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Hydrogen Sulfide in Aquariums

Hydrogen Sulfide production in anaerobic De-Nitrification for Aquarium/Pond Nitrate Removal

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By Carl Strohmeyer-PAMR 35+ years experience
Updated 1/12/19


Hydrogen Sulfide is unfortunately often a companion 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 undue amounts of Hydrogen sulfide produced, but often this is difficult since both are byproducts of organic breakdown in environments that are either mostly devoid or totally devoid of oxygen. However within the last point is part of the answer as well!!

Hydrogen sulfide (sulfate reduction) generally results from the bacterial breakdown of organic matter in the total absence of oxygen, where as de-nitirifcation (nitrate reduction) that lowers nitrates while producing free nitrogen generally happens in an environment that is mostly devoid of oxygen but not completely devoid as in hydrogen sulfide production.

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

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.
This can be demonstrated with a canister filter or FSB filter that ceases operation (due to power filter, mechanical failure, etc.).

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. This also can be demonstrated with a canister filter that is set up with products such as Matrix, Bio Home, or Volcanic Rock where as even marginal oxygen penetration should keep the filter from producing hydrogen sulfides. Ditto a FSB filter operating with a large/tall reaction chamber or using nitrate removal products such as NPX Bioplastics

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.

Product Resources:
*AAP/TMC Professional FSB Filter
*AAP NPX Bioplastics

Appearance/Evidence of Sulfate Reduction

Hydrogen Sulfide in sand 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 somewhat.
However the smell test is still useful when one stirs up substrate releasing large amounts of trapped hydrogen sulfide bubbles which if your nose is just above the water's surface, the tell tale rotten egg smell is easy to detect. If bubbles released upon stirring the substrate do not produce a smell, likely the majority of these trapped gasses is nitrogen from beneficial nitrate reduction.

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.

Being that hydrogen sulfide is heavier than air, it can accumulate at the water surface if there is not adequate ventilation above the aquarium tank which in turn cuts off oxygen from entering the water resulting in livestock deaths. Look out for gasping fish as a possible sign.

Ocean Hydrogen Sulfides 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 worry-some 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:
*Hydrogen Sulfide and the Reef Aquarium
*Wikipedia; Hydrogen sulfide

Other Suggested Resources, Products

Freshwater Aquarium Care Information
Freshwater Aquarium Care

Aquarium Sponge Filter Information
Sponge Filtration; Information How Sponge Filters Work

NPX BioPlastics; Nitrate Reducing Media

NPX BioPlastics; Nitrate & Phosphate Reducing Media

by Two Little Fishies

Aquarium Fluidized Sand Bed Filters
TMC V² Bio Fluidized Sand Bed Filters

Premium, second to NONE Aquarium Bio Filters, that with optional Oolitic Sand also maintains essential aquarium calcium levels, alkalinity, & electrolytes that are important to ALL marine & freshwater life

Algone Nitrate Reducer

Algone Nitrate Reducer

Algone is an excellent product to utilize to lower nitrates, as enzymes in Algone break down proteins, carbohydrates and metabolic waste into insoluble complex structures

Wonder Shell
Aquarium Wonder Shell; ONLY Authorized full online seller

The most simple and proven effective way to maintain healthy mineral cations in your aquarium. Beware of parasite retailers online. ONLY AAP is authorized to sell the full line of FRESH Wonder Shells, both Medicated & Regular

AAP HJ-1542 Aquarium Pump
SunSun HJ-1542 Aquarium Pump; replaces Via Aqua 1300

This pump replaces the Via Aqua 1300 and other copies such as by AquaTop as the Premier Power Head Pump for Aquariums, Ponds, Fountains, Wet/Dry Filters. This pump is submersible with Mag drive & ceramic shaft


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In Chronological order of writing with the newest at the top

  1. How to Treat Sick Fish
  2. Whirling Disease in Fish
  3. Reef Aquarium Chemistry Maintenance
  4. Use of RO, DI, Softwater in Aquariums
  5. Lighting Theory of a Planted Aquarium- RQE, PFY, PAS, & PUR
  6. Aquarium or Pond Bio Load
  7. Tuberculosis in Fish
  8. PUR vs PAR in Aquarium Lighting
  9. Head Pressure in Aquarium and Pond Water Pumps
  10. Fin/Tail Rot For Betta & ALL Fish
  11. Angelfish Virus/Aids
  12. Activated Carbon
  13. Fish Baths/Dips as an aid to treatment
  14. Streptococcus gram positive bacterium in aquariums, Eye Infections
  15. Hydrogen Sulfide
    production in anaerobic De-Nitrification for Aquarium/Ponds
  16. Fish Shipping
  17. Aquarium Size, Fish Stunting
  18. Aquarium Algae,
    BBA & Brown Algae in particular
  19. Aquarium Salt (Sodium chloride) in Freshwater Aquariums
  20. Betta Habitat; Wild Bettas to Domestic Betta environment parameters
  21. HITH; Hole in the Head Disease
  22. Aquarium Protein Skimmers, Ozonizers
  23. Power Head/ Water Pump Review
  24. Molly Disease/ Mollies in an Aquarium
  25. Basic Fish Anatomy, Fin Identification
  26. Aquarium Moving/ Power Failures
  27. Octopus as Aquarium Pets
  28. Aquarium Nitrates
  29. Ichthyophonus protists, fungus in fish
  30. Aquarium and Pond Filter Media
    Types; Mechanical, Bio, Chemical
  31. Aquarium Water Conditioners (also Pond)
  32. Fish Parasites; Trematodes & Monogeneans; Annelids and Nematodes;
    Flukes, internal worms, Detritus Worms (often confused with Planaria), Micro Worms
  33. Aquarium Silicone Application;
    DIY Aquarium Repair & Glass thickness
  34. Pond Veggie Filters; DIY Bog Filter
  35. The difference between Plaster of Paris and Aquarium Products such a Wonder Shells:
    Identification, prevention & Treatment
  37. AQUARIUM TEST KITS; Use & Importance
  38. SEXING FISH; Basics
  39. Chocolate Chip, Knobby and Fromia Starfish
  40. Freshwater Velvet & Costia
  41. Usnic Acid as a Fish Remedy
  42. Aquarium Heaters; Types, information
  43. The Lateral Line in Fish, Lateral Line Disease
    or Head and Lateral Line Erosion (HLLE)
  44. Tap Water use in Aquarium; Chloramines, Chlorine
  45. Can Black Ghost Knife fish give an electric shock?
  46. Bio Wheel Review; Do Bio-Wheels really work?
  47. How do Fish Drink?
    Use of RO Water
  48. Cyclops, and Predatory Damselfly larvae
  49. Betta with Dropsy;
    Treatment and Prevention of DROPSY in all fish
  50. pH and KH problems in African Cichlid Aquarium
  51. Aquarium Gravel, which size?
  52. Blue green algae, Cyanobacteria in Ponds/Aquariums

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