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Indian Journal of Microbiology logoLink to Indian Journal of Microbiology
. 2016 Sep 28;57(1):39–47. doi: 10.1007/s12088-016-0622-4

Microbial Cometabolism and Polyhydroxyalkanoate Co-polymers

Subhasree Ray 1,2,, Vipin Chandra Kalia 1,2
PMCID: PMC5243247  PMID: 28148978

Abstract

Polyhydroxyalkanoate (PHAs) are natural, biodegradable biopolymers, which can be produced from renewable materials. PHAs have potential to replace petroleum derived plastics. Quite a few bacteria can produce PHA under nutritional stress. They generally produce homopolymers of butyrate i.e., polyhydroxybutyrate (PHB), as a storage material. The biochemical characteristics of PHB such as brittleness, low strength, low elasticity, etc. make these unsuitable for commercial applications. Co-polymers of PHA, have high commercial value as they overcome the limitations of PHBs. Co-polymers can be produced by supplementing the feed with volatile fatty acids or through hydrolysates of different biowastes. In this review, we have listed the potential bacterial candidates and the substrates, which can be co-metabolized to produce PHA co-polymers.

Keywords: Bacillus, Biowastes, Co-metabolism, Co-polymers, Polyhydroxyalkanoate, Gram-positive, Gram-negative

Introduction

Biopolymers like polyhydroxyalkanoates (PHAs) have gained importance as these can be produced from natural and renewable substrates. Another important characteristic is their biodegradable nature. Their physical and chemical characteristics are very similar to synthetic plastics derived from petroleum products [1, 2]. The basic advantage of this biodegradable plastic is their non-polluting nature and potential to save fossil fuels. Diverse bacteria produce PHAs under nutritionally imbalanced conditions. The PHA biosynthetic pathway operates at high Carbon (C) concentrations and limitations of other nutrients (N, P, K, O, Mg, etc.) in the environment [3]. Here, instead of operating the tri-carboxylic acid cycle for generating energy, the metabolic pathway shifts towards PHA biosynthesis to produce granules, which act as C storage material [4]. Under normal physiological conditions, especially when the C:N ratio is low, i.e. N is present in sufficient quantities, NAD(P)H/NAD(P) ratio decreases and acetyl-CoA goes into the TCA cycle, releasing CoA for the next round of utilization. Accumulation of CoA inhibits the activity of β-ketothiolase, which blocks the PHA synthesis route. β-ketothiolase is the first enzyme of the PHA biosynthetic pathway. On the other hand, PHA production progresses when cell growth is reduced under N-limiting conditions. Here, NAD(P)H/NAD(P) ratio increases, which inhibits citrate synthase and isocitrate dehydrogenase activity resulting in the blockage of the TCA cycle. It leads to high acetyl-CoA concentration and lowers CoA, resulting in the activation of the enzyme—β-ketothiolase. The Phase I of PHA biosynthetic pathway become operative leading to the generation of acetoacetyl-CoA. It then gets transformed to 3-OH-butyryl-CoA, with the aid of NADPH–dependent acetoacetyl reductase in the Phase II. The whole process terminates with the production of polyhydroxybutyrate (PHB), by polymerization of 3OH-butyrate monomers with the help of PHB synthase, i.e. Phase III [5, 6] (Fig. 1). The three enzymes of the PHB biosynthetic pathway are coded by genes: phaA (1179 nucleotides, nts), phaB (738 nts), and phaC (1767 nts), which are organized as CAB operon in Ralstonia eutropha (Fig. 2). The diversity of PHA synthases can be seen in organisms like: (1) R. eutropha, which has class I type, single subunit of PhaC (60–73 kDa), (2) Pseudomonas oleovorans having class II type—single PhaC subunit (60–65 kDa), (3) Allochromaticum vinosum and Thiocapsa pfennigii having class III, composed of two subunits PhaC (40 kDa) and PhaE (40 kDa), and (4) Bacillus megaterium representing class IV composed of subunits PhaC (40 kDa) and PhaR (22 kDa) (Fig. 3). Class I, II and IV type PHA synthases result in C3-C5 PHAs, whereas class III can result in more variable chain length PHAs (Fig. 3).

