The Aquarist's Introduction to Bacteria

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What is a Bacterium?

A bacterium (bacteria, pl.) is a single prokaryotic cell and so, by definition, lacks a nucleus and is, generally, much smaller than any eukaryotic cell.

Bacterial cells come in a variety of shapes and sizes. The shapes most relevant in terms of fish health are coccus (spherical) and rod. The smallest bacterial cells are 0.2µm in diameter and are usually no larger than 50µm in diameter. However, a very unusual marine bacterium is the largest known prokaryote, and has a diameter of 0.75mm (or 750µm). This cell can actually be seen with the naked eye!

Another important distinction between bacterial cells is their variable tolerance to oxygen. Bacterial cells will fall into one of the following groups:

  • Aerobes: grow in the presence of the normal oxygen level of air (21% O2).
    • Microaerophiles: are aerobes that grow best in oxygenated environments with lower concentrations than that of air.
    • Facultative aerobes: will use oxygen if it is present, but can also grow in anoxic conditions
  • Anaerobes: do not use oxygen.
    • Aerotolerant anaerobes: tolerate the presence of oxygen, but are unable to use it.
    • Obligate anaerobes: experience either inhibition of growth or death as a result of the presence of oxygen.

Aerobes: grow in the presence of the normal oxygen level of air (21% O2).

Microaerophiles: are aerobes that grow best in oxygenated environments with lower concentrations than that of air. Facultative aerobes: will use oxygen if it is present, but can also grow in anoxic conditions Anaerobes: do not use oxygen.

 Aerotolerant anaerobes: tolerate the presence of oxygen, but are unable to use it.

Obligate anaerobes: experience either inhibition of growth or death as a result of the presence of oxygen. Bacteria which cause disease in freshwater fish include both aerobes and anaerobes. It is very common to classify most pathogenic bacteria based on their gram-staining characteristics.  The Gram Stain is classified as a differential stain because cells will stain different colors based on certain morphological characteristics. When performing the gram stain, gram-positive cells will stain purple and gram-negative cells will stain pink/red due to differences in the structure of their cell walls. Any purple cells have retained the dyes crystal violet and iodine, while pink/red cells have retained the dye safranin.  The majority of bacteria which are pathogenic to tropical aquarium fish are gram-negative. Click here to read about how the gram stain works.

Good, Bad, or Both?

As any mildly experienced aquarist knows, not all bacteria are bad news. Even though all pathogenic prokaryotes are bacteria, not all bacteria are pathogenic. In fact, the benign, nitrifying bacteria that colonize filter media (and all other hard surfaces in an aquarium) do a great service by breaking down the ammonia waste produced by fish.  The Nitrogen Cycle is further explained in our Encyclopedic-Dictionary.

Bacteria which are classified as primary pathogens will cause disease in otherwise healthy fish. In the case of such detrimental bacteria, prevention is the key to avoiding potentially massive problems.

There is also a group of bacteria which fall into the gray area of opportunistic pathogens. Opportunistic bacteria are considered a part of the normal flora and will not cause problems with healthy fish. However, any fish with an already compromised immune system can be attacked. Fish will lose the ability to resist attack when they are either very young or very old, under stress, already diseased, or experiencing malnutrition.

Bacteria capable of infecting a host will have different levels of pathogenicity as expressed by their virulence. Virulence is a measure of how many bacterial cells of a certain strain must be present in the host in order to elicit a response by the host in a certain amount of time. Another way of thinking about virulence is the ease with which bacterial toxins break down the tissues of the fish. Digestion of the fish provides nutrients that allow the bacteria to reproduce - increasing in number until they elicit a host response - occasionally, death. A highly virulent strain of bacteria can potentially kill a large number of fish in a short amount of time.

Methods of Infection

Fish are infected by bacteria when the pathogens successfully penetrate the fish's physical and chemical barriers such as skin and mucous. For example, feeding food which has gone bad can introduce the bacteria directly to the intestines of the fish - where they can be absorbed directly into the bloodstream. Transmission can also occur through parasites which may harbor the bacteria. Once introduced, the resulting bacterial infections are classified as either systemic or localized. Of the systemic infections, there are two types: acute and chronic. Acute infections come on rapidly without any clear or obvious signs of a bacterial infection. Chronic infections are long-term and often cause visible symptoms which are characteristic of bacterial infections.

Symptoms of a Bacterial Infection

Symptoms of a bacterial infection fall into two categories: Behavioral and Physical. These symptoms aren't necessarily exclusive to bacterial infections, but may also result from parasites and certain non-infectious problems.


