Transcriptomics and Lipidomics of the Environmental Strain Rhodococcus ruber Point out Consumption Pathways and Potential Metabolic Bottlenecks for Polyethylene Degradation

Multi-omics insights into the response of Aspergillus parasiticus to long-chain alkanes in relation to polyethylene modification

Plastic pollution presents a global challenge, with polyethylene (PE) being among the most persistent plastics due to its durability and environmental resilience. Long-chain alkane (lcAlk) degrading microbes are a potential source of PE-degrading enzymes, as both lcAlk and PE are large hydrophobic compounds that consist exclusively of C-C and C-H bonds. In this work, we employed a multi-omics approach to study the ability of Aspergillus parasiticus MM36, an isolate derived from Tenebrio molitor intestines, to metabolize lcAlk and secrete enzymes that are potentially capable of modifying PE. The fungus was grown with hexadecane (C16) or a mixture of lcAlk (C24 to C36) as carbon sources and culture supernatants were tested daily for their ability to modify PE. Proteomic analysis identified induced oxidases hypothetically involved in lcAlk and PE functionalization. Key enzymes include multicopper oxidases, peroxidases, an unspecific peroxygenase and FAD-dependent monooxygenases. Surfactant proteins facilitating enzymatic and cellular interaction with hydrophobic substrates, such as one hydrophobin, three hydrophobic surface-binding proteins (HsbA) and one cerato platanin, were present in all secretomes. Transcriptomic analysis comparing lcAlk to C16 cultures highlighted the enrichment of oxidoreductase activities and carboxylic acid metabolism in both lcAlk incubation days, with transmembrane transporters and transferases predominating on day 2 and biosynthetic processes on day 3. In C16 cultures, hydrolytic enzymes, including esterases, were upregulated alongside Baeyer-Villiger monooxygenases, suggesting a shift toward sub-terminal hydroxylation. Integrating transcriptomic and secretomic data, we propose a mechanism for lcAlk assimilation by A. parasiticus MM36, involving extracellular oxyfunctionalization, hydrocarbon uptake via surface-modifying proteins and channeling through membrane transporters for energy consumption and biosynthetic processes. This study provides insights into fungal mechanisms for alkane metabolism and highlights their potential relevance to plastic biotransformation.

Degradation and habitat-dependent colonization of plastics in Caribbean coastal waters and sediments by bacterial communities

This study investigates microbial colonization of plastics in Caribbean coastal waters. We deployed five polymer types, on set with a mild UV-pretreatment and one set without UV-pretreatment, for 4.5 months in the water column and sediment at two locations, and analyzed the epiplastic biofilms with 16S rRNA gene sequencing. While a significant influence of location and habitat was apparent, we could not detect notable effects related to polymer type or UV-pretreatment on microbial community composition. Nevertheless, potential plastic and hydrocarbon degraders constituted up to 43 % of sequences from epiplastic biofilms, suggesting an affinity for plastic. Indeed, utilizing 13C-labeled PE and PP, we determined incorporation of plastic-derived carbon into microbial biomass. We measured isotopically labeled fatty acids in incubations with 13C labeled plastics in both water column and sediments, whether virgin or pre-weathered with UV light. The apparent biodegradation of plastic in benthic habitats challenges the perception of marine sediments as a final sink for polyolefins.

Discovery and solution for microplastics: New risk carriers in food

Microplastics (MPs), as a kind of plastic particles with an equal volume size of less than 5 mm, similar to PM2.5 in the air, are causing severe contamination issues in food. Along with the food chain accumulation, they have been confirmed to appear in daily foods and cause serious health risks to the organisms. However, there were no unifying national and local policies on separating, extracting, and detecting MPs in food, which is an essential and imperative early-warning strategy. This review carefully and comprehensively summarized the validated contaminated food, physical and chemical characteristics, extraction methods, traditional and rapid detection techniques, as well as degradation methods of MPs. We thoroughly analyzed the differences among these traditional strategies, and innovatively generalized the existing rapid detection techniques for MPs. Finally, the shortcomings of existing research were discussed, and the possibility of novel rapid and intelligent detection techniques for MPs in food was proposed.

Phanerochaete chrysosporium hyphae bio-crack, endocytose and metabolize plastic films

Numerous studies have focused on the effect and mechanism of plastic degradation; due to their high persistence, petroleum-based plastics are difficult for microbes to mineralize. Although such plastics have been demonstrated to be mineralized by white rot fungus, the reactions at the molecular level remain unknown. Here, we show the whole mineralization model of polyethylene film, that can be summarized as follows: 1) white rot fungus colonizes on polyethylene film, using additives as dissimilated carbon sources; 2) the fungus secretes extracellular enzymes protein, combining with stearic acid as electron donor, causes oxidation and cracking of polyethylene film; and 3) partial dissociated sub-microplastic debris access to cells, further oxidizes in sequential actions of intracellular enzymes, and ultimately mineralize via β-oxidation. Our study provides new insight into the causes of polyethylene film cracking degradation model.

Polyethylene biodegradation: A multifaceted approach

The inert nature, durability, low cost, and wide applicability of plastics have made this material indispensable in our lives. This dependency has resulted in a growing number of plastic items, of which a substantial part is disposed in landfills or dumped in the environment, thereby affecting terrestrial and aquatic ecosystems. Among plastic materials, polyolefins are the most abundant and are impervious to biodegradation, owing to the presence of strong CC and CH bonds. Nevertheless, naturally occurring biodegradation of polyolefins, albeit limited, has been reported. This observation has sparked research on microbial polyolefin degradation. More efficient and targeted versions of this process could be developed also in the laboratory by designing synthetic microbial consortia with engineered enzymes. In this review, we discuss strategies for the development of such microbial consortia and identification of novel polyolefin-degrading microorganisms, as well as the engineering of polyethylene-oxidizing enzymes with greater catalytic efficacy. Finally, different techniques for the design of synthetic microbial consortia capable of successful polyolefin bioremediation will be outlined.

Genomic insights and metabolic pathways of an enriched bacterial community capable of degrading polyethylene

In the face of mounting global plastic pollution, especially concerning microplastics, biodegradation must be a sustainable solution. The key factor driving this technology is to explore efficient plastic-biodegraders from different habitats, among which activated sludge (AS) may be an important option since it holds diverse microorganisms occupying various ecological niches. Here we intend to enrich the plastic-degrading microorganisms from AS by using polyethylene (PE) plastic as the carbon and energy source. After a 28-day incubation, the weight loss of PE films reached 3% and the hydrophobicity decreased, indicating physical biodegradation. Moreover, Fourier-transform infrared spectroscopy (FTIR) results showed the formation of several new oxygen-containing functional groups on PE. Microbial analysis extracted 26 metagenome-assembled genomes (MAGs) from the enriched microbial communities. Among them MAG10, MAG21 and MAG26 displayed the increased abundance upon PE addition and harbored abundant genes related to carbohydrate transport and metabolism, suggesting their potential to degrade PE. Additionally, functional analysis revealed 14 plastic degradation-related genes, including oxidase, laccase, and lipase, indicating the significant potential in plastic degradation. Furthermore, a pathway for synergistic biodegradation of PE was proposed based on the potential PE degradation genes retrieved from MAGs. This work offers a promising and sustainable solution to plastic pollution by enriching the potential biodegraders from AS.

