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ABSTRACT: Modifications are made to an earlier thermodynamic model (TEEM1) for prediction of maximum
microbial yields from aerobic and anaerobic as well as
heterotrophic and autotrophic growth. The revised model
(TEEM2) corrects for lower yields found with aerobic
oxidations of organic compounds where an oxygenase is
involved and with growth on single-carbon (C1) compounds. TEEM1 and TEEM2 are based on energy release
and consumption as determined from the reduction potential or Gibbs free energy of -reaction reduction equations
together with losses of energy during energy transfer. Energy
transfer efficiency is a key parameter needed to make
predictions with TEEM2, and was determined through
evaluations with extensive data sets on aerobic heterotrophic
yield available in the literature. For compounds following
normal catabolic pathways, the best-fit value for energy
transfer efficiency was 0.37, which permitted accurate
predictions of growth with a precision of 15%20% as
determined by standard deviation. Using the same energy
transfer efficiency, a similar precision, but somewhat less
accuracy was found for organic compounds where oxidation
involves an oxygenase (estimates 8% too high) and for C1
compounds (estimates 17% too high). In spite of the somewhat lower accuracy, the TEEM2 modifications resulted in
improved predictions over TEEM1 and the comparison
models.
Biotechnol. Bioeng. 2007;97: 377388.
! 2006 Wiley Periodicals, Inc.
KEYWORDS: bacterial yields; thermodynamics; autotrophic; heterotrophic; oxygenase; C1 compounds
Introduction
377
TEEM1 Development
TEEM1 has been presented in detail (Rittmann and
McCarty, 2001). The model is based upon the use of
half-reaction reductive equations for electron donors and
acceptors as well as for cell synthesis, and the associated
Gibbs free energies or reduction potentials for the half
reactions. Use of such half reactions is illustrated in the
upper portion of Figure 1. The methods for developing half
reactions and computing the half-reaction reduction
potentials (DGo0 , kJ/eeq) are provided by Rittmann and
McCarty (2001). Values for the compounds evaluated in this
article are given in the Appendix, and were developed using
the standard free energy of formation for each compound
(DGof ) also listed in the Appendix. Half reactions for an
electron donor and an electron acceptor can be combined to
produce an energy reaction with its associated Gibbs free
energy (DGr). Half reactions for electron donor and cell
synthesis can be combined to produce the synthesis reaction,
from which the Gibbs free energy for synthesis is derived
(DGs). An overall reaction for cell growth is obtained by
combining in proper proportion the energy reaction and
synthesis reactions. This proportion depends upon the
energy transfer efficiency (e) and is represented by A, a value
that is obtained by consideration of the energy released by
the energy reaction and that required for synthesis:
DGs
A"
"DGr
(1)
vi lnfig
(2)
(3)
378
DGic DGpc
"n
"
(4)
(5)
feo o
1
A
; fo
; and
; f
1A e
1A
fso s
Figure 1. Example of yield calculations for aerobic oxidation of acetate with e 0.37. Here, either TEEM1 or TEEM2 could be used since neither an oxygenase nor a C1
compound is involved.
379
! "
gd o
f
gx s
(7)
gd
DGr
g x DGr " DGs ="
(8)
Modifications in TEEM2
Two basic modifications are made to TEEM1 to develop
TEEM2, the first addresses aerobic heterotrophic reactions
involving oxygenases, and the second addresses aerobic
heterotrophic oxidation of C1 organic compounds.
Oxygenase Modification
Modifications to TEEM1 to address organic electron donor
oxidation reactions involving oxygenases were developed
by VanBriesen (2001) and Yuan and VanBriesen (2002).
Oxygenases are generally used by aerobic microorganisms in
the initial oxidative steps for hydrocarbons, aromatic
compounds, and ammonia to convert them to forms that
can be used for energy. Oxygenase reactions generally
require the input of energy and reducing power in the
form of NADH. The above authors made corrections for
the energy losses involved in oxygenase reactions by
considering in detail the biochemical steps involved in
the oxidation process. This is appropriate for obtaining
information on energy losses. A somewhat simpler approach
was incorporated into TEEM2 by assuming that the energy
loss involved in each step involving an oxygenase is equal to
the standard energy associated with NADH oxidation. This
is represented by the difference between that of the oxygen
reduction equation ("78.72 kJ/eeq) and that of the NADH/
380
(9)
"m
"n
"
(10)
(11)
381
Figure 2.
