Plastic-degrading Microorganisms Research Articles

Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review.

Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.

Structural insights into polyethylene terephthalate (PET)-degrading archaeal lipase enzyme: An insilico approach

Biodegradation of plastic is the most eco-friendly degradation process conferred by various microbial enzymes, especially the lipase enzymes. The lipase enzymes depict a broad substrate range, high regio/stereoselectivity, and stability in organic solvents. However, enhancing the catalytic activity of lipases for industrial production remains a challenge, predominantly due to the need for their extensive mechanistic characterization. Here, we employed a multidisciplinary approach to illustrate the comprehensive physiochemical and mechanical properties of 102 lipase sequences from six different groups of plastic-degrading microorganisms. Molecular docking-based evaluation of the binding efficiencies of selected lipases with the most common plastic polymers- polyurethane (PUR) and polyethylene terephthalate (PET), revealed that the archaeal lipase had the lowest binding energy of −7.1 kcal/mol with PET. Remarkably, the molecular dynamic simulation studies (up to 100 ns) and very low RMSD (0.3 nm) and RMSF (0.25 nm) values further ascertained the stability of archaeal lipase after binding with PET polymer. Further, a 2.19 nm radius of gyration (Rg) within 100 ns simulation time, binding free energy ΔGTOTAL with −24.36 kcal/mol and entropy factor -TΔS 7.65 kcal/mol also indicated strong binding of archaeal lipase with PET polymer. The mechanistic exploration of archaeal lipase yielded valuable insights into its effective binding with PET polymer, paving the way for future lipase enzyme engineering and harnessing its industrial potential for plastic biodegradation.

Characteristics of low-temperature plasma for activation of plastic-degrading microorganisms

Plastic pollution is a problem that threatens the future of humanity, and various methods are being researched to solve it. Plastic biodegradation using microorganisms is one of these methods, and a recent study reported that plastic-degrading microorganisms activated by plasma increase the plastic decomposition rate. In contrast to microbial sterilization using low-temperature plasma, microbial activation requires a stable plasma discharge with a low electrode temperature suitable for biological samples and precise control over a narrow operating range. In this study, various plasma characteristics were evaluated using SDBD (Surface Dielectric Barrier Discharge) to establish the optimal conditions of plasma that can activate plastic-degrading microorganisms. The SDBD electrode was manufactured using low-temperature co-fired ceramic (LTCC) technology to ensure chemical resistance, minimize impurities, improve heat conduction, and consider freedom in designing the electrode metal part. Plasma stability, which is important for microbial activation, was investigated by changing the frequency and pulse width of the voltage applied to the electrode, and the degree of activation of plastic-degrading microorganisms was evaluated under each condition. The results of this study are expected to be used as basic data for research on the activation of useful microorganisms using low-temperature plasma.

Plastic-degrading microbial communities reveal novel microorganisms, pathways, and biocatalysts for polymer degradation and bioplastic production

Plastics derived from fossil fuels are used ubiquitously owing to their exceptional physicochemical characteristics. However, the extensive and short-term use of plastics has caused environmental challenges. The biotechnological plastic conversion can help address the challenges related to plastic pollution, offering sustainable alternatives that can operate using bioeconomic concepts and promote socioeconomic benefits. In this context, using soil from a plastic-contaminated landfill, two consortia were established (ConsPlastic-A and -B) displaying versatility in developing and consuming polyethylene or polyethylene terephthalate as the carbon source of nutrition. The ConsPlastic-A and -B metagenomic sequencing, taxonomic profiling, and the reconstruction of 79 draft bacterial genomes significantly expanded the knowledge of plastic-degrading microorganisms and enzymes, disclosing novel taxonomic groups associated with polymer degradation. The microbial consortium was utilized to obtain a novel Pseudomonas putida strain (BR4), presenting a striking metabolic arsenal for aromatic compound degradation and assimilation, confirmed by genomic analyses. The BR4 displays the inherent capacity to degrade polyethylene terephthalate (PET) and produce polyhydroxybutyrate (PHB) containing hydroxyvalerate (HV) units that contribute to enhanced copolymer properties, such as increased flexibility and resistance to breakage, compared with pure PHB. Therefore, BR4 is a promising strain for developing a bioconsolidated plastic depolymerization and upcycling process. Collectively, our study provides insights that may extend beyond the artificial ecosystems established during our experiments and supports future strategies for effectively decomposing and valorizing plastic waste. Furthermore, the functional genomic analysis described herein serves as a valuable guide for elucidating the genetic potential of microbial communities and microorganisms in plastic deconstruction and upcycling.

