The biochemical mechanisms of plastic biodegradation

Abstract

Since the invention of the first synthetic plastic, an estimated 12 billion metric tons of plastics have been manufactured, 70% of which was produced in the last 20 years. Plastic waste is placing new selective pressures on humans and the organisms we depend on, yet it also places new pressures on microorganisms as they compete to exploit this new and growing source of carbon. The limited efficacy of traditional recycling methods on plastic waste, which can leach into the environment at low purity and concentration, indicates the utility of this evolving metabolic activity. This review will categorize and discuss the probable metabolic routes for each industrially relevant plastic, rank the most effective biodegraders for each plastic by harmonizing and reinterpreting prior literature, and explain the experimental techniques most often used in plastic biodegradation research, thus providing a comprehensive resource for researchers investigating and engineering plastic biodegradation.

Keywords: biodegradation; bioremediation; engineering; metabolic; metabolism; plastic.

Figure 1.

(A) Pie chart of projected global plastics production in 2023, totaling nearly 500 million tons (PlasticsEurope , , , OECD Environment Statistics 2022). (B) Global plastics production per year by type, 1990–2019 (Geyer et al. , OECD Environment Statistics 2022). (C) Plastic waste management statistics for Europe, the USA, and the globe (Geyer et al. , PlasticsEurope , , , OECD Environment Statistics 2022). (D) Timeline of plastics development and global production of plastics from 1950 to 2023 (McIntire , Jagger , Freinkel , Geyer et al. , Bellis , , Jemully , DuPont , OECD Environment Statistics , Science Museum 2019). An estimated 12 billion tons of plastic have been produced.

Figure 2.

(A) Branched, aromatic structure of woody plant polymer lignin compared to (B) Bakelite, the first plastic. (C) Aliphatic cutin, the waxy barrier on the outside of plant tissue.

Figure 3.

Photooxidation mechanisms of PE (Albertsson et al. , Singh and Sharma 2008) and PS (Singh and Sharma , Palacios et al. 2013) under an aerobic atmosphere.

Figure 4.

Biodegradation of PE (Albertsson et al. 1987). (A–C) Highly branching, amorphous structure of low-density polyethylene (LDPE) compared to less branched structures of high-density polyethylene (HDPE) and linear low-density polyethylene (LMWPE) are subject to photooxidation or; (D–F) nonspecific oxidation via ROS generated by lignin peroxidase (LiP) (Barr and Aust 1994b), manganese-dependent peroxidase (MnP) (Cai and Tien , Iiyoshi et al. 1998), laccase (a multicopper oxidase) (Gravouil et al. , Zhang et al. , , Zadjelovic et al. 2022), and superoxide dismutase (SOD) (Zadjelovic et al. 2022). Like with photooxidation, nonspecific oxidation of PE by these enzymes results in the release of a diverse array of alkanes, alcohols, aldehydes, ketones, and fatty acids. (G–J) shows cellular mechanisms for the utilization of these metabolites. (G) Active transport of alkanes across the outer membrane is facilitated by tonB-dependent receptors, while passive diffusion of alkanes and other extracellular metabolites is allowed by various porins and long-chain fatty acid transporters (Grund et al. , van Beilen et al. , Gregson et al. , Zadjelovic et al. 2022). (H) Alkane 1-hydroxylase (AlkB) system for medium length n-alkane and LMWPE biodegradation (van Beilen et al. , Yoon et al. , Zadjelovic et al. 2022). Nonheme irons facilitate substrate binding and catalysis, while electron transfer is enabled by rubredoxin and rubredoxin reductase (Guo et al. 2023) before being successively oxidized by alcohol and aldehyde dehydrogenases (AlkJH) (Reid and Fewson , van Beilen et al. 1994). (I) Subterminal monooxygenase activity on long-chain alkanes (Minerdi et al. , Zadjelovic et al. 2022), with the resulting secondary alcohol being oxidized to a ketone and converted to an ester by a Baeyer–Villiger monooxygenase (BVMO) (Fraaije et al. , Rojo , Fürst et al. 2019), which is then hydrolyzed by an esterase to the corresponding primary alcohol and and acetate (Gregson et al. , Zadjelovic et al. , Lou et al. , Jayan et al. 2023). (J) Terminal oxidation of short-chain n-alkanes by soluble CYP153 (Funhoff et al. , van Beilen et al. 2006). Like AlkB, it relies on electron transport proteins to oxidize substrates (Maier et al. 2001). Extreme structural diversity allows for members of this family to catalyse the regioselective hydroxylation of a diverse range of substrates (van Beilen et al. , Pham et al. , Fiorentini et al. 2018). *: the depiction of alkB shows a Gram-negative cell membrane because the mechanism is best understood in Pseudomonas. However, alkB homologs are also present in Gram-positive taxa. The exact localization of subterminal monooxygenases is currently unknown.

