Water Quality and Nitrogen Cycle for Amphibians

We're an affiliate! When you purchase something through our affiliate links, We may earn commission.

The nitrogen cycle is the process by which toxic ammonia (NH3) is converted into nitrites (NO2), and then into nitrates (NO3) by the production of beneficial bacteria. In aquatic systems, especially captive environments, the nitrogen cycle must be allowed to complete before inhabitants are introduced; this is referred to as cycling the tank.

Once the nitrogen cycle has been established in a new tank, it is a continuous conversion process (hence the word cycle in nitrogen cycle).

Because captive environments are typically very tiny compared to natural habitats, this biological cycle will at some point require some assistance in the form of tank maintenance (i.e. gravel vacuuming, water changes, filter changes etc.), which will be discussed later in the article.

When an aquatic tank is first setup, the water is clean and void of the necessary bacteria to enact the nitrogen cycle. The nitrogen cycle begins when organic matter begins to decay, usually in the form of fish waste and uneaten food items.

Decaying organic matter creates toxic ammonia in a new tank and semi-toxic ammonium ions (NH3 and NH4+, respectively), which are converted into potentially toxic nitrites by the nitrifying bacteria, Nitrosomonas and Nitrococcus.

Nitrites are then converted into nitrates by another nitrifying bacteria, Nitrobacter. Nitrates are the end result of the nitrogen cycle, and are only harmful in excessive amounts.

These bacteria are often dubbed ‘beneficial bacteria’, and will reside in the substrate of the tank, and in the biological filter (if one is provided).

When organic matter initially decays, i.e. when an aquatic system is first established, the ammonia levels increase to potentially lethal levels (they spike), until Nitrosomonas and Nitrococcus bacteria are established and convert the ammonia into nitrites.

At this point, the nitrite levels will spike to potentially lethal levels, until Nitrobacter baceria are established and convert the nitrites into nitrates.

During the initial cycling of a new tank, the water is highly toxic as ammonia and nitrite levels spike, which is potentially fatal to most fish and amphibian species.

For this reason, tanks are usually cycled with very hardy fish, such as Zebra Danios (Brachydanio rerio), Guppies (Poecilia reticulata), or feeder gold fish. Still, it is common to incur fatalities even with the hardiest of fish.

An alternative to using fish to cycle an aquarium is to add small amounts of frozen or freeze dried foods. This creates decaying organic matter, which will initiate the nitrogen cycle.

This approach has the same end result as using fish, but with no fatalities, and may also be safer for amphibian tanks, as fish can carry diseases and such.

pH, Ammonia, Nitrite, and Nitrate

pH is a measurement of the acidity or alkalinity of a solution. pH stands for potential of Hydrogen, and is the negative log of the hydrogen ion concentration in grams, atoms, or moles per liter of a solution.

The pH scale ranges from 1 – 14, where 7.0 is neutral, below 7.0 is acidic, and higher than 7.0 is alkaline (or basic).

The base-10 property of the logarithmic function indicates that each unit of change of pH is equivalent to a tenfold change in acidity or alkalinity (ion concentration). As the hydrogen ion content in solution increases, the pH decreases, or becomes more acidic, and vice versa.

It is worth noting that in acid-base relationships, sometimes the pOH, potential of hydroxide ion, is relevant also. The relationship between pH and pOH is as follows: pH + pOH = 14.

It is also important to know that acids and bases are found in equilibrium in solution, such that as one increases, the other decreases, and vice versa.

Speaking in terms of water solution, such as in an aquarium, H+ acts as an acid, while OH acts as a base.

Calculating pH and pOH values
pH = -log [H+] and [H+] = 10-pH
pOH = log -[OH] and [OH] = 10-pOH

Ammonia in an aquarium results from decaying organic matter. Two forms are present in equilibrium, NH3 and NH4+, the former of which is the toxic, and potentially lethal form.

Typical ammonia tests measure both forms combined, however, individual tests are available.

The amount of NH3 present is proportional to temperature and pH, but is more dependent on pH. The percentage of NH3 increases with increased carbonate hardness, which equates to increased pH, as NH4+ ions are converted to toxic NH3 molecules.

