Supporting information (SI)
Assessment of nitric oxide (NO) redox reactions contribution to nitrous oxide (N2O)
formation during nitrification using a multispecies metabolic network model
Octavio Perez-Garciaa*, Kartik Chandranb, Silas G. Villas-Boasc, Naresh Singhala*
a
Department of Civil and Environmental Engineering, University of Auckland, New Zealand.
b
c
Department of Earth and Environmental Engineering, Columbia University, USA.
Centre for Microbial Innovation, School of Biological Sciences, University of Auckland,
New Zealand.
*Corresponding authors: Naresh Singhal and Octavio Perez-Garcia. Department of Civil and
Environmental Engineering, University of Auckland. 20 Symonds Street, Auckland,
New Zealand, 1010. Phone: +64 9 923 4512; Fax: +64 9 373 7462; Emails:
n.singhal@auckland.ac.nz and octavio.perez@auckland.ac.nz
Running title: Multispecies metabolic network model of N2O production in nitrifying mixed
cultures
1
S1. Experimental datasets
For each analyzed experiment, a dataset was calculated consisting of variables that describe a
specific metabolic steady state of the microbial community at the moment of maximum N2O
productivity. Each of the nine experimental datasets consisted of mean and standard deviation
(st.dev.) values of variables presented in Table SI of this Supporting Information (SI)
document. Datasets are of different number of variables (𝑀) because not all the 38 variables
could be calculated form the information present on the corresponding publications. The
experimental values of Table SI of SI were calculated using the reported concentration curves
of substrates together with bioreactor volume, influent flow rate and cell concentrations in the
experiments as described in Section S2. All the reaction rates are normalized per unit of
biomass expressed as grams of chemical oxygen demand (COD). COD is a standard variable
to measure biomass and organic carbon in wastewater treatment.
2
Table SI: Definition of the 38 variables that describe the metabolic performance of microbial communities. Experimental values (𝑋̂𝑡 ) were
obtained from information in previously published experiments as described in the first section of this SI. Formulas to calculate variable value
using results of FBA or RS simulations are presented on the right column. Cells in blank indicate that that variable couldn’t be calculated for that
particular experiment due lack of information on publication(s).
Variable
ID
Microbial
population
𝑋1
AOB
𝑋2
𝑋3
𝑋4
𝑋5
𝑋6
𝑋7
𝑋8
𝑋9
NOB
𝑋10
𝑋11
𝑋12
𝑋13
𝑋14
𝑋15
COM
Variable definition and units
O2/NH4+ molar yield
(mmol-O2/mmol-N)
NO2-/NH4+ molar yield
(mmol-N/mmol-N)
Cell/NH4+ molar yield
(mmol-N/mmol-N)
Specific O2 uptake rate
(mmol-O2 gCOD-1 h-1)
Specific NH4+ uptake rate
(mmol-N gCOD-1 h-1)
Specific N2O production rate
(mmol-N gCOD-1 h-1)
Specific NO production rate
(mmol-N gCOD-1 h-1)
Specific NO2- production rate
(mmol-N gCOD-1 h-1)
O2/NO2- molar yield
(mmol-O2/mmol-N)
NO3-/ NO2- molar yield
(mmol-N/mmol-N)
Cell-N/NO2- molar yield
(mmol-N/mmol-N)
Specific O2 uptake rate
(mmol-N gCOD-1 h-1)
Specific NO2- uptake rate
(mmol-N gCOD-1 h-1)
Specific NO3- production rate
(mmol-N gCOD-1 h-1)
Inorganic nitrogenous substrate
oxidation to NO2- (%)
Variable values (𝑋̂𝑡 ) in each experiment (mean±st.dev.)
C
D
E
F
G
B
2.4±1.03
3.524±0.5
1.459±0
2.406±2.1
0.99±0.002
0.963±0.01
0.975±0.14
1.005±0.06
0.032±0.016
0.053±0.006
2.26±0.34
2.225±0.34
0.203±0.03
2.111±0.7
10.20±0.1
10.25±0.05
11.73±0.042
0.019±0.002
𝐴𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑂2
2.43±0.81
1.445±0.11
0.139±0
2.720±1.6
5.43±0.33
6.96±0.5
11.28±1.12
0.049±0.013
𝐴𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝐻4
0.004±0.003
0.071±0.02
0.002±0.0007
0.013±0.012
0.01±0.002
0.02±0.001
0.06±0.11
0.005±0.002
𝐴𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑁2𝑂
I
1.43±0.042
0.98±0.04
0.419±0.1
𝐴𝑂𝐵𝑛𝑒𝑡 ⁄ 𝐴𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑂2
𝑣𝐸𝑥𝑁𝐻4
0.62±0.2
0.71±0
0.390±0.069
𝐴𝑂𝐵𝑛𝑒𝑡 ⁄ 𝐴𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂2
𝑣𝐸𝑥𝑁𝐻4
𝐴𝑂𝐵𝑛𝑒𝑡 ⁄ 𝐴𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝐶𝑒𝑙𝑙
𝑣𝐸𝑥𝑁𝐻4
0.048±0.02
0.0002±0.000
2.46±0.813
1.85±0.096
H
Variable calculation formula
A
𝐴𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂
0.0002±0.0001
1.407±0.1
0.136±0.02
2.781±1.7
0.6±0.23
0.468±0.02
-0.394±0.9
0.99±0.002
0.97±0.158
1.635±1.5
4.47±0.01
3.73±1.3
0.051±0.01
𝐴𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂2
0.413±0.12
0.493±0.15
𝑁𝑂𝐵𝑛𝑒𝑡 ⁄ 𝑁𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑂2
𝑣𝐸𝑥𝑁𝑂2
0.956±0.17
1.077±0.12
𝑁𝑂𝐵𝑛𝑒𝑡 ⁄ 𝑁𝐶𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂3
𝑣𝐸𝑥𝑁𝑂2
9.58±0
𝑁𝑂𝐵𝑛𝑒𝑡 ⁄ 𝑁𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝐶𝑒𝑙𝑙
𝑣𝐸𝑥𝑁𝑂2
0.011±0.006
0.047±0.023
0.053±0.05
0.55±0.11
0.582±0.032
0.060±0.003
0.019±0.015
0.057±0.008
0.021±0.004
𝑁𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑂2
2.3±0.81
0.303±0.26
0.129±0
0.131±0.23
0.09±0.01
0.047±0.017
𝑁𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂2
2.4±0.81
0.416±0.27
0.125±0.02
0.286±0.25
0.09±0.01
0.049±0.013
𝑁𝑂𝐵𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂3
88.6±5.4
83.42±8.5
97.6±10
83.42±8.53
103.6±10.4
𝐶𝑂𝑀𝑛𝑒𝑡 ⁄ 𝐶𝑂𝑀𝑛𝑒𝑡
(𝑣𝐸𝑥𝑁𝑂2
𝑣𝐸𝑥𝑁𝐻4 ) ∗ 100
82.39±4.1
53.52±5.3
84.89±8
3
𝑋16
(Full
𝑋17
community)
𝑋18
𝑋19
𝑋20
𝑋21
𝑋22
𝑋23
𝑋24
𝑋25
𝑋26
𝑋27
𝑋28
𝑋29
𝑋30
𝑋31
𝑋32
𝑋33
𝑋34
N-substrate oxidation to NO3(%)
NO3-/NH4+ molar yield
(mmol-N/mmol-N)
NO2-/NH4+ molar yield
(mmol-N/mmol-N)
N2O/NH4+ molar yield
(mmol-N/mmol-N)
NO/NH4+ molar yield
(mmol-N/mmol-N)
N2O/NO2- molar yield
(mmol-N/mmol-N)
O2/N substrae molar yield
(mmol-O2/mmol-N)
Cell-/N substrate molar yield
(mmol-N/mmol-N)
Specific oxygen uptake rate
(mmol-N gCOD-1 h-1)
Specific N-substrate uptake rate
(mmol-N gCOD-1 h-1)
Specific nitrate production rate
(mmol-N gCOD-1 h-1)
Specific nitrite production rate
(mmol-N gCOD-1 h-1)
Specific N2O production rate
(mmol-N gCOD-1 h-1)
Specific NO production rate
(mmol-N gCOD-1 h-1)
Specific biomass production rate
(Cell-N/gCOD*h)
N. europaea biomass fraction
(%)
N. eutropha biomass fraction
(%)
N. multiformis biomass fraction
(%)
N. oceani biomass fraction
(%)
99.6±0.21
9.51±4.9
90.0±9
9.51±4.9
0.29±0.19
0.900±0.14
0.10±0.05
0.002±0.001
0.68±0.2
0.075±0
0.91±0.05
0.002±0.002
0.05±0.02
0.016±0.001
0.01±0.01
0.0002±0.0001
0.002±0.0002
95.88±9
103.7±7.3