Figure 5.

Pathways for poly(cis-1,4 isoprene) (NR) and poly(trans-1,4 isoprene) (GP) degradation. (A–C) Comparison of NR, GP, and PP structures. (A) Initial oxidation of NR proceeds by heme oxidiases; rubber oxidase (RoxAB) in Gram-negative bacteria and latex clearing protein (Lcp) in Gram-positive bacteria. RoxA acts in an exo mechanism, while Lcp cleaves random endo double bonds in polymer chains, leading to iterative generation of smaller oligomers that can be taken up by the cell (Jendrossek and Birke 2019). (B) Initial oxidation of GP has only been demonstrated in Gram-positive Nocardia sp., putatively indicating activity of Lcp (Warneke et al. 2007). Subsequent metabolism of NR oligomers proceeds by oxygenation of a terminal aldehyde by a molybdenum-dependent oxygenase (OxiAB) (Rose et al. 2005). Following this, two cycles of β-oxidation occur per isoprene unit, involving four novel phases (Banh et al. 2005); (i) rearrangement of double bonds via 2,4-dienoyl-CoA reductase and enoyl-CoA isomerase generates a suitable substrate for enoyl-CoA hydratase. (ii) 3-hydroxyacyl-CoA dehydrogenase and thiolase release acetyl-CoA. (iii) acyl-CoA dehydrogenase and enoyl-CoA hydratase generate ⍺-methylacyl CoA racemase (Mcr) ensures that the methyl group is in the required (S) configuration for 3-hydroxyacyl-CoA dehydrogenase. (iv) β-oxidation releases propionyl-CoA. This pathway is thought to be the same in GP-degrading bacteria (Luo et al. 2013). A detailed membrane structure is not shown because both Gram-negative and Gram-positive bacteria are depicted.

Figure 6.

(A) Common examples of PAEs. (B and C) Other examples of plasticizers used in PVC: epoxidized soybean oil (ESBO), adipates, sebacates, and stearates (Bueno-Ferrer et al. 2010) (D) Generalized PAE biodegradation pathways phyla presented in Hu et al. (2021). (i) Esterases and lipases (Nakamiya et al. 2005) hydrolyze short and medium chain PAEs, respectively, releasing primary alcohols in the process. (ii) β-Oxidation of side chains can occur prior to hydrolysis. (iii) Two distinct aerobic pathways employ meta or para phthalate dioxygenases, dehydrogenases, and decarboxylases to generate TCA cycle substrates, with protocatechuate as a common metabolite between the two pathways. (iv) Anerobic metabolism directly ligates phthalic acid to CoA before decarboxylation to benzoyl-CoA. A detailed membrane structure is not shown because both Gram-negative and Gram-positive bacteria are depicted.

Figure 7.

Mechanism of PVC biodegradation proposed by Zhang et al. (2022b). A detailed membrane structure is not shown because the exact localization of enzymes is not known.

Figure 8.

(A) Iterative PS oxidation, chain scission, and ring cleavage to yield oligomers and low molecular weight metabolites. Initial oxidation is carried out by peroxidases and laccases (Nakamiya et al. , Mamtimin et al. 2023), while aromatic monooxygenase and dioxygenase enzymes catalyse ring cleavage (Sielicki et al. , Mamtimin et al. 2023). Given the structure of partially oxidized PS and the appearance of esters and fatty acids in culture media, it is likely that a BVMO and a serine hydrolase (SH) such as an esterase catalyse the release of fatty acid products (Fürst et al. , Kim et al. 2020a). The products of this initial depolymerization step are a mix of fatty acids, ketones, alcohols, and alkanes along with aromatic PS metabolites. Incidence of CYP153 and AlkB activity indicates alkanes or aromatic monomers produced during initial biodegradation are metabolized (Syranidou et al. , Hou and Majumder 2021). (B) Toluene catabolism pathway associated with PS biodegradation proposed by Shi et al. (, KEGG 2022) detected in association with PS biodegradation; TMO = toluene monooxygenase (Yen et al. 1991); HBADH = p-cresol methylhydroxylase (Kim et al. 1994); HBALDH = 4-hydroxybenzaldehyde dehydrogenase. (C) Styrene catabolism pathways associated with PS biodegradation (Santos et al. , Shi et al. , KEGG 2021); SMO = styrene monooxygenase (Santos et al. , Otto et al. 2004); SOI = styrene oxide isomerase (Santos et al. 2000); PAALDH = phenylacetaldehyde dehydrogenase (Hanlon et al. 1997); PAAH = phenylacetate-2-monooxygenase (Mingot et al. 1999); HPAAH = 2-hydroxyphenylacetate hydroxylase; HGADO = homogentisate 1,2-dioxygenase; FAH = fumarylacetoacetase; and PAAK = phenylacetate-CoA ligase (Miñambres et al. , Santos et al. 2000). A detailed membrane structure is not shown because both Gram-negative and Gram-positive bacteria are depicted.

