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Ammonia Control in Biofloc Ponds


Andrey Krutov ( Listers, we are trying to start a new shrimp farm in Vietnam.  We’re attempting to get the pond balanced before we stock any shrimp.  We add urea to the pond and then try to control the ammonia that develops by adding molasses and rice bran, hoping that heterotrophic bacteria will develop and reduce the ammonia.  We add commercial bacteria (Nitrosomonas and Nitrobacter) as well.  The problem is the more molasses and rice bran we add, the higher ammonia level rises.  Today we checked the alkalinity (raised previously by baking soda to 120 from 90 and surprisingly found it to be 160).  We run paddlewheels and bottom oxygen injection all day and all night.  After applying a serious amount of rice bran and molasses, the water started to foam and almost half-a-meter of foam piled up around obstacles, like pipes and other equipment.


My questions:


Why does the alkalinity increase?  We don’t seem to have anaerobic conditions, and we have abundant oxygen in the water.


Why does the ammonia increase?  Is it because algae populations decrease as the bacterial flocs increase?


Should we continue to use molasses, sugar and rice bran to increase the C/N ratio?


Here’s some information on our experimental pond:


• Size 1,200 m2

• Depth 1.8-2 meters

• Four paddlewheels, 2-hp each

• Bottom aeration

• Ph 7.8

• Alkalinity 160

• Salinity 4-5 ppt


Ramon Macaraig ( Andrey, how much carbon as molasses, sugar, rice bran did you put in your experimental pond?


What is your C/N Ratio?

How much ammonia are you confronted with?

How much carbon do you need to manage this?


Andrey Krutov ( Ramon, in total for one pond we used 35 kilos of rice bran and around 300 liters of molasses.  In ten days, the ammonia slowly increased from 0.25 to 2 mg/l.  Just last night we decided to switch to pure sugar (60 kg/pond), which seems to create a carbon:nitrogen ratio around 20:1.  It worked.  In 6 hours we managed to drop ammonia from 2 mg/l to almost zero.


Last night we made some calculations and taking into account that molasses contains from 40 to 67 percent sugar, it looks like it’s cheaper to buy pure sugar, containing around 100% of sucrose.


Now it is more or less clear that sugar works, but I still wonder why the alkalinity increases so much?


Daniel Gruenberg ( Andrey, you are basically feeding incompatible systems.  You mentioned urea and along with sunlight will produce algae that will increase “alkalinity” from photosynthesis.  You mentioned nitrifying bacteria along with organic carbon source.  Nitrifiers don’t use organic carbon.  That feeds the heterotrophs.  Nitrifiers get their carbon by consuming alkalinity.


You have to sit down and plot a clear strategy of what you want to do and then focus on that strategy rather than feeding multiple, competing systems.


Autotrophic systems are my thing in natural balance with heterotrophs.  I never add organic carbon.  If you desire a floc, there are others on this list that can give you advice, but it’s noteworthy that Tzachi Samocha also mentioned that he never uses organic carbon in his flocs.


Billy Setio ( Andrey, go to the Aquacultural Engineering Society’s Biofloc Working Group Page to learn more about bioflocs.


For the moment, stop adding anything, let the pre-start system find its own balance.  Biofloc cannot be forced in a 1,200 m2 pond unless the water is coming from another recirculating aquaculture system.


Andrey Krutov ( Daniel, for me all this stuff is a mystery.  I still don’t know what “heterotrophic bacteria” really means.  I can’t find any precise names of the bacteria that feed on carbon and reduces ammonia.  So I just guessed when I say “nitrifying bacteria”.  I’m very interested in biofloc, but I know I’m not ready, so I’m trying to go step by step, trying “this” and “that”.  I’ve read several articles by Tzachi Samocha and try to follow his methods, and I also know he has released a book on biofloc shrimp farming, but right now it’s unavailable for me.  So I’m trying to connect different experiences, articles and books to get a better understanding of biofloc management.  Most think algae dominated systems are unpredictable and that better control can be achieved using bacteria dominated systems.  I guess what I have today is a “semi-biofloc system”.


