Nitrocycle Modelling?

Discussion in 'General Discussions and Advice' started by zuraki, 1 Sep 2010.

  1. zuraki

    zuraki

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    Hi,
    I’m a new member to MASA as well as TASA. I used to have tropical fish and a range of Synodontis species. At the moment I have no active aquariums. Recently I’ve tried to develop a method for modeling the nitrogen cycle in an aquarium setup. The model presents a graph of the aquarium concentration levels of ammonia, nitrite, nitrate and nitrogen with respect to time. The model can be adjusted according to tank size and inlet/outlet flow rate. Needles to say the model falls far short of reality.

    It does give quite a good qualitative description of the dynamics during the startup process of a new aquarium.

    When I started this project I didn’t have marine aquariums in mind, but I was told by a user from TASA that marine fish keepers are more serious when it comes to recording and documenting their water parameters.

    My aim is to gather enough experimental data on the fluctuating levels of ammonia, nitrite and nitrate during aquarium start up to allow adjustments to the model parameters so that it more accurately represents what is actually happening in existing aquariums.

    I understand there are a lot of differences between different aquarists’ setups, water conditions and operation. Aside from this fact I believe that it is possible to obtain a generalized trend of behavior if enough experimental data can be gathered.
    So if someone is willing to share his log records of ammonia, nitrites or nitrate levels during fish tank start up along with his tank volume, flow rates and water temp, I might be able to tweak the model to be more realistic. Here is an example of the model output in Matlab:
    [​IMG]
    Or without denitrifying bacteria:

    [​IMG]

    Any comments / suggestions / critique are welcomed.
    Thank you
     
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  3. dallasg

    dallasg Moderator MASA Contributor

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    nice idea, but things are way to dynamic to even get 1% accuracy amoung 10 systems in the same lab.

    also differenct filtering types change the cycle completely. eg Prodibio removes the ammonia and prevents or slows the cycle down to nitrite etc thus having no nitrates etc.
     
  4. zuraki

    zuraki Thread Starter

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    Yes, i agree that there are so many variables that are out of one's control it becomes almost impossible to compare one system to another.

    Again i agree with the statement on filtering types, i mean just as an example having a DSB or not will affect the system considerably. The model is flexible to some extent however and can be adjusted to specific aquarium traits. It uses Monod kinetics as basis combined with a CSTR in series reactor model.

    Even with all the complications and possible shortcomings, i would still like to try my luck... if i fail ill fail gloriously :thumbup:
     
  5. dallasg

    dallasg Moderator MASA Contributor

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    by all means, i did something similar measuring the bacteria mass etc, even if it only satifies the curiosity it is fun
     
  6. zuraki

    zuraki Thread Starter

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    Well to me it is really interesting. My experience with marine aquariums are limited and its always good to get a different perspective. I was actually thinking of building my own denitrator / fluidized bed or packed bed reactor to try and test my luck. But i am also aware that the model output is a pulsed output and not a steady state response. That is why i know it only represents the start up of new aquaria and not the steady state operation. For that a step response is required and i havent adapted the model to accomodate that...yet
     
  7. 459b

    459b Moderator MASA Contributor

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    How did you come up with the graphs? Is it based on theoretical values or did you use actual data? If you did use actual data, how many sample times did you use?
     
  8. zuraki

    zuraki Thread Starter

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    No this is purely theoretical. You see its the solution of solving 7 differential mole balances involving NH3, NO2, NO3 and N2 and then also bacterial cel balances of Nitrosomonas, Nitrospira (or Nitrobacter) and Pseudomonas.

    The thing is i want people's input to give me experimental values which they have recorded in the past so that i can see how far from the reality the model falls short :)
     
  9. 459b

    459b Moderator MASA Contributor

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    thought it looked modelled. My brother used to come up with similar graphs when he did life cycle assessments and then ask me for my input (im a microbiologist).

    Best of luck with this. I think its going to be hard getting accurate measurements for all parameters with the avaialble test kits.
     