382
Substrate
2"
0.375
0.365
0.400
0.510
0.610
0.510
0.410
0.560
0.670
0.480
0.445
0.530
0.575
Malate
Citrate3"
Succinate2"
Gluconate"
Glucose
Lactate"
Acetate"
Mannitol
Glycerol
Propionate"
Acetone
Ethanol
Propanol
Average
Std. Dev.
Number
fs
YC/CCmol/Cmol
Error
0.40
0.40
0.40
0.43
0.46
0.42
0.38
0.40
0.45
0.38
0.30
0.31
0.34
0.39
0.05
13.00
0.46
0.45
0.42
0.48
0.49
0.45
0.39
0.48
0.48
0.40
0.42
0.45
0.43
0.343
0.340
0.365
0.441
0.486
0.450
0.394
0.520
0.555
0.463
0.566
0.668
0.644
0.09
0.07
0.09
0.14
0.20
0.12
0.04
0.07
0.17
0.04
"0.27
"0.26
"0.12
0.03
0.15
13.00
&
Reported
e Implied
YC/C&
fs
YC/C
Cmol/Cmol
0.220
0.280
0.238
0.390
0.385
0.406
0.505
0.569
0.558
0.32
0.35
0.32
0.42
0.39
0.38
0.38
0.38
0.32
0.53
0.48
0.43
0.45
0.42
0.39
0.49
0.48
0.45
0.263
0.301
0.285
0.340
0.365
0.394
0.486
0.555
0.668
"0.20
"0.08
"0.20
0.13
0.05
0.03
0.04
0.02
"0.20
0.441
0.434
0.448
0.559
0.595
0.490
0.455
0.692
0.424
0.446
0.617
0.48
0.42
0.45
0.47
0.45
0.37
0.42
0.46
0.29
0.28
0.35
0.45
0.46
0.42
0.48
0.49
0.49
0.39
0.48
0.45
0.45
0.45
0.340
0.384
0.365
0.441
0.486
0.486
0.394
0.555
0.568
0.618
0.668
0.23
0.12
0.18
0.21
0.18
0.01
0.13
0.20
"0.34
"0.39
"0.08
0.420
0.480
0.510
0.620
0.45
0.48
0.43
0.44
0.46
0.42
0.48
0.48
0.343
0.365
0.441
0.520
0.18
0.24
0.14
0.16
0.250
0.320
0.400
0.550
0.29
0.32
0.31
0.37
0.38
0.06
28
0.46
0.46
0.49
0.48
0.343
0.384
0.486
0.555
"0.37
"0.20
"0.22
"0.01
0.00
0.19
28
DG
&
%'
#$ pc
DGr 1 " g d g x YC=C " DGic
!0:5
(12)
!0:5
DGpc DGic
&
%'
#$
DGr 1 " g d g x YC=C
(13)
383
TEEM2
Reported
YC/C
p m
Substrate
Methane
Benzene-theoretical
Benzene-average
Toluene-theoretical
Toluene-average
Phenol-theoretical
Phenol-average
Naphthalene-average
Naphthalene-maximum
Phenanthrene-average
Phenanthrene-maximum
NTA
EDTA
Average
Std. Dev.
Number
384
0.55
0.54
0.43
0.55
0.47
0.50
0.36
0.47
0.52
0.32
0.56
0.27
0.27
8
30
30
36
36
28
28
48
48
66
66
18
34
1
1
1
1
1
1
1
1
1
1
1
1
4
fs
0.281
0.390
0.390
0.386
0.386
0.405
0.405
0.389
0.389
0.390
0.390
0.467
0.425
Yuan and
VanBriesen
(2002)
"0.02
0.10
"0.13
0.10
"0.06
0.06
"0.31
0.01
0.10
"0.44
0.18
"0.30
"0.34
"0.08
0.20
13
0.63
0.54
0.54
0.61
0.61
0.53
0.53
0.51
0.51
0.48
0.48
0.35
0.28
"0.15
0.00
"0.26
"0.11
"0.30
"0.06
"0.47
"0.09
0.02
"0.50
0.14
"0.30
"0.04
"0.16
0.19
13
DGpc
"
(14)
TEEM2
gs
Reported
YC/C
fs
YC/C
Error
YC/C
Error
1.00
2.00
2.00
2.50
2.67
3.00
3.00
3.00
3.33
3.50
3.66
4.00
4.00
4.00
4.00
4.00
4.66
5.00
0.086
0.162
0.220*
0.280*
0.238*
0.333
0.368
0.348
0.377
0.385
0.535
0.447
0.535
0.505
0.510*
0.470
0.596
0.660
0.402
0.402
0.527
0.482
0.427
0.483
0.453
0.457
0.461
0.417
0.482
0.394
0.486
0.486
0.450
0.507
0.476
0.427
0.101
0.201
0.263
0.301
0.285
0.362
0.340
0.343
0.384
0.365
0.441
0.394
0.486
0.486
0.450
0.507
0.555
0.534
"0.17
"0.24
"0.20
"0.08
"0.20
"0.09
0.08
0.01
"0.02
0.05
0.18
0.12
0.09
0.04
0.12
"0.08
0.07
0.19
0.107
0.216
0.247
0.297
0.268
0.337
0.334
0.342
0.397
0.383
0.464
0.446
0.501
0.501
0.480
0.524
0.578
0.616
"0.24
"0.33
"0.12
"0.06
"0.13
"0.01
0.09
0.02
"0.05
0.01
0.13
0.00
0.06
0.01
0.06
"0.11
0.03
0.07
6.00
6.00
0.552
0.558*
Substrate
2"
Oxalate
FormateGlyoxylate"
Tartrate2"
Malonate2"
Iminodiacetate
Citrate3"
Malate2"
Pyruvate"
Succinate2"
Gluconate"
Acetate"
Glucose
Fructose
Lactate"
Formaldehyde
Glycerol
Ethylenediamine
(ED)
Methanol
Ethanol
Average
Std. Dev.