Biodegradation of oil-derived hydrocarbons by marine actinobacteria: A systematic review

The intensive use of oil and its derivatives is related to a greater frequency of accidents involving the release of pollutants that cause harmful effects on ecosystems. Actinobacteria are cosmopolitan and saprophytic microorganisms of great commercial interest, but because they are predominantly found in soil, most research into the products of this phylum's metabolism has focused on this habitat. Marine actinobacteria exhibit unique metabolic characteristics in response to extreme conditions in their habitat, which distinguishes them from terrestrial actinobacteria. This systematic review aims to describe cultivable hydrocarbonoclastic marine actinobacteria, analyze their biodegradation rates, as well as discuss their respective potential for application in bioremediation techniques and their limitations. Twenty-one actinobacteria were found to be capable of degrading one or more hydrocarbons derived from petroleum. The majority of these bacteria belonged to the genera Rhodococcus, Gordonia, Pseudonocardia, Isoptericola, Microbacterium, Citricoccus, Kocuria, Brevibacterium, and Cellulosimicrobium. The highest degradation rate was obtained by the species R. ruber, which degraded 100 % of fluorene at a concentration of 100 mg/L. On the other hand, the species Streptomyces gougerotti and Micromonospora matsumotoense were able to degrade polyethylene and use the carbon derived from it to produce polylactic acid (PLA), which represents an excellent candidate for making safely degradable bioplastics, with a view to recycling and replacing conventional petroleum-based plastics. An approach that integrates physicochemical and biological methods, and optimized growth conditions can lead to greater success in decontaminating environments. Despite the number of bacteria found in the research, this number may be significantly higher. This review provides valuable information to support further studies.

Recent progresses and perspectives of polyethylene biodegradation by bacteria and fungi: A review

Plastics pollution has become a serious threat to the people and environment due to the mass production, unreasonable disposal and continuous pollution. Polyethylene (PE), one of the most utilized plastics all over the world, is considered as a highly recalcitrant environmental destruction problem on account of strong hydrophobicity and high molecular weight. Therefore, it is urgently necessary to seek economical and efficient treatment and disposal methods for PE. Considering microorganisms can use various carbon sources for anabolism, they are recognized to have great potential in the biodegradation of microplastics including PE. From this point of view, the present review concentrates on providing information regarding the current status of PE biodegradation microorganisms (bacteria and fungi), and the influencing factors such as PE characteristics, cellular surface hydrophobicity, physical treatments, chemicals addition, as well as environmental conditions for biodegradation are thoroughly discussed. Furthermore, the possible biodegradation mechanisms for PE involve the biofilm formation, biodeterioration, fragmentation, assimilation, and mineralization are elucidated in detail. Finally, the future research directions and application prospects of microbial degradation are prospected in this review. It is expected to provide reference and guidance for PE biodegradation and their potential applications in real contaminated sites.

Screening and isolation of polyethylene microplastic degrading bacteria from mangrove sediments in southern China

Mangrove sediments in southern China are a large reservoir for microplastics (MPs). In particular, polyethylene microplastics (PE-MPs) are environmentally toxic and have accumulated in large quantities in these sediments, posing a potential threat to the overall mangrove and the organisms that inhabit it. We screened sediments from 5 mangrove sites and identified a potential source of PE-MP degrading bacteria. We purified the bacterial strains Acinetobacter venetianus E1-1, Serratia marcescens E1-2, Chryseobacterium cucumeris E1-3 and Bacillus albus E1-4 from P1 that were able to reduce the mass of the 75 μm PE-MPs substrate by 3.67 to 6.59 %, respectively and use it as a sole carbon source. The degradation was accompanied by surface deformation of the MPs and introduction of polar oxygen-containing carbonyl and carboxylic acid functional groups thereby decreasing the hydrophobicity of the substrate. Whole-genome sequencing of S. marcescens E1-2, the most effective degrader, revealed it possesses a variety of enzymes and metabolic pathways related to PE degradation. Our results indicated that the PE-MP degrading bacteria isolated from screened mangrove sediments represent an effective strategy for in situ MP pollution remediation and uncovering mechanisms associated with PE degradation.

Comprehensive genomic and transcriptomic analyses of the anaerobic degradation of microcystin in Alcaligenes faecalis D04

Microcystin LR (MC-LR) pollution is a serious threat to aquatic ecosystems and public health in China and is an environmental problem that urgently needs to be solved. However, few studies have investigated the anaerobic degradation pathway and related molecular biological mechanisms of MC-LR. In this study, a bacterium capable of degrading MC-LR with a degradation efficiency of 0.303 µg/mL/d under anaerobic conditions was isolated from water. The strain was identified as Alcaligenes and named Alcaligenes faecalis D04. Two new anaerobic degradation products, one pentapeptide (Adda-Glu-Mdha-Ala-Leu) and one tripeptide (Adda-Glu-Mdha), were identified by chromatography and mass spectrometry, and two new anaerobic degradation pathways for microcystins were proposed. This study revealed a new connection between related functional genes (mblH, ridA, paaA, livI, soxR, gltD, marR, etc.) and bacterial degradation functions through the analysis of multiomics data. Real-time quantitative PCR analysis verified that the expression trends of the differentially expressed genes were consistent with the transcriptomic data. Our study aimed to elucidate the anaerobic degradation pathway and molecular regulatory mechanism of MC-LR in Alcaligenes faecalis D04, which offers important practical significance for microbial strategies to prevent and regulate microcystin contamination.

Insights into polyethylene biodegradative fingerprint of Pseudomonas citronellolis E5 and Rhodococcus erythropolis D4 by phenotypic and genome-based comparative analyses

Polyethylene (PE) is the most-produced polyolefin, and consequently, it is the most widely found plastic waste worldwide. PE biodegradation is under study by applying different (micro)organisms in order to understand the biodegradative mechanism in the majority of microbes. This study aims to identify novel bacterial species with compelling metabolic potential and strategic genetic repertoires for PE biodegradation. Pseudomonas citronellolis E5 is newly isolated from solid organic waste contaminated with plastic debris, and Rhodococcus erythropolis D4 was selected for its promising potential in biodegradable plastic determined by its genetic repertoire. P. citronellolis E5 was selected for its ability to grow on PE as the only carbon and energy source. Meaningful extracellular secreted laccase activity was also characterized for D4 during growth on PE (E5 and D4 strains have a laccase activity of (2 ± 1)×10-3 U mg-1 and (3 ± 1)×10-3 U mg-1, respectively). Despite the highest level of cell numbers recorded at 7 days of growth on PE for both strains, the patterns of the metabolic products obtained and degraded during 60 days on PE were dissimilar in the two bacteria at different sampling times. However, they mainly produced metabolites belonging to carboxylic acids and alkanes with varying numbers of carbons in the aliphatic chains. Whole-genome sequence analyses of P. citronellolis E5 compared to R. erythropolis D4 and genetic determinant prediction (by gene annotation and multiple sequence alignment with reference gene products) have been performed, providing a list of 16 and 42 gene products putatively related to different metabolic steps of PE biodegradation. Altogether, these results support insights into PE biodegradation by bacteria of the Pseudomonas and Rhodococcus genera from metabolic and genetic perspectives as a base to build up novel biotechnological platforms.