𝐶𝑂𝑀𝑛𝑒𝑡 ⁄ 𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂3
𝑣𝐸𝑥𝑁𝐻4
0.0019±0.0002
0.62±0.21
0.71±0
0.060±0.1
𝐶𝑂𝑀𝑛𝑒𝑡 ⁄ 𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂2
𝑣𝐸𝑥𝑁𝐻4
0.003±0.0003
0.0055±0.0005
0.124±0.06
𝐶𝑂𝑀𝑛𝑒𝑡 ⁄ 𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑁2𝑂
𝑣𝐸𝑥𝑁𝐻4
𝐶𝑂𝑀𝑛𝑒𝑡 ⁄ 𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂
𝑣𝐸𝑥𝑁𝐻4
0.0008±0.0006
0.217±0.017
𝐶𝑂𝑀𝑛𝑒𝑡 ⁄ 𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑁2𝑂
𝑣𝐸𝑥𝑁𝑂2
0.100±0.059
2.42±2.3
1.9±1
1.43±0.04
0.98±0.04
0.413±0.12
0.869±0.12
𝐶𝑂𝑀𝑛𝑒𝑡 ⁄ 𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑂2
𝑣𝐸𝑥𝑁
2.99±1.19
4.45±0.47
0.04±0.02
0.06±0.004
2.82±0.35
2.81±0.32
0.264±0.003
2.13±0.84
10.2±0.1
10.25±0.05
11.73±0.04
0.057±0
0.040±0.004
𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑂2
2.44±0.81
1.44±0.11
0.139±0
2.72±1.64
5.4±0.3
6.96±0.54
11.28±1.12
0.09±0.01
0.049±0.013
𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑁
2.43±0.81
0.42±0.27
0.125±0.02
0.29±0.25
0.09±0.01
0.049±0.013
𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂3
0.076±0.019
2.48±1.49
4.5±0.02
3.73±1.3
9.58±0
0.030±0.008
𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂2
0.002±0
0.02±0.01
0.01±0.002
0.02±0.0012
0.06±0.1
0.005±0
𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑁2𝑂
0.01±0.003
1.892±0.018
𝐶𝑂𝑀𝑛𝑒𝑡 ⁄ 𝐶𝑂𝑀𝑛𝑒𝑡
(𝑣𝐸𝑥𝑁𝑂3
𝑣𝐸𝑥𝑁𝐻4 ) ∗ 100
𝐶𝑂𝑀𝑛𝑒𝑡 ⁄ 𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝐶𝑒𝑙𝑙𝑁
𝑣𝐸𝑥𝑁
0.05±0.03
0.004±0.003
0.071±0.03
0.001±0.000
0.003±0.0005
0.002±0.001
𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝑁𝑂
0.09±.001
0.09±0
0.09±0.0
𝐶𝑂𝑀𝑛𝑒𝑡
𝑣𝐸𝑥𝐶𝑒𝑙𝑙𝑁
52.6±5.3
52.6±5.3
20±2
30±3
60.0±6.0
80.24±8
80.24±8
80.24±8
30.3±3.0
5.25±0.53
5.25±0.53
5.25±0.53
5.25±0.53
5.25±0.53
5.25±0.53
5.25±0.53
5.25±0.53
5.25±0.53
0.013±0.004
20±2
20±2
𝑛𝑒𝑢
𝐶𝑂𝑀𝑛𝑒𝑡
⁄𝑣𝐸𝑥𝑐𝑒𝑙𝑙𝑁
(𝑣𝐸𝑥𝐶𝑒𝑙𝑙𝑁
) ∗ (100 − 𝑓 𝑜 )
𝑛𝑒𝑡
𝐶𝑂𝑀𝑛𝑒𝑡
⁄𝑣𝐸𝑥𝑐𝑒𝑙𝑙𝑁
(𝑣𝐸𝑥𝐶𝑒𝑙𝑙𝑁
) ∗ (100 − 𝑓 𝑜 )
30±3
30±3
𝑛𝑚𝑢
𝐶𝑂𝑀𝑛𝑒𝑡
⁄𝑣𝐸𝑥𝑐𝑒𝑙𝑙𝑁
(𝑣𝐸𝑥𝐶𝑒𝑙𝑙𝑁
) ∗ (100 − 𝑓 𝑜 )
𝑛𝑜𝑐
𝐶𝑂𝑀𝑛𝑒𝑡
⁄𝑣𝐸𝑥𝑐𝑒𝑙𝑙𝑁
(𝑣𝐸𝑥𝐶𝑒𝑙𝑙𝑁
) ∗ (100 − 𝑓 𝑜 )
4
𝑋35
𝑋36
𝑋37
𝑋38
𝑁
N. defluvii biomass fraction
(%)
N. winogradskyi biomass
fraction (%)
N. hamburgensis biomass
fraction (%)
N. gracilis biomass fraction
(%)
Number of variables in dataset
𝑣𝑗𝐴𝑂𝐵𝑛𝑒𝑡 = 𝑣𝑗𝑛𝑒𝑢 + 𝑣𝑗𝑛𝑒𝑡 + 𝑣𝑗𝑛𝑚𝑢 + 𝑣𝑗𝑛𝑜𝑐
𝑛𝑠𝑝
𝑣𝑗𝑁𝑂𝐵𝑛𝑒𝑡 = 𝑣𝑗𝑛𝑑𝑒 + 𝑣𝑗𝑛𝑤𝑖 + 𝑣𝑗𝑛ℎ𝑎 + 𝑣𝑗
25±2.5
1.00±0.1
1.00±0.1
1.00±0.1
25±2.5
25±2.5
𝑛𝑑𝑒
𝐶𝑂𝑀𝑛𝑒𝑡
⁄𝑣𝐸𝑥𝑐𝑒𝑙𝑙𝑁
(𝑣𝐸𝑥𝐶𝑒𝑙𝑙𝑁
) ∗ (100 − 𝑓 𝑜 )
9.7±1
9.7±1
12.5±1
4.5±0.4
1.00±0.1
1.00±0.1
1.00±0.1
12.5±1
12.5±1
𝑛𝑤𝑖
𝐶𝑂𝑀𝑛𝑒𝑡
⁄𝑣𝐸𝑥𝑐𝑒𝑙𝑙𝑁
(𝑣𝐸𝑥𝐶𝑒𝑙𝑙𝑁
) ∗ (100 − 𝑓 𝑜 )
9.7±1
9.7±1
12.5±1
4.5±0.4
1.00±0.1
1.00±0.1
1.00±0.1
12.5±1
12.5±1
𝑛ℎ𝑎
𝐶𝑂𝑀𝑛𝑒𝑡
⁄𝑣𝐸𝑥𝑐𝑒𝑙𝑙𝑁
(𝑣𝐸𝑥𝐶𝑒𝑙𝑙𝑁
) ∗ (100 − 𝑓 𝑜 )
1.00±0.1
1.00±0.1
1.00±0.1
20
22
22
31
28
28
33
𝑛𝑠𝑝
𝐶𝑂𝑀𝑛𝑒𝑡
(𝑣𝐸𝑥𝐶𝑒𝑙𝑙𝑁 ⁄𝑣𝐸𝑥𝑐𝑒𝑙𝑙𝑁
) ∗ (100 − 𝑓 𝑜 )
17
26
𝑛𝑠𝑝
𝑣𝑗𝐶𝑂𝑀𝑛𝑒𝑡 = 𝑣𝑗𝑛𝑒𝑢 + 𝑣𝑗𝑛𝑒𝑡 + 𝑣𝑗𝑛𝑚𝑢 + 𝑣𝑗𝑛𝑜𝑐 + 𝑣𝑗𝑛𝑑𝑒 + 𝑣𝑗𝑛𝑤𝑖 + 𝑣𝑗𝑛ℎ𝑎 + 𝑣𝑗
𝑓 𝑜 = biomass percentage fraction of non-nitrifying organism.
5
S2. Details of analyzed nitrifying cultures
S2.1 (Ahn et al., 2011) experiments on N2O production in full and partial nitrification
systems
Analyzed experiments A, B and D were previously presented in (Ahn et al., 2011)
publication. These experiments consisted of a single 11 liters bioreactor operated in
continuous mode during 360 days; reactor’s dissolved oxygen and HRT were changed at
specific days to impose different experimental conditions. The calculated experimental data
sets A, B and D were generated from the bioreactors performance reported during the period
of those experimental conditions. Bioreactor performance was monitored twice a week by
measuring nitrogenous compounds concentrations subsequently reported as percentages of
reactor removal and accumulation efficiency.
Table SII. Experimental conditions used to calculate the experimental datasets A, B and D are
following enlisted:
Variable
Value (mean±st.dev.)
Units
A
B
D
NH4+ oxidation NH4+ oxidation
NH4+ oxidation
Experimental process
to NO3
to NO3 *
to NO2Reactor operation mode
Continuous
Continuous
Continuous
Reactor working volume (V)
11
11
11
L
Hydraulic retention time (HRT)
1.1
1.1
1.1
d
Flow rate (Q)
10
10
10
L/d
Air flow rate
3
3
3
L/min
pH
7.5
7.5
7.5
Dissolved oxygen
3.8 ± 0.38
1.5 ± 0.87
1.5 ± 0.87
mg-O2/L
Sludge retention time
8.0
3.0
3.0
d
Analyzed period from total experiment run
53 to 99
100 to 110
200 to 350
day of experiment
NH4+-N feed concentration
500
500
500
mg-N/L
NH4+-N removed from feed
88.5±5.4
73.6±8.2
83.42±8.5
%
N converted to NO2--N
0.15±0.12
67.6±19.8
91±4.6
%
N converted to NO3--N
99.6±0.21
28.7±18.6
9.5±4.9
%
N converted to N2O-N
0.16±0.20
3.5±1.12
0.66±0.15
%
N converted to NO-N
0.022±0.010
0.175±0.022
0.084±0.033
%
Oxygen uptake rate due to NH4+ oxidation
2.26±0.34
2.22±0.34
2.33±0.75
mmolO2/gCOD*h
Oxygen uptake rate due to NO2- oxidation
0.55±0.11
0.58±0.03
0.05±0.15
mmolO2/gCOD*h
AOB biomass concentration**
0.47±0.02
0.56±0.14
0.57±0.31
gCOD/L
NOB biomass concentration**
0.14±0.008
0.19±0.037
0.05±0.03
gCOD/L
Total biomass concentration**
0.54±0.19
0.68±011
0.61±0.32
gCOD/L
(*) Transition period (10 days) from NH4+ oxidation to NO3- to NH4+ oxidation to NO2-. Presence of NOB species
(**) Biomass concentrations in grams of COD were calculated by multiplying the number of 16SRNA gene copies for AOB,
NOB and bacterial cells quantified by qPCR with the conversion factor 3.9x10-13 gCOD/16Scopy reported by (Ahn et al.,
2008).
Experiment ID
6
Reported NH4+-N feed concentrations and percentages of removed nitrogen converted to
nitrogenous compounds were used to estimate absolute concentrations of nitrogenous
compounds during the analyzed period for each experiment. These nitrogenous compound
concentrations (in mmol-N/L) were multiplied by bioreactor’s flow rate (Q in L/h) and
divided by bioreactor’s AOB, NOB or total biomass (in gCOD) to obtain production and
consumption rates of nitrogenous compounds in mmol-N/gCOD*h units.
S2.2 (Wunderlin et al., 2013) experiments on quantification of N2O production pathways
using stable isotopes
Analyzed experiments C, H and I were previously presented in (Wunderlin et al., 2013;
Wunderlin et al., 2012) publications. Both publications reported the same set of 25 batch
cultures experiments, each of them initialized by adding a specific amount of nitrogenous
substrate; for our analysis; we chose three of these experiments on basis of two criteria: 1)
different initial nitrogenous substrate and 2) availability experiment’s concentration curves of
nitrogenous compounds on publications.