Number
&
Data from Heijnen and van Dijken (1992) that is also listed in Tables I
or II.
TEEM2
Substrate
FormateFormateFormateFormaldehyde
Methanol
Methanol
Methanol
Average
Std. Dev
Number
gs
Reported
YC/C&
fos
YC/C
Error
YC/C
Error
2.00
2.00
2.00
4.00
6.00
6.00
6.00
0.162
0.120
0.180
0.470
0.540
0.540
0.552
0.402
0.402
0.402
0.507
0.375
0.375
0.375
0.201
0.201
0.201
0.507
0.563
0.563
0.563
"0.24
"0.68
"0.12
"0.08
"0.04
"0.04
"0.02
"0.17
0.23
7
0.216
0.216
0.216
0.524
0.728
0.728
0.728
"0.33
"0.80
"0.20
"0.11
"0.35
"0.35
"0.32
"0.35
0.23
7
&
Data from Heijnen and van Dijken (1992) and Xiao and VanBriesen
(2006), with one reported YC/C value of 0.100 for formate not included as
value appears to be erroneous (correspondence with VanBriesen).
Discussion
TEEM2 was found to be as good as or better than the
comparison models for predicting maximum aerobic
bacterial yields. The comparisons made here were aerobic
growth because of the extensive data bank that was here
available. TEEM2 is based upon an electron equivalents
balance, with yields reported as fraction of substrate or
electron donor electron equivalents converted for synthesis.
Other models tend to report yields in moles of cell carbon
per mole of substrate carbon for organic electron donors or
in moles cell carbon per mole of electron donor for
autotrophic reactions. Conversions to such units is readily
achieved when using electron equivalents. The comparison
models also use electron equivalents for determining
reaction energies so that use for determining yield in
electron equivalents would not be a difficult transition to
make. Using electron equivalents has the advantage that
conversion factors are not needed in the models, which often
leads to confusion. An additional advantage of using
electron equivalents is that stoichiometric equations for the
overall microorganism reactions for growth and energy
production can be more directly produced.
With the large data set of aerobic heterotrophic yield
values analyzed here, the best energy transfer efficiency
found for use in TEEM2 for aerobic growth was 0.37. With
this value, predicted yields were within 13%23% of the
measured yields. Good accuracy and about the same
variation was found for organic reactions involving
oxygenases. The TEEM2 modification to address single
carbon compounds was also found to be quite accurate for
all cases using the 0.37 energy transfer efficiency, except for
formate, where yield predictions were on average 35% too
high. This larger error was affected mainly by one especially
low formate yield measurement, which may be the result of a
measurement error or to formate catabolism following a
lower energy biochemical pathway than assumed here. For
other C1 compounds, the accuracy was good and much
better than with the comparison model, especially for
methanol, which has a high degree of reduction. These
results tend to support the hypothesis proposed here that
yield measurements that are much lower than predicted by
TEEM1 are the result of energy inefficient biochemical
pathways taken in transformations of C1 compounds, rather
385
386
Acetate
Acetoin
Acetone
Acetyl-CoA
Alanine
n-Alkanes
Benzene
Benzoate
Butane
2-3 butanediol
n-Butanol
ButyrateCitrate3"
Dihydroxy-acetone
EDTA
Ethanol
Ethylene glycol
Ethylenediamine
Formaldehyde
Formate"
Fructose
Gluconate"
Glucose
Glycerol
Glycine
Glyoxylate"
Iminodiacetate
Lactate"
Lactose
Malate2"
Malonate2"
Mannitol
Methane
Methanol
NADH
Naphthalene
NTA
Oxalate2"
Phenanthrene
Phenol
Phenylalanine
n-Propanol
Propionate"
Pyruvate"
Succinate2"
Sucrose
Tartrate2"
Toluene
Xylose
NH4
CO2
H
H (pH 7)
H2CO3
H2O
HCO"
3
DGof (kJ/mol)
Reference
aq.
