A deep sand bed without the proper amount of water movement to bring in the needed organic carbon and nitrate will not function well as a denitrifier. On the other hand too much fluidization will bring in too much oxygen. On the third hand, too much carbon and too little nitrate will set the stage for the bacteria to turn to SO4 for the oxygen they need with the potential for hydrogen sulfide formation as a by product. After that they will move on to metals and other nasty by products.Hence, the caveat on dosing organic carbon when deep sand beds are in play . Although some have suggested seeding a deep bed with sulfur or vodka et al. as a means of sourcing an energy source in a deep bed. I think it's dangerous.
Again a functional deep sand bed needs a force to insure the movement of oxygen depleted water( stripped by autorphic and faculative bacteria)laden with nitrate and a source of organic carbon for the heterotrophic bacteria to thrive and reduce the nitrate .
A bed that is allowed to clog or pack down or is just too deep for things to pass down just wont do very much.Benthic fauna in a live bed can help to maintain viability through channeling activities and assist in transport of organic materials..
Diffusion is a relatively weak force and will not in my opinion provide enough material to promote denitrification.
Advection, can enhance the process multifold( as many as 50 fold see reference (2) putting more water in play in which diffusion can occur.
The study by Tonnen and Wee from the Advanced Aquarist Magazine:
http://www.advancedaquarist.com/2008/8/aafeature3
concludes:
Each sediment-based aquarium design appeared capable of handling nutrient inputs up to 0.5 mg / L / day of NH4+ - which is equivalent to a well-stocked reef aquarium. At this input level, final concentrations of ammonia, nitrite and nitrate did not differ significantly among aquaria 1) with or without plenums, 2) containing deep (9.0 cm) or shallow (2.5cm) sediments, or 3) containing coarse (2.0mm) or fine (0.2mm) mean particle sizes."
So for my money ,deep (9inches or more of sand ) buckets with limited surface area, brisk flow to avoid detritus accumulation and no wave action except perhaps at the perimeter will not denitrify to any significant degree beyond the first few inches if that.
Live deep beds within a display with live rock will do better if the sand is kept live which may require periodic replenishment with fresh live sand..
These beds may also benefit from the effects of advection as the upwelling water passes upward under and through live rock. It seems ensuring sand is under the rock will enhance the process. Issues with the stability of the stack could be handled with pylon pvc structures under the rock backfilled with sand. I have these on my 7 year old in tank deep sand bed.
A remote deep sand bed (ie not in the display) can be more productive in denitrification with a larger surface area since even the small sand grains cause advective wave action and upwelling. Placing live rock on a bed can enhance it's effectivenes as a denitrifier since the effects of advection will enhance water movement under the rock to a depth equal to the height of the submerged rock per the model presented by Sprung and Delbeek.It will also enhance movement of water through the rock.
Nitrate removal can be accomplished by a number of means other than the substratum or rock such as: coil denitrifiers, carbon fed denitriers, sulfur denitrifiers,macroalgae refugia,carbon dosing , the use of granular activated carbon to remove organic material before it turns to nitrate as well as strong skimming and perhaps to some extent ozone in conjunction with granulated activated carbon.
Refernces:
(1)Sprung and Delbeek, The Reef Aquarium Vol 3.
(2)
http://aslo.org/lo/toc/vol_48/issue_4/1674.pdf
(3)
http://www2.hawaii.edu/~toonen/files/Toonen-Wee-05.pdf
If you'd like to tune this up some feel free , Tom. Your input is always appreciated.
__________________
Tom
Hobby Experience: 40yrs+overall,6yrs reef,9tanks,largest is a 120g reef
Current Tanks: 500g system consisting of a 120g reef sps mixed,a 90g lps,a 90g sps dominant,a 30g breeder lps frag tank ,a 40g sps frag tank,a 20g refugium,a29g refugium, an 88gal sump with live rock and rubble. Calcium reactor and kalk doser , mh pc and vho
Interests: Marine aquariums,fishing,reading,Bill's football, Sabres' hockey
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Old Post 05/19/2009 03:11 PM
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WaterKeeper
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It seems all the Chemistry Forum gang are on vacation. I was called in to the discussion just to keep things on a civil basis. Anyway, since I formerly moderated this forum when Randy was on sabbatical I will chime in.
quote:Trickle filters or towers : support high oxygen ,oxic areas and thus produce nitrate as an end product since they do not support heterotrophic bacteria which perish in the presence of oxygen.
You sure you didn't mean obligate anaerobes here. Most heterotrophs handle oxygen very well.
quote:After that they will move on to metals and other nasty by products.Hence, the caveat on dosing organic carbon when deep sand beds are in play . Although some have suggested seeding a deep bed with sulfur or vodka et al. as a means of sourcing an energy source in a deep bed. I think it's dangerous.
The principle post nitrate electron acceptor in water are usually sulfates, which exist in an abundance in seawater. Metals, on the other hand, are at fairly low levels, so fully oxidized iron and manganese would not be a major oxidative source. I've always agreed that the amount of DOM entering a DSB will be a sufficient carbon sink to allow active denitrification. Supplementation should not be required unless the remaining DOM is too refractory for effective electron donation.
quote:A bed that is allowed to clog or pack down or is just too deep for things to pass down just wont do very much.Benthic fauna in a live bed can help to maintain viability through channeling activities and assist in transport of organic materials.
Now there we get to the heart of the matter. Indeed the bio-agitation of a DSB is the key to its success. The movement of of countless ciliated protozoa, burrowing of worms and movement of things like mini starfish is what moves water through the bed. The same organism's respiration also release buoyant gas bubbles that further increase water movement throughout the bed. The bed exists in a state of constant, biologically induced, mechanical agitation and therefore serves as a major detritus processing component to the tank.
I've previously replied about that article by Rob and while I do not reject it I have some doubts about the statements on the bed not being able to process nutrient beyond the first inch or two of sand. My above paragraph explains why I disagree to some extent.
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Tom
Hobby Experience: Nearly 28 years in SW and a little over 10 years in Reef Tanks (and Still waiting on the OTS to strike)
Current Tanks: 130 Now out of service and a 29
Interests: Reef and ridding the world of unsightly Newbies
Last edited by WaterKeeper on 05/19/2009 at 03:17 PM
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Old Post 05/19/2009 03:36 PM
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Thanks Tom.
Obligate anerobes it is.Hey, how about obligate anaerobic chemotrophic heterotrophs?
Yep, sulfate is probably too abundant for the bacteria to move on to metals in most practical situations.
I also think a deeper bed with bio agitiation works.Keeping that going as you've noted in the past with live sand replenishment is a key.
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. OK maybe just a retired electrician hobbiest, but physics is physics and sand clogs.
including Waterkeeper.
I'll be back. 
