A matter of trust?

In the last years it has become very popular the use of all types of bacteria as a convenient and smart solution to solve some of the most common problems in the marine aquarium (high levels of nitrates and phosphates, cyanobacteria, dirty substrate, seaweed, diseases and infections…). Almost all manufacturers have rushed to launch their own bottles “miraculous”, cocktails of unknown content that are positioned as the best solution to these problems.

Some hobbyists say they work awesome, others see little change or improvements. Could it be that we do not know to use it? Is it just another one of those snake oil elixirs bottled in attractive color bottles?

And it seems that every manufacturer has its own system to facilitate these bacteria reach the aquarium in perfect condition: Some are bottled in vials that we must keep in the fridge, others do not seem to need the preservative power of cold because they come encapsulated in a nitrogen atmosphere, other bottles are coated with a protective substance and unknown preservative, some separate them in different bottles and say they do not need any conservation measure but the most fascinating is the system of those who come dry, accompanying other products such as activated carbon, zeolites or even grains of salt.

And all of them with the same noble and generous objective: turn our aquarium into a healthy system, clean and natural. So little.

It is perfectly understandable, sensible and reasonable: we are skeptical and so must be.

Types of bacteria

They can be classified in many ways, but we will focus on the two groups that interest us, the nitrifying bacteria and the denitrifying bacteria.

As we know, Nitrogen compounds are major pollutants in a marine aquarium. It all starts with secretions of fish and invertebrates and release of ammonium / ammonia: at a pH of 8,3 there is approximately 10% ammonia (NH3) and a 90% ammonium (NH4), being the first one much more toxic. The more densely populated is the tank and the more we feed the fish, the higher the concentration of these compounds will be.

This is where they begin their important work the nitrifying bacteria, especially nitrosomonas and nitrosococcus, which oxidize these molecules converting them in nitrite (NO2), much less toxic. For this process to be effective these oxidizing bacteria need a well oxygenated media so they are frequently found on the outer surfaces of rocks, sand and even the walls of the aquarium (biofilm).

However, nitrites remain a serious threat, especially for fish and not so much for invertebrates, because when they reach the bloodstream through their gills, they turn hemoglobin into meta-hemoglobin, which is unable to capture oxygen molecules causing the fish to die asphyxiated (fish that die poisoned by nitrites usually have a cyanotic appearance and bluish guts).

That's when another group of bacteria show up, the nitrobacter, which transform nitrites (NO2) into nitrates (NO3) by a second oxidation. Besides oxygen, these bacteria make use of CO2 as a major carbon source to perform a process called aerobic digestion.

But our problems with nitrogen compounds do not end here . The nitrate ions are less toxic than nitrites, but they have a drawback: they are the best fertilizer for algae. We must reduce the nitrates concentration, or the tank will soon fill up of algae which eventually end up suffocating any coral inside.

And how to remove nitrates? Just doing the opposite that what we've been doing so far: removing the oxygen atoms from the NO3 molecule until it becomes free nitrogen: N2

And who is able to remove the oxygen from these molecules? No more no less than denitrifying bacteria, the real film stars. It is very easy to transform the ammonia into nitrite and then nitrate, just wait for the nitrifying bacteria colonies to settle and feed our animals to provide enough ammonia. But removing nitrates…that's a little more complicated.

By full name

All this theory is great and most of the hobbyists already knew it. Let's get a deeper knowledge about them and what every bacteria strain can do for our aquarium.

Nitrosomonas Europaea acuario

Nitrosomonas Europaea

It is a gram negative very common on any surface containing oxygen and nitrogen. It tolerates a relatively high pH range (between 6 and 9) which makes it be frequently found in both fresh and salt water, on the ground, grass, and even buildings and vehicles in moderate or highly polluted cities.

They are chemoautotrophs and only require ammonia and oxygen to thrive, they do not depend on light as many other bacteria. The result of the aerobic digestion of these bacteria are nitrite molecules, a very toxic compound for any animal with blood circulation. Because of their heavy dependence on ammonia, their reproduction is very slow and it takes several days to divide.

Nitrosococcus Mobilis acuario

Nitrosococcus Mobilis

Ellipsoidal and provided with a small flagella, these bacteria feed on oxygen and ammonium to produce nitrite (NO2). Quimioautótrofa and gram negative it can be found in fresh and salt water as well as soil and any surface containing ammonium. It can survive in anaerobic conditions producing nitrous oxide (N2O). It can be inhibited by metals like zinc.

Nitrobacter Winogradskyi acuario

Nitrobacter Winogradski

Like the previous one, it is a bacterium gram negative easy to find on the ground and freshwater / seawater. This bacterium has flagella and a double cell membrane, able to live in both oxygenated areas and those deprived of this element. They will only be able to process nitrites in the presence of oxygen, thus providing nitrate molecules.