  • Weakness evident as motionlessness
  • Swimming in circles
  • Unusual swimming orientation due to loss of spatial orientation


  • Hemorrhages (bleeding)
  • Ulcerations (Inflamed tissue surrounding an area of dead tissue; no pus)
  • Skin erosions (Fin rot, tail rot, body rot, cloudy eye)
  • Ascites (Bloat): an enlarged abdomen may be accompanied by exophthalmia, or "popeye"

The above symptoms have varying degrees of severity and some can be treated successfully. However, it is our experience that a fish with ascites is very unlikely to survive, despite any amount of treatment. Many cases of bloat are due to a chronic Mycobacterium infection. The fluid accumulation is due to disruptions of osmotic regulation as a result of the destruction of kidney tissue. Treatment is futile, as the damage is irreversible.

Treatment with Antibiotics

There are many different antibiotics on the market for treating ornamental fish. They function by either slowing down bacterial reproduction long enough for the fish's immune system to wipe out the infection - known as a static antibiotic, or by killing the bacterial cells as with cidal antibiotics. Due to different modes of operation, antibiotics may only treat certain bacteria. For example penicillin interferes with the synthesis of the cell wall of bacteria (since animal cells do not have a cell wall, they are not harmed). With a weakened or absent cell wall, osmotic pressure differences between the interior and exterior of the cell cause it to lyse (burst). This is only effective against gram-positive bacteria which depend on an extensive cell wall for survival. The structure of gram-negative cell walls is different enough that it isn't affected by penicillin. However, ampicillin, a synthetic penicillin-like drug, has been modified to act as a broad-spectrum antibiotic and will eliminate both gram-positive and some gram-negative cells.

How to Choose an Antibiotic

Short of some fairly elaborate laboratory assays, it is nearly impossible to know for certain the absolute best antibiotic to use in any given situation. This is why most aquarists stick to trial and error - add an antibiotic and observe the results. If the fish get better...success! No improvement and you will have to continue experimenting.

Antibiotic Resistance

Continuous use of antibiotics will lead to the emergence of antibiotic-resistant strains of bacteria. The antibiotic resistance may arise as a random mutation in a single bacterial cell, which due to its beneficial nature is selected for and becomes increasingly predominant in the future generations of bacteria. Once the population is mainly comprised of antibiotic-resistant strains, continuing to use the medication will only be harmful. The antibiotic-resistance can also arise from the transfer of resistance-factors on plasmids via conjugation between bacteria. Thus, it is wise to use antibiotics sparingly, and as stated on the label directions. Continuous use is not only costly, but is also not a cure-all solution. Many Mycobacterium strains can remain safely protected from antibiotics in a dormant state in the body for long periods of time and reemerge at a later point. Mycobacterium tuberculosis is the species responsible for tuberculosis in humans. Another Mycobacterium, M. leprae, causes leprosy. This particular bacterium genus can be spread from fish to humans. This is why it is important to never submerge an open wound in an aquarium.

Medication in a bath versus Medicated Foods

The following chart is a quick summary of the pros and cons of both medicated foods and medications which are added directly to the tank water. We will also note here, that contrary to a fish-keeping "urban legend", medicated foods will not cause a fish to become sterile.

Adding Medications to Water
  • Dosing is based on gallons of water in the tank, and therefore is easy
  • All fish in the tank are uniformly exposed to the medication
  • Cons
  • Tank pollutants have the ability to interfere with adsorption of the medication by the fish
  • Bactericidal meds will kill the beneficial nitrifying bacteria. While bacteriostatic will slow their growth
  • Medicated Food
  • Allows easy absorption of meds in the gut of the fish
  • Less antibiotic can be used compared to treating the water., therefor it's less costly
  • Dosing is based on a fish's food intake
  • Environmentally friendly
  • Cons
  • Sick fish may not eat the food
  • Prevention

    A rampant bacterial infection would be a nightmare for any aquarist - have they one or many tanks. It can not only wipe out an entire population, but it can remain inconspicuously dormant in survivors as well as in endospores with the intent to similarly destroy the next generation of fish. This is why we stress the importance of prevention. We strongly recommend the implementation of a very strict quarantine procedure. (To read about it, click here.) This is the same procedure that we have faithfully upheld for over 30 years and is the reason we can produce quality, disease-free fish. If you are planning to purchase your fish from us, congratulations, you're making a great investment! However, keep in mind that without proper quarantine practice, any other fish you introduce to your population can (and probably will) infect the fish you buy from us. Our fish are very high quality for many reasons - among them being the assurance of health. If you choose our breeding stock to start your own lines, protect your investment and quarantine.

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