nitrification, denitrification, the COMPLETE cycle & perfect water

Planted-Pete™

New Member
Joined
Jan 31, 2021
Messages
27
Reaction score
17
Location
USA
There are many cycling how-to's out there and they will all get you from ammonia, to nitrate which is removed by water changes, this is called the nitrification process. Any of these guides can and should be followed, however with minor modifications to your tank setup, you and also harbor beneficial anaerobic bacteria that will complete your nitrogen cycle, breaking nitrates into oxygen (which is used) and nitrogen gas which harmlessly offgasses from your tank. This process is called denitrification. There are many sources for this information out there, it's amazingly unknown in the aquarium community.
I've received push back and don't understand why.. here I will post some info and sources for you to make your own informed decision.

Nitrification is the biological oxidation of ammonia to nitrite followed by the oxidation of the nitrite to nitrate occurring in separate organisms

Denitrification is a microbially facilitated process where nitrate (NO3−) is reduced and ultimately produces molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products.

Source: Wikipedia

Thiobacillus denitrificans, Micrococcus denitrificans, and some species of Serratia, Pseudomonas, and Achromobacter are implicated as denitrifiers. Pseudomonas aeruginosa can, under anaerobic conditions (as in swampy or water-logged soils), reduce the amount of fixed nitrogen (as fertilizer) by up to 50 percent. Without denitrification, however, the Earth’s supply of nitrogen would eventually accumulate in the oceans, since nitrates are highly soluble and are continuously leached from the soil into nearby bodies of water.

source: encyclopedia brittanica


By Tony Griffitts:
Aerobic bacteria, also known as the good bacteria in the aquarium ecosystem that helps oxidize ammonia into nitrite and then into nitrate (NO3) is the most common bacteria written about in freshwater aquarium articles and books. Often what is left out in publications about the freshwater aquarium hobby is the lesser known beneficial anaerobic bacteria. Anaerobic bacteria live in areas devoid of oxygen. Anaerobic bacteria use the oxygen attached to the nitrate to respire, which frees up nitrogen gas that then can escape into the atmosphere. The most common areas within the aquarium ecosystem you can find anaerobic bacteria is in the lower layer of sand and deep gravel beds. It can also be found in the gastrointestinal tract of animals, including fish. To encourage large populations of anaerobic bacteria the environment must not have easy access to the oxygen rich water column.

This is a lengthy but quick read and should be referred to for further info

Source:http://www.aquaworldaquarium.com/Articles/TonyGriffitts/AnaerobicBacteria.html

WHAT IS A FULL CYCLE? *If someone tells you the aquarium nitrogen cycle ends with the production of nitrate that is incorrect - please read on* A full cycle is completed by bacteria - the aerobic part of biological filtration which processes ammonia to nitrite and nitrite to nitrate followed by an anaerobic part which processes nitrate into soluble nitrogen which bubbles off to the atmosphere. Therefore it requires a suitable amount of excellent quality filter media to be able to provide the environment for both aerobic AND anaerobic bacteria - that is what Biohome ultimate does perfectly but even with such good media there are limitations and we recommend the following amounts for different stocking scenarios: (1 US gallon = 3.8 litres) (1kg = 2.2 lbs) Average community tropical aquarium = 1kg per 100 litres Average coldwater aquarium = 1kg - 1.5kg per 100 litres Predator aquarium = 1.5kg - 2kg per 100 litres Large cichlid aquarium = 1.5kg - 2kg per 100 litres Malawi / Tanganyikan aquarium = 1.5kg - 2kg per 100 litres Marine aquarium = 1.5kg - 2kg per 100 litres Average mixed fish pond = 1kg per 200 litres Average koi pond = 1kg per 150 litres Avoid using any products which claim to remove, detoxify or bind ammonia, nitrite and nitrate as they will have a noticeable starving effect on the bacteria which will manifest as an inability to achieve a full cycle due to a low population of bacteria on a starvation diet. Let Nature do the work and as long as you have a suitable sized, well set up filter there is no reason why a full cycle won't be achieved. You may be disagreeing with the above figures but remember that the recommendations are for a FULL CYCLE not half a job - achieving 0 ammonia and 0 nitrite is quite easy since aerobic bacteria grows freely on any surface but the anaerobic bacteria responsible for COMPLETING the cycle needs more a specialized habitat. Size a filter properly, set it up sensibly and you will have perfect water - it's that simple....and your filter won't be the dreaded 'Nitrate factory'.