At lower pH levels, NH3 converts to NH4+ (in aqueous solution, ammonia acts as a weak base, and ammonium ion as a weak acid). If the pH increases, the released H+ (hydrogen ion) rapidly forms NH3 ions with the present NH4+ ions, resulting in high levels of toxic NH3 molecules.

In summary, it can be said that at low pH levels NH4+ ions predominate, while at higher pH levels, the more toxic NH3 molecules predominate.

It should be clear that higher ammonia test results at lower pH levels are less lethal to fish and other animals than the same ammonia test results at higher pH levels, assuming a combined test kit is used.

Ammonia Equilibrium
NH3(aq) + H2O(l) <======> NH4+(aq) + OH(aq)
        NH4+(aq)  <======> NH3(aq) + H+(aq)

It should also be understood that although ammonia test results are less lethal at lower pH levels, toxic nitrite levels are higher at such pH levels.

A similar acid/base equilibrium occurs between nitrite (NO2) and nitrous acid (HNO2), where the acidic form is predominate in acidic water, and vice versa.

However, in the case of nitrites, the opposite is true in terms of toxicity, that is, the acidic form is more toxic than the basic form. 

Introducing New Inhabitants – The Bio Load

The bio-load is the amount of organic matter present in an aquarium, in regards to the nitrogen cycle, and is measured by its proportionality to the volume of water for which it is contained.

For example, a 55 gallon aquarium housing 5 Cynops pyrrhogaster will have a larger bio-load than a 100 gallon aquarium with the same inhabitants because the amount of organic matter present at any time is more concentrated in the 55 gallon, and more diluted in the 100 gallon.

Also, the bio-load is increased or decreased when life forms are added or subtracted, and the bacteria present in the tank must compensate when the bio-load changes.

Each time a new member is introduced, the bio-load increases, and the nitrogen cycle attempts to compensate by increased bacterial growth.

Similarly, when a member is removed, there is a slight excess in bacteria for which the nitrogen cycle will attempt to compensate.

In turn, this disruption of the nitrogen cycle can cause spikes in ammonia, nitrites, and nitrates, and reduced pH levels. To avoid shocking the system, it is necessary to introduce new inhabitants moderation (i.e. few at a time).

Cycling and Maintenance of Aquatic Tanks

Beneficial bacteria will reside in two key places in an aquarium: the substrate, and biological filter.

Once the bacteria is established, it should never be completely removed by thorough cleaning of the gravel or removal of the biological filter.

If the bacteria is completely removed from the tank, the nitrogen cycle will restart, which is potentially fatal to fish and amphibians.

However, bacteria can grow in excess in small aquarium environments, and will require some maintenance to ensure stable levels.

Excess food and waste should be removed from the gravel by a 1/3 gravel vacuum every month or so, depending on the size of the tank, the number of inhabitants, and the type of inhabitants.

This will keep ammonia levels at 0 ppm (parts per million), which will in turn help regulate nitrite and nitrate levels, as well as influence the stability of pH levels.

The biological filter should be lightly cleaned of clogging debris and algae every month, or so, depending on the size of the tank, the number of inhabitants, and the type of inhabitants.

General Hardness (GH), Carbonate Hardness (KH), Alkalinity, CO2, and pH

Aquarium water contains dissolved ions in varying amounts, which determine the hardness of the water. Water hardness is a general term that refers to water hardness as a whole, however, in the aquarium world, there are two measurements of water hardness: Carbonate hardness (KH), and general hardness (GH).

In a freshwater system, such as an aquarium, cations (ions with a positive charge) of magnesium and calcium are present in varying amounts, and form salts with anions (ions with a negative charge) present in the water.

General hardness (GH) is a measurement of the amount of dissolved magnesium, and calcium in the water source. For clarity, iron, aluminum, strontium, and barium may also be present, but provide negligible contributions to water hardness.

Some confusion of terms has resulted from the original translation of the German word, Gesamthaerte, abbreviated GH, which means “Total Hardness”. Somewhere in the translation to English, the definition was obscured to “General Hardness”, still abbreviated GH, which is used in the U.S. In summary, “General Hardness” is synonymous with “Total Hardness”, both abbreviated by GH. Similarly, the abbreviation KH was derived from the German word Karbonathaerte, meaning “carbonate hardness”.