Unveiling the Power Microbial Degradation by Plastic-Degrading Microorganisms

Unveiling the Power Microbial Degradation by Plastic-Degrading Microorganisms

Strategies for biofilm optimization of plastic-degrading microorganisms and isolating biofilm formers from plastic-contaminated environments

Abstract The perpetual disposal of plastic waste, combined with ineffective waste management strategies, has resulted in widespread environmental plastic pollution. Microbial plastic biodegradation represents an emerging solution to this problem. However, biodegradation studies tend to overlook the fundamental prerequisite of initial surface colonization via biofilm formation. This study had two independent but connected aims relating to plastic surface colonization by microorganisms: to enhance biofilm formation by known plastic degraders, with translational potential for improved plastic degradation, and to isolate microorganisms from microplastic contaminated environments with the ability to colonize plastic surfaces. Planktonic and biofilm responses to diverse carbon and energy sources were investigated over 7 days, using Bacillus subtilis 168, Fusarium solani (Martius) Saccardo, Ideonella sakaiensis 201-F6, Pseudomonas putida KT2440, and Rhodococcus ruber C208. This enabled optimal conditions for biofilm formation by each strain to be determined. In parallel, environmental samples containing synthetic or natural polymeric substances (anaerobic digestate, landfill leachate, and microplastic contaminated compost) were incubated with polyethylene and polyethylene terephthalate films, to isolate microorganisms capable of colonizing their surfaces. This yielded eight bacterial isolates from three genera: Bacillus, Lysinibacillus, and Proteus. These genera contain species that have been shown to degrade plastics and other recalcitrant synthetic polymers, demonstrating the success of our approach. This study also suggests that discrete plastic types may create different ecological niches which can be exploited by unique bacterial colonizers. Our findings underscore the importance of considering plastic colonization by microbial biofilms in the context of their biodegradation.

PET-degrading microorganisms isolated from residues of the SAV biosphere reserve and identification of carboxylic ester hydrolase activity during their growth in the presence of polymer

The “Sistema Arrecifal Veracruzano” (SAV) is a vital marine ecosystem; its resources are continually perturbed due to contamination by anthropogenic activities, with multiple contaminants such as plastics. In aquatic ecosystems, plastics are almost immediately coated by inorganic and organic matter, which is then colonized by microbes to form a biofilm on plastic surfaces. This work aimed to isolate and identify plastic-degrading microorganisms isolated mainly from plastic residues of the SAV biosphere reserve. Eight bacteria and three fungi were isolated from a biofilm in plastic residues from islands of SAV. All the bacteria and one fungus showed evidence of degrading PET, over 10% for two bacteria and 17% for the fungus. All fungi belong to the genus Aspergillus, and bacteria belong to the genera Aneurinibacillus, Bordetella, Bacillus, and Lysinibacillus. Aneurinibacillus migulanus and Aspergillus flavus showed the highest values for PET degradation. Carboxylic ester hydrolase (CEH) activity was detected in all crude extracts from fungi and bacteria growing with PET triturates as a carbon source; the maximum CEH in bacteria was 255 U mg-1 and 780 U mg-1 for fungi.

Novel insight into the aging process of microplastics: An in-situ study in coastal wetlands

Coastal wetlands, the critical interface between the terrestrial and marine environments, provide a dynamic and unique environment for the aging of microplastics (MPs). Nevertheless, both abiotic and biotic processes that contribute to the aging of MPs in coastal wetlands have been largely neglected. In this study, the aging of MPs was continuously characterized in Hangzhou Bay, a representative coastal wetland in Zhejiang, China. Three-month exposure of polymers in sediment-water interface induced the aging phenomenon with embrittlement and exfoliation, as evidenced by simultaneous observed alternations in crystallinity and functional groups. A first-order kinetic model was fitted to describe the rate and degree of aging quantitatively. As evidenced by the carbonyl index, the residence time of all the examined MPs exhibited significant variance, ranging from 335 to 661 days. These variations might be caused by the selective attachment of plastic-degrading microorganisms (such as Moraxella sp. and Rhodococcus sp.). A positive correlation between the carbonyl index, the number of OTUs in the MP-associated biofilm, and irradiation was observed (p < 0.001), suggesting that the aging process may be co-regulated by natural sunlight and wetland microbial colonization. This study sheds new light on the long-term environmental fate of MPs and their associated ecological risks.