Fig. 1.

Fig. 1

Polyhydroxyalkanoate biosynthetic pathway. PHA is a synthesized by the action of enzymes: PhbA (β-keto thiolase), PhbB (acetoacetyl-CoA reductase) and PhbC (PHA plymerase). TCA tricarboxylic acid cycle

Fig. 2.

Fig. 2

phaCAB operon organization in Ralstonia eutropha

Fig. 3.

Fig. 3

Diversity of Polyhydroxyalkanoate (PHA) synthases

Polyhydroxyalkanoate (PHAs)

Bacteria have the potential to gather C in the form of PHAs to the extent of 90 % of the total dry cell mass (DCM). The composition of the PHAs depends upon the C chain length, which varies from: (1) C3–C5 i.e., short chain length PHA e.g., in R. eutropha, and (2) C6–C14 i.e., medium chain length PHA e.g., in Pseudomonas oleovorans [3]. The nature of the biopolymers depends upon the growth medium, type and quantity of C source, bacterium, supplements, etc. Most bacteria produce homopolymers as PHB, however, a few have the potential to produce co-polymers, but need specific co-substrate to be present in the medium [1]. R. eutropha and Chromobacterium violaceum grown in the presence of valeric acid (VA) as supplemented material results in PHA co-polymers. The commercial value of PHBs is lower as compared to co-polymers because of the following reasons: (1) brittle nature, (2) low strength, (3) high cost of production, (4) low elasticity, (5) low mechanical resistance, etc. [1]. PHA copolymers have characteristics, which can be compared to petroleum plastics. Here, the improvement in PHA strength is because of high molecular weight and variation in monomeric compositions. These changes can be achieved through variation in: (1) co-substrate, (2) feeding, (3) physiological conditions, (4) genetic modifications, (5) heterologous gene expressions (6) metabolic pathway modification [1, 7, 8]. 3HV monomers when incorporate into a PHA polymer chain, increase material characteristics of PHA co-polymer, such as: (1) melting point, (2) crystallinity, (3) stiffness, and (4) toughness. Co-polymers are thermoplastics, which have a melting temperature of 140 °C, which is  close to that of polylactic acids [9].

PHA Co-polymers by Co-metabolism of Diverse Substrates

Gram-Negative Bacteria

Most PHA producers generally belong to gram-negative group of bacteria (Table 1) [1035]. Ralstonia species are among the most widely studied PHA producers. They have an ability to produce homopolymers and co-polymers. R. eutropha could utilize mixtures of: (1) gluconoate + octanoate, and (2) glycerol + casein hydrolysate (CH) to produce PHB homopolymers, where PHA yield varied from 40 to 50 % of DCM [13, 18]. Different strains of Cupriavidus necator could produce P(3HB-3HV-3HHx) from vegetable oils, and glycerol supplemented with VA or levulinic acid, where 3HV and 3HHx components varied from 6 to 7 mol%. C. necator DSM545 produced homopolymers of PHB from glucose and VA, but co-polymers from FAME + VA [25, 33]. Similarly, Pseudomonas spp. could metabolize mixtures of sugars to PHB homopolymers. However, switching over to substrates such as dodecanoate and gluconaote mixtures resulted in PHA co-polymers—P(HD-HDD-HO-HHx) with P. putida and P(3HB-3HHx) with Aeromonas hyrophila CQ4. A variation in feed to dodecanoate + PA allowed A. hydrophila GAK4 to produce P(3HB-3HV-3HHx) [10, 1922]. Mixed cultures of Burkholderia and Acidobacteria and other bacteria proved instrumental in transforming acetate and PA combination to P(3HB-3HV) [34]. A few other organisms, which produce PHA copolymers through co-metabolism of substrates are Comamonas and Escherichia coli, whereas others like Azotobacter, Haloferax, Methylobacterium and Azohydromonas did not produce co-polymers inspite of being provided with mixed substrates as feed [11, 13, 15, 17, 27].