Figure 9.

Mechanisms of PVA utilization adapted from Masayuki Shimao (Shimao 2001). PVADH = PQQ-dependent PVA dehydrogenase (pvaA) from Pseudomonas sp. VM15C (Masayuki et al. 1996). SAO = secondary alcohol dehydrogenase from Pseudomonas sp. (Sakai et al. 1986) OPH = oxidized PVA hydrolase (pvaB) from VM15C (Shimao et al. 2000) or β-ketol hydrolase from Pseudomonas sp (Sakai et al. 1986). Af-PVADH holoenzyme = PQQ-bound PVA dehydrogenase from A. faecalis KK314 (Matsumura et al. 1999). Af-PVADH apoenzyme = PVA dehydrogenase from A. faecalis KK314 (Matsumura et al. 1999) with aldolase activity when not bound to PQQ. A detailed membrane structure is not shown because the exact localization of enzymes is not known.

Figure 10.

(A) PEG biodegradation mechanism reported by Fusako Kawai (Kawai 2010a). PEG is brought into periplasmic space by PegB = TonB-dependent receptors (Charoenpanich et al. , Tani et al. 2007); PegA = FAD-dependent homodimeric PEG dehydrogenase (Sugimoto et al. , Ohta et al. 2006); PegC = NADP-dependent homotetrameric PEG-aldehyde dehydrogenase (Ohta et al. 2005); PegD = permease transporter for small PEG molecules or metabolites (Tani et al. 2007). Oxidiase = glycolic acid oxidase with activity on PEG-carboxylate, producing glyoxylate (Yamanaka and Kawai , Enokibara and Kawai , Yamashita et al. , , Enokibara and Kawai 1997). PegE = ATP-dependent PEG-carboxylate acyl-CoA synthetase, possibly involved in translocation across inner membrane (Somyoonsap et al. , Tani et al. 2008). (B) PEG operon showing AraC and GalR regulation sites (Charoenpanich et al. 2006). pegR = PEG-induced AraC-type regulator, which positively regulates expression of pegBCD pegAE is inhibited by a GalR-type regulator. GST = glutathione-S-transferase downstream from PEG operon. The end product, glyoxylate, is converted to malate and utilized in the TCA cycle.

Figure 11.

Mechanism of PET biodegradation by I. sakaiensis (Yoshida et al. 2016). Protocatechuate, a key intermediate in the metabolism of many aromatic compounds, is labeled (bottom, center) (Johnson and Beckham 2015). Top left inset: PETase from I. sakaiensis can hydrolyze PET analogue poly(ethylene-2,5-furandicarboxylate), but MHETase has no effect on the resulting mono(2-hydroxyethyl furanoate) (Knott et al. 2020). Left inset: a membrane-bound chimera of PETase and MHETase connected by a glycine–serine linker (Li et al. 2023). TPATP = TPA transporter; TPADO = TPA 1,2-dioxygenase; DCDDH = 1,2-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylate dehydrogenase; Pca34 = protocatechuate 3,4-dioxygenase; IsPedE, IsPedH = alcohol dehydrogenase (Hachisuka et al. 2022); IsPedI = aldehyde dehydrogenase; and GlcDEF = glycolic acid oxidase.

Figure 12.

