Hydrogen Sulfide production in anaerobic De-Nitrification for Aquarium/Pond Nitrate Removal
Updated 12/07/09

Hydrogen Sulfide is unfortunately a bi-product of anaerobic de-nitrification, of which denitrification is an important aspect of keeping low nitrate levels in both salt and freshwater. This said, it is important to achieve de-nitrification without undo amounts of Hydrogen sulfide produced
The production of Hydrogen Sulfide in aquariums (both salt and even more so freshwater) is a controversial subject, often with unclear answers as to whether anaerobic de-nitrification is beneficial in freshwater due to the POSSIBLE production of Hydrogen Sulfide. The keyword is “possible” as in saltwater, you CAN have de-nitrification with no or low hydrogen sulfide production.

With the most current research (although admittedly not conclusive in my view), you CAN have anaerobic de-nitrification and NOT have dangerous levels of Hydrogen Sulfide produced in both fresh & saltwater. With healthy de-nitrification it is possible to have low nitrate levels below 20 ppm

Points to achieving De-Nitrification (removal of nitrates) without hydrogen sulfide production

• One study showed that even though sulfate reduction (the production of hydrogen sulfides from Nitrates/Sulfur) took place maximally at ¾ inch (1-2 cm) depth, free hydrogen sulfide was present only below a depth of 2-1/2 inches (6-7 cm), above which Fe++ (Iron) was available for precipitation as iron sulfides.
So with this study in mind, keeping your substrate sand bed mixed at depths deeper than 2.5 inches and/or minimally aerated can prevent this process. This will also allow for better de-nitrification (lower nitrate levels) as nitrate will be allowed to better permeate the deeper sand depths allowing for more nitrate reduction and less sulfur reduction.

• Care should be especially taken with Under Gravel Filters as these filters can allow much compaction of gravel when gravel is much over 2.5 inches, as well mulm/sludge can build up under the under gravel plates and the biggest risk is when the filter is shut down either manually or by a power filter as this decomposing mulm can quickly go sulfur reducing anaerobic and not only produce hydrogen sulfide, but the more immediate danger is a sudden decrease of dissolved oxygen levels from the die off of aerobic nitrifying bacteria trapped/dying in the deeper layers of gravel or under the plates.

• Along this same line of thought as the previous point, a good surface flow of water and correct vacuuming procedures which includes surface vacuuming of top layers of gravel (in marine tanks I recommend a ½ inch layer over the several inch deep bet of fine #00 oolite sand), AND as well occasional and gentle vacuuming of deeper layers except where plant roots would be damaged.
One test/study I read showed that organics in totally oxygen deprived test tubes made little difference in the production of hydrogen sulfides, HOWEVER it was the total lack of oxygen and nitrates in these layers that allow for sulfate reduction to start.

• Another study showed that when 300 ppb hydrogen sulfide was added to Biscayne Bay and Gulf Stream waters off of Florida, the half life of the sulfide was 49 and 147 minutes, respectively. Such studies found that sunlight (both ultraviolet and visible) was able to significantly accelerate the oxidation.
This speaks “loudly” for strong lighting whether it be healthy 6400 K SHO lamps or Metal Halide (which my previous notes in reef keeping showed NO hydrogen sulfide production when these lights were employed). This also shows one more reason why a UV Sterilizer should be used, whether fresh or saltwater if they can at all be afforded (of which UV Sterilizers are not all that expensive, even for good quality models such as the Terminator).

• In freshwater aquariums, plant roots have been shown to not only remove ammonia directly, but as well (and more importantly as to the subject of this article) prohibit the total anaerobic conditions that promote production of hydrogen sulfides

What these points show is that the hydrogen sulfide production in substrate is only common when the area of sulfate reduction in question is totally deprived of oxygen and nitrates. As long as very small amounts of oxygen and nitrates can penetrate into the substrate (or live rock), this will not become a problem. This same general idea holds true for man made de-nitrators that have no oxygen whatsoever and are not bathed in adequate nitrates.
Light energy has also been shown to be a factor in destroying rogue hydrogen sulfide molecules in the water and penetrating into some layers of substrate as well.

Appearance/Evidence of sulfate reduction
A tell-tale sign of Hydro Sulfide production is black areas in the deep areas of sand or substrate, whether freshwater, marine, or especially ponds. The rotten egg odor is another sign although as Hydrogen Sulfide levels in the air increase, research has shown that human’s olfactory senses tend to block out the smell.
Please see the picture to the left of what the "black" Hydrogen Sulfide producing layers look like in sand (click picture to enlarge).

Hydrogen sulfide is toxic to a wide range of organisms, including people, which is a FACT that has been known for many years. It is just now becoming clear, however, that hydrogen sulfide also appears to play important roles in normal biochemical processes in animals. Neurons and muscles, for example, may use it in various ways, but exactly how this takes place has not been made clear scientifically.
One way that hydrogen sulfide exerts its toxicity is by inhibiting a mitochondrial enzyme called cytochrome c oxidase. It can be inhibited at hydrogen sulfide levels in solution as low as 30 ppb.12 Such inhibition limits the ability of mitochondria to produce energy for cells. Another enzyme, catalase, is inhibited at concentrations of 6,000 ppb.12 Other mechanisms of toxicity are also likely, and have recently been studied.

Hydrogen sulfide eruptions happen frequently off the shore of Namibia because of patterns in the ocean currents called upwelling. In this region, cold water pushes nutrients from the ocean floor to the surface, where ocean life thrives. In particular, large colonies of microscopic ocean plants, phytoplankton, grow in the nutrient rich water, forming the dark green swirls seen in this image. As the plants use all of the nutrients, they die and sink to the sea floor where bacteria consume them. The bacteria release toxic hydrogen sulfide gas into the soil. Eventually, the toxic gas erupts from the soil. In addition to the bright waters seen by satellites, the event is marked by massive fish die-offs and a strong smell that resembles rotten eggs. To date, hydrogen sulfide eruptions have only been observed off the shore of Namibia
Please click the picture to the left to enlarge.

HOWEVER hydrogen sulfide toxicity problems aside, I have observed and the most up to date scientific evidence supports that an aquarist or pond keeper CAN maintain de-nitrification without the worriesome production of hydrogen sulfides

For Further information about the Aquarium/Pond Nitrogen Cycle, please see this very well researched article:
"The Aquarium & Pond Nitrogen Cycle"

Further references:
http://www.agu.org/pubs/crossref/1997.../96JD03817.shtml
http://www.fhsu.edu/biology/eastrauss/Courses/MicrobEcol/Papers/Gerhardt%20et%20al%202005%20Biogeochem.pdf
http://reefkeeping.com/issues/2005-12/rhf/index.php