Daniel Gruenberg ( Ok, I see where you’re coming from.  Nitrifiers use carbon from inorganic sources (carbonate alkalinity) and heterotrophs use organic carbon such as sugars.  If you are adding organic carbon you are growing heterotrophs.  Nitrifiers can’t compete with heterotrophs so no need to add Nitrosomonas.


Algae systems are only unstable when you don’t have the right tools to manage them.  We have been doing diatom-based systems for decades and have our own system of management.


Andrey Krutov ( Daniel, could you give me of some names of heterotrophic bacteria so I know what to look for?


Daniel Gruenberg ( Look for species in the following genera Bacillus, Lactobacillus, Pseudomonas.


York Wong ( Andrey, I think there are two possible reasons for the rise in your ammonia.  The first is the gradual break down of urea into ammonia by soil bacteria.  The second is the degradation of rice bran over time.  I think the first is more likely to have a greater effect.  I didn’t know how much urea was added to your pond.  It is possible that the molasses you added did not provide enough carbon to remove the ammonia, so when you added more sugar, the ammonia level went down.


I understand the frustration you are going through.  I have been there.  Sometimes it is hard to see the big picture, and some papers could even be a little bit misleading.  Anyway, below is my understanding of biofloc.


There are several types of biofloc systems.


Heterotrophic Biofloc Systems encourage the growth of heterotrophic bacteria by adding organic carbon, like sugar or starch, or using low protein feed.  Heterotrophic bacteria are bacteria that use organic carbon as their carbon source and energy source.  And at the same time, heterotrophic bacteria take up the ammonia or nitrate in the water as their nitrogen source.


Pros: No need to do shrimpless cycling; provide a microbial protein source.

Cons: More waste; higher cost; fluctuations in ammonia levels.


Autotrophic Biofloc Systems encourage the growth of autotrophic/nitrifying bacteria by providing enough surface area (e.g. by adding rice bran), ammonia (if you are doing shrimpless cycling) and sufficient aeration.  Nitrifying bacteria are mostly autotrophic bacteria and don’t require organic carbon for growth.  They fix carbon dioxide as carbon source kind of like plants, but instead of getting energy from sunlight, they oxidize ammonia to nitrite, or nitrite to nitrate for energy.


Pros: No need to add organic carbon; less waste; lower cost; more stable ammonia levels.

Cons: It takes a little bit longer to get the system up and running; nitrate accumulates over time.


There are also Mixotrophic Biofloc Systems.  But in my opinion, heterotrophic biofloc systems will become mixotrophic if they are run long enough, when nitrifying bacteria are established.  And autotrophic biofloc system will become mixotrophic once you start feeding because the carbon content in the feed promotes some degree of heterotrophic growth.


Personally, I prefer the Autotrophic Biofloc Systems.  I think they are a more elegant way to control ammonia and nitrite.


I agree with Daniel that you need to be clear which type of biofloc system to use.  If you want an autotrophic biofloc system, then there is no need to add molasses or sugar, and it is better to maintain a high ammonia level (e.g. TAN 4-6mg/L by adding ammonium chloride) to speed up the process.  If you want a heterotrophic system, then there is no need to do shrimpless cycling.  Heterotrophic bacteria (there’s plenty of them in natural water) replicate quickly and should be up and working in several hours.


Andrey Krutov ( York, thank you for the detailed explanation, now I’m beginning to understand how these systems work.  The problem is we stocked shrimp yesterday when ammonia was zero and today it’s back to 2 mg/l.  I would like to have an autotrophic system (that’s why I started shrimpless cycling) but it seems to take too long, so now I have no other way but to try reducing ammonia with sugar.  If you think that a heterotrophic system can slowly become autotrophic, that’s a good piece of news for me.  I hope one day we can establish a sustainable system.  The only thing I worry about is if the shrimp can stand the high levels of ammonia.  Today I put some phosphoric acid in the experimental pond to reduce toxic levels of nh3, because we ran out of sugar.  I’m not sure if I really should continue with an heterotrophic approach as it’s too expensive and lasts for only one night


York Wong ( Andrey, what’s your stocking density and the size of your PLs?  Are you feeding the PLs?  How much?  Also how much urea did you add to the pond?