Table 1.

Polyhydroxyalkanoate co-polymer production by co-metabolism of diverse substrates by gram-negative microorganism

Organism Substrate Homo-polymers Co-polymer References
PHB Type Ratio
mol (%)
Yield (% DCM)
mol (%) Yield (% DCM)
Alcaligenes eutrophus Glucose + (NH4)2SO4 100 78 [16]
Ralstonia eutropha PHB-4 Gluconate + octanoate 100 40.89 [18]
R. eutropha Glycerol + caesin hydrolysate (CH) 100 50 [13]
Cupriavidus necator H16 Palm kernel oil + propionic acid (PA) P(3HB-3HV-3HHx) 93:0:7 55.5 [25]
Palm kernel oil + valeric acid (VA) P(3HB-3HV-3HHx) 89:6:5 52.3
C. necator DSM545 Glucose + VA 100 64.5 [33]
FAME + VA P(3HB-3HV) 4.3 63.4
C. necator DSM7237 Glycerol + sunflower meal + levulinic acid 27 g/L 72.9 P(3HB-3HV) 22.5 66.4 [35]
C. necator Crude glycerol + rapeseed meal P(3HB-3HV) 2.8−8:55.6 NA [32]
Cupriavidus sp. USMAA1020 γ-butyrolactone P(3HB-4HB) NA 52.4 [23]
Pseudomonas pseudoflava Glucose + xylose 100 22 [10]
P. putida KTOY06 Dodecanoate + gluconate P(3HD-3HDD-3HO- 3HHx) NA 84.3 [19]
P. putida KT2440 Glucose + nonanoic acid 100 75 NA NA [21]
Burkholderia + Acidobacteria Acetic acid (AA) + PA 100 NA P(3HB-3HV) 0–74 NA [34]
Aeromonas hydrophila CQ4 Dodecanoate + gluconoate P(3HB-3HHx) 44.67 [20]
A. hydrophila 4AK4 Dodecanoate + PA P(3HB-3HV-3HHx) NA 37.2 [22]
Lauric acid + 1,4-butanediol P(3HB-4HB—3HHx) NA 23.6 [28]
Azotobacter sp. Glucose (5 % w/v) + FP (Fish peptone) 100 85 [11]
Glucose (3 % w/v) + FP + NH4Cl 100 74
Glucose (3 % w/v) + FP 100 79
A. vinelandii UWD P(3HB-3HV) 4.3 58.3 [12]
Comamonas acidovorans Glucose + 1,4-butanediol 100 53 P(4HB) 0–96 40 [15]
Haloferax mediterranei Rice bran + corn starch (1:8) 100 55.6 [17]
Wheat bran + Corn Starch (1:2) 100 40.2
Methylobacterium rhodesianum Glycerol + CH + Casamino acids 100 65 [13]
E. coli JM109 Glucose P(3HHx-3HO) NA 54.0 [27]
Azohydromonas australica Sucrose + Nitrogen 100 77.0 [31]
Mixed culture AA + PA + Lactic acid P(3HB-3HV) 31 NA [14]
Mixed culture Fermented molasses (VFAs) 100 65 P(3HB-3HV) 13 30 [30]
Mixed culture AA + PA 100 78 P(3HB-3HV) 15–20 NA [26]
Mixed culture (Waste activated sludge) AA + Glucose 100 30 P(3HB-3HV) 3.1 NA [27]
AA + Bovine serum albumin (BSA) 100 29.1 P(3HB-3HV) 2.7 NA
AA + Glucose + BSA 100 30.8 P(3HB-3HV) 3.7 NA
Mixed culture (Activated sludge) VFAs (AA + PA + VA + butyrate) 100 31–47 P(3HB-3HV) 53–69 48 [24]