Source: youtube.com "pimp my filter series"

Please do your research, it's valid info that will benefit the livelyhood of our beloved fish. I've had perfect water for months in an overstocked tank that's well overfed by using a super thick substrate and proper media DESIGNED to harbor the anaerobic bacteria. Remember these bacteria are slow growing and can take several months to build up sufficient colonies to completely remove nitrate.
 
Last edited:
I have to admit having watched Pond Gurus videos I've been very interested in this process but I dont have my tank set up in a way to test this. I love his filter pimping videos and I've followed them on 2 filters but I've never been totally convinced on this process mainly because 1. most people will come across Pond Guru at the start of their hobby and will likely buy his media if convinced but then 2. he states it takes about 6 months for the anaerobic bacteria to colonise which is also when most people leave the hobby because they have had a string of common mistakes and simply give up. Which when combined really brings the cynic in me out.

I am really open to changing this view as it will massively help me. But it feels worth mentioning that with our collective knowledge on this forum no one has reached this level of filtration with a way of actively reducing nitrates so I would describe myself as sceptical at this point. I do have a lot of questions though :)

Alongside the filter media how would you go about setting up the substrate? Are you layering different substrates that allow for the anaerobic to grow and develop? How deep is the substrate? I've always had issues with deep sand substrates developing bad anaerobic bacteria so how do you get around this?

One thing we often try and do is make the tank water oxygenated for the fish and the aerobic bacteria for the first 2 stages of the cycle, how does having deep substrates and specific media allow for water to loose its oxygen and then come into contact with bacteria that will remove the nitrate?

We are very lucky to have a couple of highly educated scientists on this forum so very interested to see what they say too :).

Wills
 
2021-02-01 14.24.58.jpg
So here is my tank now, the substrate is fluval stratum and it's between 3.5 and 4" throughout the tank.

I realize that people may think the plants are playing a role (which they are), but I've had perfect water for months, since the plants were negligible...

It's 36 gallon with a fluval 307 and biohone media. Pondguru doesn't own biohome, he just believes in it, the best US supplier is greatwaveengineering, that's who I bought from.

I've got 2 kilos of biohome ultimate with biohome gravel filling the voids.

HOWEVER....

I've had perfect water for about a month before I installed the 307. I was just using the HOB that came with the tank.

I know I'm gonna get crap for this, but when cycling the tank I added a full 12 oz bottle of bacteria on two separate occasions and that's why I believe my substrate colonized in 6 weeks and I've had perfect water ever since.

The danger with this is the bacteria can potentially consume all the oxygen in the water column and kill the fish.

It only stands to reason that this state of equilibrium would have been achieved naturally without the added bacteria, given enough time.

Also my tank is acidic and the anaerobic bacteria are supposed to be suppressed in acidic environments, another testament to the value and efficacy of deep substrate beds.


I've got 60 odd shrimp in there
12 harlequin rasbora's
12 neon tetras
6 Cory's
5 oto's
14 forktailed rainbow fish
6 adult guppies
Approx 20 odd juveniles
40 assassin snails Ramshorn's and mts

P.s. I love to feed. I feed 3-4 times a day
 
Last edited:
That's cool, hope to speak to some fellow scientists. I'm a mycologist and I've studied soil biology for 25 years
 
The big issue with anaerobic (lacking oxygen) bacteria in an aquarium is there aren't many places for it to grow. Aquariums are designed to house fish and other aquatic organisms and these require aerobic (oxygen) conditions. This makes it hard to have both aerobic and anaerobic conditions in the same tank. That doesn't mean you can't do it, just most aquariums are not suitable for having both conditions together.

