Characteristics and polyethylene biodegradation function of a novel cold-adapted bacterial laccase from Antarctic sea ice psychrophile Psychrobacter sp. NJ228

Comparative analysis of Polyethylene-Degrading Laccases: Redox Properties and Enzyme-Polyethylene Interaction Mechanism

Laccases that oxidize low-density polyethylene (LDPE) represent a promising strategy for bioremediation purposes. To rationalize or optimize their PE-oxidative activity, two fundamental factors must be considered: the enzyme's redox potential and its binding affinity/mode towards LDPE. Indeed, a stable laccase-PE complex may facilitate a thermodynamically unfavorable electron transfer, even without redox mediators. In this study, we compared the redox potential and the LDPE-binding properties of three different PE-oxidizing laccases: a fungal high-redox potential laccase from Trametes versicolor, a bacterial low-redox potential laccase from Bacillus subtilis, and the recently characterized LMCO2 from Rhodococcus opacus R7. First we found that LMCO2 is a low-potential laccase (E°=413 mV), as reported in other bacterial variants. Using computational tools, we simulated the interactions of these laccases with a large LDPE model and highlighted the key role of hydrophobic residues surrounding the T1 site. Notably, a methionine-rich loop in LMCO2 appears to enhance the formation of a stable complex with LDPE, potentially facilitating electron transfer. This study underscores the necessity for comprehensive computational strategies to analyze enzyme-polymer interactions beyond simplistic models, uncovering critical binding determinants and informing future mutagenesis experiments, in order to enhance laccase performance and rationalize variations in enzymatic activity.

Biodegradation characterization and mechanism of low-density polyethylene by the enriched mixed-culture from plastic-contaminated soil

Plastic pollution poses significant ecological and health risks. In this study, we enriched microbial consortia from plastic-contaminated soil capable of degrading low-density polyethylene (LDPE) film over a 28-day incubation period. Using two kinds of enriched cultures, the mean film weight loss rate (WLR) of 0.27 ± 0.04 % (p < 0.01) was 9 times higher than the control. Scanning electron microscopy (SEM) revealed a average hole occurrence area of 0.67 ± 0.11 μm2 in the topmost sample, while the control had no change. Fourier transform infrared (FTIR) revealed specific changes in hydrophilicity (increased by 5.70 ± 0.02 times) and crystallinity (decreased by 15.73 ± 3.26 %). Meanwhile, FTIR analyses including peak occurrence at 3741 cm-1, carbonyl index and Lambert-Beer law calculations revealed moisture infiltration and predominant aldehyde carbonyl formation (88.69 % in total carbonyl). The results of high-throughput sequencing indicated Brevibacillus, Bacillus and Sporosarcina were dominate genera in the mixed-cultures, and PICRUSt2 implied they could use LDPE as the sole carbon source. Our study aims to provided theoretical basis driving plastic degradation and to mitigate plastic pollution based on microbial resource development.

Metagenomic investigation of bacterial laccases in a straw-amended soil

Background

Bacterial laccases play a crucial role in the degradation of lignin and the turnover of soil organic matter. Their advantageous properties make them highly suitable for a wide range of industrial applications. However, the limited identification of these potential enzymes has impeded their full utilization. The straw-amended soil provides materials for the development of bacterial laccases.

Methods

Metagenomic sequencing of a straw-amended soil was conducted to explore novel bacterial laccases. The putative bacterial laccases were then screened using profile hidden Markov models for further analysis. The most abundant gene, lacS1, was heterologously expressed in Escherichia coli and the recombinant laccase was purified for enzymatic characterization.

Results

A total of 322 putative bacterial laccases were identified in the straw-amended soil. Among them, 45 sequences had less than 30% identity to any entries in the Carbohydrate-Active Enzyme database and only 4.66% were more than 75% similar to proteins in the NCBI environmental database, exhibiting their novelty. These enzymes were found across various bacterial orders, demonstrating substantial diversity. Phylogenetic analysis revealed a number of the bacterial laccase sequences clustered with homologs characterized by favorable enzymatic properties. Five full-length representative bacterial laccase genes were obtained by modified thermal asymmetric interlaced PCR. The laccase activity of lacS1 was validated. It was a mesophilic enzyme with alkaline stability and halotolerance, indicating its promise for industrial applications.