Screening and degradation characteristics of plastic-degrading microorganisms in film-mulched vegetable soil

In recent years, the incomplete recycle of residual mulch film (RMF) leads to the increasing richness of plastic fragment in soil, which poses a serious threat to the soil ecological environment. Therefore, the degradation of RMF in soil has aroused the interest of researchers. In this study, the degradation microorganisms were screened from film-mulched vegetable field, the results showed that seven potential plastic-degradation microorganisms were screened and identified, including four bacteria (Burkholderia cepacia, Burkholderia diffusa, Burkholderia aenigmatica, Chrysebacterium nepalense) and three fungi (Geotrichum candidum, Fusarium oxysporum and Trichoderma sp.). The results of degradation ability experiments showed that the weight loss rate of single strains ranges from 1.58 to 2.44% after 90 d. The loss rate of weight-average molecular weight (Mw) and number-average molecular weight (Mn) for single strains after 30 d were 2.61–22.40% and 17.92–39.18%, respectively. In addition, the weight loss rate of the mixed strains ranges from 1.34 to 1.62% after 90 d. The loss rate of Mw and Mn for mixed strains after 30 d were 8.04–10.06% and 20.06–39.25%, respectively. The comparing results showed that there may be inhibitory interactions between microorganisms in mixed strains are culture. This research can provide theoretical basis and data support for the control and disposal measures of RMF pollution.

Biodegradation of plastics: mining of plastic-degrading microorganisms and enzymes using metagenomics approaches.

Plastic pollution exacerbated by the excessive use of synthetic plastics and its recalcitrance has been recognized among the most pressing global threats. Microbial degradation of plastics has gained attention as a possible eco-friendly countermeasure, as several studies have shown microbial metabolic capabilities as potential degraders of various synthetic plastics. However, still defined biochemical mechanisms of biodegradation for the most plastics remain elusive, because the widely used culture-dependent approach can access only a very limited amount of the metabolic potential in each microbiome. A culture-independent approach, including metagenomics, is becoming increasingly important in the mining of novel plastic-degrading enzymes, considering its more expanded coverage on the microbial metabolism in microbiomes. Here, we described the advantages and drawbacks associated with four different metagenomics approaches (microbial community analysis, functional metagenomics, targeted gene sequencing, and whole metagenome sequencing) for the mining of plastic-degrading microorganisms and enzymes from the plastisphere. Among these approaches, whole metagenome sequencing has been recognized among the most powerful tools that allow researchers access to the entire metabolic potential of a microbiome. Accordingly, we suggest strategies that will help to identify plastisphere-enriched sequences as de novo plastic-degrading enzymes using the whole metagenome sequencing approach. We anticipate that new strategies for metagenomics approaches will continue to be developed and facilitate to identify novel plastic-degrading microorganisms and enzymes from microbiomes.

Microplastics spatiotemporal distribution and plastic-degrading bacteria identification in the sanitary and non-sanitary municipal solid waste landfills

The municipal solid waste landfill (MSWL) is an important source of microplastics (MPs) and a huge bioreactor for plastic-degrading microorganisms (PDM). However, the spatiotemporal distribution and degradation mechanisms of MPs in MSWLs are unclear. Therefore, they were studied using the samples drilled in a sanitary landfill (SL) and an non-sanitary landfill (NSL). The results showed that there were a lot of polyethylene (PE), polypropylene (PP), polystyrene (PS), polyurethane (PU), Polyamide (PA), Polyethylene terephthalate (PET) and Polyvinyl chloride (PVC) in the landfill, and their abundance ranged from 0 to 80 items/g. The MPs surface gradually faded, became rough and even yielded cracks and holes with the landfill depth and age increase. The tiny-size MPs (< 100 µm) were the most abundant and their amount significantly increased from 28.14% to 49.13% in SL and from 24.54% to 59.51% in NSL, respectively, while large-size MPs were significantly reduced from the top to the bottom. Lysinibacillus (0.21%~67.87%) and Bacillus (0.10%~67.00%) were the dominate PDMs in SL and Candidatus_Caldatribacterium (5.06%~73.48%) was the dominate in NSL. The PE degradation was closely related to Candidatus_Cloacimonas (r = 0.688*) and Candidatus_Caldatribacterium (r = 0.680*); PS and PA were closely related to Candidatus_Contubernalis (r = 0.595*~0.705*) and PVC was closely related to Candidatus_Caldatribacterium (r = 0.547*). In addition to physical and chemical effects, biological effects can also promote the MPs formation in MSWLs.