Big marine tanks often have a 6 inch layer of sand in them and the bottom few inches of this can become anaerobic and convert nitrates into nitrogen gas. These tanks often have big pieces of limestone rock, which is porous and anaerobic bacteria live in the middle of the rock and also convert nitrates into nitrogen gas.

Most smaller aquariums don't have the room for a 6 inch layer of sand or large pieces of limestone rock.

-------------------
Most freshwater aquariums can use plants to remove nitrates, and floating plants are great at this. You simply harvest the plants and remove them from the aquarium, and that removes the nitrates too.

Marine tanks can grow various algae like Halimeda and Caulerpa species and these will also remove nitrates.

-------------------
I have never heard of or used the substance you are talking about (Biohome ultimate) so can't comment on how well it works. It might be good and from the website I looked at, it would probably work better if it was in its own filter with a slower flow rate of water, rather than being put in a normal filter with a high flow of water. However, it appears to be designed for fast flowing water with small cavities inside the media that allow for anaerobic conditions. Only time will tell how good it is and whether it becomes part of the average filter media for an aquarium. It appears to have potential.

-------------------
Having said all this, aquariums should still get big regular water changes even if they don't have any nitrates in the water.

Fish live in a soup of microscopic organisms including bacteria, fungus, viruses, protozoans, worms, flukes and various other things that make your skin crawl. Doing a big water change and gravel cleaning the substrate on a regular basis will dilute these organisms and reduce their numbers in the water, thus making it a safer and healthier environment for the fish.

So if you don't want to do water changes to reduce nitrates, do it to reduce the microscopic organisms that the fish live with.

Fish live in their own waste. Their tank and filter is full of fish poop. The water they breath is filtered through fish poop. Cleaning filters, gravel and doing big regular water changes, removes a lot of this poop and makes the environment cleaner and healthier for the fish.
 
The big issue with anaerobic (lacking oxygen) bacteria in an aquarium is there aren't many places for it to grow. Aquariums are designed to house fish and other aquatic organisms and these require aerobic (oxygen) conditions. This makes it hard to have both aerobic and anaerobic conditions in the same tank. That doesn't mean you can't do it, just most aquariums are not suitable for having both conditions together.

Big marine tanks often have a 6 inch layer of sand in them and the bottom few inches of this can become anaerobic and convert nitrates into nitrogen gas. These tanks often have big pieces of limestone rock, which is porous and anaerobic bacteria live in the middle of the rock and also convert nitrates into nitrogen gas.

Most smaller aquariums don't have the room for a 6 inch layer of sand or large pieces of limestone rock.

-------------------
Most freshwater aquariums can use plants to remove nitrates, and floating plants are great at this. You simply harvest the plants and remove them from the aquarium, and that removes the nitrates too.

Marine tanks can grow various algae like Halimeda and Caulerpa species and these will also remove nitrates.

-------------------
I have never heard of or used the substance you are talking about (Biohome ultimate) so can't comment on how well it works. It might be good and from the website I looked at, it would probably work better if it was in its own filter with a slower flow rate of water, rather than being put in a normal filter with a high flow of water. However, it appears to be designed for fast flowing water with small cavities inside the media that allow for anaerobic conditions. Only time will tell how good it is and whether it becomes part of the average filter media for an aquarium. It appears to have potential.

-------------------
Having said all this, aquariums should still get big regular water changes even if they don't have any nitrates in the water.

Fish live in a soup of microscopic organisms including bacteria, fungus, viruses, protozoans, worms, flukes and various other things that make your skin crawl. Doing a big water change and gravel cleaning the substrate on a regular basis will dilute these organisms and reduce their numbers in the water, thus making it a safer and healthier environment for the fish.

So if you don't want to do water changes to reduce nitrates, do it to reduce the microscopic organisms that the fish live with.

Fish live in their own waste. Their tank and filter is full of fish poop. The water they breath is filtered through fish poop. Cleaning filters, gravel and doing big regular water changes, removes a lot of this poop and makes the environment cleaner and healthier for the fish.
Absolutely, water changes are a must ( but not for nitrate removal in a properly set up tank) And I still vacuum the gravel, not much surface area I can get to, but I vacuum what I can....lol besides...I gotta feed the detritus worms or the planaria might starve?
 