a Not applicable NA Not available

PHA Polyhydroxyalkanoae

PHB Polyhydroxybutyrate

3HB 3-Hydroxybutyric acid

3HV 3-Hydroxyvaleric acid

4HB 4-Hydroxybutyric acid

3HO 3-Hydroxyoctanoate

3HHx 3-Hydroxyhexenoate

6HHx 6Hydroxyhexanoate

3HD 3-Hydroxydecanoate

3HDD 3Hydroxydodecanoate

Gram-Positive Bacteria

Among gram-positive bacteria, Streptomyces, Corynebacteria, Clostridium, Nocardia, Rhodococcus, Staphylococcus are capable of producing PHA co-polymers [4]. Bacillus spp. are among those few gram-positive bacteria, which have been gaining importance as PHA producers because of their unique metabolic characterstics. These are perhaps the only bacteria in this category, which can produce homopolymers and co-polymers of PHA from sugars and complex biowastes (Table 2) [1, 2, 7, 3649]. Bacillus species are generally regarded as safe (GRAS) organisms [3, 7]. Bacillus megaterium OU303A and Bacillus sp. 88D utilized glucose, glycerol and acetate to produce PHB homopolymers, whereas addition of PA (<2.5 ml/L) allowed them to convert these mixtures into P(3HB-3HV). Here, 3HV content varied from 2.5 to 6.3 mol% [42, 43]. Bacillus sp. INT005 utilized butyrate to produce PHB, however, glucose in combination with different fatty acids (1 % v/v) resulted in PHA co-polymers with HV content varying from 1.5 to 29 mol% and total PHA yield ranging from 13 to 64.5 % DCM [38].

Table 2.

Polyhydroxyalkanoate Co-polymer production by co-metabolism of diverse substrates by Bacillus sp