Implications

These findings highlight novel bacterial laccase resources with potential for industrial applications and enzyme engineering.

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.

Microbial degradation of polyethylene polymer: current paradigms, challenges, and future innovations

Polyethylene (PE) is the second most commonly used plastic worldwide, mainly used to produce single-use items such as bags and bottles. Its significant resistance to natural biodegradation results in the accumulation of PE in landfills, leading to various ecological and toxicological consequences. Despite extensive research on the microbial degradation of PE, achieving complete biodegradation remains a challenge. Comparing experimental outcomes is complicated by the diverse array of microbes involved in PE biodegradation, variations in culture conditions, and differences in assessment tools. This review discusses the critical hurdles in PE biodegradation experiments, including the chemical complexity of PE substrates and the challenges of isolating effective microbes and forming stable consortia. The review also delves into the difficulties in accurately assessing microbial metabolic activity and understanding the biochemical pathways involved in PE degradation. Furthermore, it addresses the pressing issues of metabolic byproducts, slow degradation rates, scalability concerns, and the challenges in measuring biodegradation levels effectively. In addition to outlining the technical challenges associated with PE experiments, this review offers recommendations for future research directions to enhance PE biodegradation outcomes. Overcoming these challenges and implementing the proposed future strategies will improve the reliability, comparability, and practicality of current PE biodegradation experiments, ultimately contributing to better comprehension and management of PE waste in the environment.

Review of key issues and potential strategies in bio-degradation of polyolefins

Polyolefins are the most widely used plastic product and a major contributor to white pollution. Currently, studies on polyolefin degradation systems are mainly focused on microorganisms and some redox enzymes, and there is a serious black-box phenomenon. The use of polyolefin-degrading enzymes is limited because of the small number of enzymes; in addition, the catalytic efficiency of these enzymes is poor and their catalytic mechanism is unclear, which leads to the incomplete degradation of polyolefins to produce microplastics. In this review, three questions are addressed: the generation and degradation of action targets that promote the degradation of polyolefins, the different modes by which enzymes bind substrates and their application scenarios, and possible multienzyme systems in a unified system. This review will be valuable for mining or modifying polyolefin degradation enzymes and constructing polyolefins degradation systems and may provide novel ideas and opportunities for polyolefin degradation.

A Novel Cold-Adapted Nitronate Monooxygenase from Psychrobacter sp. ANT206: Identification, Characterization and Degradation of 2-Nitropropane at Low Temperature

Aliphatic nitro compounds cause environmental pollution by being discharged into water with industrial waste. Biodegradation needs to be further explored as a green and pollution-free method of environmental remediation. In this study, we successfully cloned a novel nitronate monooxygenase gene (psnmo) from the genomic DNA library of Psychrobacter sp. ANT206 and investigated its ability to degrade 2-nitropropane (2-NP). Homology modeling demonstrated that PsNMO had a typical I nitronate monooxygenase catalytic site and cold-adapted structural features, such as few hydrogen bonds. The specific activity of purified recombinant PsNMO (rPsNMO) was 97.34 U/mg, rPsNMO exhibited thermal instability and reached maximum catalytic activity at 30 °C. Moreover, rPsNMO was most active in 1.5 M NaCl and remained at 104% of its full activity in 4.0 M NaCl, demonstrating its significant salt tolerance. Based on this finding, a novel bacterial cold-adapted enzyme was obtained in this work. Furthermore, rPsNMO protected E. coli BL21 (DE3)/pET28a(+) from the toxic effects of 2-NP at 30 °C because the 2-NP degradation rate reached 96.1% at 3 h and the final product was acetone. These results provide a reliable theoretical basis for the low-temperature degradation of 2-NP by NMO.