I forgot to add that denitrating filters have been around for years. Sera brought out a denitrating filer in the 1980s and it took a few months to get going but worked well at removing nitrates. It was just a brown plastic filter that hung on the back of the tank and had a very slow flow of water moving through it. This allowed the filter to turn anaerobic. You added a small carbon tablet each day to feed the bacteria. These tablets were hideously overpriced. I eventually stopped using the tablets even though I was getting them at cost price, and it didn't seem to affect the anaerobic bacteria. The filter continued to keep the nitrates at 0ppm for several years while it was being used.

The tank was a marine tank with a bit of rock and some Caulerpa, but it also had lots of fish and they were fed heavily 3 times a day. I did a big water change about once a month. There was no protein skimmer on the tank.
 
I forgot to add that denitrating filters have been around for years. Sera brought out a denitrating filer in the 1980s and it took a few months to get going but worked well at removing nitrates. It was just a brown plastic filter that hung on the back of the tank and had a very slow flow of water moving through it. This allowed the filter to turn anaerobic. You added a small carbon tablet each day to feed the bacteria. These tablets were hideously overpriced. I eventually stopped using the tablets even though I was getting them at cost price, and it didn't seem to affect the anaerobic bacteria. The filter continued to keep the nitrates at 0ppm for several years while it was being used.

The tank was a marine tank with a bit of rock and some Caulerpa, but it also had lots of fish and they were fed heavily 3 times a day. I did a big water change about once a month. There was no protein skimmer on the tank.
That's interesting about the filters, the link I attached to my OP mentions that it's been known about in the marine aquarium hobby for decades, but it's almost unheard of in the freshwater community.

I had to use very specific search terms to find sources outside of pondguru
 
I think the main reason it's not commonly known or talked about in freshwater circles is because in most countries, freshwater is cheap and easy to get. Turn on a tap and you can do water changes to get rid of nitrates. Whereas marine tanks were more work when it came to water changes. I tried natural sea water and artificial marine salts and found natural sea water was easier and cheaper for me. But for people using artificial marine salts, they had to make the water up 24 hours before using it, and the marine salts were expensive.

This high cost of marine salts encouraged people to look at ways of keeping nitrates lower so they didn't have to do as many water changes. Protein skimmers were the first item used, then ozone, but that was stopped pretty shortly after it started. Then the denitrator filters appeared and whilst they worked, they were costly and most people didn't touch them. Then they started bringing out products that go in the filter to remove nitrates. Now there is the Biohome ultimate media.

The other reason these types of things aren't often spoken about is because most shop workers don't know about the products. The boss or manager does the ordering and might be the only person who talks to the sale's reps. I was fortunate when I started working in the pet industry, our sale's reps would bring in all the new products for us to look at. Quite often they would leave a sample with us to test and try out. If we liked the item and thought it was good, then wholesalers would carry them. If we didn't like it and pointed out flaws or possible issues, they wouldn't carry the product. There were lots of new products that came in and I would spend a couple of minutes fiddling about with them and they were sent back with a list of issues. :)
 
I think the main reason it's not commonly known or talked about in freshwater circles is because in most countries, freshwater is cheap and easy to get. Turn on a tap and you can do water changes to get rid of nitrates. Whereas marine tanks were more work when it came to water changes. I tried natural sea water and artificial marine salts and found natural sea water was easier and cheaper for me. But for people using artificial marine salts, they had to make the water up 24 hours before using it, and the marine salts were expensive.

This high cost of marine salts encouraged people to look at ways of keeping nitrates lower so they didn't have to do as many water changes. Protein skimmers were the first item used, then ozone, but that was stopped pretty shortly after it started. Then the denitrator filters appeared and whilst they worked, they were costly and most people didn't touch them. Then they started bringing out products that go in the filter to remove nitrates. Now there is the Biohome ultimate media.