Biotransformation of microplastics from three-layer face masks by nitrifying-denitrifying consortia

COVID-19 increased microplastics (MP) contamination due to the extensive use of single-use personal protective equipment, particularly three-layer face masks. MP from face masks enter wastewater treatment plants (WWTPs), which were not designed to remove them. We utilized nitrifying-denitrifying microbial consortia and synthetic urban wastewater to evaluate the biotransformation of MP from each layer of three-layer face masks made of polypropylene (PP). The biotransformation carried out by the nitrifying-denitrifying consortia altered the surface of the outer, middle, and inner layers, as a consequence of the chemical modification of the PP-MP structure. Abiotic controls did not show changes on the physicochemical and thermal properties of PP-MP. Biotic tests showed increments in both the carbonyl and hydroxyl indices of the three layers in 42 days. The outer layer showed the greatest degree of biotransformation, which was consistent with morphological changes detected by scanning electron microscopy and in physicochemical properties such as crystallinity, evaporation, and fusion temperature. The nitrifying-denitrifying consortia, which removed 99 % of the total nitrogen from the synthetic urban wastewater, had several genera with proven capacity to biotransform MP such as Cephaloticoccus and Pseudomonas.

Metagenomic analysis of soil from landfill site reveals a diverse microbial community involved in plastic degradation

In this study, we have investigated microbial communities structure and function using high throughput amplicon sequencing and whole metagenomic sequencing of DNA extracted from different depths of a plastic-laden landfill site. With diverse taxonomic groups inhabiting the plastic-rich soil, our study demonstrates the remarkable adaptability of microbes to use this new substrate as a carbon source. FTIR spectroscopic analysis of soil indicated degradation of plastic as perceived from the carbonyl index of 0.16, 0.72, and 0.44 at 0.6, 0.9 and 1.2 m depth, respectively. Similarly, water contact angles of 108.7 degree, 99.7 degree, 62.7 degree, and 77.8 degree of plastic pieces collected at 0.3, 0.6, 0.9, and 1.2 m depths respectively showed increased wettability and hydrophilicity of the plastic. Amplicon analysis of 16S and 18 S rRNA revealed a high abundance of several plastic-degrading bacterial groups, including Pseudomonas, Rhizobiales, Micrococcaceae, Chaetomium, Methylocaldum, Micromonosporaceae, Rhodothermaceae and fungi, including Trichoderma, Aspergillus, Candida at 0.9 m. The co-existence of specific microbial groups at different depths of landfill site indicates importance of bacterial and fungal interactions for plastic. Whole metagenome analysis of soil sample at 0.9 m depth revealed a high abundance of genes encoding enzymes that participate in the biodegradation of PVC, polyethylene, PET, and polyurethane. Curation of the pathways related to the degradation of these materials provided a blueprint for plastic biodegradation in this ecosystem. Altogether, our study has highlighted the importance of microbial cooperation for the biodegradation of pollutants. Our metagenome-based investigation supports the current perception that consortia of fungi-bacteria are preferable to axenic cultures for effective bioremediation of the environment.

Direct evidence for selective microbial enrichment with plastic degradation potential in the plastisphere

Plastisphere, characterized by microbial colonization on plastic debris, has attracted concern with its adverse environmental effects. The microbial features have been increasingly investigated; however, there lacks direct evidence for microplastics serving as carbon sources and enriching plastic-degrading microorganisms. Here, we obtained microbial communities from soil microplastics, analyzed the dissimilarity compared with soil, and characterized the plastic-degrading potential of isolates from plastisphere. Results showed the plastisphere communities significantly differed from soil communities and exhibited a higher relative abundance of Nocardia and Rhodococcus. To verify the selective enrichment of plastic-degrading microorganisms in the plastisphere, culture-based strategies were employed to evaluate the polyethylene (PE) degradation potential of two isolates Nocardia asteroides No.11 and Rhodococcus hoagii No.17. They could grow solely on PE and led to significant weight loss. FTIR and SEM analysis revealed the formation of new functional groups and the destruction of structural integrity on PE surfaces. Genes related to PE biodegradation were identified by genome-wide sequencing thus recognizing relevant enzymes and elucidating potential pathways. Overall, this report combined culture-free and culture-based approaches to confirm the plastic degradation potential of selectively enriched microorganisms in soil plastisphere, providing a positive perspective toward promoting microplastic biodegradation in farmland soil by enhancing natural microbial processes.

Interactions between microplastics and organic contaminants: The microbial mechanisms for priming effects of organic compounds on microplastic biodegradation

The co-presence of plastics and other organic contaminants is pervasive in various ecosystems, particularly in areas with intensive anthropogenic activities. Their interactions inevitably impact the composition and functions of the plastisphere microbiome, which in turn determines the trajectory of these contaminants. Antibiotics are a group of organic contaminants that warrant particular attention due to their wide presence in environments and significant potential to disseminate antibiotic resistance genes (ARGs) within the plastisphere. Therefore, this study investigated the impacts of sulfadiazine (SDZ), a prevalent environmental antibiotic, on the composition and function of the plastisphere microbial community inhabiting micro-polyethylene (mPE), one of the most common microplastic contaminants. Our findings indicated that the presence of SDZ increased the overall plastisphere microbial abundance and enriched populations that are capable of degrading both SDZ and mPE. The abundance of Aquabacterium, a dominant plastisphere population that is capable of degrading both SDZ and mPE, increased over the course of SDZ exposure, while another abundant mPE-degrading population, Ketobacter, remained stable. Accordingly, the removal of SDZ was enhanced in the presence of mPE. Moreover, the results further revealed that not only SDZ but also other labile organic contaminants (e.g., aniline and hexane) could accelerate mPE biodegradation through a priming effect. This investigation underscores the complex dynamics among microplastics, organic contaminants, and the plastisphere microbiome, offering insights into the environmental fate of plastic and antibiotic pollutants.

The biochemical mechanisms of plastic biodegradation

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.

Metatranscriptomics of microbial biofilm succession on HDPE foil: uncovering plastic-degrading potential in soil communities

BACKGROUND

Although plastic pollution is increasing worldwide, very little is known about the microbial processes that take place once plastic debris is incorporated into the soil matrix. In this study, we conducted the first metatranscriptome analysis of polyethylene (PE)-associated biofilm communities in highly polluted landfill soil and compared their gene expression to that of a forest soil community within a 53-day period.

RESULTS

Our findings indicate that the microbial population present in soil contaminated with plastic debris is predisposed to both inhabit and degrade plastic surfaces. Surprisingly, the microbial community from undisturbed forest soil contained a diverse array of plastic-associated genes (PETase, alkB, etc.), indicating the presence of an enzymatic machinery capable of plastic degradation. Plastic-degrading taxa were upregulated in the early stages of biofilm formation. During the maturation of the biofilm, the alkB1/alkM transcripts, which encode PE-degrading enzymes, and transporters such as fadL, livG, livF, livH, and livM were upregulated, along with transcripts associated with the fatty acid β-oxidation pathway.