Table SIII. Experimental variables used to calculate the experimental datasets C, H and I are
following enlisted:
Variable
Experiment ID
Experimental process
Reactor operation mode
Reactor working volume (V)
Total suspended solids (TSS)
Air flow rate
pH
Dissolved oxygen
Nitrogenous substrate in feed
N concentration in feed
Experiment duration
Absolute value
C
NH4+ oxidation to
NO3Batch
6.9
4.1
1
7.1
1.9 ± 0.2
NH4+
25
180
H
NO2- oxidation to
NO3Batch
6.9
4.1
1
7.1
1.1 ± 0.2
NO215.5
120
Units
I
NH2OH oxidation
to NOx
Batch
6.9
4.1
1
7.1
1.1 ± 0.2
NH2OH
9.8
360
L
g/L
L/min
mg-O2/L
d
mg-N/L
min
7
Specific N2O production rates were taken directly form (Wunderlin et al., 2012) publication.
Nitrogenous substrate uptake rate and NO2--N, NO3--N production rates were estimated using
the formula 𝑟𝑎𝑡𝑒 = (𝐶1 − 𝐶0 )/(𝑡1 − 𝑡0 ) along with the reported concentration data (𝐶)
respectively observed at times 𝑡1 and 𝑡0 (in hours) (Dorian, 1995). In particular these rates
were estimated for the reaction phase time period, where concentration curves of these three
compounds presented a straight trend (constant slope) therefore indication a temporal steady
state in the system. Specific oxygen uptake rates (sOUR) were estimated using the Activated
Sludge (ASM) model “C” presented in (Law et al., 2012) (implemented in MS Excel® sheet)
by fitting estimated NH4+ and NO2- and NO3+ concentration curves to the corresponding
concentration data of experiments’ C, H and I. All calculated rates were normalized by
bioreactor’s AOB, NOB or total biomass expressed as gCOD (measured in Wunderlin et al.,
(2013) and (2012) studies as TSS and converted to gCOD suing the factor 1.42gCOD/gTSS
(Grady et al., 1999)).
S2.3 (Law et al., 2012) experiments on the effect of pH and dissolved oxygen on N2O
production by partial nitrification systems
Analyzed experiments E, F and G were previously presented in (Law et al., 2011; Law et al.,
2012) publications. These experiments consisted of batch cultures enriched with nitrifying
biomass and initial ammonium concentration of 500mg-N/L; reactor pH and dissolved
oxygen were changed at specific times of the reaction phase to impose different experimental
conditions. The calculated experimental data sets E, F and G were generated from the
bioreactors performance reported during the period of those experimental conditions.
Bioreactor performance was monitored by measuring nitrogenous compounds concentrations.
8
Table SIV. Experimental variables used to calculate the experimental datasets E, F and G are
following enlisted:
Variable
Experiment ID
Experimental process
Reactor operation mode
Reactor working volume (V)
Volatile suspended solids (MLVSS)
Air flow rate
pH
Dissolved oxygen
Initial NH4+-N concentration in feed
Experimental condition duration
Value (mean±st.dev.)
E
NH4+ oxidation
to NO2Batch
1.1
750±50
2.5
7
0.55 ± 0.05
500
0.5
F
NH4+ oxidation
to NO2Batch
1.1
750±50
2.5
8
0.55 ± 0.05
500
1.1
Units
G
NH4+ oxidation
to NO2Batch
1.1
750±50
2.5
8
1.25 ± 0.05
500
0.5
L
mg/L
L/min
mg-O2/L
mg-N/L
hours
Specific N2O production and NH4+-N consumption rates were directly reported on Law et al.,
(2011) publication. NO2--N production rates were estimated using the formula 𝑟𝑎𝑡𝑒 = (𝐶1 −
𝐶0 )/(𝑡1 − 𝑡0 ) along with the reported concentration data (𝐶) observed at times 𝑡1 and 𝑡0 (in
hours) (Dorian, 1995). NO2--N production rates were estimated for the reaction phase time
period, where concentration curves of this compound presented a straight trend (constant
slope) therefore indication a temporal steady state in the system. Specific oxygen uptake rates
(sOUR) were estimated using the Activated Sludge (ASM) model “C” presented in (Law et
al., 2012) (implemented in MS Excel® sheet). All calculated rates were normalized by
bioreactor’s AOB, NOB or total biomass expressed as gCOD (measured in Law et al., 2012
and 2011 studies as MLVSS and converted to gCOD suing the factor 1.42gCOD/gVSS
(Grady et al., 1999)).
9
S3. Monte Carlo random sampling method
For each analyzed experiment and using each of the eight model variants, 11,000 FBA
simulations were performed iteratively using random combinations of values sampled for
𝐴𝑂𝐵
sOUR, sAUR, 𝑓 𝑘 and 𝛽𝐶𝑦𝑡𝑎𝑎3
. The sOUR and sAUR parameter values were randomly
sampled from a uniform probabilistic distribution spanning the experimentally observed
mean ± std. dev. values (Table I); similarly, values for 𝑓 𝑘 fractions were obtained assuming a
± 50 % variability in experimental values (Table II). The rate of AOB’s terminal oxidase
greatly influenced the sN2OPR estimated for AOB (Ni et al., 2013; Perez-Garcia et al., 2014).
𝐴𝑂𝐵
𝐴𝑂𝐵
Therefore, a full range of 𝛽𝐶𝑦𝑡𝑎𝑎3
values was explored by adjusting the input 𝛽𝐶𝑦𝑡𝑎𝑎3
value as
𝐴𝑂𝐵
function of the observed sOUR for AOB so that 𝛽𝐶𝑦𝑡𝑎𝑎3
= 𝑥 ∗ 𝑠𝑂𝑈𝑅 𝐴𝑂𝐵 ; where 𝑥 is one of
11 fraction numbers 0, 0.1, 0.2 until 1.
10
S4. Calculation of absolute percent error
The fitness between model-estimated and experimental datasets was quantified using the
absolute percent error (Δ) using the following formula:
∆=
𝑆𝑎𝑚𝑝 𝑒𝑥𝑝
∑𝑁
− 𝑋𝑡𝑒𝑠𝑡 |
𝑡=1 ∑𝑠=1 |𝑋𝑡
𝑆𝑎𝑚𝑝 𝑒𝑥𝑝
∑𝑉𝑎𝑟
|
𝑡=1 ∑𝑠=1 |𝑋𝑡
∗ 100
(S1)
where 𝑋𝑡𝑒𝑠𝑡 is the estimated value of the 𝑡𝑡ℎ variable defined in Table II of SI; 𝑋𝑡𝑒𝑥𝑝 is the
𝑒𝑥𝑝
experimentally observed mean value of the 𝑡𝑡ℎ variable; the expression ∑𝑆𝑎𝑚𝑝
−
𝑠=1 |𝑋𝑡
𝑋𝑡𝑒𝑠𝑡 | represents the sum of the absolute errors resulting from the 1000 FBAs ran using the
sampled values of model’s input parameters and 𝑁 is the number of dataset variables, 𝑁 vary
in all the analyzed experiments because not all the variables could be estimated from the
experiments’ descriptions and graphs presented in publications.
11
Figures
Figure S1. Relationship between the rate of the reaction catalyzed by terminal oxidase
𝐴𝑂𝐵
cytochrome aa3 (𝛽𝐶𝑦𝑡𝑎𝑎3
) and the specific N2O production rate (sN2OPR) of nitrifying
cultures. Solid lines represent mean values obtained from 1000 FBA simulations using the
Monte Carlo procedure while break line represent the 10th and 90th percentiles.
12
Complete SMN model
Table SV. Stoichiometric equations of the nitrifying community SMN model. Reaction description
column specify reaction’s compartment as follows: Exchange reactions (EX), common environment
(ENV); Nitrosomonas europaea (NEU); Nitrosomonas eutropha (NET); Nitrosospira multiformis
(NMU); Nitrosococcus oceani (NOC); Candidatus Nitrospira defluvii (NDE); Nitrobacter
winogradskyi (NWI); Nitrobacter hamburgensis (NHQ); and Nitrospina gracilis (NSP).