The other reason these types of things aren't often spoken about is because most shop workers don't know about the products. The boss or manager does the ordering and might be the only person who talks to the sale's reps. I was fortunate when I started working in the pet industry, our sale's reps would bring in all the new products for us to look at. Quite often they would leave a sample with us to test and try out. If we liked the item and thought it was good, then wholesalers would carry them. If we didn't like it and pointed out flaws or possible issues, they wouldn't carry the product. There were lots of new products that came in and I would spend a couple of minutes fiddling about with them and they were sent back with a list of issues. :)
This is a great insight And it makes perfect sense, and as you stated before water changes are necessary from time to time. I do them weekly....but I'm not forced to do it because of nitrates, and my fish don't need to suffer because I'm lazy and forgetful.

Truth is, most people have severely undersized filters and they couldn't stuff enough biohome in there to reduce everything to zero.

I'm using a filter that's rated for double my tanks volume and should have gone bigger . I'm going to be running 2 fx6 with around 10kg biohome total on the 120 gallon I'm building

I trust pondguru's numbers, I'm sure there are other media that can work but I don't know anyone knowledgeable enough with the product to give concrete numbers
 
View attachment 128123So here is my tank now, the substrate is fluval stratum and it's between 3.5 and 4" throughout the tank.

I realize that people may think the plants are playing a role (which they are), but I've had perfect water for months, since the plants were negligible...

It's 36 gallon with a fluval 307 and biohone media. Pondguru doesn't own biohome, he just believes in it, the best US supplier is greatwaveengineering, that's who I bought from.

I've got 2 kilos of biohome ultimate with biohome gravel filling the voids.

HOWEVER....

I've had perfect water for about a month before I installed the 307. I was just using the HOB that came with the tank.

I know I'm gonna get crap for this, but when cycling the tank I added a full 12 oz bottle of bacteria on two separate occasions and that's why I believe my substrate colonized in 6 weeks and I've had perfect water ever since.

The danger with this is the bacteria can potentially consume all the oxygen in the water column and kill the fish.

It only stands to reason that this state of equilibrium would have been achieved naturally without the added bacteria, given enough time.

Also my tank is acidic and the anaerobic bacteria are supposed to be suppressed in acidic environments, another testament to the value and efficacy of deep substrate beds.


I've got 60 odd shrimp in there
12 harlequin rasbora's
12 neon tetras
6 Cory's
5 oto's
14 forktailed rainbow fish
6 adult guppies
Approx 20 odd juveniles
40 assassin snails Ramshorn's and mts

P.s. I love to feed. I feed 3-4 times a day
That a very nice tank Planted-Pete. It more than nice enough to enter it in our Tank of the Month contest which is accepting entries for tanks sized at 31 gallons and larger. Entry thread is here:
 
That a very nice tank Planete-Pete. It more than nice enough to enter it in our Tank of the Month contest which is accepting entries for tanks sized at 31 gallons and larger. Entry thread is here:
Thanks, I appreciate that! I was thinking about it, just real overgrown and jungle like right now.
 
The thing about our contest is that you can enter at any stage of your goal. Enter what you have now and, if you don't win, then in a few months show off the improvements by entering again. You tanks looks really nice in my opinion.
 
The thing about our contest is that you can enter at any stage of your goal. Enter what you have now and, if you don't win, then in a few months show off the improvements by entering again. You tank looks really nice in my opinion.
Thank you so much! I think it's gorgeous, I love it, it brings me so much peace and joy. You've got me convinced, But I've seen ones that brought tears to my eyes (international aquascaping competition I think) so I've set a pretty high bar for myself ?, it's so much more than "pets" ....it's a living art installation and it moves me. That's why I'm building the 120 gallon with low iron glass.
 
Truth is, most people have severely undersized filters and they couldn't stuff enough biohome in there to reduce everything to zero.

I'm using a filter that's rated for double my tanks volume and should have gone bigger . I'm going to be running 2 fx6 with around 10kg biohome total on the 120 gallon I'm building
I have gone in completely the opposite direction. All of my tanks are seriously under filtered and have enough plants to deal with the ammonia without all that tedious mucking about with bacteria. Chances are the bacteria have died of starvation - but on the plus side I never see nitrate and I have no fear of filter failures :whistle:
 

Most reactions

Back
Top