aq.
aq.
"369.41
"280
"161.17
aq.
aq.
aq.
aq.
g
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
g
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
aq.
g
aq.
aq.
aq.
l
aq.
"371.54
60
133.9
"245.6
"15.707
"322
"171.84
"352.63
"1168.34
"450
"1209.15
"181.75
"323.21
"10.05
"130.54
"351.0
"915.38
"1128.3
"917.22
"488.52
"370.788
"658.1
"655.2
"517,81
"1515.24
"845.08
"700
"942.61
"50.75
"175.39
State
219.97
"954.79
"674.9
310.99
"47.5
"207.1
"175.81
"361.08
"474.63
"690.23
"1551.85
"1010
127
1077
"79.37
"394.36
0
"39.87
"623.16
"237.18
"586.85
c
a
a
a
f
d
e
c
a
a
a
c
b
a
a
b
a
a
a
a
a
a
a
a
b
a
a
a
a
a
a
a
a
b
b
a
b
f
a
a
a
a
a
a
c
f
g
a
Oxidized form
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
NAD
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
CO2
DGo (kJ/mol)
p eeq/mol
C mol/mol
g degree of reduction
27.40
33.59
29.62
30.88
31.37
27.48
28.34
27.34
27.56
32.25
29.26
27.72
33.08
41.67
33.66
31.18
39.01
29.80
46.53
39.19
41.27
40.21
41.35
38.88
39.80
51.30
40.56
32.29
42.09
34.17
29.78
39.89
23.53
36.84
30.88
27.80
33.97
52.10
27.62
29.50
29.42
29.94
27.63
35.09
29.09
42.00
40.24
27.85
41.35
8
20
16
2
4
3
4.00
5.00
5.33
12
92
30
30
26
22
24
20
18
12
34
12
10
10
4
2
24
22
24
14
6
4
12
12
48
12
8
26
8
6
2
48
18
2
66
28
40
18
14
10
14
48
10
36
20
3
15
6
7
4
4
4
4
6
3
10
2
2
2
1
1
6
6
6
3
2
2
4
3
12
4
3
6
1
1
4.00
6.13
5.00
4.29
6.50
5.50
6.00
5.00
3.00
4.00
3.40
6.00
5.00
5.00
4.00
2.00
4.00
3.67
4.00
4.67
3.00
2.00
3.00
4.00
4.00
3.00
2.67
4.33
8.00
6.00
10
6
2
14
6
9
3
3
3
4
12
4
7
5
4.80
3.00
1.00
4.71
4.67
4.44
6.00
4.67
3.33
3.50
4.00
2.50
5.14
4.00
a
a
a
a
a
a
387
References
Blackmore MA, Quayle JR. 1970. Microbial growth on oxalate by a route
not involving glyoxylate carboligase. Biochem J 118:5359.
Burkhead CE, McKinney RE. 1969. Energy concepts of aerobic microbial
metabolism. J Sanitary Eng Div, Proc Amer Soc Civil Eng 95 SA2:253
268.
Heijnen JJ, van Dijken JP. 1992. In search of a thermodynamic description
of biomass yields for the chemotrophic growth of microorganisms.
Biotechnol Bioeng 39(8):833858.
Kornberg HL. 1966. Anaplerotic sequences and their role in metabolism. In:
Campbell PN, Greville GD, editors. London: Academic Press. p 131.
Madigan MT, Martinko JM, Parker J. 1997. Brock biology of microorganisms. Upper Saddle River, NJ: Prentice Hall. 986 p.
McCarty PL. 1965. Thermodynamics of biological synthesis and growth. Int
J Air Water Pollut 9:621639.
McCarty PL. 1971. Energetics and bacterial growth. In: Faust SD, Hunter JV,
editors. Organic compounds in aquatic environments. New York:
Marcel Dekker, Inc. p 495531.
388