Reaction
name
Rx1
Rx2
Rx3
Rx4
Rx5
Rx6
Rx7
Rx8
Rx9
Rx10
Rx11
Rx12
Rx13
Rx14
Rx15
Rx16
Rx17
Rx18
Rx19
Rx20
Rx21
Rx22
Rx23
Rx24
Rx25
Rx26
Rx27
Rx28
Rx29
Rx30
Rx31
Rx32
Rx33
Rx34
Rx35
Rx36
Rx37
Rx38
Rx39
Rx40
Rx41
Rx42
Rx43
Rx44
Rx45
Rx46
Rx47
Rx48
Rx49
Rx50
Rx51
Rx52
Rx53
Rx54
Rx55
Rx56
Rx57
Rx58
Rx59
Rx60
Rx61
Rx62
Rx63
Rx64
Rx65
Rx66
Rx67
Rx68
Rx69
Rx70
Rx71
Rx72
Rx73
Rx74
Rx75
Rx76
Rx77
Reaction description
EX. NH4
EX. O2
EX. NO2
EX. NO3
EX. N2O
EX. NO
EX. N2
EX. NH2OH
EX. Biomass
EX. Pi
EX. H2O
EX. CO2
EX. H
ENV. Tr1
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Equation
Associated
Genes
Reference
nh4[e] <==>
o2[e] <==>
no2[e] <==>
no3[e] <==>
n2o[e] <==>
no[e] <==>
n2[e] <==>
nh2oh[e] <==>
biomass[e] <==>
pi[e] <==>
h2o[e] <==>
co2[e] <==>
h[e] <==>
nh4[e] <==> nh4[a]
nh4[e] <==> nh4[b]
nh4[e] <==> nh4[c]
nh4[e] <==> nh4[d]
nh4[e] <==> nh4[f]
nh4[e] <==> nh4[g]
nh4[e] <==> nh4[h]
nh4[e] <==> nh4[i]
o2[e] <==> o2[a]
o2[e] <==> o2[b]
o2[e] <==> o2[c]
o2[e] <==> o2[d]
o2[e] <==> o2[f]
o2[e] <==> o2[g]
o2[e] <==> o2[h]
o2[e] <==> o2[i]
no2[e] <==> no2[a]
no2[e] <==> no2[b]
no2[e] <==> no2[c]
no2[e] <==> no2[d]
no2[e] <==> no2[f]
no2[e] <==> no2[g]
no2[e] <==> no2[h]
no2[e] <==> no2[i]
no3[e] <==> no3[b]
no3[e] <==> no3[d]
no3[e] <==> no3[f]
no3[e] <==> no3[g]
no3[e] <==> no3[h]
no3[e] <==> no3[i]
n2o[e] <==> n2o[a]
n2o[e] <==> n2o[b]
n2o[e] <==> n2o[c]
n2o[e] <==> n2o[d]
n2o[e] <==> n2o[f]
n2o[e] <==> n2o[h]
no[e] <==> no[a]
no[e] <==> no[b]
no[e] <==> no[c]
no[e] <==> no[d]
no[e] <==> no[f]
no[e] <==> no[g]
no[e] <==> no[h]
no[e] <==> no[i]
n2[e] <==> n2[c]
n2[e] <==> n2[d]
nh2oh[e] <==> nh2oh[a]
nh2oh[e] <==> nh2oh[b]
nh2oh[e] <==> nh2oh[c]
nh2oh[e] <==> nh2oh[d]
biomass[e] <==> biomass[a]
biomass[e] <==> biomass[b]
biomass[e] <==> biomass[c]
biomass[e] <==> biomass[d]
biomass[e] <==> biomass[i]
biomass[e] <==> biomass[f]
biomass[e] <==> biomass[g]
biomass[e] <==> biomass[h]
pi[e] <==> pi[a]
pi[e] <==> pi[b]
pi[e] <==> pi[c]
pi[e] <==> pi[d]
pi[e] <==> pi[i]
pi[e] <==> pi[f]
13
Rx78
Rx79
Rx80
Rx81
Rx82
Rx83
Rx84
Rx85
Rx86
Rx87
Rx88
Rx89
Rx90
Rx91
Rx92
Rx93
Rx94
Rx95
Rx96
Rx97
Rx98
Rx99
Rx100
Rx101
Rx102
Rx103
Rx104
Rx105
Rx106
Rx107
Rx108
Rx109
Rx110
Rx111
Rx112
Rx113
Rx114
Rx115
Rx116
Rx117
Rx118
Rx119
Rx120
Rx121
Rx122
Rx123
ENV. Tr65
ENV. Tr66
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ENV. Tr68
ENV. Tr69
ENV. Tr70
ENV. Tr71
ENV. Tr72
ENV. Tr73
ENV. Tr74
ENV. Tr75
ENV. Tr76
ENV. Tr77
ENV. Tr78
ENV. Tr79
ENV. Tr80
ENV. Tr81
ENV. Tr82
ENV. Tr83
ENV. Tr84
ENV. Tr85
ENV. Tr86
ENV. Tr87
ENV. Tr88
ENV. Tr89
ENV. Tr90
NEU. Tr1
NEU. Tr2
NEU. Tr3
NEU. Tr4
NEU. Tr5
NEU. Tr6
NEU. Tr7
NEU. Tr8
NEU. Tr9
NEU. Tr10
NEU. Tr11
NEU. Tr12
NEU. Tr13
NEU. Tr14
NEU. Tr15
NEU. Tr16
NEU. Tr17
NEU. Tr18
NEU. Tr19
NEU. AMO Ammonia oxidation to
hydroxylamine using ubiquinol as e
donor
pi[e] <==> pi[g]
pi[e] <==> pi[h]
h2o[e] <==> h2o[a]
h2o[e] <==> h2o[b]
h2o[e] <==> h2o[c]
h2o[e] <==> h2o[d]
h2o[e] <==> h2o[i]
h2o[e] <==> h2o[f]
h2o[e] <==> h2o[g]
h2o[e] <==> h2o[h]
co2[e] <==> co2[a]
co2[e] <==> co2[b]
co2[e] <==> co2[c]
co2[e] <==> co2[d]
co2[e] <==> co2[i]
co2[e] <==> co2[f]
co2[e] <==> co2[g]
co2[e] <==> co2[h]
h[e] <==> h[a]
h[e] <==> h[b]
h[e] <==> h[c]
h[e] <==> h[d]
h[e] <==> h[i]
h[e] <==> h[f]
h[e] <==> h[g]
h[e] <==> h[h]
nh4[a] <==> nh3[j] + h[j]
o2[a] <==> o2[j]
no2[a] + h[a] <==> hno2[j]
n2o[a] <==> n2o[j]
no[a] <==> no[j]
nh2oh[a] <==> nh2oh[j]
biomass[a] <==> biomass[j]
pi[a] <==> pi[j]
h2o[a] <==> h2o[j]
co2[a] <==> co2[j]
h[a] <==> h[j]
h[a] <==> h[r]
nh3[j] <==> nh3[r]
o2[j] <==> o2[r]
biomass[j] <==> biomass[r]
pi[j] <==> pi[r]
h2o[j] <==> h2o[r]
co2[j] <==> co2[r]
h[j] <==> h[r]
nh3[j] + o2[j] + q8h2[r] --> nh2oh[j] + h2o[r] + q8[r]
amoABC
Rx124
NEU. HAO Hydroxylamine oxidation to
nitrite 1
nh2oh[j] + cyt554[j] --> noh[j] + cyt554e[j] + 2 h[j]
haoAB
Rx125
NEU. HAO Hydroxylamine oxidation to
nitrite 2
noh[j] + 0.5 cyt554[j] --> no1[j] + h[j] + 0.5 cyt554e[j]
haoAB
Rx126
NEU. HAO Hydroxylamine oxidation to
nitrite 3
no1[j] + h2o[j] + 0.5 cyt554[j] --> hno2[j] + h[j] + 0.5
cyt554e[j]
haoAB
Rx127
NEU. ETC Partition of electron flow by
cyt554
cyt554e[j] + cyt552[r] --> cyt552e[r] + cyt554[j]
cycA
Rx128
NEU. ETC Ubiquinone to ubiquinol for
AMO
q8[r] + cyt552e[r] + 2 h[j] --> q8h2[r] + cyt552[r]
Rx129
NEU. ETC NADH production by NADHubiquinone reductase using ubiquinol
nad[r] + q8h2[r] + 4 h[j] --> nadh[r] + q8[r] + 6 h[r]
nouA-M
Rx130
NEU. ETC proton pump by CytCbc1
reductase using ubiquinol
q8h2[r] + 2 cyt552[j] + 0 h[r] --> 2 h[j] + q8[r] + 2
cyt552e[j]
cyt b, cyt 1
Rx131
NEU. ETC proton pump by Cytaa3,
Oxygen as final electron acceptor OXIC
.5 o2[r] + 4 h[r] + 2 cyt552e[j] --> h2o[r] + 2 h[j] + 2
cyt552[j]
coxABC
NEU. CytP460 NO2 synthesis from
NH2OH + NO
NEU. NO availability to NOR and
Cytp460
0.5 nh2oh[j] + 0.5 no[j] + 2 cyt552[j] + h2o[j] --> hno2[j] +
2 cyt552e[j] + 3 h[j]
cyp
no1[j] --> no[j]
haoAB
hno2[j] + cyt552e[j] + h[j] --> no[j] + cyt552[j] + h2o[j]
nirK
Rx132
Rx133
Rx134
NEU. R1 - NIR Nitrite reduction to nitric
oxide
Rx137
NEU. R2 - NOR Nitric oxide reduction to
nitrous oxide
NEU. Nitric oxide activity by cytochrome
C554
NEU. ATP production
R138
NEU. Protein synthesis
Rx139
NEU. ATP maintenance consumption
Rx140
NEU. Biomass synthesis.
