Supplementary Online Material

S3: Catabolic network

r0	128.10^-6 THF + 14.10^-6Methyl-THF + 293.10^-6Methenyl-THF + 200.10^-6 Formyl-THF + 555.10^-6 Sulfur + 0.010 Ammonia + 0.052 ATP + 4699.10^-6NADH + 0.012 NADPH + 3239.10^-6 Acetyl-CoA + 361.10^-6 Erythrose-P + 93.10^-6 Fructose-P + 423.10^-6 Glucose-P + 1727.10^-6 -Ketoglutarate + 2358.10^-6 Oxaloacetate + 597.10^-6 Pentoses-P + 769.10^-6 PEP + 1676.10^-6 Glycerate-P + 2488.10^-6 Pyruvate + 440.10^-6 Succinyl-CoA + 107.10^-6 O2	→	1683.10^-6 CO2 + 718.10^-6 Acetate + 440.10^-6 Succinate +19.10^-6 Glycerol-P + 3679.10^-6 CoA-SH + 634.10^-6 Methylene-THF + 1 g of Biomass
r1	1 ATP + 1 CoA-SH + 1 Butyric acid	→	1 Butyryl-CoA
r2	1 Butyryl-CoA	→	1 FADH + 1 Crotonyl-CoA
r3	1 Crotonyl-CoA	→	1 S-3Hydroxybutyryl-CoA
r4	1 S-3Hydroxybutyryl-CoA	→	1 NADH + 1 AcetoacetylCoA
r5	1 AcetoacetylCoA + 1 NADPH	→	1 R-3 Hydroxybutyryl -CoA
r6	1 R-3 Hydroxybutyryl -CoA	→	1 CoA-SH + 1 HydroxyButyrate monomer
r7	1 CoA-SH + 1 AcetoacetylCoA	→	2 Acetyl CoA
r8	1 Acetyl CoA + 1 Oxaloacetate	→	1 CoA-SH + 1 Isocitrate
r9	1 Isocitrate	→	1 NADH+ 1 -ketoglutarate + 1 CO2
r10	1 Isocitrate	→	1 NADPH+ 1 -ketoglutarate + 1 CO2
r11	1 -ketoglutarate + 1 CoA-SH	→	1 NADH+ 1 CO2 + 1 Succinyl-CoA
r12	1 Succinyl-CoA	→	1 ATP + 1 Succinate + 1 CoA-SH
r13	1 Succinate	→	1 Fumarate + 1 FADH
r14	1 Fumarate	→	1 Malate
r15	1 Malate	→	1 NADH+ 1 Oxaloacetate
r16	1 ATP + 1 Oxaloacetate	← →	1 PEP + 1 CO2
r17	1 Malate	→	1 NADPH+ 1 Pyruvate + 1 CO2
r18	1 Pyruvate + 1 CoA-SH	→	1 NADH+ 1 Acetyl CoA + 1 CO2
r19	1 PEP	← →	1 ATP + 1 Pyruvate
r20	1 PEP	→	1 Glycerate-P
r21	1 ATP + 1 Glycerate-P	→	1 Glycerate-1,3 diP
r22	1 NADH+ 1 Glycerate-1,3 diP	→	1 Triose-P
r23	2 Triose-P	→	1 Fructose di-P
r24	1 Fructose di-P	→	1 Fructose-P
r25	1 Fructose-P	→	1 Glucose-P
r26	1 Glucose-P	→	1 NADPH+ 1 Gluconate 6-P
r27	1 Gluconate 6-P	→	1 2-Keto-3-deoxygluconate 6-P
r28	1 2-Keto-3-deoxygluconate 6-P	→	1 Pyruvate + 1 Triose-P
r29	1 Isocitrate	→	1 Succinate + 1 Glyoxylate
r30	1 Acetyl CoA + 1 Glyoxylate	→	1 CoA-SH + 1 Malate
r31	1 Ribose-P	→	1 Pentose-P
r32	1 Xylulose-P	→	1 Pentose-P
r33	1 Triose-P + 1 SedoHeptulose-P	→	1 Ribose-P + 1 Xylulose-P
r34	1 Fructose-P + 1 Triose-P	→	1 Erythrose-P + 1 Xylulose-P
r35	1 Fructose-P +1 Erythrose-P	→	1 Triose-P + 1 SedoHeptulose-P
r36	1 ATP + 1 Acetate + 1 CoA-SH	→	1 Acetyl CoA
r37	1 Glycerol-P	→	1 NADH+ 1 Triose-P
r38	1 THF + 1 NADPH+ 1 CO2	→	1 Formyl-THF
r39	1 Methylene-THF + 1 NADPH	→	1 Methyl-THF
r40	1 Methylene-THF	→	1 Methenyl-THF + 1 NADH
r41	1 Methylene-THF	→	1 THF + 1 CO2

r42	1 NADH+ 0.5 Oxygen	→	6 Proton
r43	0.5 Oxygen + 1 FADH	→	3 Proton
r44	3 Proton	→	1 ATP
r45	1 ATP	→