Isolation of marine polyethylene (PE)-degrading bacteria and its potential degradation mechanisms

Microbial degradation of polyethylene (PE) offers a promising solution to plastic pollution in the marine environment, but research in this field is limited. In this study, we isolated a novel marine strain of Pseudalkalibacillus sp. MQ-1 that can degrade PE. Scanning electron microscopy and water contact angle results showed that MQ-1 could adhere to PE films and render them hydrophilic. Analyses using X-ray diffraction, fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy showed a decrease in relative crystallinity, the appearance of new functional groups and an increase in the oxygen-to‑carbon ratio of the PE films, making them more susceptible to degradation. The results of gel permeation chromatography and liquid chromatography-mass spectrometry indicated the depolymerization of the long PE chains, with the detection of an intermediate, decanediol. Furthermore, genome sequencing was employed to investigate the underlying mechanisms of PE degradation. The results of genome sequencing analysis identified the genes associated with PE degradation, including cytochrome P450, alcohol dehydrogenase, and aldehyde dehydrogenase involved in the oxidative reaction, monooxygenase related to ester bond formation, and esterase associated with ester bond cleavage. In addition, enzymes involved in fatty acid metabolism and intracellular transport have been identified, collectively providing insights into the metabolic pathway of PE degradation.

An integrated approach for plastic polymer degradation by the gut bacterial resident of superworm, Zophobas morio (Coleoptera:Tenebrionidae)

The potential of superworm to remove certain plastic polymers has recently been noted. In this study, aerobic bacterial strains were isolated from the gut of Zophobas morio larvae which were fed with polyethylene (PE), polyethylene terephthalate (PET), polypropylene (PP), and polystyrene (PS) polymers. Strains P2 (Leminorella), P6 (Bacillus), P9 (Bacillus), and P5 (Citrobacter) were associated with the highest PS (2.7%), PP (1.3%), PET (1.1%), and PE (0.42%) weight loss after 28 days, respectively. Pretreatments including thermal treatment (80 °C for 10 days), weathering (4 months in the free environment), and nitric and sulfuric acids (1 N, 10 days) improved the degradation of PE (1.3%), PET (1.9%), PP (5.2%), and PS (8.3%) by the same strains, respectively. Further analyses on the PS degradation by Leminorella sp. P2 revealed acid pretreatment promoted the formation of the C = C, C = O, and O-H functional groups. Surface irregularities, as well as a 3.6-fold increase in surface roughness, were observed in the PS film subjected to biodegradation. The contact angle dropped from 98.4° to 42.2° following the biodegradation. Bacterial depolymerization was confirmed by the 8.7% and 3.4% reduction of Mn and Mw and the change in polydispersity from 1.65 to 1.75. The results suggest that Zophobas morio microbiota in combination with abiotic pretreatment can be considered for plastic waste management.

Enterobacter cloacae-mediated polymer biodegradation: in-silico analysis predicts broad spectrum degradation potential by Alkane monooxygenase

Plastic pollution poses a significant environmental challenge. In this study, the strain Enterobacter cloacae O5-E, a bacterium displaying polyethylene-degrading capabilities was isolated. Over a span of 30 days, analytical techniques including x-ray diffractometry, scanning electron microscopy, optical profilometry, hardness testing and mass spectrometric analysis were employed to examine alterations in the polymer. Results revealed an 11.48% reduction in crystallinity, a 50% decrease in hardness, and a substantial 25-fold increase in surface roughness resulting from the pits and cracks introduced in the polymer by the isolate. Additionally, the presence of degradational by-products revealed via gas chromatography ascertains the steady progression of degradation. Further, recognizing the pivotal role of alkane monooxygenase in plastic degradation, the study expanded to detect this enzyme in the isolate molecularly. Molecular docking studies were conducted to assess the enzyme's affinity with various polymers, demonstrating notable binding capability with most polymers, especially with polyurethane (- 5.47 kcal/mol). These findings highlight the biodegradation potential of Enterobacter cloacae O5-E and the crucial involvement of alkane monooxygenase in the initial steps of the degradation process, offering a promising avenue to address the global plastic pollution crisis.