Rx141
Rx142
Rx143
Rx144
NET. Tr1
NET. Tr2
NET. Tr3
NET. Tr4
Rx135
Rx136
no[j] + cyt552e[j] + h[j] --> 0.5 n2o[j] + cyt552[j] + 0.5
h2o[j]
no[j] + h[j] + 0.5 cyt554e[j] --> 0.5 n2o[j] + 0.5 cyt554[j] +
0.5 h2o[j]
adp[r] + pi[r] + 6.8 h[j] --> atp[r] + h2o[r] + 4.8 h[r]
2.244 atp[r] + nh3[r] + 4 co2[r] --> 2.244 adp[r] + 2.244
pi[r] + 2.244 h[r] + 0.25 protein[r]
atp[r] + h2o[r] --> adp[r] + pi[r] + h[r] + m[r]
15 atp[r] + 12 nadh[r] + 0.25 protein[r] + 32 m[r] --> 15
adp[r] + 12 nad[r] + 15 pi[r] + 15 h[r] + biomass[r]
nh4[b] <==> nh3[k] + h[k]
no2[b] + h[b] <==> hno2[k]
no2[b] + no2[b] <==> n2o4[k]
o2[b] <==> o2[k]
norCB
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000);
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000);
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000)
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Whittaker et
al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Whittaker et
al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
(Chandran et al., 2011; Elmore et al., 2007; Numata et
al., 1990)
(Chandran et al., 2011; Poughon et al., 2001)
(Beaumont et al., 2002; Cantera and Stein, 2007; Colliver
and Stephenson, 2000; Hooper et al., 1997; Stein, 2011;
Yu et al., 2010)
(Chandran et al., 2011; Colliver and Stephenson, 2000;
De Vries et al., 2007; Stein, 2011; Yu et al., 2010)
cycA
(Stein, 2011; Upadhyay et al., 2006)
atpα- ε F-type
(Thiele and Palsson, 2010)
(Thiele and Palsson, 2010)
14
Rx145
Rx146
Rx147
Rx148
Rx149
Rx150
Rx151
Rx152
Rx153
Rx154
Rx155
Rx156
Rx157
Rx158
Rx159
Rx160
Rx161
Rx162
Rx163
Rx164
Rx165
Rx166
NET. Tr5
NET. Tr6
NET. Tr7
NET. Tr8
NET. Tr9
NET. Tr10
NET. Tr11
NET. Tr12
NET. Tr13
NET. Tr14
NET. Tr15
NET. Tr16
NET. Tr17
NET. Tr18
NET. Tr19
NET. Tr20
NET. Tr21
NET. Tr22
NET. Tr23
NET. Tr24
NET. AMO Ammonia oxidation to
hydroxylamine using ubiquinol as e
donor
NET. AMO-ANX Ammonia oxidation to
hydroxylamine using ubiquinol as e
donor
n2o[b] <==> n2o[k]
no[b] <==> no[k]
nh2oh[b] <==> nh2oh[k]
no3[b] <==> no3[k]
biomass[b] <==> biomass[k]
pi[b] <==> pi[k]
h2o[b] <==> h2o[k]
co2[b] <==> co2[k]
h[b] <==> h[k]
h[b] <==> h[s]
nh3[k] <==> nh3[s]
o2[k] <==> o2[s]
no[k] <==> no[s]
no3[k] <==> no3[s]
n2o[k] <==> n2o[s]
biomass[k] <==> biomass[s]
pi[k] <==> pi[s]
h2o[k] <==> h2o[s]
co2[k] <==> co2[s]
h[k] <==> h[s]
nh3[k] + o2[k] + q8h2[s] --> nh2oh[k] + h2o[s] + q8[s]
amoABC
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
nh3[k] + n2o4[k] + q8h2[s] --> nh2oh[k] + h2o[s] + q8[s] +
2 no[k]
amoABC
(Schmidt, 2008)
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000)
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000)
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Whittaker et
al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Whittaker et
al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
Rx167
NET. HAO Hydroxylamine oxidation to
nitrite 1
nh2oh[k] + cyt554[k] --> noh[k] + cyt554e[k] + 2 h[k]
haoAB
Rx168
NET. HAO Hydroxylamine oxidation to
nitrite 2
noh[k] + 0.5 cyt554[k] --> no1[k] + h[k] + 0.5 cyt554e[k]
haoAB
Rx169
NET. HAO Hydroxylamine oxidation to
nitrite 3
no1[k] + h2o[k] + 0.5 cyt554[k] --> hno2[k] + h[k] + 0.5
cyt554e[k]
haoAB
Rx170
NET. ETC Partition of electron flow by
cyt554
cyt554e[k] + cyt552[s] --> cyt552e[s] + cyt554[k]
cycA
Rx171
NET. ETC Ubiquinone to ubiquinol for
AMO
q8[s] + cyt552e[s] + 2 h[k] --> q8h2[s] + cyt552[s]
Rx172
NET. ETC NADH production by NADHubiquinone reductase using ubiquinol
nad[s] + q8h2[s] + 4 h[k] --> nadh[s] + q8[s] + 6 h[s]
nouA-M
Rx173
NET. ETC proton pump by CytCbc1
reductase using ubiquinol
q8h2[s] + 2 cyt552[k] + 0 h[s] --> 2 h[k] + q8[s] + 2
cyt552e[k]
cyt b, cyt 1
Rx174
NET. ETC proton pump by Cytaa3,
Oxygen as final electron acceptor OXIC
.5 o2[s] + 4 h[s] + 2 cyt552e[k] --> h2o[s] + 2 h[k] + 2
cyt552[k]
coxABC
NET. CytP460 NO2 synthesis from
NH2OH + NO
NET. NO availability to NOR and
Cytp460
0.5 nh2oh[k] + 0.5 no[k] + 2 cyt552[k] + h2o[k] -->
hno2[k] + 2 cyt552e[k] + 3 h[k]
cyp
no1[k] --> no[k]
haoAB
hno2[k] + cyt552e[k] + h[k] --> no[k] + cyt552[k] + h2o[k]
nirK
no[k] + cyt552e[k] + h[k] --> 0.5 n2o[k] + cyt552[k] + 0.5
h2o[k]
norCB
no[k] + h[k] + 0.5 cyt554e[k] --> 0.5 n2o[k] + 0.5 h2o[k]
cycA
(Stein, 2011; Upadhyay et al., 2006)
no[s] + o2[s] + 0.5 nadh[s] --> no3[s] + 0.5 nad[s] + 0.5
h[s]
hmp
(Stein, 2011)
no[s] + 0.5 nadh[s] --> n2o[s] + 0.5 nad[s] + 0.5 h[s]
hmp
(Stein, 2010)
adp[s] + pi[s] + 6.8 h[k] --> atp[s] + h2o[s] + 4.8 h[s]
atpα- ε F-type
(Thiele and Palsson, 2010)
R175
Rx176
Rx177
NET. R1 - NIR Nitrite reduction to nitric
oxide
Rx182
Rx183
Rx184
NET. R2 - NOR Nitric oxide reduction to
nitrous oxide
NET. Nitric oxide activity by cytochrome
C554
NET. Nitric oxide oxidoreductase,
flavohemoglobin involved in nitric oxide
detoxification
NET. Nitric oxide oxidoreductase,
flavohemoglobin involved in nitric oxide
detoxification
NET. ATP production
NET. Protein synthesis
NET. ATP maintenance consumption
Rx185
NET. Biomass synthesis
Rx186
Rx187
Rx188
Rx189
Rx190
Rx191
Rx192
Rx193
Rx194
Rx195
Rx196
Rx197
Rx198
Rx199
Rx200
Rx201
Rx202
Rx203
Rx204
Rx205
Rx206
NMU. Tr1
NMU. Tr2
NMU. Tr3
NMU. Tr4
NMU. Tr5
NMU. Tr6
NMU. Tr7
NMU. Tr8
NMU. Tr9
NMU. Tr10
NMU. Tr11
NMU. Tr12
NMU. Tr13
NMU. Tr14
NMU. Tr15
NMU. Tr16
NMU. Tr17
NMU. Tr18
NMU. Tr19
NMU. Tr20
NMU. Tr21
Rx178
Rx179
Rx180
Rx181
atp[s] + h2o[s] --> adp[s] + pi[s] + h[s] + m[s]
15 atp[s] + 12 nadh[s] + 0.25 protein[s] + 32 m[s] --> 15
adp[s] + 12 nad[s] + 15 pi[s] + 15 h[s] + biomass[s]
nh4[c] <==> nh3[l] + h[l]
no2[c] + h[c] <==> hno2[l]
o2[c] <==> o2[l]
n2o[c] <==> n2o[l]
no[c] <==> no[l]
nh2oh[c] <==> nh2oh[l]
n2[c] <==> n2[l]
biomass[c] <==> biomass[l]
pi[c] <==> pi[l]
h2o[c] <==> h2o[l]
co2[c] <==> co2[l]
h[c] <==> h[l]
h[c] <==> h[t]
nh3[l] <==> nh3[t]
hno2[l] <==> h[t] + no2[t]
n2[l] <==> n2[t]
o2[l] <==> o2[t]
biomass[l] <==> biomass[t]
pi[l] <==> pi[t]
h2o[l] <==> h2o[t]
co2[l] <==> co2[t]
(Chandran et al., 2011; Elmore et al., 2007)
(Chandran et al., 2011; Numata et al., 1990; Poughon et
al., 2001)
(Beaumont et al., 2002; Cantera and Stein, 2007; Colliver
and Stephenson, 2000; Hooper et al., 1997; Stein, 2011;
Yu et al., 2010)
(Chandran et al., 2011; Colliver and Stephenson, 2000;
De Vries et al., 2007; Stein, 2011; Yu et al., 2010)
(Thiele and Palsson, 2010)
15
Rx207
Rx208
NMU. Tr22
NMU. AMO Ammonia oxidation to
hydroxylamine using ubiquinol as e
