The Nitrogen Cycle Refresher Course

In essence, the Nitrogen Cycle is the infinitely complicated path, set of paths, overlapping and diverging paths, twisted and sinister paths, etc. by which Nitrogen circles around and through the earth, air and water.   Thank goodness we don't need to know all that much about it.   I painfully recall, and perhaps some readers of this article do too, being required to memorize the basics of the Nitrogen Cycle in school.   I can also remember rolling my eyes thinking 'when am I ever going to need to know this?'   Huh, well, believe it or not, here it is again.  The breakdown of nitrogenous wastes (largely from animals), occurs via the Nitrogen Cycle.  This is not unique to aquariums.  I'm sure any self-respecting farmer could tell you just as much or more about the in-soil manifestation of the Nitrogen Cycle as any DSB-loving reef aquarist could tell you about the in-aquarium manifestation of this process.   Grossly over-simplified,  it's the pathways by which:

1)      Ammonia is fixed (by nitrogen fixing bacteria) to make Ammonium. 

2)      Ammonium is converted into nitrogen oxides (nitrites and nitrates) by nitrifying bacteria. 

3)      Nitrogen oxides are converted into nitrogen gas and water.

Aerobic bacteria accomplish the first two steps.  Anaerobic bacteria accomplish the third.  Anaerobic bacteria absolutely need an oxygen depleted space in order to live and do their thing.  In a DSB, the goal is to have the top layer be aerobic (containing oxygen), with oxygen concentration gradually declining to zero down into the sand bed.   In this way, a DSB can become an excellent natural filter.  Essentially, all biological aquarium filters work this way (with an aerobic zone in juxtaposition to an anaerobic zone).   However, in all such filters, the biological filtration capacity is limited by the surface area available for bacterial colonization.  In a DSB, this surface area is truly immense.  If you do the math, the surface area can get up to an acre or more in the average DSB!   

Of course, as with any over-simplification of a biological process, I'm leaving out countless side reactions and other by products.  For example, hydrogen sulfide is a significant by product of denitrification which is toxic to fish if it doesn't exit the system in the form of gas (which it is at room temperature).  When hydrogen sulfide precipitates iron sulfides, this is what turns areas of sand substrate black.  This phenomenon is why some zealous bare bottom advocates call DSBs 'ticking time bombs.'  According to the ticking time bomb theory, the anaerobic layer of sand in a DSB accumulates toxins and will eventually 'erupt' in a sudden cataclysmic release of a myriad of denitrification by products (such as hydrogen sulfide), causing a total tank 'crash' (sudden death of all live stock).   While I suppose it's possible for such a thing to happen, I doubt that it often does.   For one thing, as mentioned, hydrogen sulfide is a gas.  Thus, so long as the DSB is well populated with benthic organisms and the aquarium system employs good circulation and gas exchange, hydrogen sulfide should bubble out along with nitrogen gas and carbon dioxide, etc.  More poignant for myself personally, I had an experience with one of my own systems that caused me to seriously question the DSB time bomb idea. 