    Last edited: 1 Sep 2010
  10. zuraki

    zuraki Thread Starter

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    Ah thank you. Its good to have some input from a biologists point of view. Let me explain the model in a bit more detail:


    The model input variables are as follows:
    • Volumetric flow rate
    • Aquarium dimentions
    • Initial concentrations of NH3, NO2 and NO3 in mmol/liter
    • Initial hypothetical bacterial concentraions of Nitrosomonas, Nitrospira and Pseudomonas
    • Temperature
    No relation between organic waste and NH3 concentration has been made because of an unknown conversion factor.


    Model paramaters:
    • Maximum specific growth reaction rates for all bacterial species (Temp dependent)
    • Monod Constants for all bacterial species (Temp dependent)
    • Bacterial Death rate constants (Unknown) (Temp dependent)
    • Bacterial Toxin Constants (Unknown)
    • Toxin Concentrations (Unknown)
    • Bacterial Yield coefficients (Bacterial mass produced per mol substrate utilized) (Temp dependent)
    • Bacterial Maintenance consumption coefficients (unknown)
    • Stoichiometric Constants
    Even though most of the parameters are temperature dependent, only two values were reported as functions of temperature and the rest as single values determined at set temperatures. The 7 equations are evaluated using the above inputs. It doesnt take inhibitory effects into account and also no pH and ignores other chemical species.

    There is no doubt that the model is an over simplification of the real dynamics. But it will be interesting to find out how far from reality it really is. So if anyone can post ballpark answers to NO3 or NO2 concentrations after x amount of time since aquarium start up and also supply me with tank volume and average flow rates, i can plot some experimental data along with the theoretical model.

    On its own the model output responses from a single aquarium might be meaningless, but we might gain value or insight when comparing it to that of a different aquarium.
     
  11. 459b

    459b Moderator MASA Contributor

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    You have gone into depth with this. I agree it is an over simplification, but still a decent start.

    for interests sake..what were your hypothetical concentrations?
    And how do the graphs change if you change the initial conc. of the bacteria?
     
  12. zuraki

    zuraki Thread Starter

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    ok give me a sec and ill post the results. To have dimensional consistency in the equations, i am forced to use molar units for the bacterial concentrations. It carries no meaning however because if i specify 1 millimol of bacterial cells present at the start, how do i relate the capacity of that amount of bacteria to reduce say 1ppm of ammonia to 0.5ppm? Until i can find a relation between how much NH3 a single bacterial cell can consume at certain operating conditions, it doesn’t carry any meaning to try and estimate the exact bacterial count. Some authors have used mass or biological increase in mass against decrease in substrate (for example NH3) in models but again that can’t be factored into a model working with exact quantities.

    Ill post the output response for different initial bacterial counts now...
     
  13. zuraki

    zuraki Thread Starter

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    Here is the response if the hypothetical bacterial inputs are 0.001 with Pseudomonas being 0:

    [​IMG]

    Here is the response if the hypothetical bacterial inputs are 0.01 with Pseudomonas being 0:

    [​IMG]

    Here is the response if the hypothetical bacterial inputs are 0.1 with Pseudomonas being 0:

    [​IMG]

    Basically the bacteria just establish faster when their initial count is increased
     
  14. zuraki

    zuraki Thread Starter

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    Here is the same set of responses from 0.001, 0.01 and 0.1 but it is the bacterial growth responses:

    [​IMG]
     
  15. 459b

    459b Moderator MASA Contributor

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    are you using the same "formula" for each bacteria? Fairly preditable that increasing the conc would result if faster rection rate. Have you tried changing the conc of each bacteria? So what if for example you start with 0.01 Nitrosoma 0.001 Nitrospira etc.


    how long before the Psedomonas and Nitrospira reach stationery phase?
     
  16. zuraki

    zuraki Thread Starter

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    The equations are basically the same. It is the different parameters (Monod, specific growth rates etc.) that have differing literature values that make the responses behave differently. Each individual bacterial concentration can be adjusted to any arbitrary value irrespective of the other values.