Biodegradation of Plastic Waste

Plastic waste has greatly contributed to water and land pollution worldwide and marine plastic waste has caused havoc on numerous biological species. Most plastics are fossil-based and cannot be fully degraded by microorganisms. Bio-based plastics derived from biomass, such as starch or cellulose, can be generally degraded into CO2 and microbial biomass. Recent scientific studies have shown that several pro-degradant additives did not perform, as claimed by plastic processors, under standard biodegradation conditions. Life cycle assessment studies in the United States and Canada confirm that the standard polyethylene grocery bag has significantly lower environmental impacts than a 30% recycled content paper bag. Major factors that differentiate cradle-to-grave impacts of plastics and alternative packaging materials include: (a) less weight of plastic material required to perform same packaging function, (b) lower water consumption per kg of plastics compared to alternatives, (d) no methane releases for land-filled plastics and (e) higher energy credits for plastics disposed via waste-to-energy combustion. A Dutch study showed that substitution of fossil-based plastics by bio-based polymers generally leads to lower non-renewable energy use and reduced greenhouse gas emission. Research at the University of the Philippines (UP) deals with the utilization of agricultural by-products, such as chitin and cellulose, to make bioplastic film for packaging. Nanoclay was also incorporated to produce a nano-composite polymer. Plastic degrading microorganisms have been isolated by UP researchers from local sources including plant root nodules, alkaline spring and soil samples. The following policies regarding plastic products are being recommended under Philippine conditions: (a) government incentives for processors/manufacturers of biodegradable plastic products, (b) restricted importation and sale of non-biodegradable, esp. single-use, plastic products, and (c) funding and logistical support for R &amp; D on commercial additives for plastic biodegradation, local production of bioplastics and isolation of plastic-degrading microorganisms.

Fluorescence-activated droplet sorting of PET degrading microorganisms

Enzymes that can decompose synthetic plastics such as polyethylene terephthalate (PET) are urgently needed. Still, a bottleneck remains due to a lack of techniques for detecting and sorting environmental microorganisms with vast diversity and abundance. Here, we developed a fluorescence-activated droplet sorting (FADS) pipeline for high-throughput screening of PET-degrading microorganisms or enzymes (PETases). The pipeline comprises three steps: generation and incubation of droplets encapsulating single cells, picoinjection of fluorescein dibenzoate (FDBz) as the fluorogenic probe, and screening of droplets to obtain PET-degrading cells. We characterized critical factors associated with this method, including specificity and sensitivity for discriminating PETase from other enzymes. We then optimized its performance and compatibility with environmental samples. The system was used to screen a wastewater sample from a PET textile mill. We successfully obtained PET-degrading species from nine different genera. Moreover, two putative PETases from isolates Kineococcus endophyticus Un-5 and Staphylococcus epidermidis Un-C2-8 were genetically derived, heterologously expressed, and preliminarily validated for PET-degrading activities. We speculate that the FADS pipeline can be widely adopted to discover new plastic-degrading microorganisms and enzymes in various environments and may be utilized in the directed evolution of degrading enzymes using synthetic biology.

Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

Enhanced Bioavailability and Microbial Biodegradation of Polystyrene in an Enrichment Derived from the Gut Microbiome of Tenebrio molitor (Mealworm Larvae).

As the global threat of plastic pollution has grown in scale and urgency, so have efforts to find sustainable and efficient solutions. Research conducted over the past few years has identified gut environments within insect larvae, including Tenebrio molitor (yellow mealworms), as microenvironments uniquely suited to rapid plastic biodegradation. However, there is currently limited understanding of how the insect host and its gut microbiome collaborate to create an environment conducive to plastic biodegradation. In this work, we provide evidence that T. molitor secretes one or more emulsifying factor(s) (30-100 kDa) that mediate plastic bioavailability. We also demonstrate that the insect gut microbiome secretes factor(s) (<30 kDa) that enhance respiration on polystyrene (PS). We apply these insights to culture PS-fed gut microbiome enrichments, with elevated rates of respiration and degradation compared to the unenriched gut microbiome. Within the enrichment, we identified eight unique gut microorganisms associated with PS biodegradation including Citrobacter freundii, Serratia marcescens, and Klebsiella aerogenes. Our results demonstrate that both the mealworm itself and its gut microbiome contribute to accelerated plastic biodegradation. This work provides new insights into insect-mediated mechanisms of plastic degradation and potential strategies for cultivation of plastic-degrading microorganisms in future investigations and scale-up.