The rise in ammonia (2mg/L) could be due to feeding and shrimp activity and the gradual breakdown of urea over a period of a few weeks.  You can figure out how much each of the factors contributes to the ammonia rise by doing a little math.  The average N content of protein is about 16%.  And about 50% of the N will end up in the water as ammonia.  Another way to find out the cause is to set up a small tank (any size) with pond water and aeration (without PLs).  Then monitor the ammonia levels in the tank over time.


If the rise in ammonia is caused primarily by the slow breakdown of urea, you’ll only have to add sugar for a short period of time before the urea is used up.  And I recommend using other sources of ammonia (e.g. ammonium chloride) instead of urea when doing shrimpless cycling because it is hard to get an accurate ammonia reading with urea.


There are a few things you can try right now to keep the ammonia below toxic levels:

• A partial water exchange

• Add a proper amount of sugar (but don’t overdo it, both nitrifying
  bacteria and algae need nitrogen to grow as well)

• Cut down on the feed

• Use enough aeration and mixing for algae and nitrifying bacteria to develop.
  In my freshwater autotrophic biofloc system, it took about 7 days for
  Nitrosomonas to develop and about 12 days for Nitrospira to develop.


I think those with more experience in shrimp farming will be able to give you more practical advice regarding safe levels of ammonia for PLs and other things related to pond management after stocking.


Andrey Krutov (  York, thank you very much for your advice, we just stocked last night, so I haven’t fed the shrimps yet, but previously I used around 25 kg of urea per pond.  I added a couple of kilos and the next day ammonia was zero, then I doubled the dose and it rose to 0.25, then I added more and more and the next day it was 0.5 (which is not enough for shrimpless cycling), but the next week it suddenly rose very high when we added molasses.  Then I found a report that had the same outcome.  If there’s not enough molasses, ammonia levels will rise.  So that’s how I came to the conclusion that there was not enough sugar in water.


My stocking density is currently 160 PL-12 per m2.  I’m running oxygen as much as possible, day and night.  The salinity is around 5 ppt, so I use Nitrosomonas and Nitrobacter, which are supposed to work under 6 ppt salinity.  Nitrospira (as far as I know) is meant for salinities higher than 6 ppt.  It’s not available in Vietnam, even though many people have salinities higher than 10 ppt.


Nelson Gerundo ( Andrey, it’s an open pond exposed to sunlight, right?  What is your plankton profile?  Please upload some pictures of your pond?


Andrey Krutov ( Nelson, yes, an exposed pond.  I will upload pictures tomorrow morning.  Not sure about my plankton profile because I don’t have the equipment to measure it.


Nelson Gerundo ( Andrey, your pictures did not upload.  Email attachments sent to The Shrimp List don’t work.


You can click “Visit Your Group” at the bottom of the page in your comment then click “Photo” and then click on “+ New Album” and you can begin uploading your pictures there.


Andrey Krutov ( Nelson, unfortunately I couldn’t upload the photos to the group, but I found a webpage that provides that service.  Please check the pictures of my pond at the following links:


York, last night we had another huge spike in ammonia, and today I found some info that it could be due to a sudden die-off of some of heterotrophic bacteria because we stopped feeding them with sugar and they starved.  This makes some sense.  So I guess we have to continue with sugar slowly until we have a transition from a heterotrophic to an autotrophic system.


Billy Setio ( Andrey, my guess is that stopping sugar won’t make a big difference because your feed and algae contain organic carbon.  Actually, if you don’t supply any organic carbon, your system will be in the middle.


If you don’t supply any organic carbon (your organic C comes from dead algae and feed and shrimp feces), your system will revert to algae after 70 days of culture.  It will go to floc if you only top-off with new water (very minimal water exchange).


Chandran Ravichandran ( I saw the picture of your pond.  Is it lined?


Andrey Krutov ( Semi-lined, banks only with a soil bottom.


Sources: 1. The Shrimp List (a mailing list for shrimp farmers).  Subject: Alkalinity and Ammonia Unexpected Rise.  July 8 to 11, 2017.  2. Bob Rosenberry, Shrimp News International, July 13, 2017.


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