CONCLUSIONS

In this study, we address the underlying patterns of gene expression during biofilm development in a PE-associated plastisphere in soil and address the pressing question of whether natural microbial communities have the potential to biodegrade petrochemical-based plastic in the soil environment.

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.

The assembly and ecological roles of biofilms attached to plastic debris of Ashmore reef

Plastic pollution in the ocean is a global environmental hazard aggravated by poor management of plastic waste and growth of annual plastic consumption. Microbial communities colonizing the plastic's surface, the plastisphere, has gained global interest resulting in numerous efforts to characterize the plastisphere. However, there are insufficient studies deciphering the underlying metabolic processes governing the function of the plastisphere and the plastic they reside upon. Here, we collected plastic and seawater samples from Ashmore Reef in Australia to examine the planktonic microbes and plastic associated biofilm (PAB) to investigate the ecological impact, pathogenic potential, and plastic degradation capabilities of PAB in Ashmore Reef, as well as the role and impact of bacteriophages on PAB. Using high-throughput metagenomic sequencing, we demonstrated distinct microbial communities between seawater and PAB. Similar numbers of pathogenic bacteria were found in both sample types, yet plastic and seawater select for different pathogen populations. Virulence Factor analysis further illustrated stronger pathogenic potential in PAB, highlighting the pathogenicity of environmental PAB. Furthermore, functional analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed xenobiotic degradation and fatty acid degradation to be enriched in PABs. In addition, construction of metagenome-assembled genomes (MAG) and functional analysis further demonstrated the presence of a complete Polyethylene (PE) degradation pathway in multiple Proteobacteria MAGs, especially in Rhodobacteriaceae sp. Additionally, we identified viral population presence in PAB, revealing the key role of bacteriophages in shaping these communities within the PAB. Our result provides a comprehensive overview of the various ecological processes shaping microbial community on marine plastic debris.

Current paradigms and future challenges in harnessing gut bacterial symbionts of insects for biodegradation of plastic wastes

The ubiquitous incorporation of plastics into daily life, coupled with inefficient recycling practices, has resulted in the accumulation of millions of metric tons of plastic waste, that poses a serious threat to the Earth's sustainability. Plastic pollution, a global problem, disrupts the ecological balance and endangers various life forms. Efforts to combat plastic pollution are underway, with a promising avenue being biological degradation facilitated by certain insects and their symbiotic gut microorganisms, particularly bacteria. This review consolidates existing knowledge on plastic degradation by insects and their influence on gut microbiota. Additionally, it delves into the potential mechanisms employed by insects in symbiosis with gut bacteria, exploring the bioconversion of waste plastics into value-added biodegradable polymers through mineralization. These insights hold significant promise for the bio-upcycling of plastic waste, opening new horizons for future biomanufacturing of high-value chemicals from plastic-derived compounds. Finally, we weigh the pros and cons of future research endeavors related to the bioprospection of plastic-degrading bacteria from underexplored insect species. We also underscore the importance of bioengineering depolymerases with novel characteristics, aiming for their application in the remediation and valorization of waste plastics.

Bottlenecks in biobased approaches to plastic degradation

Plastic waste is an environmental challenge, but also presents a biotechnological opportunity as a unique carbon substrate. With modern biotechnological tools, it is possible to enable both recycling and upcycling. To realize a plastics bioeconomy, significant intrinsic barriers must be overcome using a combination of enzyme, strain, and process engineering. This article highlights advances, challenges, and opportunities for a variety of common plastics.

Towards consolidated bioprocessing of biomass and plastic substrates for semi-synthetic production of bio-poly(ethylene furanoate) (PEF) polymer using omics-guided construction of artificial microbial consortia

Poly(ethylene furanoate) (PEF) plastic is a 100% renewable polyester that is currently being pursued for commercialization as the next-generation bio-based plastic. This is in line with growing demand for circular bioeconomy and new plastics economy that is aimed at minimizing plastic waste mismanagement and lowering carbon footprint of plastics. However, the current catalytic route for the synthesis of PEF is impeded with technical challenges including high cost of pretreatment and catalyst refurbishment. On the other hand, the semi-biosynthetic route of PEF plastic production is of increased biotechnological interest. In particular, the PEF monomers (Furan dicarboxylic acid and ethylene glycol) can be synthesized via microbial-based biorefinery and purified for subsequent catalyst-mediated polycondensation into PEF. Several bioengineering and bioprocessing issues such as efficient substrate utilization and pathway optimization need to be addressed prior to establishing industrial-scale production of the monomers. This review highlights current advances in semi-biosynthetic production of PEF monomers using consolidated waste biorefinery strategies, with an emphasis on the employment of omics-driven systems biology approaches in enzyme discovery and pathway construction. The roles of microbial protein transporters will be discussed, especially in terms of improving substrate uptake and utilization from lignocellulosic biomass, as well as from depolymerized plastic waste as potential bio-feedstock. The employment of artificial bioengineered microbial consortia will also be highlighted to provide streamlined systems and synthetic biology strategies for bio-based PEF monomer production using both plant biomass and plastic-derived substrates, which are important for circular and new plastics economy advances.

Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes

Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.

Assessing microbial plastic degradation requires robust methods

Plastics are versatile materials that have the potential to propel humanity towards circularity and ultimate societal sustainability. However, the escalating concern surrounding plastic pollution has garnered significant attention, leading to widespread negative perceptions of these materials. Here, we question the role microbes may play in plastic pollution bioremediation by (i) defining polymer biodegradability (i.e., recalcitrant, hydrolysable and biodegradable polymers) and (ii) reviewing best practices for evaluating microbial biodegradation of plastics. We establish recommendations to facilitate the implementation of rigorous methodologies in future studies on plastic biodegradation, aiming to push this field towards the use of isotopic labelling to confirm plastic biodegradation and further determine the molecular mechanisms involved.

Biodegradation of polyethylene terephthalate by Tenebrio molitor: Insights for polymer chain size, gut metabolome and host genes

Polyethylene terephthalate (PET or polyester) is a commonly used plastic and also contributes to the majority of plastic wastes. Mealworms (Tenebrio molitor larvae) are capable of biodegrading major plastic polymers but their degrading ability for PET has not been characterized based on polymer chain size molecular size, gut microbiome, metabolome and transcriptome. We verified biodegradation of commercial PET by T. molitor larvae in a previous report. Here, we reported that biodegradation of commercial PET (Mw 29.43 kDa) was further confirmed by using the δ13C signature as an indication of bioreaction, which was increased from - 27.50‰ to - 26.05‰. Under antibiotic suppression of gut microbes, the PET was still depolymerized, indicating that the host digestive enzymes could degrade PET independently. Biodegradation of high purity PET with low, medium, and high molecular weights (MW), i.e., Mw values of 1.10, 27.10, and 63.50 kDa with crystallinity 53.66%, 33.43%, and 4.25%, respectively, showed a mass reduction of > 95%, 86%, and 74% via broad depolymerization. Microbiome analyses indicated that PET diets shifted gut microbiota to three distinct structures, depending on the low, medium, and high MW. Metagenome sequencing, transcriptomic, and metabolic analyses indicated symbiotic biodegradation of PET by the host and gut microbiota. After PET was fed, the host's genes encoding degradation enzymes were upregulated, including genes encoding oxidizing, hydrolyzing, and non-specific CYP450 enzymes. Gut bacterial genes for biodegrading intermediates and nitrogen fixation also upregulated. The multiple-functional metabolic pathways for PET biodegradation ensured rapid biodegradation resulting in a half-life of PET less than 4 h with less negative impact by PET MW and crystallinity.