donor
h[l] <==> h[t]
nh3[l] + o2[l] + q8h2[t] --> nh2oh[l] + h2o[t] + q8[t]
amoABC
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000)
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000)
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Whittaker et
al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Whittaker et
al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
Rx209
NMU. HAO Hydroxylamine oxidation to
nitrite 1
nh2oh[l] + cyt554[l] --> noh[l] + cyt554e[l] + 2 h[l]
haoAB
Rx210
NMU. HAO Hydroxylamine oxidation to
nitrite 2
noh[l] + 0.5 cyt554[l] --> no1[l] + h[l] + 0.5 cyt554e[l]
haoAB
Rx211
NMU. HAO Hydroxylamine oxidation to
nitrite 3
no1[l] + h2o[l] + 0.5 cyt554[l] --> hno2[l] + h[l] + 0.5
cyt554e[l]
haoAB
Rx212
NMU. ETC division of electron flow by
cyt554
cyt554e[l] + cyt552[t] --> cyt552e[t] + cyt554[l]
cycA
Rx213
NMU. ETC Ubiquinone to ubiquinol for
AMO
q8[t] + cyt552e[t] + 2 h[l] --> q8h2[t] + cyt552[t]
Rx214
NMU. ETC NADH production by NADHubiquinone reductase using ubiquinol
nad[t] + q8h2[t] + 4 h[l] --> nadh[t] + q8[t] + 6 h[t]
nouA-M
Rx215
NMU. ETC proton pump by CytCbc1
reductase using ubiquinol
q8h2[t] + 2 cyt552[l] + 0 h[t] --> 2 h[l] + q8[t] + 2
cyt552e[l]
cyt b, cyt 1
Rx216
NMU. ETC proton pump by Cytaa3,
Oxygen as final electron acceptor OXIC
.5 o2[t] + 4 h[t] + 2 cyt552e[l] --> h2o[t] + 2 h[l] + 2
cyt552[l]
coxABC
NMU. ETC proton pump by cytaa3,
nitrite as final electron acceptor ANOXIC
NMU. NO availability to NOR and
Cytp460
no2[t] + 3 h[t] + 3 cyt552e[l] --> 0.5 n2[t] + 2 h2o[t] + 3
cyt552[l]
coxA2
(Kampschreur et al., 2008; Schmidt, 2008)
no1[l] --> no[l]
haoAB
(Chandran et al., 2011; Poughon et al., 2001)
hno2[l] + cyt552e[l] + h[l] --> no[l] + cyt552[l] + h2o[l]
nirK
Rx217
Rx218
Rx219
NMU. R1 - NIR Nitrite reduction to nitric
oxide
Rx221
Rx222
Rx223
NMU. R2 - NOR Nitric oxide reduction to
nitrous oxide
NMU. ATP production
NMU. Protein synthesis
NMU. ATP maintenance consumption
Rx224
NMU. Biomass synthesis
Rx225
Rx226
Rx227
Rx228
Rx229
Rx230
Rx231
Rx232
Rx233
Rx234
Rx235
Rx236
Rx237
Rx238
Rx239
Rx240
Rx241
Rx242
Rx243
Rx244
Rx245
Rx246
Rx247
Rx248
Rx249
Rx250
NOC. Tr1
NOC. Tr2
NOC. Tr3
NOC. Tr4
NOC. Tr5
NOC. Tr6
NOC. Tr7
NOC. Tr8
NOC. Tr9
NOC. Tr10
NOC. Tr11
NOC. Tr12
NOC. Tr13
NOC. Tr14
NOC. Tr15
NOC. Tr16
NOC. Tr17
NOC. Tr18
NOC. Tr19
NOC. Tr20
NOC. Tr21
NOC. Tr22
NOC. Tr23
NOC. Tr24
NOC. Tr25
NOC. Tr26
NOC. AMO Ammonia oxidation to
hydroxylamine using ubiquinol as e
donor
Rx220
Rx251
no[l] + cyt552e[l] + h[l] --> 0.5 n2o[l] + cyt552[l] + 0.5
h2o[l]
adp[t] + pi[t] + 6.8 h[l] --> atp[t] + h2o[t] + 4.8 h[t]
atp[t] + h2o[t] --> adp[t] + pi[t] + h[t] + m[t]
atp[t] + h2o[t] --> adp[t] + pi[t] + h[t] + m[t]
15 atp[t] + 12 nadh[t] + 0.25 protein[t] + 32 m[t] --> 15
adp[t] + 12 nad[t] + 15 pi[t] + 15 h[t] + biomass[t]
nh4[d] <==> nh3[m] + h[m]
no2[d] + h[d] <==> hno2[m]
o2[d] <==> o2[m]
n2o[d] <==> n2o[m]
no[d] <==> no[m]
nh2oh[d] <==> nh2oh[m]
n2[d] <==> n2[m]
no3[d] <==> no3[m]
biomass[d] <==> biomass[m]
pi[d] <==> pi[m]
h2o[d] <==> h2o[m]
co2[d] <==> co2[m]
h[d] <==> h[m]
h[d] <==> h[u]
nh3[m] <==> nh3[u]
hno2[m] <==> h[u] + no2[u]
no3[m] <==> no3[u]
n2o[m] <==> n2o[u]
n2[m] <==> n2[u]
o2[m] <==> o2[u]
no[m] <==> no[u]
biomass[m] <==> biomass[u]
pi[m] <==> pi[u]
h2o[m] <==> h2o[u]
co2[m] <==> co2[u]
h[m] <==> h[u]
norCB
atpα- ε F-type
(Beaumont et al., 2002; Cantera and Stein, 2007; Colliver
and Stephenson, 2000; Hooper et al., 1997; Stein, 2011;
Yu et al., 2010)
(Chandran et al., 2011; Colliver and Stephenson, 2000;
De Vries et al., 2007; Stein, 2011; Yu et al., 2010)
(Thiele and Palsson, 2010)
(Thiele and Palsson, 2010)
nh3[m] + o2[m] + q8h2[u] --> nh2oh[m] + h2o[u] + q8[u]
amoABC
Rx252
NOC. HAO Hydroxylamine oxidation to
nitrite 1
nh2oh[m] + cyt554[m] --> noh[m] + cyt554e[m] + 2 h[m]
haoAB
Rx253
NOC. HAO Hydroxylamine oxidation to
nitrite 2
noh[m] + 0.5 cyt554[m] --> no1[m] + h[m] + 0.5
cyt554e[m]
haoAB
Rx254
NOC. HAO Hydroxylamine oxidation to
nitrite 3
cyt554e[m] + cyt552[u] --> cyt552e[u] + cyt554[m]
haoAB
Rx255
NOC. ETC Partition of electron flow by
cyt554
cyt554e[m] + cyt552[u] --> cyt552e[u] + cyt554[m]
cycA
Rx256
NOC. ETC Ubiquinone to ubiquinol for
AMO
q8[u] + cyt552e[u] + 2 h[m] --> q8h2[u] + cyt552[u]
Rx257
NOC. ETC NADH production by NADHubiquinone reductase using ubiquinol
nad[u] + q8h2[u] + 4 h[m] --> nadh[u] + q8[u] + 6 h[u]
nouA-M
Rx258
NOC. ETC proton pump by CytCbc1
reductase using ubiquinol
q8h2[u] + 2 cyt552[m] + 0 h[u] --> 2 h[m] + q8[u] + 2
cyt552e[m]
cyt b, cyt 1
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000)
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000)
(Arp et al., 2002; Cabail and Pacheco, 2003; Chain et al.,
2003; Colliver and Stephenson, 2000; Ferguson et al.,
2007; Kostera et al., 2008; Poughon et al., 2001; Stein,
2011; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Whittaker et
al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Whittaker et
al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
16
2001; Whittaker et al., 2000)
(Arp et al., 2002; Chain et al., 2003; Colliver and
Stephenson, 2000; Ferguson et al., 2007; Poughon et al.,
2001; Whittaker et al., 2000)
NOC. ETC proton pump by Cytaa3,
Oxygen as final electron acceptor OXIC
.5 o2[u] + 4 h[u] + 2 cyt552e[m] --> h2o[u] + 2 h[m] + 2
cyt552[m]
coxABC
NOC. ETC proton pump by cytaa3, nitrite
as final electron acceptor ANOXIC
NOC. NO availability to NOR and
Cytp460
no2[u] + 3 h[u] + 3 cyt552e[m] --> 0.5 n2[u] + 2 h2o[u] +
3 cyt552[m]
coxA2
(Kampschreur et al., 2008; Schmidt, 2008)
no1[m] --> no[m]
haoAB
Chandran et al., 2011; Poughon et al., 2001)
NOC. R1 - NIR Nitrite reduction to nitric
oxide
hno2[m] + cyt552e[m] + h[m] --> no[m] + cyt552[m] +
h2o[m]
nirK
no[m] + cyt552e[m] + h[m] --> 0.5 n2o[m] + cyt552[m] +
0.5 h2o[m]
norCB
no[u] + o2[u] + 0.5 nadh[u] --> no3[u] + 0.5 nad[u] + 0.5
h[u]
hmp
(Stein, 2011)
no[u] + 0.5 nadh[u] --> n2o[u] + 0.5 nad[u] + 0.5 h[u]
hmp
(Stein, 2010)
Rx266
NOC. R2 - NOR Nitric oxide reduction to
nitrous oxide
NOC. Nitric oxide oxidoreductase,
flavohemoglobin involved in nitric oxide
detoxification
NOC. Nitric oxide oxidoreductase,
flavohemoglobin involved in nitric oxide
detoxification
NOC. ATP production
(Thiele and Palsson, 2010)
NOC. Protein synthesis
Rx268
NOC. ATP maintenance consumption
Rx269
NOC. Biomass synthesis.