Enhanced degradation of phenolic pollutants by a novel cold-adapted laccase from Peribacillus simplex

Laccase (EC 1.10.3.2), as eco-friendly biocatalysts, holds immense potential for sustainable applications across various environmental and industrial sectors. Despite the growing interest, the exploration of cold-adapted laccases, especially their unique properties and applicability, remains limited. In this study, we have isolated, cloned, expressed, and purified a novel laccase from Peribacillus simplex (GenBank: PP430751), which was derived from permafrost layer. The recombinant laccase (PsLac) exhibited optimal activity at 30 °C and a pH optimum of 3.5. Remarkably, PsLac exhibited remarkable stability in the presence of organic solvents, with its enzyme activity increasing by 20 % after being incubated in a 30 % trichloromethane solution for 12 h, compared to its initial activity. Furthermore, the enzyme preserved 100 % of its activity after undergoing eight freeze-thaw cycles. Notably, the catalytic center of PsLac contains Zn2+ instead of the typically observed Cu2+ found in other laccases, and metal-ion substitution experiments raised the catalytic efficiency to 3-fold when Zn2+ was replaced with Fe2+. Additionally, PsLac has demonstrated a proficient ability to degrade phenolic pollutants, such as hydroquinone, even at a low temperature of 16 °C, positioning it as a promising candidate for environmental bioremediation and contributing to cleaner production processes.

Chemo-Enzymatic Depolymerization of Functionalized Low-Molecular-Weight Polyethylene

Polyethylene (PE) is the most commonly used plastic type in the world, contributing significantly to the plastic waste crisis. Microbial degradation of PE in natural environments is unlikely due to its inert saturated carbon-carbon backbones, which are difficult to break down by enzymes, challenging the development of a biocatalytic recycling method for PE waste. Here, we demonstrated the depolymerization of low-molecular-weight (LMW) PE using an enzyme cascade that included a catalase-peroxidase, an alcohol dehydrogenase, a Baeyer Villiger monooxygenase, and a lipase after the polymer was chemically pretreated with m-chloroperoxybenzoic acid (mCPBA) and ultrasonication. In a preparative experiment with gram-scale pretreated polymers, GC-MS and weight loss determinations confirmed ~27 % polymer conversion including the formation of medium-size functionalized molecules such as ω-hydroxycarboxylic acids and α,ω-carboxylic acids. Additional analyses of LMWPE-nanoparticles using AFM showed that enzymatic depolymerization reduced the sizes of these mCPBA- and enzyme-treated LMWPE-nanoparticles. This multi-enzyme catalytic concept with distinct chemical steps represents a unique starting point for future development of bio-based recycling methods for polyolefin waste.

Ancestral sequence reconstruction of the prokaryotic three-domain laccases for efficiently degrading polyethylene

Biodegradation of polyethylene (PE) plastics is environmentally friendly. To obtain the laccases that can efficiently degrade PE plastics, we generated 9 ancestral laccases from 23 bacterial three-domain laccases through ancestral sequence reconstruction. The optimal temperatures of the ancestral laccases were between 60 °C-80 °C, while their optimal pHs were at 3.0 or 4.0. Without substrate pretreatment and mediator addition, all the ancestral laccases can degrade low-density polyethylene (LDPE) films at pH 7.0 and 60 °C. Among them, Anc52, which shared low sequence identity (18 %-41.7 %) with the reported PE-degrading laccases, was the most effective for LDPE degradation. After the catalytic reactions at 90 °C for 14 h, Anc52 (0.2 mg/mL) induced clear wrinkles and deep pits on the PE film surface detected by scanning electron microscope, and its carbonyl and hydroxyl indices reached 2.08 and 2.42, respectively. Then, we identified the residues 203 and 288 critical for PE degradation through site-directed mutation on Anc52. Moreover, Anc52 be activated by heat treatment (60 °C and 90 °C) at pH 7.0, which gave it a high catalytic efficiency (kcat/Km= 191.73 mM-1·s-1) and thermal stability (half-life at 70 °C = 13.70 h). The ancestral laccases obtained here could be good candidates for PE biodegradation.