These bacteria get their energy from the nitrite oxidation (NO2) and fixing the carbon dioxide (CO2), but when oxygen is no longer available they behave as chemoheterotrophic feeding on nitrate (NO3) and producing nitrites (NO2), nitrous oxide (N2O) and nitric oxide (NO).

Alcaligenes Denitrificans acuario

Alcaligenes Denitrificans

Bacteria heterotrophic and gram negative capable to reduce nitrates (NO3) by reduction. As a result of the anaerobic digestion nitrogen molecules are released to the surrounding media. Like any organism heterotrophic besides nitrogen it also needs a carbon source to thrive.

We can find these bacteria on any surface, especially on soil and contaminated water (fresh and saltwater).

Paracoccus Denitrificans acuario

Paracoccus Denitrificans

Like the previous ones, Paracoccus Denitrificans is a bacterium gram negative, which means that it has a double membrane. It is a roller-shaped bacterium that can adopt a spherical shape under certain conditions. It has no flagella and therefore lacks motility.

It is very useful in the aquarium because of its high capacity to convert nitrates (NO3) into free nitrogen.

This bacterium chemoautotrophic stands out from the previous ones beacause of its adaptability to almost any media, so it is considered extremophile. It can thrive in aerobic and anaerobic conditions and within very wide temperature and pH ranges, a fact that makes it very easy to find it in any media containing nitrogen and carbon.

In the absence of nitrates it is able to digest molecules of methanol and methylamine, and even inorganic compounds containing hydrogen and sulfur, such as thiosulfate.

Pseudomonas Stutzeri bacteria

Pseudomonas Stutzeri

Bacteria gram negative cylinder shaped up to 3 microns in length and equipped with a single flagellum that provides some mobility. They are considered universal bacteria because of their usual presence in almost all media, especially soil and sea.

They are chemoheterotrophic and usually they get their energy from organic molecules and dissolved sugars, amino acids and acetates.

Depending on oxygen availability, they can become denitrifying taking nitrate molecules and reducing them to nitrogen.

Their adaptability to a wide variety of media and ability to act as nitrifying or denitrifying bacteria depending on the availability of oxygen, makes this bacteria some of the most used ones for wastewater treatment and as a fundamental element in bioremediation.

Pseudomonas citronellolis acuario

Pseudomonas Citronellolis

Bacteria gram negative, cylindrical and approximately 1 um length, equipped with a single flagellum that allows certain motility. Usually aerobic (they can survive without oxygen in the presence of nitrate).

They are very useful in the aquarium because they eliminate building fats, phospholipids, oils and other toxic hydrocarbon compounds.

Plasticizers are partly converted to less harmful compounds. These bacteria can link to phosphates temporarily, permitting they can be partially removed through the skimmer.

They are very hardy and thrive in a range of temperatures between 4 and 42ºC.

Flavobacterium acuario

Flavobacterium Aquatile

They are bacteria gram negative, cylindrical, elongated and are provided with flagella that allow them some motility. Aerobic and dependent on nitrogen, they can be found in sludge and marine or freshwater sediments.

Flavobacterium Oceanosedimentum

Similar to the previous ones, they are direct consumers of nitrogen molecules in the presence of oxygen and thus contribute to the oxidation of ammonia and nitrite.

Rhodopseudomonas acuario

Rhodopseudomonas sp

Bacteria gram negative cylinder shaped and tendency to cluster radially forming spheres (etymological interpretation of the name is “fake rose”). It can be found in wetlands and flooded areas, such as marshes and swamps, lakes and coastal areas forming a kind of viscous orange-brown sludge.

Rhodopseudomonas stands out bacause of its ability to change its metabolism depending on the conditions in which it is, it can behave like photoautotrophic, photoheterotrophic (usual), chemoautotrophic and chemoheterotrophic.

Its metabolic flexibility is amazing: It can thrive with or without oxygen, take advantage on sunlight or not and synthesize organic and inorganic compounds

They are especially useful in the aquarium when operating as photoheterotrophic by eliminating halogenated carboxylic acids (very toxic). To accomplish this they only need light, a carbon source such as CO2 and oxygen.

Rhodospirillum rubrum acuario

Rhodospirillum Rubrum

Bacteria gram negative with the shape of a spiro and small (less than 1 µm). It has great motility due to multiple flagella on each pole (usually seven).

It is a facultative typically employing anaerobic bacteriochlorophyll for light energy. In the presence of oxygen photosynthesis ceases and it loses its characteristic pink color.

It is significant that for photosynthesis they use bacteriochlorophyll, instead of chlorophyll A as most of the organisms do. This makes it can absorb light of wavelengths between 800 and 925 nm (chlorophyll A does it between 660 and 680 nm). This wavelength corresponds to the red part of the spectrum, which it is more abundant in shallow areas.

These bacteria are especially useful in the aquarium because of their ability to fix nitrogen from denitrification and thus compete against cyanobacteria which can also fix nitrogen. This makes it a particularly useful bacteria to prevent and combat the appearance of cyanobacteria in our aquariums.