Organism Substrate Homo-polymers Co-polymer References
PHB Type Ratio
mol (%)
Yield (% DCM)
mol (%) Yield (% DCM)
Bacillus megaterium OU303A Glucose (2 % w/v) 100 62 [42]
Glucose (2 % w/v) + PA (<2.5 mL/L) P(3HB-3HV) 97.5:2.5 58.6
Glycerol (2 % w/v) P(3HB-3HV) 95:5 52
Glycerol (2 % w/v) + PA (<2.5 mL/L) P(3HB-3HV) 86:14 57
Acetate (2 % w/v) 100 49
Acetate (2 % w/v) + PA (<2.5 mL/L) P(3HB-3HV) 96.5:3.5 59
B. megaterium DSM90 Glycerol 100 62.4 [46]
B. cereus ATCC14579 Caprolactone + octanoate 3HHx
P(3HHx-3HO)
NA 2–4 [36]
B. cereus UW85 γ- caprolactone P(3HB-3HV-6HHx) NA NA [37]
Bacillus sp.
INT005
Butyrate 100 NA [38]
Glucose (0.1 % w/v) + Butyrate (1 % v/v) P(3HB-3HHx)
P(3HB-4HB-3HHx)
98.5:1.5 32.9
Glucose (0.1 % w/v) + valerate (1 % v/v) P(3HB-3HV) 51.5:48.5 18.8
Glucose (0.1 % w/v) + hexanoate (1 % v/v) P(3HB-3HHx) 97.7:2.3 13.0
Glucose (0.1 % w/v) + octanoate (1 % v/v) P(3HB-3HHx) 97.1:2.9 64.5
Glucose (0.1 % w/v) + decanoate (1 % v/v) P(3HB-3HHx) 97.1:2.9 23.5
Glucose (0.1 % w/v) + γ- caprolactone (1 % v/v) P(3HB-6HHx-3HHx) 97.3:2.7 23.2
Bacillus sp. 88D Glucose (2 % w/v) P(3HB-3HV) 96:4 64.6 [43]
Glucose (2 % w/v) + PA (<2.5 mL/L) P(3HB-3HV) 87:13 59.8
Glycerol (2 % w/v) P(3HB-3HV) 85:15 60.5
Glycerol (2 % w/v) + PA (<2.5 mL/L) P(3HB-3HV) 96:4 60
Acetate (2 %w/v) 100:0 48
Acetate (2 %w/v) + PA (<2.5 mL/L) P(3HB-3HV) 93.7:6.3 42
Bacillus (Defined mixed strains:
B. cereus strains EGU3, EGU43 + EGU44 + EGU520 +
B. thuringiensis EGU45
Pea-shell slurry (PSS) + glucose 100 18.8 P(3HB-3HV) 87:13 16.9 [47]
PSS + glucose + PA P(3HB-3HV) 89:11 21.6
PSS + glucose + VA P(3HB-3HV) 90:10, 93:7 16–23
B. cereus EGU44 PSS + glucose 100 30.0 [47]
PSS + glucose + PA (0.5–2 % v/v) P(3HB-3HV) 89:11, 84:16, 85:15 16 -22
PSS + glucose + VA (0.5–2 % v/v) P(3HB-3HV) 83:17, 90:10 16 -24
B. thuringiensis EGU45 Effluent from H2-stage + glucose (1 % w/v) + [49]
 1. M9 + GM2 media: 1X + 0.25X NA NA P(3HB-3HV) 61:39 10
 2. M9 + GM2 media: 1X + 0.5X NA NA P(3HB-3HV) 62:38 7.6
 3. M9 + GM2 media: 1X + 1X NA NA P(3HB-3HV) 77:23 18
 4. M9 + GM2 media: 1X + 2X NA NA P(3HB-3HV) 95:5 21
B. thuringiensis EGU45 Crude glycerol (CG) + Peptone (PE) + Yeast extract (YE) + [48]
 1. PA (0.5 % v/v) P(3HB-3HV) 89:11 53.9
 2. PA (1.0 % v/v) P(3HB-3HV) 94.7:5.3 37.3
 3. PA (2.0 % v/v) P(3HB-3HV) 98.2:1.8 44.2
 4. VA (0.5 % v/v) P(3HB-3HV) 95.7:4.3 37.8
 5. VA (1.0 % v/v) P(3HB-3HV) 98.2:1.8 48.5
 6. VA (2.0 % v/v) P(3HB-3HV) 99:1.0 56.3
CG + nutrient broth +
 1. PA (0.5 % v/v) P(3HB-3HV) 86.6:13.4 55
 2. PA (1.0 % v/v) P(3HB-3HV) 95.7:4.3 29
 3. PA (2.0 % v/v) P(3HB-3HV) 98.3:1.7 36
 4. VA (0.5 % v/v) P(3HB-3HV) 96.3:3.7 29.7
 5. VA (1.0 % v/v) P(3HB-3HV) 98.7:1.3 53.1
 6. VA (2.0 % v/v) P(3HB-3HV) 98.9:1.1 52.2
PSS 100 5.8 [2]
PSS + glucose (1 % w/v) 100 7.7
Apple pomace (AP) P(3HB-3HV) 64.3:35.7 3.8
AP + glucose (1 % w/v) P(3HB-3HV) 75.9:24.1 7.5
Onion peels (OP) P(3HB-3HV) 80:20 8.4
OP + glucose (1 % w/v) P(3HB-3HV) 97.5:2.5 11.7
Potato peels (PP) P(3HB-3HV) 33:67 2.6
PP + glucose (1 % w/v) P(3HB-3HV) 90.9:9.1 38.2
PS:AP:2:1 + glucose (1 % w/v) P(3HB-3HV) 78.8:21.2 16.4
PS:OP:1:2 + glucose (1 % w/v) P(3HB-3HV) 63.4:36.6 20.5
PS:PP:2:1 + glucose (1 % w/v) P(3HB-3HV) 77:23 27.1
Bacillus sp. Glycerol NA NA 25–52 [39]
Bacillus sp. Madhuca sp. Flowers (Sugars + malic acid) P(3HB-3HV) 90:10 51 [41]
B. licheniformis PHA007 Glycerol 100 68.8 [45]
B. licheniformis DSM394 Glycerol 100 17 [45]
B. subtilis DSM10 Glycerol 100 18.9 [45]
B. cereus PHA037 Glucose 100 60.7
B. thuringiensis R1 Glycerol 100 64.1 [40]
B. sphaericus NII0838 Glycerol 100 31.0 [44]