Respiratory Chain according to Ishaque and Aleem, 1970 and ATP spilling reaction

S4: Metabolites list

i	name
0	Xr (Biomass)
1	Butyric acid
2	Butyryl-CoA
3	Crotonyl-CoA
4	S-3Hydroxybutyryl-CoA
5	AcetoacetylCoA
6	R-3 Hydroxybutyryl -CoA
7	HydroxyButyrate monomer
8	Acetyl CoA
9	Oxaloacetate
10	Isocitrate
11	-ketoglutarate
12	Succinyl-CoA
13	Succinate
14	Fumarate
15	Malate
16	PEP
17	Pyruvate
18	Glycerate-P
19	Glycerate-1,3 diP
20	Triose-P
21	Fructose di-P
22	Fructose-P
i	name
23	Glucose-P
24	Gluconate 6-P
25	2-Keto-3-deoxygluconate 6-P
26	Glyoxylate
27	Ribose-P
28	Pentose-P
29	Xylulose-P
30	SedoHeptulose-P
31	Erythrose-P
32	Acetate
33	Glycerol-P
34	Formyl-THF
35	Methyl-THF
36	Methylene-THF
37	Methenyl-THF
38	Oxygen
39	CO2
40	CoA-SH
41	FADH
42	NADH
43	NADPH
44	Proton
45	ATP

S5: Feeding strategy and indicators used to readjust the flow to the biological requirement

In order to avoid inhibitory effect of volatile fatty acids, the cultivation was carried out in Fed-Batch condition at limiting carbon concentration (null residual concentration or lower than 0.25 g.L^-1) monitored by an exponential or linear profile adjusted to the biological demand.

Figure 1: System considered for mass balance calculations

1. Calculation of exponential feed performed according to mass balance:

,

assuming a null residual concentration of substrate ( and ) :

with  :

during the exponential growth phase, , yielding ,

with a constant growth rate, and ,

assuming a constant biomass on substrate yield:

- during PHB production associated with growth (phosphorus feeding), exponential feeding was applicable considering an apparent growth rate and a global carbon yield :

- during PHB production without phosphorus feeding, we were not able to apply an exponential carbon feeding rate, the carbon flow was manually readjusted as successive constant or linear flows with the help of the indicators listed below.

2. Indicators used to readjust the feeding to biological requirement:

The following measurements and online calculations enabled culture monitoring and feeding readjustments:

1. 
   pO₂: an increase in the O₂ partial pressure value (pO₂) without action on airflow or stirring speed indicated a limitation (carbon or of another element) or an inhibition of the strain resulting of acid accumulation in the broth
   
2. 
   N/C: nitrogen fed on carbon fed ratio was calculated with added mass (estimated instantly by weighing). This ratio indicated the partitioning of nitrogen (exclusively fed by pH regulation) between biomass production and neutralization of residual acids in the media:
   
   1. 
      During biomass production stage, the N/C must be about 0.25 mole.Cmole^-1 (according to biomass composition : C₁H_1.77O_0.44N_0.25, 4% ash, Aragao, 1996). The accumulation of butyric acid cannot be detected since the N/C corresponding to its neutralization was also 0.25 mole.Cmole^-1. However with others acids (e. g., acetic acid or propionic acid), the N/C increased if nitrogen was used for neutralization (see Figure 2 below).
      
   2. 
      During PHB or PHV production, N/C should asymptotically approach the limit value of 0.04 mole.Cmole^-1 (corresponding to a PHB or PHV accumulation of 80% of the DCW) regardless of the substrate. An increase in this ratio revealed an accumulation of the acid in the fermentation broth.
      

Figure 2: Expected evolution of nitrogen fed on carbon fed ratio (N/C) during a Fed-Batch culture depending on nitrogen distribution

3. 
   RQ: the respiratory quotient calculated from dioxygen and carbon dioxyde measurement in outlet gazes indicated the partitioning of butyric acid between biomass (RQ between 0.61 and 0.63 according to the metabolic descriptor), PHB (RQ between 0.45 and 0.67) and CO₂ if the substrate was totally decarboxylated because of the toxicity of the substrate (RQ of 0.8)
   
4. 
   Acid concentration: residual butyric acid concentration in the fermentation broth can be quantified in 10 minutes by CPG as described in the Material and Methods section. The substrate flux adapted to biological requirements can be subsequently recalculated, if necessary.
   

S6: Schematic flux distribution during growth at maximal growth rate (A), during PHB production without any growth (B), during PHB production associated with a low growth rate (C) - of 0.05h^-1 (D)



References

1 - Aragao, G.M.F., 1996. Production de poly-beta-hydroxyalcanoates par Alcaligenes eutrophus : caractérisation cinétique et contribution à l'optimisation de la mise en oeuvre des cultures Génie Biochimique et Alimentaire. Institut National des Sciences Appliquées de Toulouse, Thèse n° d'ordre : 403, Toulouse.

2 - Ingraham, J.L., Maaloe, O., Neidhardt, F.C., 1983. Growth of the bacterial cell. Sinauer Associates, Inc, Sunderland, Massachusetts.

3 - Ishaque, M., Aleem, M.I.H., 1970. Energy coupling in Hydrogenomonas eutropha. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 223, 388.



* Corresponding author: Estelle GROUSSEAU, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés – INSA, UMR INSA/CNRS 5504 - UMR INSA/INRA 792, 135 Avenue de Rangueil, 31077 TOULOUSE CEDEX 4, France. Tel. [phone]. Email: [e-mail]