Nitrogen Cycle Help

This is quite good, as are some of their other videos. Thanks for posting.

A minor point as it doesn't affect the aim of the video, but he is wrong on the second-stage bacteria strain. Nitrosomonas bacteria do the ammonia to nitrite, but we now know that the nitrite to nitrate is not Nitrobacter but probably Nitrospira. I use the word "probably" because the team of scientists led by Dr. Hovanec that determined the true bacteria responsible for nitrification in the 1990's couldn't determine the specific bacteria handling the nitrite to nitrate part in their freshwater aquaria, so they assumed it was a strain of Nitrospira similar to those in marine environments. Nitrobacter was definitely ruled out as this bacteria only operates in soil, not water.

While we're on the topic, even more recent research in the last few years has determined that these bacteria only appear in new aquaria. Once an aquarium is established, these bacteria disappear and no longer perform this nitrification. A strain of archaea colonize and carry out nitrification. Another and very large topic.

Byron.

Byron Amazonas said:

This is quite good, as are some of their other videos. Thanks for posting.

A minor point as it doesn't affect the aim of the video, but he is wrong on the second-stage bacteria strain. Nitrosomonas bacteria do the ammonia to nitrite, but we now know that the nitrite to nitrate is not Nitrobacter but probably Nitrospira. I use the word "probably" because the team of scientists led by Dr. Hovanec that determined the true bacteria responsible for nitrification in the 1990's couldn't determine the specific bacteria handling the nitrite to nitrate part in their freshwater aquaria, so they assumed it was a strain of Nitrospira similar to those in marine environments. Nitrobacter was definitely ruled out as this bacteria only operates in soil, not water.

While we're on the topic, even more recent research in the last few years has determined that these bacteria only appear in new aquaria. Once an aquarium is established, these bacteria disappear and no longer perform this nitrification. A strain of archaea colonize and carry out nitrification. Another and very large topic.

Byron.

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Interesting assertion...please link to any articles on this information. I'm interested in the mechanism of how/why the bacteria are replaced by archaea. Also, hopefully an explanation of why media from an older, established aquarium can be used to initiate the colonization of bacteria, which are apparently no longer present, in a new aquarium.
thanks,

Mark

wesleydnunder said:

Interesting assertion...please link to any articles on this information. I'm interested in the mechanism of how/why the bacteria are replaced by archaea. Also, hopefully an explanation of why media from an older, established aquarium can be used to initiate the colonization of bacteria, which are apparently no longer present, in a new aquarium.
thanks,

Mark

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Here is the link to the 2011 scientific study that first brought this archaea issue to light for aquarists:
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023281

Both of your questions are answered therein, but I will just copy/paste the last two paragraphs which summarize this. [AOA = Ammonia-oxidizing archaea, and AOB = Ammonia-oxidizing bacteria.]

Although the detectable ammonia concentrations in established freshwater aquaria are typically low as a result of biological ammonia oxidation, a preference for high ammonia concentrations by AOB suggests a possible role for their involvement in first establishing an aquarium when ammonia concentrations may approach levels associated with fish toxicity. In addition, ammonium concentration was positively and significantly correlated with the number of fish per gallon of aquarium water (Tables S2 and S3), suggesting that AOB may also be important for heavily stocked tanks that experience chronic high ammonia concentrations.


This study has identified that AOA are the dominant ammonia oxidizing microorganisms in freshwater aquarium biofilters. Aquarium ammonium concentrations were significantly and inversely correlated with AOA:AOB ratios. Freshwater aquarium AOA amoA gene sequences largely clustered with other freshwater-associated sequences. This work provides a foundation for future studies of aquarium nitrification and AOA ecology. Aquaria may serve as valuable microcosms to investigate the factors affecting AOA and AOB dynamics in both natural and engineered aquatic communities, including wastewater treatment systems, aquaculture, lakes, rivers and oceans.

Byron.

Fascinating! Thanks.

I'm interested in denitrification to get rid of or maintain a low level of nitrate. Would like to know how I can increase the population of these BB.

Byron Amazonas said:

Here is the link to the 2011 scientific study that first brought this archaea issue to light for aquarists:
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023281

Both of your questions are answered therein, but I will just copy/paste the last two paragraphs which summarize this. [AOA = Ammonia-oxidizing archaea, and AOB = Ammonia-oxidizing bacteria.]

Although the detectable ammonia concentrations in established freshwater aquaria are typically low as a result of biological ammonia oxidation, a preference for high ammonia concentrations by AOB suggests a possible role for their involvement in first establishing an aquarium when ammonia concentrations may approach levels associated with fish toxicity. In addition, ammonium concentration was positively and significantly correlated with the number of fish per gallon of aquarium water (Tables S2 and S3), suggesting that AOB may also be important for heavily stocked tanks that experience chronic high ammonia concentrations.


