Module SedimentQuality

Overview

This is the 0D module that handles sediment biological processes made by bacteria as organic matter mineralization, nitrification, denitrification and immobilization.

Main Processes

Main processes in SedimentQuality are organic matter mineralization, nitrification, denitrification and immobilization. These processes are simulated using a standard rate (s.day-1.pop-1) that is afected by temperature, pH, oxygen in case of aerobic processes and sustrate concentrations if exist. A maximum rate is computed calculating the standard rate at the actual temperature (day-1.pop-1) times bacteria population that conducts the process.

$MaxRate (day-1) = Standard Rate at actual Temperature (day-1.pop-1) * BacteriaPopulation$

$ActualRate (day-1) = MaxRate (day-1) * Aerobiose/AnaerobioseTerm * pHTerm * OxygenTerm * SubstrateTerm$

Organic Matter Mineralization

Organic matter is mineralized to ammonia with heterotrophic bacteria and also immobilization may occur in order to maintain bacteria C:N ratios.

Heterotrophic LPOM mineralization rate

$Insert formula here$

Heterotrophic RPOM mineralization rate

$Insert formula here$

Immobilization rate

$Insert formula here$

Nitrification

Nitrification rate

$Insert formula here$

Denitrification

Denitrification rate

$Insert formula here$

Other Features

Outputs

Output is done in terms of timeseries, HDF, and boxes following the MOHID standards.

References

Data File

Keywords

Properties Units:
dissolved                 - as from called - in MOHID Land mg/L
adsorbed/particulated     - as from called - in MOHID Land mg/kgsoil
gases:
CO2 and CH4               - same as adsorbed/particulated properties
N2                        - same as dissolved properties
exceptions:
oxygen                    - mol/L
hydrogen                  - mol/L
microorganisms population - #org/kgsoil
wind                      - km/day

OXYGEN   	            :  [0/1]       0      !Connect/Disconnect Oxygen computation 
SOL_BACTERIA 	            :  [0/1]       0	  !Connect/Disconnect Solubilizing bacteria computation 

DTSECONDS                  :  [s]       86400.   !dt to evaluate
NO3_LIMIT                  :  [mg/L]      0.     !Minimum value for denitrification or maximum value for 
                                                   !methane production in organic matter decay
NEW_RATES                  : [0/1]        0      !Connect/Disconnect new rates formulation using maximum * factors
IMOBILIZATION              : [0/1]        1      !Connect/Disconnect immobilization

EXPLICIT                   : [0/1]        1      !Explicit computation for time dicretization

Sample

!!!!!!!!!!!!!!!!!MAIN SEDIMENT OPTIONS!!!!!!!!!!!!!!!!
!++++++++++++++++++++++++++++++++++++++++++++++++++++++

!NITROGEN 	: 1
!CARBON   	: 1
!PHOSPHORUS  	: 1	
OXYGEN   	: 1 
SOL_BACTERIA 	: 0	 

DTSECONDS    : 86400.
NO3_LIMIT    : 0. ![mg/L] Minimum value for denitrification or maximum value for methane production in organic matter decay
CHANGE_RATES : 0  !0 - original rates; 1-changed rates (removing concentrations from rates so do not change units)
NEW_RATES    : 1  !1 - new rates using maximum * factors
!IMOBILIZATION : 0

EXPLICIT : 1
!IMPLICIT  ! not working?
!SEMIIMP




!!!!!!!!!!!!!!!!!!!!!!RATES!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!++++++++++++++++++++++++++++++++++++++++++++++++++++++

	!!!! Organic Matter Decay !!!!

<begin_Labil_OM_C_Rate>
AE           : 15.1         ![kcal.mole-1] Initial Activation Energy
Acoef        : 0.391E-9     !same rate as original rates   !1E-7         ![s.day-1.pop-1] Rate Coefficient
kp 	     : 12.3	    ![L/mol] Salinity coefficient		
Temperature  : 35           ![ºC] Optimal Temperature     

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Labil_OM_C_Rate>

<begin_RefractOM_C_Rate>
AE           : 15.1
Acoef        : 0.653E-11     !0.653E-10    !same rate as original rates   !1.67E-8
kp 	     : 12.3
Temperature  : 35

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_RefractOM_C_Rate>
 

	!!!! Microorganisms Death !!!!!

<begin_Heterotrophs_Rate>
AE           : 15.19
Acoef        : 1.01E-33    !5.00E-34    !5.00E-35 testing
kp 	     : 12.3
Temperature  : 35

ConcMinCarbon : 1000.         ![kg/kgsoil] - labil and refractary organic carbon. below rate is maximum
OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Heterotrophs_Rate>

<begin_Autotrophs_Rate>
AE           : 12.64
Acoef        : 1.35E-25     !1.34E-25      !same rate as original rates  !6.68E-30  testing
kp 	     : 12.3
Temperature  : 35 

ConcMinAmmonia : 1.           ![mg/L] - ammonia min. below rate is maximum
OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Autotrophs_Rate>

<begin_Anaerobic_Rate>
AE           : 12.83
Acoef        : 4.522E-30     !4.76E-33      !4.76E-30       !4.76E-23
kp 	     : 12.3
Temperature  : 35 

ConcMinNitrate : 1.           ![mg/L] - nitrate min. below rate is maximum
ConcMinCarbon : 1000.         ![kg/kgsoil] - labil and refractary organic carbon. below rate is maximum
OptimumpH    : 7            ![] Optimum pH for reaction
<end_Anaerobic_Rate>
 

	!!!! Nitrification !!!!!