The terms KH, and carbonate hardness are used synonymously with the term alkalinity, which often causes confusion in the aquarium world.

The terms KH and carbonate hardness should be used carefully, as they are not accurate descriptions of what is actually measured by a typical KH test. A KH test is supposed to measure the buffering capacity of only the carbonate/bicarbonate buffering relationship in a given water source.

Although carbonate and bicarbonate are the main contributors to the buffering ability of a water source, there are other contributing ions present, as well.

In actuality, a KH test measures the total alkalinity, or buffering capacity, of the water source because it also takes into account other contributing ions.

Essentially, a KH test measures alkalinity as a whole, and does not discriminate between carbonate/bicarbonate ions and other contributing ions.

This is because alkalinity is measured by acid titration, which does not discriminate between ions; any significant base present in the solution will be titrated.

A true carbonate hardness test would measure only the buffering capabilities of the carbonate and bicarbonate system. Although the alkalinity in an aquarium is usually a reflection mainly of carbonate & bicarbonate, this is not always the case. 

When using pH/KH/CO2 tables to determine CO2 concentration, errors can occur as a result of carbonate hardness test results that include other ion measurements, in addition to bicarbonate.

This is because such tables are based on true carbonate hardness measurements, not alkalinity.

In general, KH test results of soft water, where phosphates or other salts are not present or are negligible, bicarbonate is the major buffer component, and so levels of KH are very close to the alkalinity value.

In this case, because KH is equal, or nearly equal to alkalinity, pH/KH/CO2 tables are virtually accurate.

However, in the case of hard water, where phosphates or other buffers are present, the measurement of alkalinity and carbonate hardness will be significantly different values.

In this case, a KH test will read higher than accurate, and inaccurate values from pH/KH/CO2 tables will result.

Although there is not a direct method of measuring true carbonate hardness, the value can be calculated indirectly by using a pH/KH/CO2 tables, in conjunction with accurate CO2 and pH tests. After determining the pH and CO2, the tables can be used to determine the true KH measurement.  

Permanent and temporary hardness are terms that also appear ambiguously in the aquarium world. Permanent hardness is essentially GH minus the hardness resultant from salts of magnesium and calcium, other than carbonates and bicarbonates.

Temporary hardness is essentially the GH minus the permanent hardness, that is, the hardness resultant from magnesium and calcium carbonates and bicarbonates.

This is not to say that you should actually subtract units, however, this may give a mental perspective of what is actually meant by the terms permanent and temporary hardness.

To soften hard water, diluted de-ionized or spring waters are sometimes, and are usually more effective than chemical alternatives.

De-ionized water should never be used alone with amphibians because it is void of ions, and can disrupt the chemical composition of amphibian cells (Water Quality and Amphibians).

Instead, de-ionized, distilled, or spring waters are usually mixed in some ratio with hard water to form a softer solution. 

To maintain hardened water, crushed coral can be added to the substrate, or placed in mesh bags and added to the tank or filter.

A few natural additions, such as driftwood or peat, can be used to lower pH values.

With any method, the pH should be incremented very slowly, so as not to shock the inhabitants. A change of no more than .3 units per day is recommended.

  • Carbonate Hardness (KH) = measurement of alkalinity, or buffering capacity, resultant only from carbonates and bicarbonates of calcium and magnesium
  • Permanent Hardness (PH) = measurement of waters total, or general, hardness minus the carbonate hardness. The permanent hardness is a measurement of salts of calcium and magnesium, other than carbonates and bicarbonates
  • General Hardness (GH) = measurement of total water hardness.
  • Alkalinity = the ability of a solution to resist changes to pH; buffering capacity.
  • pH = negative logarithm of the hydrogen ion concentration present in a solution; potential of Hydrogen. This equates to the measurement of acidity
CO2 + H20 <======> H2CO2 (Carbon Dioxide + water = Carbonic Acid)
H2CO2 <======> H+ + HCO3 (Carbonic Acid => Hydrogen ion & Bicarbonate)
HCO3 <======> H+ + CO32- (= Bicarbonate => Hydrogen ion & Carbonate)