ANECDOTE: The following is a mere anecdote and should not be taken more or less seriously than any other anecdote.  I once had the good fortune of watching my 65g aquarium start to leak along the bottom rim.  It started as a drip, then a steady stream.  Well, you know how this goes.  In less than an hour, I was forced to drain the tank (water, sand and all).  I'm embarrassed to admit that I was terribly unprepared for such an undertaking and did not have nearly enough pre-mixed water or anywhere for the livestock to go except a few empty aquariums of various sizes and plenty of spare Maxi Jet power heads.   When I got down to my DSB (about 4 inches deep), I started to scoop it out in 20oz slushy-cup-fulls at a time.  The rotten egg smell was room-filling and noxious.  The sand just an inch or two below the surface was black.  There was every sign that at least parts of my DSB had turned into an all-out hydrogen sulfide toxic waste dump.  How long it had been this way, I don't know.   Regardless, all my fish, corals and invertebrates had no choice but to sit in that same water and sand for at least 3 days before I could replace the leak tank.  And yet, nothing died.  Of course, this is, as forewarned, a mere anecdote.   While I was happy to see that my sand bed had, obviously, a significant anaerobic zone, I was not happy to see so much evidence of hydrogen sulfide (and iron sulfide).  This is not ideal.  Thus, having learned of what was going on in my sand bed, I made a concerted effort to obtain more benthic organisms (worms, micro-crustaceans, seed shrimp, etc.) which would provide the necessary subtle movement in the sand to allow hydrogen sulfide to more readily exit the sand bed.  So while I'll concede that a poorly maintained sand bed with insufficient benthic life can result in significant hydrogen sulfide production, I'm not ready to concede that DSBs (even at their worst) are 'ticking time bombs' that will (or could) crash your tank and kill your animals at any time.

The Significance of Grain Size, Grain Composition and Sand Bed Dimensions

Grain Size:

Arguably, even sugar-fine is likely too large a grain size to get the full functionality of a sand bed as a source of nitrogenous waste filtration.    The reason for this is, the functionality of a sand bed as a biological filter is dependent on the existence of an anaerobic zone where anaerobic, denitrifying bacteria can carry out denitrification (in large part, the conversion of nitrogen oxides into nitrogen gas and water).   The coarser the sand, the less anaerobic space there will be.  To understand this concept, ask yourself; 'would I rather be buried under marbles or mud?'   Buried under marbles, you might stand a chance of survival since all the spaces between the marbles allow at least some air to get through.  Buried under mud, you'd suffocate in a minute or so (depending on how long you could hold your breath).   By the same general principle, a sand bed of coarse sand is going to be more oxygenated all the way through even if left undisturbed.  With a sand bed of sugar fine sand (i.e. a grain size of ~0.5mm), at the bottom of 4 inches, you'll likely get at least some anaerobic zones, but not nearly as much as with finer sand.  I'll note here that this might be the actual advantage of some 'mud' products sold as substrates for marine aquariums.  Marine mud is, after all, just very fine sand/substrate.  

All this said about the theoretical importance of grain size for creating anaerobic environments, I must tell you that some denitrification will occur even if you use marbles for substrate.   But there's even more to this issue of grain size.  The truth is that a lot of benthic (sand dwelling) organisms are very picky about the range of sediment grain size they will tolerate.   Some of them are picky to an extreme such that they will not reproduce or live a normal life span if stuck in sediment of a grain size even just 0.01mm outside of their preference.  Some organisms will just refuse to live in finer or coarser substrate.    And unfortunately, you just can't make everybody happy.  Dr. Shimek opines that a sand grain size of 0.125mm is likely a good middle ground compromise for enough benthic organisms.  Alternatively, some equally intelligent aquarists recommend using substrate of mixed grain sizes, with grains occurring across a range of 0.05mm to 0.5mm in size.  For those who wish to know more about this topic of sand grain size and the functionality of sand beds, I refer you to many articles on the subject written by Dr. Ron Shimek, Dr. Robert Toonen and others.  

In short, the thought is that finer the sand, the more effective the sand bed will be as a processor of nitrogenous waste. Keep in mind though, that, no matter how fine or coarse your sand might be, the filtration capacity of your sand bed will not appreciably increase beyond a depth of about 5 or 6 inches.  In fact, there's likely not much to be gained by having a sand bed deeper than even four inches.

 Sand Bed Dimensions:

Generally speaking, the dimensions of the 'foot print' (length x width--not depth) of a DSB should be at least ~4.5 square feet (or roughly the footprint of a 40g breeder).  Unfortunately, this recommendation is routinely given and taken without much explanation.  Generally, it's thought that this is the threshold dimension needed to maintain a healthy population of benthic organisms.  Empirically, for whatever reason, it looks like the filtration and other benefits of a DSB aren't so apparent when the dimensions are much smaller than this. Also, again, if you want to make your sand bed bigger, make it longer and/or wider (rather than deeper). 