Selective bacterial colonization processes on polyethylene waste samples in an abandoned landfill site

The microbial colonization of plastic wastes has been extensively studied in marine environments, while studies on aged terrestrial wastes are scarce, and mostly limited to the isolation of plastic-degrading microorganisms. Here we have applied a multidisciplinary approach involving culturomics, next-generation sequencing analyses and fine-scale physico-chemical measurements to characterize plastic wastes retrieved in landfill abandoned for more than 35 years, and to assess the composition of bacterial communities thriving as biofilms on the films’ surfaces. All samples were characterized by different colors but were all of polyethylene; IR and DSC analyses identified different level of degradation, while FT-Raman spectroscopy and X-ray fluorescence further assessed the degradation level and the presence of pigments. Each plastic type harbored distinct bacterial communities from the others, in agreement with the differences highlighted by the physico-chemical analyses. Furthermore, the most degraded polyethylene films were found to host a bacterial community more similar to the surrounding soil as revealed by both α- and β-diversity NGS analyses. This work confirms the novel hypothesis that different polyethylene terrestrial waste samples select for different bacterial communities, and that structure of these communities can be correlated with physico-chemical properties of the plastics, including the degradation degree.

Bacterial Candidates for Colonization and Degradation of Marine Plastic Debris.

With the rising plastic pollution in the oceans, research on the plastisphere-the microorganisms interacting with marine plastic debris-has emerged. Microbial communities colonizing plastic have been characterized from several ocean regions and they are distinct from the communities of the surrounding waters, and a few plastic-degrading microorganisms have been isolated from other environments. Therefore, we propose that marine microorganisms have adapted to plastic as a surface for colonization and potentially degradation. When comparing the taxonomic patterns of plastic-associated, marine bacteria, recurring groups and families such as the families Erythrobacteraceae and Rhodobacteraceae (Alphaproteobacteria), Flavobacteriaceae (Bacteriodetes), and the phylum of cyanobacteria (such as the Phormidium genus) can be identified. Thereby, we provide a perspective on which bacterial candidates could play a role in the colonization and possible degradation of plastic in the oceans due to their occurrence on marine plastic debris. We emphasize the need for extended and reproducible collection of data to assess the existence of a core microbiome or core functionalities of the plastisphere and confirm the capability of these bacterial candidates for biodegradation of plastic. Furthermore, we suggest the next steps in research to elucidate the level of natural bioremediation and the exploitation of bacterial degradative mechanisms of plastic.

Plastic waste management, a matter for the 'community'.

Plastic waste management, a matter for the 'community'.

Phyllosphere yeasts rapidly break down biodegradable plastics

The use of biodegradable plastics can reduce the accumulation of environmentally persistent plastic wastes. The rate of degradation of biodegradable plastics depends on environmental conditions and is highly variable. Techniques for achieving more consistent degradation are needed. However, only a few microorganisms involved in the degradation process have been isolated so far from the environment. Here, we show that Pseudozyma spp. yeasts, which are common in the phyllosphere and are easily isolated from plant surfaces, displayed strong degradation activity on films made from poly-butylene succinate or poly-butylene succinate-co-adipate. Strains of P. antarctica isolated from leaves and husks of paddy rice displayed strong degradation activity on these films at 30°C. The type strain, P. antarctica JCM 10317, and Pseudozyma spp. strains from phyllosphere secreted a biodegradable plastic-degrading enzyme with a molecular mass of about 22 kDa. Reliable source of biodegradable plastic-degrading microorganisms are now in our hands.

Early microbial biofilm formation on marine plastic debris

An important aspect of the global problem of plastic debris pollution is plastic buoyancy. There is some evidence that buoyancy is influenced by attached biofilms but as yet this is poorly understood. We submerged polyethylene plastic in seawater and sampled weekly for 3weeks in order to study early stage processes. Microbial biofilms developed rapidly on the plastic and coincided with significant changes in the physicochemical properties of the plastic. Submerged plastic became less hydrophobic and more neutrally buoyant during the experiment. Bacteria readily colonised the plastic but there was no indication that plastic-degrading microorganisms were present. This study contributes to improved understanding of the fate of plastic debris in the marine environment.