Rx270
Rx271
Rx272
Rx273
Rx274
Rx275
Rx276
Rx277
Rx278
Rx279
Rx280
Rx281
Rx282
Rx283
Rx284
Rx285
Rx286
Rx287
Rx288
Rx289
Rx290
Rx291
Rx292
NDE. Tr1
NDE. Tr2
NDE. Tr3
NDE. Tr4
NDE. Tr5
NDE. Tr6
NDE. Tr7
NDE. Tr8
NDE. Tr9
NDE. Tr10
NDE. Tr11
NDE. Tr12
NDE. Tr13
NDE. Tr14
NDE. Tr15
NDE. Tr16
NDE. Tr17
NDE. Tr18
NDE. Tr19
NDE. Tr20
NDE. Tr21
NDE. Transport mediated NO2 transport
NDE. Transport mediated NO3 transport
NDE. NXR Periplasmic Nitrite oxidation
to nitrate
NDE. Terminal oxidase Cytbd, Oxygen
as final electron acceptor OXIC
NDE. ETC proton pump by CytCbc1
reductase using ubiquinol
NDE. ETC NADH production by NADHubiquinone reductase using ubiquinol
NDE. ETC ferredoxin production
NDE. Nitrite reductase nitric oxide
forming
NDE. Dissimilatory reduction of Nitrate to
Nitrite NXR mediated
NDE. Assimilatory reduction of Nitrite to
Ammonia by NAR
NDE. Assimilatory reduction of Nitrite to
Ammonia by NAR
NDE. Nitric oxide oxidoreductase,
flavohemoglobin involved in nitric oxide
detoxification
NDE. Nitric oxide oxidoreductase,
flavohemoglobin involved in nitric oxide
detoxification
NDE. ETC ATP transmembrane
synthesis (four protons per ATP)
adp[u] + pi[u] + 6.8 h[m] --> atp[u] + h2o[u] + 4.8 h[u]
2.244 atp[u] + nh3[u] + 4 co2[u] --> 2.244 adp[u] + 2.244 pi[u]
+ 2.244 h[u] + 0.25 protein[u]
atp[u] + h2o[u] --> adp[u] + pi[u] + h[u] + m[u]
15 atp[u] + 12 nadh[u] + 0.25 protein[u] + 32 m[u] --> 15
adp[u] + 12 nad[u] + 15 pi[u] + 15 h[u] + biomass[u]
nh4[f] <==> nh3[n] + h[n]
o2[f] <==> o2[n]
no2[f] <==> no2[n]
no3[f] <==> no3[n]
no[f] <==> no[n]
n2o[f] <==> n2o[n]
biomass[f] <==> biomass[n]
pi[f] <==> pi[n]
h2o[f] <==> h2o[n]
co2[f] <==> co2[n]
h[f] <==> h[n]
h[f] <==> h[v]
nh3[n] <==> nh3[v]
o2[n] <==> o2[v]
biomass[n] <==> biomass[v]
no[n] <==> no[v]
n2o[n] <==> n2o[v]
pi[n] <==> pi[v]
h2o[n] <==> h2o[v]
co2[n] <==> co2[v]
h[n] <==> h[v]
no2[n] --> no2[v]
no3[v] --> no3[n]
no2[n] + 2 cyt550[v] + h2o[n] --> no3[n] + 2 cyt550e[v] +
2 h[n]
atpα- ε F-type
Rx267
0.5 o2[v] + 2 h[v] + 2 cyt550e[v] --> h2o[v] + 2 cyt550[v]
cydAB
(Ferguson et al., 2007; Lücker et al., 2010)
qcrABC
(Ferguson et al., 2007; Poughon et al., 2001)
nouA-M
(Ferguson et al., 2007; Poughon et al., 2001)
hcaD
(Ferguson et al., 2007; Poughon et al., 2001)
(Ferguson et al., 2007; Lücker et al., 2010; Starkenburg
et al., 2008b)
Rx259
Rx260
Rx261
Rx262
Rx263
Rx264
Rx265
Rx293
Rx294
Rx295
Rx296
Rx297
Rx298
Rx299
Rx300
Rx301
Rx302
Rx303
Rx304
Rx305
Rx306
Rx307
Rx308
Rx309
Rx310
Rx311
Rx312
Rx313
Rx314
Rx315
Rx316
Rx317
Rx318
Rx319
Rx320
Rx321
Rx322
NDE. Protein synthesis from ammonia
NDE. Maintenance ATP consumption
(non-growth associated energy
consumption)
NDE. Biomass synthesis ATP
consumption
NWI. TR1
NWI. TR2
NWI. TR3
NWI. TR4
NWI. TR5
NWI. TR6
NWI. TR7
NWI. TR8
NWI. TR9
NWI. TR10
NWI. TR11
NWI. TR12
NWI. TR13
NWI. TR14
NWI. TR15
q8[v] + 2 cyt550e[v] + 4 h[n] --> q8h2[v] + 2 cyt550[v] +
2 h[v]
nad[v] + q8h2[v] + 2 h[n] + 2 h[v] --> nadh[v] + q8[v] + 5
h[v]
nadh[v] + 2 fe[v] <==> nad[v] + 2 fee[v] + h[v]
(Beaumont et al., 2002; Cantera and Stein, 2007; Colliver
and Stephenson, 2000; Hooper et al., 1997; Stein, 2011;
Yu et al., 2010)
(Chandran et al., 2011; Colliver and Stephenson, 2000;
De Vries et al., 2007; Stein, 2011; Yu et al., 2010)
(Thiele and Palsson, 2010)
narK
narK
nxrAB
(Ferguson et al., 2007; Starkenburg et al., 2008b)
(Ferguson et al., 2007; Starkenburg et al., 2008b)
(Ferguson et al., 2007; Lücker et al., 2010; Starkenburg
et al., 2008b)
no2[n] + cyt550e[v] + 2 h[n] --> no[n] + cyt550[v] + h2o[n]
nirK
no3[n] + nadh[v] + h[v] --> no2[n] + nad[v] + h2o[v]
nxrAB
(Ferguson et al., 2007; Poughon et al., 2001)
no2[v] + 4 h[v] + 3 nadh[v] --> nh3[v] + 2 h2o[v] + 3
nad[v]
nirA
(Lücker et al., 2010; Starkenburg et al., 2008b)
no2[v] + 6 fee[v] + 7 h[v] --> nh3[v] + 2 h2o[v] + 6 fe[v]
nirA
(Lücker et al., 2010; Starkenburg et al., 2008b)
no[v] + o2[v] + 0.5 nadh[v] --> no3[v] + 0.5 nad[v] + 0.5
h[v]
hmp
(Stein, 2011)
no[v] + 0.5 nadh[v] --> n2o[v] + 0.5 nad[v] + 0.5 h[v]
hmp
(Stein, 2011)
adp[v] + pi[v] + 3 h[n] --> atp[v] + h2o[v] + 3 h[v]
atpA-I
(Lücker et al., 2010; Starkenburg et al., 2011)
2.244 atp[v] + nh3[v] + 4 co2[v] --> 2.244 adp[v] + 2.244
pi[v] + 2.244 h[v] + 0.25 protein[v]
atp[v] + h2o[v] --> adp[v] + pi[v] + h[v] + m[v]
(Thiele and Palsson, 2010)
15 atp[v] + 12 nadh[v] + 0.25 protein[v] + 200 m[v] --> 15
adp[v] + 12 nad[v] + 15 pi[v] + 15 h[v] + biomass[v]
o2[g] <==> o2[o]
nh4[g] <==> nh3[o] + h[o]
no2[g] <==> no2[o]
no3[g] <==> no3[o]
no[g] <==> no[o]
biomass[g] <==> biomass[o]
pi[g] <==> pi[o]
h2o[g] <==> h2o[o]
co2[g] <==> co2[o]
h[g] <==> h[o]
h[g] <==> h[w]
nh3[o] <==> nh3[w]
o2[o] <==> o2[w]
biomass[o] <==> biomass[w]
pi[o] <==> pi[w]
17
Rx323
Rx324
Rx325
Rx326
Rx327
Rx328
Rx329
Rx330
Rx331
Rx332
Rx333
Rx334
Rx335
Rx336
Rx337
Rx338
Rx339
Rx340
Rx341
Rx342
Rx343
Rx344
Rx345
Rx346
Rx347
Rx348
Rx349
Rx350
Rx351
Rx352
Rx353
Rx354
Rx355
Rx356
Rx357
Rx358
Rx359
Rx360
Rx361
Rx362
Rx363
Rx364
Rx365
Rx366
Rx367
Rx368
Rx369
Rx370
Rx371
Rx372
Rx373
Rx374
Rx375
Rx376
Rx377
Rx378
Rx379
Rx380
Rx381
Rx382
Rx383
Rx384
Rx385
Rx386
Rx387
Rx388
NWI. TR16
NWI. TR17
NWI. TR18
NWI. Transport mediated NO2 transport
NWI. Transport mediated NO3 transport
NWI. NXR Periplasmic Nitrite oxidation
to nitrate
NWI. Terminal oxidase Cytbd, Oxygen
as final electron acceptor OXIC
NWI. ETC proton pump by CytCbc1
reductase using ubiquinol
NWI. ETC NADH production by NADHubiquinone reductase using ubiquinol
NWI. Nitrite reductase nitric oxide
forming
NWI. Nitric oxide reductase NADH
forming
NWI. Dissimilatory reduction of Nitrate to
Nitrite NXR mediated
NWI. Dissimilatory reduction of Nitrate to
Nitrite NAR mediated
NWI. Assimilatory reduction of Nitrite to
Ammonia by NAR
NWI. ETC ATP transmembrane
synthesis (four protons per ATP)
NWI. Protein synthesis from ammonia
NWI. Maintenance ATP consumption
(non-growth associated energy
consumption)
NWI. Biomass synthesis ATP
consumption
NHA. Tr1
NHA. Tr2
NHA. Tr3
NHA. Tr4
NHA. Tr5
NHA. Tr6
NHA. Tr7
NHA. Tr8
NHA. Tr9
NHA. Tr10
NHA. Tr11
NHA. Tr12
NHA. Tr13
NHA. Tr14
NHA. Tr15
NHA. Tr16
NHA. Tr17
NHA. Tr18
NHA. Tr19
NHA. Transport mediated NO2 transport
NHA. Transport mediated NO3 transport
NHA. NXR Periplasmic Nitrite oxidation
to nitrate
NHA. Terminal oxidase Cytbd, Oxygen
as final electron acceptor OXIC
NHA. ETC proton pump by CytCbc1
reductase using ubiquinol
NHA. ETC NADH production by NADHubiquinone reductase using ubiquinol
NHA. ETC ferredoxin production
NHA. P460 NO2 shynthesis from
NH2OH + NO
NHA. NOR Nitric oxide reduction to
nitrous oxide
NHA. Assimilatory reduction of Nitrite to
Ammonia by NAR
NHA. Nitrite reductase nitric oxide
forming
NHA. Dissimilatory reduction of Nitrate to
Nitrite NXR mediated
NHA. Assimilatory reduction of Nitrite to
Ammonia by NAR
NHA. ETC ATP transmembrane
synthesis (four protons per ATP)
NHA. Protein synthesis from ammonia
NHA. Maintenance ATP consumption
(non-growth associated energy
consumption)
NHA. Biomass synthesis ATP
consumption
NSP. Tr1
NSP. Tr2
NSP. Tr3
NSP. Tr4
NSP. Tr5
NSP. Tr6
NSP. Tr7
NSP. Tr8
NSP. Tr9
NSP. Tr10
NSP. Tr11
NSP. Tr12
h2o[o] <==> h2o[w]