Biodegradation mechanisms for various polyesters and biosynthesis mechanisms for poly[(R)-3-hydroxybutyrate] (PHB) and other PHA’s (Senior and Dawes , Jendrossek et al. , , Kavitha et al. 2018). PHB is synthesized from acetyl-CoA while heavier PHA precursors are derived from fatty acids in β-oxidation or fatty acid biosynthesis (Madison and Huisman 1999). PHA depolymerases cleave 2–3 units away from the hydroxyl end of the chain. Poly[lactic acid] (PLA) biodegradation proceeds via lactate dehydrogenase (da Silva et al. 2018). Proteinase K exhibits activity on poly[(l)-lactic acid] while esterase-type PLA depolymerases can biodegrade racemic mixtures of PLA and show stereoselectivity for poly[(d)-lactic acid] (Pranamuda et al. , Tokiwa and Calabia 2006). Biodegradation mechanism of polycaprolactone (PCL) proceeds via ω- and β-oxidation, producing adipic acid as an intermediate and succinyl-CoA as a product (Goldberg , Nakasaki et al. 2006). β-oxidation and TCA cycle pathways are shown in full. A detailed membrane structure is not shown because both Gram-negative and Gram-positive bacteria are depicted.

Figure 13.

Mechanism of Nylon-6 degradation by Flavobacterium spp. Crystalline regions of Nylon-6 are stabilized by hydrogen bonds, while NylC catalyses endo-type degradation of oligomers and amorphous polymer regions. NylB catalyses exo-hydrolysis of dimers and trimers while NylA is specific for cyclic dimers. nylA = 6-aminohexanoate cyclic dimer hydrolase (Kinoshita et al. 1975); nylB = aminohexanoate dimer hydrolase (Kinoshita et al. 1981); nylC = Endo-Type 6-Aminohexanoate oligomer hydrolase (Negoro et al. 1992); OPP = oligopeptide permease (Kato et al. 1995); nylD = 6-aminohexanoate aminotransferase; nylE = adipate semialdehyde oxidoreductase (Takehara et al. 2018); and PLP = pyridoxal 5′-phosphate. A detailed membrane structure is not shown because both Gram-negative and Gram-positive bacteria are depicted.

Figure 14.

Monomers used by Darby and Kaplan (1968) to assess the fungal susceptibility of various PURs. Addition between diisocyanates and polyesters results in polyester PURs, while addition between diisocyanates and polyols results in polyether PUR.

Figure 15.

PUR synthesis by Nakajima-Kambe et al. (1995) and biodegradation by C. acidovorans TB-35 (Nakajima-Kambe et al. 1997). The membrane-bound PUR esterase identified contains a hydrophobic-binding domain that attaches to the PUR surface and a catalytic serine hydrolase domain to cleave the ester bond (Akutsu et al. 1998). A detailed membrane structure is not shown because both Gram-negative and Gram-positive bacteria are depicted.

Figure 16.

Proposed chemical structure of Impranil™ DLN (de Witt et al. 2024a) with carbamate bonds on the left and ester bonds on the right. Multiple hydrolases were detected. One designated Hfor_PE-H catalysed the hydrolysis of ester bonds, metabolizing adipic acid and GA as the sole carbon source. 1,6-hexanediol was not utilized by the strain, instead being exported back to the culture supernatant in the form of 4-hydroxybutyrate. A detailed membrane structure is not shown because because the exact localization of enzymes is not known.

Figure 17.

(A) Proporosed structure of PolyLack^® deduced by Gaytán et al. (2020). (B) Biodegradation pathways of PolyLack^® additives by Microbial Community BP8.

Figure 18.

(A) Different types of bisphenols used in the synthesis of PC. (B) Traditional phosgene route for the synthesis of PC using BPA under basic conditions with methylene chloride as a solvent. (C) Melt process for PC synthesis in which diphenyl carbonate is directly reacted with bisphenols at high temperatures requiring no additional solvents but creating phenol as a biproduct. (D) Synthesis and structure of Tritan™, a BPA PC alternative produced by Eastman used to make Nalgene water bottles.

Figure 19.

(A) Biodegradation of PC by Pseudomonas sp. BP2 (Artham and Doble 2009); inner inset = breakdown products detected in seawater-weathered BPA PC film; enveloping inset = breakdown products from PC biodegradation by Pseudomonas sp. BP2. (B) Biodegradation products of BPA PC by Pseudoxanthomonas sp. NyZ600 (Yue et al. 2021). (C) Compounds generated via the photooxidation and subsequent treatment of P. chrysosoporium NCIM 1170 (Artham and Doble 2010).