Molecular docking and metagenomics assisted mitigation of microplastic pollution

Microplastics, tiny, flimsy, and direct progenitors of principal and subsidiary plastics, cause environmental degradation in aquatic and terrestrial entities. Contamination concerns include irrevocable impacts, potential cytotoxicity, and negative health effects on mortals. The detection, recovery, and degradation strategies of these pollutants in various biota and ecosystems, as well as their impact on plants, animals, and humans, have been a topic of significant interest. But the natural environment is infested with several types of plastics, all having different chemical makeup, structure, shape, and origin. Plastic trash acts as a substrate for microbial growth, creating biofilms on the plastisphere surface. This colonizing microbial diversity can be glimpsed with meta-genomics, a culture-independent approach. Owing to its comprehensive description of microbial communities, genealogical evidence on unconventional biocatalysts or enzymes, genomic correlations, evolutionary profile, and function, it is being touted as one of the promising tools in identifying novel enzymes for the degradation of polymers. Additionally, computational tools such as molecular docking can predict the binding of these novel enzymes to the polymer substrate, which can be validated through in vitro conditions for its environmentally feasible applications. This review mainly deals with the exploration of metagenomics along with computational tools to provide a clearer perspective into the microbial potential in the biodegradation of microplastics. The computational tools due to their polymathic nature will be quintessential in identifying the enzyme structure, binding affinities of the prospective enzymes to the substrates, and foretelling of degradation pathways involved which can be quite instrumental in the furtherance of the plastic degradation studies.

Flying toward a plastic-free world: Can Drosophila serve as a model organism to develop new strategies of plastic waste management?

The last century was dominated by the widespread use of plastics, both in terms of invention and increased usage. The environmental challenge we currently face is not just about reducing plastic usage but finding new ways to manage plastic waste. Recycling is growing but remains a small part of the solution. There is increasing focus on studying organisms and processes that can break down plastics, offering a modern approach to addressing the environmental crisis. Here, we provide an overview of the organisms associated with plastics biodegradation, and we explore the potential of harnessing and integrating their genetic and biochemical features into a single organism, such as Drosophila melanogaster. The remarkable genetic engineering and microbiota manipulation tools available for this organism suggest that multiple features could be amalgamated and modeled in the fruit fly. We outline feasible genetic engineering and gut microbiome engraftment strategies to develop a new class of plastic-degrading organisms and discuss of both the potential benefits and the limitations of developing such engineered Drosophila melanogaster strains.

Exploring genetic landscape of low-density polyethylene degradation for sustainable troubleshooting of plastic pollution at landfills

Plastic pollution increases globally due to the high volume of its production and inadequate mismanagement, leading to dumps in landfills affecting terrestrial and aquatic ecosystems. Landfills, as sink for plastics, leach various toxic chemicals and microplastics into the environment. We scrutinized the genetic expression for low-density polyethylene (LDPE) degradation via microorganisms to investigate cell viability and metabolic activities for biodegradation and genetic profiling. Samples were collected from the Pirana waste landfill at Ahmedabad, Gujarat, which is one of the largest and oldest municipal solid waste (MSW) dump sites in Asia. Results analyzed that isolated bacterial culture PN(A)1 (Bacillus cereus) is metabolically active on LDPE as carbon source during starvation conditions when incubated for up to 60 days, which was confirmed via 2,3,5-triphenyl-tetrazolium chloride (TTC) reduction test, reported cell viability and LDPE degradation. Abrasions, surface erosions, and cavity formations were analyzed via scanning electron microscopy (SEM), whereas the breakdown of high molecular polymers converted to low molecules, i.e., depolymerization, was also observed via Fourier-transform infrared (FTIR) spectroscopy over 90 days, along with changes in functional groups of carboxylic acids and aldehyde as well as the formation of polysulfide, aliphatic compounds, aromatic ethers, alcohols, and ether linkages. Further, transcriptomic analysis was performed via DESeq2 analysis to understand key gene expression patterns and pathways involved in LDPE degradation. During the initial phase of LDPE degradation, genes related to biological processes, like membrane transportation, ABC transporters, carbon and lipid metabolism, fatty acid degradation/oxidation, and TCA cycle, are likely to indicate pathways for stress response and molecular functions, like oxidoreductase, catalytic, lyase, transferase, and hydrolase activities were expressed. Interlinking between metabolic pathways indicates biodegradation process that mineralizes LDPE during subsequent incubation days. These pathways can be targeted for increasing the efficiency of LDPE degradation using microbes in future studies. Thus, considering microbial-mediated biodegradation as practical, eco-friendly, and low-cost alternatives, healthy biomes can degrade polymers in natural environments explored by understanding the genetic and enzymatic expression, connecting their role in the process to the likely metabolic pathways involved, thereby increasing the rate of their biodegradation.

Mechanistic understanding on the uptake of micro-nano plastics by plants and its phytoremediation

Contaminated soil is one of today's most difficult environmental issues, posing serious hazards to human health and the environment. Contaminants, particularly micro-nano plastics, have become more prevalent around the world, eventually ending up in the soil. Numerous studies have been conducted to investigate the interactions of micro-nano plastics in plants and agroecosystems. However, viable remediation of micro-nano plastics in soil remains limited. In this review, a powerful in situ soil remediation technology known as phytoremediation is emphasized for addressing micro-nano-plastic contamination in soil and plants. It is based on the synergistic effects of plants and the microorganisms that live in their rhizosphere. As a result, the purpose of this review is to investigate the mechanism of micro-nano plastic (MNP) uptake by plants as well as the limitations of existing MNP removal methods. Different phytoremediation options for removing micro-nano plastics from soil are also described. Phytoremediation improvements (endophytic-bacteria, hyperaccumulator species, omics investigations, and CRISPR-Cas9) have been proposed to enhance MNP degradation in agroecosystems. Finally, the limitations and future prospects of phytoremediation strategies have been highlighted in order to provide a better understanding for effective MNP decontamination from soil.

Bioremediation of environmental organic pollutants by Pseudomonas aeruginosa: Mechanisms, methods and challenges

The development of the chemical industry has led to a boom in daily consumption and convenience, but has also led to the release of large amounts of organic pollutants, such as petroleum hydrocarbons, plastics, pesticides, and dyes. These pollutants are often recalcitrant to degradation in the environment, whereby the most problematic compounds may even lead to carcinogenesis, teratogenesis and mutagenesis in animals and humans after accumulation in the food chain. Microbial degradation of organic pollutants is efficient and environmentally friendly, which is why it is considered an ideal method. Numerous studies have shown that Pseudomonas aeruginosa is a powerful platform for the remediation of environmental pollution with organic chemicals due to its diverse metabolic networks and its ability to secrete biosurfactants to make hydrophobic substrates more bioavailable, thereby facilitating degradation. In this paper, the mechanisms and methods of the bioremediation of environmental organic pollutants (EOPs) by P. aeruginosa are reviewed. The challenges of current studies are highlighted, and new strategies for future research are prospected. Metabolic pathways and critical enzymes must be further deciphered, which is significant for the construction of a bioremediation platform based on this powerful organism.