co2[o] <==> co2[w]
h[o] <==> h[w]
no2[o] <==> no2[w]
no3[o] <==> no3[w]
no2[w] + 2 cyt550[w] + h2o[w] <==> no3[w] + 2 cyt550e[w] +
2 h[o]
0.5 o2[w] + 4 h[w] + 2 cyt550e[w] --> h2o[w] + 2 h[o] + 2
cyt550[w]
q8[w] + 2 cyt550e[w] + 4 h[o] --> q8h2[w] + 2 cyt550[w] + 2
h[w]
nad[w] + q8h2[w] + 2 h[o] + 2 h[w] --> nadh[w] + q8[w] + 5
h[w]
no2[o] + cyt550e[w] + 2 h[o] --> no[o] + cyt550[w] +
h2o[o]
no[o] + 0.5 nad[w] + h2o[w] --> no2[o] + 0.5 nadh[w] +
1.5 h[o]
narK
narK
nxrA-K
cydAB
qcrABC
nouA-M
nirK,
nirK
(Ferguson et al., 2007; Starkenburg et al., 2011)
(Ferguson et al., 2007; Starkenburg et al., 2011)
(Ferguson et al., 2007; Starkenburg et al., 2011;
Starkenburg et al., 2006; Yamanaka and Fukumori, 1988)
(Starkenburg et al., 2006; Yamanaka et al., 1981;
Yamanaka and Fukumori, 1988)
(Ferguson et al., 2007; Poughon et al., 2001; Starkenburg
et al., 2006)
(Ferguson et al., 2007; Poughon et al., 2001; Starkenburg
et al., 2006)
(Ferguson et al., 2007; Lücker et al., 2010; Poughon et
al., 2001; Starkenburg et al., 2006)
(Freitag and Bock, 1990; Poughon et al., 2001;
Starkenburg et al., 2011; Starkenburg et al., 2008a)
((Starkenburg et al., 2011; Starkenburg et al., 2006;
Starkenburg et al., 2008a)
(Starkenburg et al., 2011; Starkenburg et al., 2006;
Starkenburg et al., 2008a)
no3[o] + nadh[w] + h[w] --> no2[o] + nad[w] + h2o[w]
nxrAB
no3[o] + q8h2[w] --> no2[o] + q8[w] + h2o[o]
narJI
no2[w] + 4 h[w] + 3 nadh[w] --> nh3[w] + 2 h2o[w] + 3
nad[w]
nirBD
(Lücker et al., 2010b; Starkenburg et al., 2011)
adp[w] + pi[w] + 3 h[o] --> atp[w] + h2o[w] + 3 h[w]
atpA-I
(Lücker et al., 2010b; Starkenburg et al., 2011)
2.244 atp[w] + nh3[w] + 4 co2[w] --> 2.244 adp[w] +
2.244 pi[w] + 2.244 h[w] + 0.25 protein[w]
atp[w] + h2o[w] --> adp[w] + pi[w] + h[w] + m[w]
15 atp[w] + 12 nadh[w] + 0.25 protein[w] + 200 m[w] -->
15 adp[w] + 12 nad[w] + 15 pi[w] + 15 h[w] + biomass[w]
o2[h] <==> o2[p]
nh4[h] <==> nh3[p] + h[p]
no2[h] <==> no2[p]
no3[h] <==> no3[p]
no[h] <==> no[p]
n2o[h] <==> n2o[p]
biomass[h] <==> biomass[p]
pi[h] <==> pi[p]
h2o[h] <==> h2o[p]
co2[h] <==> co2[p]
h[h] <==> h[p]
h[h] <==> h[x]
nh3[p] <==> nh3[x]
o2[p] <==> o2[x]
biomass[p] <==> biomass[x]
pi[p] <==> pi[x]
h2o[p] <==> h2o[x]
co2[p] <==> co2[x]
h[p] <==> h[x]
no2[p] <==> no2[x]
no3[p] <==> no3[x]
no2[x] + 2 cyt550[x] + h2o[x] <==> no3[x] + 2 cyt550e[x]
+ 2 h[p]
0.5 o2[x] + 4 h[x] + 2 cyt550e[x] --> h2o[x] + 2 h[p] + 2
cyt550[x]
q8[x] + 2 cyt550e[x] + 4 h[p] --> q8h2[x] + 2 cyt550[x] +
2 h[x]
nad[x] + q8h2[x] + 2 h[p] + 2 h[x] --> nadh[x] + q8[x] + 5
h[x]
(Thiele and Palsson, 2010)
narK
narK
nxrA-K
cydAB
qcrABC
nouA-M
(Ferguson et al., 2007; Starkenburg et al., 2011)
(Ferguson et al., 2007; Starkenburg et al., 2011)
(Ferguson et al., 2007; Starkenburg et al., 2011;
Starkenburg et al., 2006; Yamanaka and Fukumori, 1988)
(Starkenburg et al., 2006; Yamanaka et al., 1981;
Yamanaka and Fukumori, 1988)
(Ferguson et al., 2007; Poughon et al., 2001; Starkenburg
et al., 2006)
(Ferguson et al., 2007; Poughon et al., 2001; Starkenburg
et al., 2006)
(Starkenburg et al., 2011; Starkenburg et al., 2006;
Starkenburg et al., 2008b)
(Starkenburg et al., 2011; Starkenburg et al., 2006;
Starkenburg et al., 2008b)
(Starkenburg et al., 2011; Starkenburg et al., 2006;
Starkenburg et al., 2008b)
(Starkenburg et al., 2011; Starkenburg et al., 2006;
Starkenburg et al., 2008b)
Starkenburg et al., 2011; Starkenburg et al., 2006;
Starkenburg et al., 2008b)
(Starkenburg et al., 2011; Starkenburg et al., 2006;
Starkenburg et al., 2008b)
nadh[x] + 2 fe[x] <==> nad[x] + 2 fee[x] + h[x]
hcaD
no[p] + cyt550[x] + h2o[x] --> no2[p] + cyt550e[x] + 2 h[p]
cyp
no[p] + cyt550e[x] + h[p] --> 0.5 n2o[p] + cyt550[x] + 0.5
h2o[p]
norCB
no2[x] + 6 fee[x] + 7 h[x] --> nh3[x] + 2 h2o[x] + 6 fe[x]
nirA
no2[p] + cyt550e[x] + 2 h[p] --> no[p] + cyt550[x] + h2o[p]
nirK,
no3[o] + nadh[w] + h[w] --> no2[o] + nad[w] + h2o[w]
nxrAB
no2[x] + 4 h[x] + 3 nadh[x] --> nh3[x] + 2 h2o[x] + 3
nad[x]
nirBD
(Lücker et al., 2010; Starkenburg et al., 2011)
adp[x] + pi[x] + 3 h[p] --> atp[x] + h2o[x] + 3 h[x]
atpA-I
(Lücker et al., 2010; Starkenburg et al., 2011)
2.244 atp[x] + nh3[x] + 4 co2[x] --> 2.244 adp[x] + 2.244
pi[x] + 2.244 h[x] + 0.25 protein[x]
atp[x] + h2o[x] --> adp[x] + pi[x] + h[x] + m[x]
(Thiele and Palsson, 2010)
15 atp[x] + 12 nadh[x] + 0.25 protein[x] + 200 m[x] --> 15
adp[x] + 12 nad[x] + 15 pi[x] + 15 h[x] + biomass[x]
o2[i] <==> o2[q]
nh4[i] <==> nh3[q] + h[q]
no2[i] <==> no2[q]
no3[i] <==> no3[q]
no[i] <==> no[q]
biomass[i] <==> biomass[q]
pi[i] <==> pi[q]
h2o[i] <==> h2o[q]
co2[i] <==> co2[q]
h[i] <==> h[q]
h[i] <==> h[y]
nh3[q] <==> nh3[y]
18
Rx389
Rx390
Rx391
Rx392
Rx393
Rx394
Rx395
Rx396
Rx397
Rx398
Rx399
Rx400
Rx401
Rx402
Rx403
Rx404
Rx405
Rx406
Rx407
NSP. Tr13
NSP. Tr14
NSP. Tr15
NSP. Tr16
NSP. Tr17
NSP. Tr18
NSP. Transport mediated NO2 transport
NSP. NXR Periplasmic Nitrite oxidation
to nitrate
NSP. Terminal oxidase Cytbd, Oxygen
as final electron acceptor OXIC
NSP. ETC proton pump by CytCbc1
reductase using ubiquinol
NSP. ETC NADH production by NADHubiquinone reductase using ubiquinol
NSP. ETC ferredoxin production
NSP. NO2 synthesis from NH2OH + NO
NSP. Assimilatory reduction of Nitrite to
Ammonia by NAR
NSP. Nitrite reductase nitric oxide
forming
NSP. ETC ATP transmembrane
synthesis (four protons per ATP)
NSP. Protein synthesis from ammonia
NSP. Maintenance ATP consumption
(non-growth associated energy
consumption)
NSP. Biomass synthesis ATP
consumption
o2[q] <==> o2[y]
biomass[q] <==> biomass[y]
pi[q] <==> pi[y]
h2o[q] <==> h2o[y]
co2[q] <==> co2[y]
h[q] <==> h[y]
no2[q] <==> no2[y]
no2[q] + 2 cyt550[y] + h2o[q] --> no3[q] + 2 cyt550e[y] +
2 h[q]
0.5 o2[y] + 4 h[y] + 2 cyt550e[y] --> h2o[y] + 2 h[q] + 2
cyt550[y]
q8[y] + 2 cyt550e[y] + 4 h[q] --> q8h2[y] + 2 cyt550[y] +
2 h[y]
nad[y] + q8h2[y] + 2 h[q] + 2 h[y] --> nadh[y] + q8[y] + 5
h[y]
nadh[y] + 2 fe[y] <==> nad[y] + 2 fee[y] + h[y]
no[q] + cyt550[y] + h2o[y] --> no2[q] + cyt550e[y] + 2 h[p]
narK
hcaD
cyp
(Ferguson et al., 2007; Starkenburg et al., 2011)
(Lücker et al., 2010; Lücker et al., 2013; Starkenburg et
al., 2011)
(Starkenburg et al., 2006; Yamanaka et al., 1981;
Yamanaka and Fukumori, 1988)
(Ferguson et al., 2007; Poughon et al., 2001; Starkenburg
et al., 2006)
(Ferguson et al., 2007; Poughon et al., 2001; Starkenburg
et al., 2006)
(Lücker et al., 2013)
(Lücker et al., 2013)
no2[y] + 6 fee[y] + 7 h[y] --> nh3[y] + 2 h2o[y] + 6 fe[y]
nirA
(Lücker et al., 2013)
no2[q] + cyt550e[y] + 2 h[q] --> no[q] + cyt550[y] + h2o[q]
nirK,
(Lücker et al., 2013)
adp[y] + pi[y] + 3 h[q] --> atp[y] + h2o[y] + 3 h[y]
atpA-I
(Lücker et al., 2010; Starkenburg et al., 2011)
nxrABC
cydAB
qcrABC
nouA-M
2.244 atp[y] + nh3[y] + 4 co2[y] --> 2.244 adp[y] + 2.244
pi[y] + 2.244 h[y] + 0.25 protein[y]
atp[y] + h2o[y] --> adp[y] + pi[y] + h[y] + m[y]
(Thiele and Palsson, 2010)
15 atp[y] + 12 nadh[y] + 0.25 protein[y] + 200 m[y] --> 15
adp[y] + 12 nad[y] + 15 pi[y] + 15 h[y] + biomass[y]
19
Supporting Information and model references
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21
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