<begin_AmmoniaToNitrate_Rate>
AE           : 21
Acoef        : 0.    !3.33E-04           ! 3.33E-01                          !Need for a standard value.
kp 	     : 12.3
Temperature  : 35

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_AmmoniaToNitrate_Rate>


	!!!! Ammonia Immobilization !!!!!

<begin_AmmoniaImobilization_Rate>
AE           : 15.1
Acoef        : 5E-07
kp 	     : 12.3
Temperature  : 35
<end_AmmoniaImobilization_Rate>


	!!!! Denitrification !!!!!

<begin_NitrateToNgas_Rate>
AE           : 12.6
Acoef        : 1.431E-10   !1.746E-8       !1.00E-13   2E-7 gave similar results as original rates with 1E-13
kp 	     : 0
Temperature  : 35 

ConcOptCarbon : 10000.         ![kg/kgsoil] - labil and refractary organic carbon. below rate is maximum
OptimumpH    : 7            ![] Optimum pH for reaction
<end_NitrateToNgas_Rate>
 

	!!!! Nitrate Immobilization !!!!!

<begin_NitrateImobilization_Rate>
AE           : 15.1
Acoef        : 5E-07
kp 	     : 12.3
Temperature  : 35
<end_NitrateImobilization_Rate>


	!!!! Urea hydrolysis !!!!!

<begin_Urea_Hydrolysis>
AE	     : 12.6					
Acoef        : 2.50E-04
kp 	     : 0			
Temperature  : 35
<end_Urea_Hydrolysis>


	!!!! Phsphorus Immobilization !!!!!

<begin_PhosphorusImobilization_Rate>
AE	     : 15.1					
Acoef        : 1.955E-9    !5E-10         !5E-07 testing
kp 	     : 12.3			
Temperature  : 35

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_PhosphorusImobilization_Rate>


	!!!! Methane Production !!!!! -> testing

<begin_methane_production>
AE	     : 12.6					
Acoef        : 1.252E-12      !same rate as original rates !1E-13  testing
kp 	     : 0		
Temperature  : 35 

OptimumpH    : 7            ![] Optimum pH for reaction
<end_methane_production>


	!!!! Solubilizing Bacteria  !!!!!

<begin_Sol_Rate>	               
AE           : 15.19
Acoef        : 5.00E-35
kp 	     : 12.3 
Temperature  : 35

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Sol_Rate>

<begin_Labil_OM_C_sol_Rate>
AE           : 1.64E-04
Acoef        : 7.92E-10
kp 	     : 12.3
Temperature  : 35     

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Labil_OM_C_sol_Rate>


<begin_RefractOM_C_sol_Rate>
AE           : 2.02E-04
Acoef        : 2.58E-10
kp 	     : 12.3
Temperature  : 35

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_RefractOM_C_sol_Rate>


<begin_Solubilizing_Rate>	        
AE           : 12.6	                
Acoef        : 1.10E-13			
kp 	     : 0
Temperature  : 35 

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Solubilizing_Rate>




!!!!!!!!!!!!!!!!!!MICROORGANISMS!!!!!!!!!!!!!!!!!!!!!!!
!++++++++++++++++++++++++++++++++++++++++++++++++++++++

<begin_Heterotrophs>
CN_RATIO                : 3.40        !
CP_RATIO		: 12.09       !
POPULATION_CARBON_RATIO : 950         !950         ![(#org/kgsoil)/(mgC/kgsoil)]
CARBON_EFICIENCY        : 0.13        !
NITROGEN_EFICIENCY      : 0           !
MINIMUM_POPULATION      : 50000.      ![#org/kgsoil]
<end_Heterotrophs>

<begin_Autotrophs>
CN_RATIO                : 2.01 
CP_RATIO		: 13.82    
POPULATION_CARBON_RATIO : 9500       !9500
CARBON_EFICIENCY        : 0
NITROGEN_EFICIENCY      : 0.01
MINIMUM_POPULATION      : 500.
<end_Autotrophs>

<begin_Anaerobic>
CN_RATIO                : 3.40
CP_RATIO		: 13.82    
POPULATION_CARBON_RATIO : 9500       !9500
CARBON_EFICIENCY        : 0.1
NITROGEN_EFICIENCY      : 0.1
MINIMUM_POPULATION      : 5000.
<end_Anaerobic>

<begin_Sols>
CN_RATIO                :8
CP_RATIO		:60    
POPULATION_CARBON_RATIO :950         !950
CARBON_EFICIENCY        :0.1
NITROGEN_EFICIENCY      :0.1
<end_Sols>

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Module SedimentQuality

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Contents

Overview

Main Processes

Organic Matter Mineralization

Nitrification

Denitrification

Other Features

Outputs

References

Data File

Keywords

Sample