Grain Composition:

When it comes to substrate composition, marine aquarists often find themselves choosing between aragonite and silica.  Though aragonite is usually favored, marine substrate does not necessarily have to be aragonite.  There's reason to believe, theoretically, experimentally and anecdotally, that aragonite provides *localized* alkalinity benefits which might be advantageous for any number of reasons.   For example, it might aid in phosphate precipitation and/or dinitrification.   However, any potential contribution (if any) it makes to the overall alkalinity and/or pH balance of the system as a whole is not likely significant.  Even with a sand bed of fine aragonite, you will still need to balance your system's calcium and alkalinity by some other means.  If you want to use silica sand (or 'quartz sand') and you're worried about soluble silicates, I would advise rinsing the sand *a lot.*   While quartz (SiO2) itself will not add silicates to your water (since pure quartz is virtually insoluble in water), you might be hard pressed to find 100% pure quartz sand.   Less than pure quartz sand will inevitably have some contaminates of soluble silica compounds.   However, it should be easy enough to rinse away any contaminate that's water soluble.

 Now, if I could put a side bar within a side bar, I'd discuss different commercial sources for substrate of different grain sizes and compositions.   Instead I'll just note here that there are places outside of your local aquarium store or pet store where you can find cheap substrate suitable for marine aquariums.   In addition to browsing your local aquarium store's substrate selection, don't hesitate to venture into a hardware store and/or construction supply store.   However, do be sure you know what you're getting and what you're putting in your aquarium (potential contaminates and all).

The Jaubert System

Though arguably not a 'DSB' under my previously given definition, I'll discuss it here since it's closer to a DSB than it is to any other substrate choice.   The Jaubert system was developed by French marine biologist, Professor Jean Jaubert, in the late 1980s, and became popular in early 1990s.   In brief, this is a system with a layer of sand on top of a layer of gravel that is suspended over a thin layer of empty space.  This empty space at the bottom of the aquarium, underneath the gravel, is called the 'plenum.'  In the Jaubert system, two different types of substrate are used to create the aforementioned aerobic and anaerobic zones/layers.  Additionally, there's this 'plenum' underneath it all.  Therefore, there is water both below and above the substrate.  Supposedly and apparently, setting up the substrate in this way reduces hydrogen sulfide production and according to some aquarists, reduces nitrate levels.   Though I've never attempted to use this method myself, I (and others) have enjoyed theorizing as to what might be going on in these systems.   One such theory is that water moves through the layers by way of convection which results from a difference in temperature of the water above and below the substrate layers.  If the water on one side of the substrate layers is warmer or cooler than the plenum, convection will create a very subtle, steady 'flow' through the substrate layers.  This flow could possibly create the gas exchange needed to allow hydrogen sulfide, when/if produced, to exit the system more easily.   Or, if the gas exchange is significant enough, it might decrease the size and number of available anaerobic areas in which hydrogen sulfide production could occur.  However, this writer wonders, if the Jaubert system creates fewer anaerobic areas, how could it accomplish just as much denitrification (which also requires an anaerobic environment)?  Perhaps the reactions resulting in hydrogen sulfide production are more sensitive to the presence of oxygen than are the desired denitrification reactions.  If this is the case, then having a hypoxic environment that's not quite completely anaerobic might allow for all the same nitrate reduction while limiting hydrogen sulfide production.  However, I dare not delve too far into any detailed discussion of Jaurbert systems as this has already been done by writers far more experienced with them than myself.   There has even been some dabbling into controlled experiments aimed at comparing the Jaubert system to 'traditional' DSBs and other methods (see list of references at conclusion of this article).  Thus, I refer anyone wishing to know more about Jaubert systems to articles written by Dr. Toonen and others.