Designing biodegradable alternatives to commodity polymers

The development and widespread adoption of commodity polymers changed societal landscapes on a global scale. Without the everyday materials used in packaging, textiles, construction and medicine, our lives would be unrecognisable. Through decades of use, however, the environmental impact of waste plastics has become grimly apparent, leading to sustained pressure from environmentalists, consumers and scientists to deliver replacement materials. The need to reduce the environmental impact of commodity polymers is beyond question, yet the reality of replacing these ubiquitous materials with sustainable alternatives is complex. In this tutorial review, we will explore the concepts of sustainable design and biodegradability, as applied to the design of synthetic polymers intended for use at scale. We will provide an overview of the potential biodegradation pathways available to polymers in different environments, and highlight the importance of considering these pathways when designing new materials. We will identify gaps in our collective understanding of the production, use and fate of biodegradable polymers: from identifying appropriate feedstock materials, to considering changes needed to production and recycling practices, and to improving our understanding of the environmental fate of the materials we produce. We will discuss the current standard methods for the determination of biodegradability, where lengthy experimental timescales often frustrate the development of new materials, and highlight the need to develop better tools and models to assess the degradation rate of polymers in different environments.

Enzymatic polyethylene biorecycling: Confronting challenges and shaping the future

Polyethylene (PE) is a widely used plastic known for its resistance to biodegradation, posing a significant environmental challenge. Recent advances have shed light on microorganisms and insects capable of breaking down PE and identified potential PE-degrading enzymes (PEases), hinting at the possibility of PE biorecycling. Research on enzymatic PE degradation is still in its early stages, especially compared to the progress made with polyethylene terephthalate (PET). While PET hydrolases have been extensively studied and engineered for improved performance, even the products of PEases remain mostly undefined. This Perspective analyzes the current state of enzymatic PE degradation research, highlighting obstacles in the search for bona fide PEases and suggesting areas for future exploration. A critical challenge impeding progress in this field stems from the inert nature of the C-C and C-H bonds of PE. Furthermore, breaking down PE into small molecules using only one monofunctional enzyme is theoretically impossible. Overcoming these obstacles requires identifying enzymatic pathways, which can be facilitated using emerging technologies like omics, structure-based design, and computer-assisted engineering of enzymes. Understanding the mechanisms underlying PE enzymatic biodegradation is crucial for research progress and for identifying potential solutions to the global plastic pollution crisis.

Recent advances in biodegradation of emerging contaminants - microplastics (MPs): Feasibility, mechanism, and future prospects

Plastics have become an essential part of life. When it enters the environment, it migrates and breaks down to form smaller size fragments, which are called microplastics (MPs). Compared with plastics, MPs are detrimental to the environment and pose a severe threat to human health. Bioremediation is being recognized as the most environmentally friendly and cost-effective degradation technology for MPs, but knowledge about the biodegradation of MPs is limited. This review explores the various sources of MPs and their migration behavior in terrestrial and aquatic environments. Among the existing MPs removal technologies, biodegradation is considered to be the best removal strategy to alleviate MPs pollution. The biodegradation potential of MPs by bacteria, fungi and algae is discussed. Biodegradation mechanisms such as colonization, fragmentation, assimilation, and mineralization are presented. The effects of MPs characteristics, microbial activity, environmental factors and chemical reagents on biodegradation are analyzed. The susceptibility of microorganisms to MPs toxicity might lead to decreased degradation efficiency, which is also elaborated. The prospects and challenges of biodegradation technologies are discussed. Eliminating prospective bottlenecks is necessary to achieve large-scale bioremediation of MPs-polluted environment. This review provides a comprehensive summary of the biodegradability of MPs, which is crucial for the prudent management of plastic waste.

An integrated metagenomic model to uncover the cooperation between microbes and magnetic biochar during microplastics degradation in paddy soil

The free radicals released from the advanced oxidation processes can enhance microplastics degradation, however, the existence of microbes acting synergistically in this process is still uncertain. In this study, magnetic biochar was used to initiate the advanced oxidation process in flooded soil. paddy soil was contaminated with polyethylene and polyvinyl chloride microplastics in a long-term incubation experiment, and subsequently subjected to bioremediation with biochar or magnetic biochar. After incubation, the total organic matter present in the samples containing polyvinyl chloride or polyethylene, and treated with magnetic biochar, significantly increased compared to the control. In the same samples there was an accumulation of "UVA humic" and "protein/phenol-like" substances. The integrated metagenomic investigation revealed that the relative abundance of some key genes involved in fatty acids degradation and in dehalogenation changed in different treatments. Results from genome-centric investigation suggest that a Nocardioides species can cooperate with magnetic biochar in the degradation of microplastics. In addition, a species assigned to the Rhizobium taxon was identified as a candidate in the dehalogenation and in the benzoate metabolism. Overall, our results suggest that cooperation between magnetic biochar and some microbial species involved in microplastic degradation is relevant in determining the fate of microplastics in soil.

Increasing concentration of pure micro- and macro-LDPE and PP plastic negatively affect crop biomass, nutrient cycling, and microbial biomass

Over the last 50 years, the intense use of agricultural plastic in the form of mulch films has led to an accumulation of plastic in soil, creating a legacy of plastic in agricultural fields. Plastic often contains additives, however it is still largely unknown how these compounds affect soil properties, potentially influencing or masking effects of the plastic itself. Therefore, the aim of this study was to investigate the effects of pure plastics of varying sizes and concentrations, to improve our understanding of plastic-only interactions within soil-plant mesocosms. Maize (Zea mays L.) was grown over eight weeks following the addition of micro and macro low-density polyethylene and polypropylene at increasing concentrations (equivalent to 1, 10, 25, and 50 years mulch film use) and the effects of plastic on key soil and plant properties were measured. We found the effect of both macro and microplastic on soil and plant health is negligible in the short-term (1 to <10 years). However, ≥ 10 years of plastic application for both plastic types and sizes resulted in a clear negative effect on plant growth and microbial biomass. This study provides vital insight into the effect of both macro and microplastics on soil and plant properties.