a Not applicable

NA Not available

PHA Polyhydroxyalkanoate

PHB Polyhydroxybutyrate

3HB 3-Hydroxybutyric acid

3HV 3-Hydroxyvaleric acid

4HB 4-Hydroxybutyric acid

3HO 3-Hydroxyoctanoate

3HHx 3-Hydroxyhexenoate

6HHx 6-Hydroxyhexanoate

3HD 3-Hydroxydecanoate

3HDD 3Hydroxydodecanoate

Bacillus licheniformis, B. cereus, B. subtilis and other Bacillus spp. could not produce PHA co-polymers from glucose or glycerol. However, use of defined mixed cultures of B. cereus and B. thuringiensis produced interesting results: (1) on pea-shell slurry (PSS) + glucose—only PHB 18.8 % of DCM was recorded, whereas (2) PSS + glucose + PA resulted in P(3HB-3HV::87:13), with a yield of 16.9 % of DCM. Addition of VA to PSS + glucose was also quite effective in producing co-polymer having 7–10 mol% of 3HV. In contrast, B. cereus EGU44 was also reported to show results which are quite similar to those recorded with defined mixed cultures of Bacillus [47]. Bacillus thuringiensis EGU45 was able to metabolize effluent from hydrogen production stage and yielded co-polymers of PHA with a 3HV content of 5–39 mol% [48].

Bacillus thuringiensis EGU45 could metabolize CG to PHA co-polymers. The composition of these co-polymers varied with the amount of PA or VA used as a supplement. With PA in Peptone + Yeast extract (PE + YE) medium, PHA co-polymer had 3HV content in the range of 1.8–11 mol%. However, with VA in PE + YE medium, 3HV content varied from 1 to 4.3 mol%. On the other hand, CG + Nutrient broth (NB) supplemented with (1) PA resulted in 1.7–13.4 mol% of 3HV, and (2) VA resulted in 1.1–3.7 mol% of 3HV [49]. A very interesting result was recorded in an effort to provide supplemental fatty acids by hydrolysing different biowastes as mixtures in a wide range of ratios. Hydrolysates of PS was found to produce only AA, whereas apple poamace (AP) hydrolysates had only isovaleric acid. Hydrolysates of potato peels (PP) and onion peels (OP) produced mixtures of AA, butyric acid, and PA. This initial information was found to prove helpful in producing PHA co-polymers by co-metabolizing these biowatses by B. thuringiensis EGU45. PS alone was able to produce only homopolymers i.e., PHB, however, mixtures: (1) PS + AP, (2) PS + OP, and (3) PS + PP resulted in P(3HB-3HV), where HV content varied i.e., 21.2, 36.6, and 23.4 mol%, respectively. It implied that by co-metabolism, it is possible to divert PHA biosynthetic pathway from producing only homopolymers to different co-polymers [2].

Opinion

In order to produce co-polymers of PHA, it seems that in addition to bacterial genetic potential, we also need to choose a right combination of substrates and supplements. Thus co-metabolism is an important approach for producing PHA co-polymers of desired compositions. Among the PHA producers, Bacillus spp. are perhaps the most persistent. They have the ability to produce homopolymers and co-polymers as well from the cometabolizing substrates. It implies how Bacillus can engineer its metabolic pathway to produce PHA co-polymer. This property enables it to be a strong competitor as an industrial PHA producer in future.

Acknowledgments

We are thankful to the Director of CSIR-Institute of Genomics and Integrative Biology (IGIB), and CSIR Project INDEPTH (BSC0111) for providing the necessary funds, facilities and moral support. Authors are also thankful to Academy of Scientific and Innovative Research (AcSIR), New Delhi.

Compliance with Ethical Standards

Conflict of interest

Authors declare no conflict of interests.

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