This study has identified that AOA are the dominant ammonia oxidizing microorganisms in freshwater aquarium biofilters. Aquarium ammonium concentrations were significantly and inversely correlated with AOA:AOB ratios. Freshwater aquarium AOA amoA gene sequences largely clustered with other freshwater-associated sequences. This work provides a foundation for future studies of aquarium nitrification and AOA ecology. Aquaria may serve as valuable microcosms to investigate the factors affecting AOA and AOB dynamics in both natural and engineered aquatic communities, including wastewater treatment systems, aquaculture, lakes, rivers and oceans.

Byron.

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Interesting study...thank you Byron.

Mark

FishFanMan said:

I'm interested in denitrification to get rid of or maintain a low level of nitrate. Would like to know how I can increase the population of these BB.

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Many aquarists neglect denitrification, but as you seem to realize it is an important part of the biological system.

The bacteria responsible for denitrification are heterotrophic, meaning bacteria that cannot synthesize their own food so they need organic material such as fish waste, dead bacteria, fish and plant matter, etc. While some are aerobic (which means, requiring oxygen to be present), many are facultative anaerobes, meaning that they can survive in either the presence or absence of free oxygen. Anaerobes are organisms that do not require free oxygen for growth. This has significant consequences in aquaria.

There are several species of heterotrophic bacteria that utilize nitrate by consuming the oxygen within nitrate and releasing nitrogen gas. They do not require free oxygen in the water so they are facultative anaerobes, and generally occur in what we term “dead spots,” which occur when water movement is stopped and thus no oxygen is available. These are the good guys among heterotrophs, since de-nitrification is important in a healthy aquarium. And they will naturally occur in the lower level of the substrate, which is a good reason for not disturbing it with deep cleaning, at least in several areas such as under chunks of wood and rock.

The greatest population of bacteria in a healthy balanced aquarium occurs in the substrate, not the filter. The floc or humic compost that collects in the substrate is the host for the biofilms; this is why the substrate in planted tanks should never be disturbed, and many aquarists apply this to non-planted tanks as well.

In very general terms, aerobic nitrification takes place in the top 1-2 inches of the substrate; anaerobic de-nitrification takes place approximately 2-4 inches down, and anaerobic bacteria producing hydrogen sulfide occurs in substrates deeper than 3-4 inches. In all three cases, it will be deeper in coarse substrates (like pea gravel) and more shallow in finer substrates such as sand. These generalities will also vary with the presence of live plant roots and substrate “diggers” such as snails and worms, since these factors result in more oxygen being made available in the substrate, reducing anaerobic bacteria activity. An oxygen level in the substrate of as little as 1 ppm promotes nitrogen reduction rather than sulfur reduction (hydrogen sulfide).

Having explained the processes (I hope), the answer to your question is to leave at least some of the substrate alone. I have tanks in which I never vacuum the sand at all, and some tanks I do just the top of the front sand. I also have a great many chunks of wood in my tanks, and the sand under these is never disturbed.

Byron.

What the heck is denitrifucatrion =P Just put frogbit and it'll eat up all the bad stuff.

Russian_Girl said:

What the heck is denitrifucatrion =P Just put frogbit and it'll eat up all the bad stuff.

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Nitrification refers to the change of ammonia to nitrite to nitrate, and the bacteria responsible for this nitrification process are termed nitrifying. But the nitrogen cycle is only complete (in aquaria) when it includes de-nitrification; in this stage, different bacteria that are termed denitrifying convert nitrate into nitrogen gas which is released back into the atmosphere. Another component of the complete nitrogen cycle in nature but not present in our aquaria involves the “fixing” of atmospheric nitrogen by cyanobacteria and other life forms. So there is a full cycle, so to speak.

Ending the process, or assuming it should end, with only nitrification leaves nitrate, and nitrate is also highly toxic. We aquarists have for decades worried about the nitrification, but assumed the nitrate was relatively safe. But this is now being shown to be erroneous thinking, and many fish species we keep are in fact more negatively affected by nitrate than we once thought. The aim is to keep nitrate as low as possible, certainly below 20 ppm, though some fish will in time have difficulty at even this level. Below 10 ppm is now being recommended. Partial water changes (assuming there is no nitrate present in the tap water) are one way to achieve this, along with not overstocking. And of course live plants.

The plants in most cases do not take up nitrate, since they prefer ammonium (ammonia) as their nitrogen source. Studies have shown that only when ammonium is not present will plants then turn to nitrate. This is because the plants have to change the nitrate back into ammonium in order to use it as food, and this takes significantly more effort and energy. And floating plants as you mention are fastest in all this, because they have what Walstad terms the aerial advantage. The floating leaves can assimilate CO2 directly from the air, which is a process about four times faster than in water. And unlike the limited volume of CO2 in aquarium water, there is more than sufficient CO2 in the air for the needs of plants. Thus, surface plants are faster growing, which means they are using more ammonium.

Byron.