Responses of gut microbiomes to commercial polyester polymer biodegradation in Tenebrio molitor Larvae

Polyethylene terephthalate (PET) is a mass-produced fossil-based plastic polymer that contributes to catastrophic levels of plastic pollution. Here we demonstrated that Tenebrio molitor (mealworms) was capable of rapidly biodegrading two commercial PET resins (microplastics) with respective weight-average molecular weight (M_w) of 39.33 and 29.43 kDa and crystallinity of 22.8 ± 3.06% and 18 ± 2.25%, resulting in an average mass reduction of 71.03% and 73.28% after passage of their digestive tract, and respective decrease by 9.22% and 11.36% in M_w of residual PET polymer in egested frass. Sequencing of 16 S rRNA gene amplicons of gut microbial communities showed that dominant bacterial genera were enriched and associated with PET degradation. Also, PICRUSt prediction exhibited that oxidases (monooxygenases and dioxygenases), hydrolases (cutinase, carboxylesterase and chitinase), and PET metabolic enzymes, and chemotaxis related functions were up-regulated in the PET-fed larvae. Additionally, metabolite analyses revealed that PET uptake caused alterations of stress response and plastic degradation related pathways, and lipid metabolism pathways in the T. molitor larvae could be reprogrammed when the larvae fed on PET. This study provides new insights into gut microbial community adaptation to PET diet under nutritional stress (especially nitrogen deficiency) and its contribution to PET degradation.

Isolation of a polyethylene-degrading bacterium, Acinetobacter guillouiae, using a novel screening method based on a redox indicator

Plastic, a polymer synthesized from petrochemicals, is used worldwide. However, natural degradation of plastic is difficult, causing environmental pollution, with microplastics posing a serious threat to human health. In this study, we aimed to use a new screening method based on the oxidation-reduction indicator, 2,6-dichlorophenolindophenol, to isolate a polyethylene-degrading bacterium, Acinetobacter guillouiae, from insect larvae. Plastic-degrading strains are identified by the color change in the redox indicator from blue to colorless as plastic metabolism occurs. Polyethylene biodegradation by A. guillouiae was verified through weight loss, surface erosion, physiological evidence, and chemical changes on the plastic surface. In addition, we analyzed the characteristics of hydrocarbon metabolism in polyethylene-degrading bacteria. Results suggested that alkane hydroxylation and alcohol dehydrogenation were key steps in polyethylene degradation. This novel screening method will pave the way for high-throughput screening of polyethylene-degrading microorganisms and extending its application to other types of plastics may potentially address plastic pollution.

Insights into characteristics of white rot fungus during environmental plastics adhesion and degradation mechanism of plastics

Since the 1980s, plastic waste in the environment has been accumulating, and little is known about fungi biodegradation, especially in dry environments. Therefore, the research on plastic degradation technology is urgent. In this study, we demonstrated that Phanerochaete chrysosporium (P. chrysposporium), a typical species of white rot fungi, could react as a highly efficient biodegrader of polylactic acid (PLA), and 34.35 % of PLA degradation was obtained during 35-day incubation. A similar mass loss of 19.71 % could be achieved for polystyrene (PS) degradation. Here, we presented the visualization of the plastic deterioration process and their negative reciprocal on cell development, which may be caused by the challenge of using PS as a substrate. The RNA-seq analysis indicated that adaptations in energy metabolism and cellular defense were downregulated in the PS group, while lipid synthesis was upregulated in the PLA-treated group. Possible differentially expressed genes (DEG) of plastic degradation, such as hydrophobic proteins, lignin peroxidase (LiP), manganese peroxidase (MnP) and laccase (Lac), Cytochrome P450 (CYP450), and genes involved in styrene or benzoic acid degradation pathways have been recorded, and we proposed a PS degradation pathway.

Enzymes' Power for Plastics Degradation

Plastics are everywhere in our modern way of living, and their production keeps increasing every year, causing major environmental concerns. Nowadays, the end-of-life management involves accumulation in landfills, incineration, and recycling to a lower extent. This ecological threat to the environment is inspiring alternative bio-based solutions for plastic waste treatment and recycling toward a circular economy. Over the past decade, considerable efforts have been made to degrade commodity plastics using biocatalytic approaches. Here, we provide a comprehensive review on the recent advances in enzyme-based biocatalysis and in the design of related biocatalytic processes to recycle or upcycle commodity plastics, including polyesters, polyamides, polyurethanes, and polyolefins. We also discuss scope and limitations, challenges, and opportunities of this field of research. An important message from this review is that polymer-assimilating enzymes are very likely part of the solution to reaching a circular plastic economy.

Biodegradation of MC-LR and its key bioactive moiety Adda by Sphingopyxis sp. YF1: Comprehensive elucidation of the mechanisms and pathways

Microcystins (MCs) are harmful to the ecology and public health. Some bacteria can degrade MCs into Adda, but few can destroy Adda. Adda is the key bioactive moiety of MCs and mainly contributes to hepatotoxicity. We had previously isolated an indigenous novel bacterial strain named Sphingopyxis sp. YF1 that can efficiently degrade MCs and its key bioactive moiety Adda, but the mechanisms remained unknown. Here, the biodegradation mechanisms and pathways of Adda were systematically investigated using multi-omics analysis, mass spectrometry and heterologous expression. The transcriptomic and metabolomic profiles of strain YF1 during Adda degradation were revealed for the first time. Multi-omics analyses suggested that the fatty acid degradation pathway was enriched. Specifically, the expression of genes encoding aminotransferase, beta oxidation (β-oxidation) enzymes and phenylacetic acid (PAA) degradation enzymes were significantly up-regulated during Adda degradation. These enzymes were further proven to play important roles in the biodegradation of Adda. Simultaneously, some novel potential degradation products of Adda were identified successfully, including 7‑methoxy-4,6-dimethyl-8-phenyloca-2,4-dienoic acid (C₁₇H₂₂O₃), 2-methyl-3‑methoxy-4-phenylbutyric acid (C₁₂H₁₆O₃) and phenylacetic acid (PAA, C₈H₈O₂). In summary, the Adda was converted into PAA through aminotransferase and β-oxidation enzymes, then the PAA was further degraded by PAA degradation enzymes, and finally to CO₂ via the tricarboxylic acid cycle. This study comprehensively elucidated the novel MC-LR biodegradation mechanisms, especially the new enzymatic pathway of Adda degradation. These findings provide a new perspective on the applications of microbes in the MCs polluted environment.

Assembly strategies for polyethylene-degrading microbial consortia based on the combination of omics tools and the "Plastisphere"

Numerous microorganisms and other invertebrates that are able to degrade polyethylene (PE) have been reported. However, studies on PE biodegradation are still limited due to its extreme stability and the lack of explicit insights into the mechanisms and efficient enzymes involved in its metabolism by microorganisms. In this review, current studies of PE biodegradation, including the fundamental stages, important microorganisms and enzymes, and functional microbial consortia, were examined. Considering the bottlenecks in the construction of PE-degrading consortia, a combination of top-down and bottom-up approaches is proposed to identify the mechanisms and metabolites of PE degradation, related enzymes, and efficient synthetic microbial consortia. In addition, the exploration of the plastisphere based on omics tools is proposed as a future principal research direction for the construction of synthetic microbial consortia for PE degradation. Combining chemical and biological upcycling processes for PE waste could be widely applied in various fields to promote a sustainable environment.