    Well since at this stage the input is only a single initial value of ammonia, the growth of Nitrospira and Pseudomonas are limited by the amount of NO3 and NO2 that are produced from the initial ammonia concentration.

    (NOTE : In the bacterial responses in the 13th post, i forgot to zero the Pseudomonas bacterial count at the beginning, that is why there is Pseudomonas growth. In this case the N2 concentrations will rise as opposed to the zero N2 concentration indicated in the chemical responses of post 12.

    The reason the stationary phases of Nitrospira and Pseudomonas are not included in the graph is because my scaling is wrong. I will have to increase the concentration limit in order to see the stationary phases.

    Being a microbiologist, cant you maybe give me some death rate constants of known strains of Nitrosomonas, Nitrospira and Pseudomonas? I am aware that the odds are that there are many different strains of each?
     
    Last edited: 1 Sep 2010
  17. Nemos Janitor

    Nemos Janitor

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    1) pH ?? influence.

    2) Nitrification involves bacteria oxidation. What DO levels?

    3) ORP influence.

    4) KH and Mg effects??

    A few thoughts for your model
     
  18. 459b

    459b Moderator MASA Contributor

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    Unfortunately im not that sort of microbiologist. I worked on marine microbes and was more involved in isolating/characterising than doing fermentation studies on them.

    Not only will there be different strains but ther will also be many diffeent species within in genus.

    can you please draw one that includes the addition of more ammonia (but less that initial) at around 150hrs?
     
  19. zuraki

    zuraki Thread Starter

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    Thank you for all the comments and suggestions! I apologize for only replying to this thread now, i was busy the past two days.

    Thank you for the suggestions Nemos Janitor.

    The dissolved oxygen is assumed to be at the saturation limit of the water at the specific water temperature and atmospheric pressure. I have found no relation as to how the DO levels rise and fall during the day/night or with different fish stocking levels. Not to mention trying to quantify those values.

    pH is in the pipeworks, but remember that i started this project out with regard to fresh water aquaria and pH variation under saline conditions are different.

    Other ions such as Ca and Mg are not considered simply because i have no idea how they impact the bacterial communities. Whether Nitrosomonas, Nitrospira or Pseudomonas fares better in alkaline or acidic environments is also unknown to me.

    I do not have the microbiological back ground, experimental capability or literature sources to answer those questions. That is why i was hoping for members of MASA to give me some data.

    459b:

    I have not yet adjusted the algorithm to enable continuous Ammonia additions. Unfortunately i am still working on that. That is why i stressed the fact that this model will only approximate the start up of a new tank and not the continuous operation thereof.

    What i can do is let you tell me in what ratios you want me to set the initial conditions (i.e. Bacterial concentrations, NH3, NO2 and NO3) and then give me a tank volume and flow rate to work with and ill plot the result for you. Specify if you have a large or small sump/refugium/DSB.


    If there is anyone that can give me a very crude answer as to estimate how much ammonia (in say mg) will be produced from a set amount of fish stock (say in grams), it will be most helpful. I am aware that this will vary with fish species, time of year etc. etc. but just humor me ok?
     
  20. Ash

    Ash Coral biologist

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    I have plenty of data from up and running systems (with high seawater turnover rates however). Will be starting four new 500lt systems soon and a 12000 lt system. all water quality params are measured weekly. I'd like to collaborate and explore this topic further. Sent you a PM
     
  21. zuraki

    zuraki Thread Starter

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    Thank you very much Ash! Just let me know if you received my reply to your PM. I am very interested and would be happy to explore this project further with you.
    Send me your model expectations/deliverables and we can discuss what is possible and what is not. I do intend to implement an algorithm in the model that allows for continuous NH3 addition. Let me know if you have any suggestions of how to bring the pH, KH, ORP or DO into the model. Looking forward to your response!
     
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