Friendly aquarium bacteria include the scavenging, decomposing bacteria digesting uneaten fish food, plant matter, dead algae, and basically everything that consist of organic matter.

The nitrifying bacteria aka nitrifiers aka beneficial bacteria, convert ammonia (resulting from bacterial activity, fish waste etc.) into the less toxic compounds of nitrite and nitrate. On rare occasions, denitrifying bacteria can settle in oxygen free areas and transform nitrate into oxygen and nitrogen gas.

‘Unfriendly’ bacteria are summarized as pathogenic, disease causing bacteria.

Pathogenic bacteria are opportunistic, meaning as long as the fish is healthy, it will not be bothered. Some bacteria are present at all times and in a constant fight with the fishs’ immune system. A strong immune system allows the survival of the bacteria strain without harming the fish.

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Bacterial infections are secondary diseases, they can only prevail if the fish is weakened under stressful conditions (heat, ammonia, nitrite, high organics, low dissolved oxygen etc.), resulting in rapidly multiplying pathogens.

A stressed and weak fish with pathogenic bacteria present results in a bacterial infection, which will be fatal if left untreated. A bacterial infection can therefore be defined as by pathogens outgrowing the defending cells of the immune system.

Any time a bacterial disease occurs adjustments in the aquatic environment need to be made in order to lessen and to eliminate stress causing factors to the fish. Bacterial diseases should be treated with antibiotics, preferably in a quarantine/hospital tank.

Antibiotics function by slowing down the pathogens thus increasing the immune systems efficiency. Nevertheless, it is the immune system that cures the disease not the antibiotic.

To achieve a slowdown, antibiotics interfere with the reproductive mechanisms of the pathogen by interrupting its lifecycle.

The two relating terms are antibiotics and antibacterial. While antibiotics are naturally produced by a microorganism to kill another microorganism, antibacterial substances such as sulfa and furans are manufactured artificially. (The term antibiotic is further used in this text referring to both, antibiotic and antibacterial).

To apply the correct antibiotic to a given pathogen the pathogens cell wall is decisive for the determination. Pathogens have either a thin or a thick cell wall.

The method to differentiate between the two main types of bacterial cell walls is called the “Gram Staining Technique”. Developed by the Danish physician Hans Christian Gram, Gram stained bacteria samples with the coloring agent crystal violet then applied potassium iodide resulting in a water insoluble blue-purple discoloration of the bacteria. Adding ethanol-alcohol as a decolorizing compound, the bacteria either retained the blue-purple color or turned red following a treatment with Safranin a counter-stain used for visibility purposes.

The blue-purple color indicates a thick cell wall and is called “gram positive”, while red indicates a thin cell wall and is referred to as “gram negative”.

This is of importance because of the response towards certain antibiotics.

Antibiotics against (thick wall) gram positive pathogens prevent the build up and repair of the cell wall whicheventually will lead to the cell content leaching out, consequently killing the pathogen. Antibiotics against (thin wall) gram negative attack by interfering with the protein synthesis (metabolic process) therefore eliminating the cells ability to produce food.

Gram positive antibiotics will not have any effect on gram negative bacteria nor will gram negative antibiotics have an effect on gram positive bacteria.

The most common pathogen in the aquarium are the aeromonad species for freshwater and its counterpart vibrionaceae in marine and reefs. Both are gram negative and everywhere present in the aquarium as part of the bacterial flora.

Aeromonads/vibrionaceae can be responsible for dropsy, abdominal swellings, skin ulcers, red patches, fin and tail rot and pop-eye.

General indicators of bacterial diseases can be disformed frayed fins, open sores, red steaks on fins or along the fish body, grey film on eyes, swollen or bloated belly, lethargic behavior, loss of appetite to name a few.

Antibiotics for use in the aquarium come in all forms and shapes – liquid, powder, or tablets.

It is essential to determine the disease causing bacteria in order to apply the correct antibiotic. The application dosage and time frame should be followed according to manufacturer’s recommendations.

Some common antibiotics used in aquariums

Erythromycin which treats gram positive bacteria and is best used in an alkaline environment (pH of 7 and up).

which treats gram positive bacteria and is best used in an alkaline environment (pH of 7 and up). Aminoglycosides marketed as neomycin, kanamycin and streptomycin are active against gram negative bacteria and work well in alkaline water conditions.

marketed as neomycin, kanamycin and streptomycin are active against gram negative bacteria and work well in alkaline water conditions. Sulfonamide known as sulfa or triple sulfa have antibacterial characteristics inhibiting the growth of bacteria. An alkaline environment is preferred and sulfonamide as well as aminoglycosides can be used in marine environments.

known as sulfa or triple sulfa have antibacterial characteristics inhibiting the growth of bacteria. An alkaline environment is preferred and sulfonamide as well as aminoglycosides can be used in marine environments. Nitrofurans (furane, nitrofurazone) are also antibacterial but will loose their potency with increasing pH levels. They are therefore preferred freshwater treatments as is the tetracycline group.

(furane, nitrofurazone) are also antibacterial but will loose their potency with increasing pH levels. They are therefore preferred freshwater treatments as is the tetracycline group. Tetracycline is bacteriostatic, inhibiting protein synthesis. This drug will get less effective in hard waters as it readily binds with calcium and magnesium.

is bacteriostatic, inhibiting protein synthesis. This drug will get less effective in hard waters as it readily binds with calcium and magnesium. Quinolones, antibacterial to treat gram negative bacteria, prevents DNA synthesis and can be used in a broad pH spectrum.

Bacterial diseases in fish can face antibiotic resistance, which means that the bacteria strain has mutated leaving it unaffected by the antibiotic. Another antibiotic will have to be used should this occur.

Bacterial diseases are not contagious and infected fish should be treated separately in a well aerated hospital tank. Antibiotics are potent by themselves and never meant to be used in combination, as some of them can eliminate each other or create toxic effects for fish.

Keep in mind that the beneficial bacteria are gram negative as well.