Microbial strategies for degradation of microplastics generated from COVID-19 healthcare waste

COVID-19 pandemic has led to the generation of massive plastic wastes, comprising of onetime useable gloves, masks, tissues, and other personal protective equipment (PPE). Recommendations for the employ of single-use disposable masks made up of various polymeric materials like polyethylene, polyurethane, polyacrylonitrile, and polypropylene, polystyrene, can have significant aftermath on environmental, human as well as animal health. Improper disposal and handling of healthcare wastes and lack of proper management practices are creating serious health hazards and an extra challenge for the local authorities designated for management of solid waste. Most of the COVID-19 medical wastes generated are now being treated by incineration which generates microplastic particles (MPs), dioxin, furans, and various toxic metals, such as cadmium and lead. Moreover, natural degradation and mechanical abrasion of these wastes can lead to the generation of MPs which cause a serious health risk to living beings. It is a major threat to aquatic lives and gets into foods subsequently jeopardizing global food safety. Moreover, the presence of plastic is also considered a threat owing to the increased carbon emission and poses a profound danger to the global food chain. Degradation of MPs by axenic and mixed culture microorganisms, such as bacteria, fungi, microalgae etc. can be considered an eco-sustainable technique for the mitigation of the microplastic menace. This review primarily deals with the increase in microplastic pollution due to increased use of PPE along with different disinfection methods using chemicals, steam, microwave, autoclave, and incineration which are presently being employed for the treatment of COVID-19 pandemic-related wastes. The biological treatment of the MPs by diverse groups of fungi and bacteria can be an alternative option for the mitigation of microplastic wastes generated from COVID-19 healthcare waste.

A stable isotope assay with 13C-labeled polyethylene to investigate plastic mineralization mediated by Rhodococcus ruber

Methods that unambiguously prove microbial plastic degradation and allow for quantification of degradation rates are necessary to constrain the influence of microbial degradation on the marine plastic budget. We developed an assay based on stable isotope tracer techniques to determine microbial plastic mineralization rates in liquid medium on a lab scale. For the experiments, ¹³C-labeled polyethylene (¹³C-PE) particles (irradiated with UV-light to mimic exposure of floating plastic to sunlight) were incubated in liquid medium with Rhodococcus ruber as a model organism for proof of principle. The transfer of ¹³C from ¹³C-PE into the gaseous and dissolved CO₂ pools translated to microbially mediated mineralization rates of up to 1.2 % yr^-1 of the added PE. After incubation, we also found highly ¹³C-enriched membrane fatty acids of R. ruber including compounds involved in cellular stress responses. We demonstrated that isotope tracer techniques are a valuable tool to detect and quantify microbial plastic degradation.

Mycobacteriaceae Mineralizes Micropolyethylene in Riverine Ecosystems

Microplastic (MP) contamination is a serious global environmental problem. Plastic contamination has attracted extensive attention during the past decades. While physiochemical weathering may influence the properties of MPs, biodegradation by microorganisms could ultimately mineralize plastics into CO₂. Compared to the well-studied marine ecosystems, the MP biodegradation process in riverine ecosystems, however, is less understood. The current study focuses on the MP biodegradation in one of the world's most plastic contaminated rivers, Pearl River, using micropolyethylene (mPE) as a model substrate. Mineralization of ¹³C-labeled mPE into ¹³CO₂ provided direct evidence of mPE biodegradation by indigenous microorganisms. Several Actinobacteriota genera were identified as putative mPE degraders. Furthermore, two Mycobacteriaceae isolates related to the putative mPE degraders, Mycobacterium sp. mPE3 and Nocardia sp. mPE12, were retrieved, and their ability to mineralize ¹³C-mPE into ¹³CO₂ was confirmed. Pangenomic analysis reveals that the genes related to the proposed mPE biodegradation pathway are shared by members of Mycobacteriaceae. While both Mycobacterium and Nocardia are known for their pathogenicity, these populations on the plastisphere in this study were likely nonpathogenic as they lacked virulence factors. The current study provided direct evidence for MP mineralization by indigenous biodegraders and predicted their biodegradation pathway, which may be harnessed to improve bioremediation of MPs in urban rivers.

Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future

Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.

Genome-Based Exploration of Rhodococcus Species for Plastic-Degrading Genetic Determinants Using Bioinformatic Analysis

Plastic polymer waste management is an increasingly prevalent issue. In this paper, Rhodococcus genomes were explored to predict new plastic-degrading enzymes based on recently discovered biodegrading enzymes for diverse plastic polymers. Bioinformatics prediction analyses were conducted using 124 gene products deriving from diverse microorganisms retrieved from databases, literature data, omic-approaches, and functional analyses. The whole results showed the plastic-degrading potential of Rhodococcus genus. Among the species with high plastic-degrading potential, R. erythropolis, R. equi, R. opacus, R. qingshengii, R. fascians, and R. rhodochrous appeared to be the most promising for possible plastic removal. A high number of genetic determinants related to polyester biodegradation were obtained from different Rhodococcus species. However, score calculation demonstrated that Rhodococcus species (especially R. pyridinivorans, R. qingshengii, and R. hoagii) likely possess PE-degrading enzymes. The results identified diverse oxidative systems, including multicopper oxidases, alkane monooxygenases, cytochrome P450 hydroxylases, para-nitrobenzylesterase, and carboxylesterase, and they could be promising reference sequences for the biodegradation of plastics with C-C backbone, plastics with heteroatoms in the main chain, and polyesters, respectively. Notably, the results of this study could be further exploited for biotechnological applications in biodegradative processes using diverse Rhodococcus strains and through catalytic reactions.

Polyvinyl chloride degradation by a bacterium isolated from the gut of insect larvae

Evidence for microbial degradation of polyvinyl chloride (PVC) has previously been reported, but little is known about the degrading strains and enzymes. Here, we isolate a PVC-degrading bacterium from the gut of insect larvae and shed light on the PVC degradation pathway using a multi-omic approach. We show that the larvae of an insect pest, Spodoptera frugiperda, can survive by feeding on PVC film, and this is associated with enrichment of Enterococcus, Klebsiella and other bacteria in the larva's gut microbiota. A bacterial strain isolated from the larval intestine (Klebsiella sp. EMBL-1) is able to depolymerize and utilize PVC as sole energy source. We use genomic, transcriptomic, proteomic, and metabolomic analyses to identify genes and proteins potentially involved in PVC degradation (e.g., catalase-peroxidase, dehalogenases, enolase, aldehyde dehydrogenase and oxygenase), and propose a PVC biodegradation pathway. Furthermore, enzymatic assays using the purified catalase-peroxidase support a role in PVC depolymerization.

Microbial communities on plastic particles in surface waters differ from subsurface waters of the North Pacific Subtropical Gyre

The long-term fate of plastics in the ocean and their interactions with marine microorganisms remain poorly understood. In particular, the role of sinking plastic particles as a transport vector for surface microbes towards the deep sea has not been investigated. Here, we present the first data on the composition of microbial communities on floating and suspended plastic particles recovered from the surface to the bathypelagic water column (0-2000 m water depth) of the North Pacific Subtropical Gyre. Microbial community composition of suspended plastic particles differed from that of plastic particles afloat at the sea surface. However, in both compartments, a diversity of hydrocarbon-degrading bacteria was identified. These findings indicate that microbial community members initially present on floating plastics are quickly replaced by microorganisms acquired from deeper water layers, thus suggesting a limited efficiency of sinking plastic particles to vertically transport microorganisms in the North Pacific Subtropical Gyre.