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The Importance of Beneficial Bacteria in the Nitrogen Cycle of Your Aquarium

beneficial bacteria in your aquarium

The importance of beneficial bacteria in the nitrogen cycle of your aquarium can not be overstated. Understanding the nitrogen cycle and how it works is crucial for maintaining a healthy aquatic ecosystem. In this article, we will explore the nitrogen cycle in water, why it is so important, and the role that nitrogen fixation bacteria play in this process. We will also discuss the steps of the nitrogen cycle and how it impacts the overall health of your aquarium’s ecosystem. By the end of this article, you will have a better understanding of how to maintain a healthy and thriving aquarium environment.

The Nitrogen Cycle: Understanding the Basics

Have you ever wondered how your aquarium is able to maintain a healthy environment for your fish? The answer lies in the nitrogen cycle.This process is crucial for the survival of aquatic life, and it all starts with beneficial bacteria.

In the nitrogen cycle, beneficial bacteria convert harmful ammonia from fish waste and decaying organic matter into less harmful compounds such as nitrite and then into nitrate. Nitrate is then taken up by corals or removed through water changes to prevent it from building up to toxic levels.

Water’s ammonia concentrations are typically measured as total ammonia, which accounts for both free ammonia (NH3) and ammonium ion (NH4+). The ratio of each of these components is influenced by the water’s pH,temperature, and salinity. When the pH is higher, the proportion of free ammonia (NH3) is greater in comparison to ammonium ion (NH4+).

Free ammonia (NH3) is more toxic than ammonium ion (NH4+) because it can enter the circulatory system of fish, causing damage to their neurological and physiological functions. Ammonium ion is less harmful because it cannot pass through the gills of the fish. Organisms that are exposed to ammonia experience symptoms such as apathy, hyperventilation, and convulsions. It has been reported that the maximum tolerance level is 0.1mg/l (ppm).

Nitrogen Cycle Stages: What’s Happening at Each Step?

An aquarium needs a nitrifying bacterial community to handle the generated ammonia. This community mainly consists of bacteria that utilize ammonia molecules as energy sources, and they carry out the nitrification process. The final outcome of this process is the nitrate ion(NO3), which happens in two stages:

1. Ammonia (NH4+undergoes a process of oxidation and is converted into nitrite ion (NO2).This transformation is carried out by bacteria belonging to the Nitrosomonas genus, including N. europaeaN. oceanusand N. mobilis

Nitrite ion (NO2) can enter freshwater fish through their gills and compete with the chloride ion in their tissues. This can lead to poisoning similar to that caused by ammonia. However, in marine fish, nitrite toxicity is generally low due to the high concentration of chloride ions resulting from salinity. Nitrite ions are displaced by chloride ions in the gills of marine fish.

2. The nitrite ion (NO2 undergoes oxidation to form the nitrate ion (NO3).This process involves bacteria belonging to the Nitrobacter genus, such as N. winogradski, Nitrococcus genus, such as N. mobilis, and Nitrospira genus, such as N. gracilis.



Nitrate (NO3) is a crucial nutrient for our system, but when it is present in high concentrations, it can have harmful effects. Even though it is less toxic than Nitrite, concentrations above 50mg/l (ppm) can cause negative consequences for corals and certain invertebrates. High nitrate levels can cause excessive algae growth, which can compete with corals for nutrients and space. Additionally, high nitrate levels can lead to poor water quality, which can stress and harm fish and other aquatic organisms.

It’s important to understand that the nitrogen cycle is a delicate balance. If there are not enough beneficial bacteria to convert ammonia, then toxic levels can build up, leading to fish stress, illness, and even death. Conversely, if there are too many bacteria, then the excess nitrate can cause algae blooms and other undesirable effects.

How to set up a nitrogen cycle in your saltwater aquarium.

To keep a healthy nitrogen cycle in your aquarium, you may wonder what steps to take. Follow these steps to establish a saltwater nitrogen cycle in your aquarium:

Step 1: Add Live Rock and Sand Bed

The first step in establishing a saltwater nitrogen cycle is to add live rock and sand bed to your aquarium. Live rock is porous and provides a surface area for beneficial bacteria to grow. Sand bed, on the other hand, provides a home for other beneficial organisms that play a crucial role in the nitrogen cycle.

Step 2: Add an Ammonia Source

The next step is to add an ammonia source to your aquarium.This can be done by adding fish food, pure ammonia, or live animals such as hermit crabs. Ammonia is the primary source of nitrogen in the nitrogen cycle and is essential for the growth of beneficial bacteria.

Step 3: Test Ammonia and Nitrite Levels

After adding an ammonia source, you should test the ammonia and nitrite levels in your aquarium regularly. Ammonia levels should be between 2-4 ppm, and nitrite levels should be between 0-0.5 ppm. High ammonia and nitrite levels can harm your fish and other marine life in the aquarium.

Step 4: Add Beneficial Bacteria

Once the ammonia and nitrite levels have stabilized, you can add beneficial bacteria to your aquarium. These bacteria convert ammonia into nitrite and then nitrite into nitrate. Nitrate is a less harmful compound that can be removed by performing regular water changes.

Step 5: Perform Regular Water Changes

Finally, you should perform regular water changes to keep nitrate levels in check. Water changes help to remove excess nitrate and other harmful compounds from the aquarium. It is recommended to perform a 20-25% water change every two weeks.

Following these steps will help you establish a saltwater nitrogen cycle in your aquarium. Remember to be patient as the nitrogen cycle can take several weeks to establish fully. Regular testing and maintenance are essential to keep your aquarium healthy and thriving.


Understanding the nitrogen cycle is essential for anyone who keeps an aquarium. By maintaining a healthy population of beneficial bacteria, you can ensure that your fish and other aquatic creatures have a safe and stable environment to live in. So the next time you perform a water change or add a new fish to your aquarium, remember the crucial role that the nitrogen cycle and its bacteria play in keeping your aquatic world thriving.

In conclusion, the nitrogen cycle is an essential process for maintaining a healthy aquatic environment. By understanding the basics of this cycle and taking steps to maintain the proper balance, you can ensure the long-term health and vitality of your fish and plants.

Sources & References:
«Evidence for behavioural thermoregulation by the world’s largest fish» (Article)
«Temperature acclimation and metabolism in ectotherms with particularreference to teleost fish» (Article)

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About the author

Picture of Ana M. López

Ana M. López

Ana holds a degree in Marine Sciences and has completed a Master's Program in Aquaculture with a specialization in ornamental species. Additionally, Ana is a certified Dive Master and Cave Diver, taking her passion for marine life to new depths. Ana has gained years of experience in the aquarium industry.