Thiobacillus thiooxidans acuario

Thiobacillus Thiooxidans

Another bacteria gram negative really useful in our aquarium. Cylinder shaped and provided with a polar flagellum, Thiobacillus Thiooxidans presents moderate motility. It has predilection for acidic environments, with a pH value near 4 so it is not as common as above described species.

These tiny bacteria autotrophic (capable of synthesizing inorganic compounds) is particularly useful for their ability to oxidize very toxic sulfur compounds such as hydrogen sulphide (H2S), so we can only find them in aerobic and well oxygenated areas. Their carbon demands are not very high and it will be enough with the dissolved CO2 in the water.

Curiously, say that it is a bacterium widely used in agriculture for their ability to acidify excessively alkaline soils.

Thiobacillus Denitrificans acuario

Thiobacillus Denitrificans

If you found useful the previous bacterial strain , wait to meet this one.

Alike the previous one it is a bacterium gram negative cylinder shaped, small size (up to 3 µm) and reduced motility. Thiobacillus Denitrificans is also chemoautotrophic, but their presence is not limited to, well-oxygenated aerobic areas as it is facultative (it can thrive with or without oxygen)

It likes neutral soils or with a slightly acidic pH and temperatures in the range of 30°C so , unlike the previous, we can find it virtually on any soil and especially on marine sediments and degraded areas.

Being facultative allows it to follow two metabolic pathways:

  • In aerobic zones it will behave as the previous one, oxidizing hydrogen sulphide (H2S).
  • In anaerobic zones will keep consuming sulfur, in addition to large amounts of nitrogen in the form of nitrate and ammonium:

H2S + HS + NO3 + CO2 + HCO3 + NH4+ –> SO42- + N2 + C5H7O2N (biomass) + H+ + H2O

And if this wasn't enough, this bacterial strain has the competitive advantage of requiring small amounts of carbon in relation to the nitrogen that it can process (it will be enough with some CO2 in the water). It is the kind of bacteria that inhabit the typical sulfur reactors, less used.

Thiobacillus Thioparus acuario

Thiobacillus Thioparus

Bacteria gram negative small size, poor motility and cylindrical. It is an obligate chemoheterotrophic aerobic, which means that it needs organic compounds and oxygen to thrive.

It is common to see colonies of Thiobacillus Thioparus forming yellow efflorescences on the surface of some rocks such as the one shown on the left.

It is of high utility because of its ability to degrade dangerous organic compounds such as sulfur carbon disulphide, metanotiol, dimethylsulphide and dimethyl disulphide before they can form hydrogen sulphide gas which is highly toxic.

Clostridium Nitrophenollicum acuario

Clostridium Nitrophenolicum

This time we are talking about a bacterium gram positive, cylinder shaped and with certain motility. Obligate anaerobic and occasional inhabitant of some substrates, it has the ability to degrade p-nitrophenol which is very toxic to the aquarium inhabitants.

This bacterium is able to produce spores, allowing it to appear again when conditions improve.

Bacillus Pumilus acuario

Bacillus Pumilus

Another bacteria gram positive and with the ability to release spores. Aerobic and quite common on any terrain or substrate.

Its spores have the amazing ability to resist ultraviolet light, prolonged periods of extreme drought and even contact with moderate concentrations of hydrogen peroxide.

It is especially useful in the aquarium for its ability to combat fungal infections like Rhizoctonia and Fusarium. As if that wasn't enough it is very effective inhibiting bacteria of the genus vibrio (responsible for the death of many fish).

Comamonas Testosteroni acuario

Comamonas Testosteroni

Bacteria gram negative, moderately sized, cylinder shaped and with some motility. It is a very ubiquitous aerobic bacteria, and can be found in most flooded areas of land and fresh or salt water.

It is very useful in industry wastewater treatment for its ability to accelerate the degradation of certain contaminants, which is known as bioaugmentation.


As we have seen, most bacteria available for use in marine aquaria are gram negative, namely, they have a double membrane (cytoplasmic and outer). Another common features in the analyzed bacteria strains is their high strength (capable of proliferating in large ranges of pH and temperature) and their ubiquity (most are present on all types of media, either dry or wet).

Moreover, many are able to adapt to new circumstances deviating from their usual metabolic pathway when they lack the necessary conditions and have no food. Some even are facultative and can adapt their metabolism to the presence or absence of oxygen.

Bacteria are ubiquitous microorganisms and keep a constant interspecific balance. In a healthy aquarium, without heavy metals, inhibitory substances or limiting elements (in general it is required the presence of nitrogen, phosphorus, carbon, sulfur and oxygen) there must be a large population of bacteria of different species, although it is true that multi-bacterial balance is usually adversely affected overtime and cause some of them be located on the brink of extinction (what it is known as a monoculture in a closed system).

Therefore periodic inoculation of different bacterial strains is advisable, which will ensure adequate maintenance and biodiversity.