Hotspots lurking underwater: Insights into the contamination characteristics, environmental fates and impacts on biogeochemical cycling of microplastics in freshwater sediments

The widespread presence of microplastics (MPs) in aquatic environments has become a significant concern, with freshwater sediments acting as terminal sinks, rapidly picking up these emerging anthropogenic particles. However, the accumulation, transport, degradation and biochemical impacts of MPs in freshwater sediments remain unresolved issues compared to other environmental compartments. Therefore, this paper systematically revealed the spatial distribution and characterization information of MPs in freshwater (rivers, lakes, and estuaries) sediments, in which small-size (<1 mm), fibers, transparent, polyethylene (PE), and polypropylene (PP) predominate, and the average abundance of MPs in river sediments displayed significant heterogeneity compared to other matrices. Next, the transport kinetics and drivers of MPs in sediments are summarized, MPs transport is controlled by the particle diversity and surrounding environmental variability, leading to different migration behaviors and transport efficiencies. Also emphasized the spatio-temporal evolution of MPs degradation processes and biodegradation mechanisms in sediments, different microorganisms can depolymerize high molecular weight polymers into low molecular weight biodegradation by-products via secreting hydrolytic enzymes or redox enzymes. Finally, discussed the ecological impacts of MPs on microbial-nutrient coupling in sediments, MPs can interfere with the ecological balance of microbially mediated nutrient cycling by altering community networks and structures, enzyme activities, and nutrient-related functional gene expressions. This work aims to elucidate the plasticity characteristics, fate processes, and potential ecological impact mechanisms of MPs in freshwater sediments, facilitating a better understanding of environmental risks of MPs in freshwater sediments.

Characterization of Potential Plastic-Degradation Enzymes from Marine Bacteria

Polyethylene terephthalate (PET) and polyethylene (PE) are prominent polymer materials that comprise a significant portion of commercial plastic waste. Their durability and slow degradation rate have resulted in significant accumulation of plastic on Earth. In a recent study, macrotranscriptomic profiling of a reconstituted marine bacterial community identified 10 putative enzymes capable of directly acting on PE or PET (PEases or PETases). Among these enzymes, three recombinant proteins were reported to possess PE degradation activity. To select potential plastic degrading enzyme candidates for protein engineering efforts, we expressed and purified eight out of the 10 candidates, excluding two due to poor expression and/or solubility. Notably, several candidate proteins displayed significant esterase activity on p-nitrophenyl butyrate and exhibited unexpected thermostability despite their marine origin. Additionally, we observed dose- and time-dependent hydrolytic activity on the PET trimer substrate. Structural analysis and mutagenesis of a candidate protein confirmed the presence of catalytic triad residues, classifying it as an esterase. Furthermore, we elucidated the structural importance of the two disulfide bonds. Through point mutation experiments, we observed an enhanced hydrolytic activity of a selected enzyme candidate on PET nanoparticles. Our findings challenge the classification of the enzymes directly acting on PE and highlight the significance and complexity of validating PE degradation enzymes identified through metagenomic analysis.

Synergistic functional activity of a landfill microbial consortium in a microplastic-enriched environment

Plastic pollution of the soil is a global issue of increasing concern, with far-reaching impact on the environment and human health. To fully understand the medium- and long-term impact of plastic dispersal in the environment, it is necessary to define its interaction with the residing microbial communities and the biochemical routes of its degradation and metabolization. However, despite recent attention on this problem, research has largely focussed on microbial functional potential, failing to clearly identify collective adaptation strategies of these communities. Our study combines genome-centric metagenomics and metatranscriptomics to characterise soil microbial communities adapting to high polyethylene and polyethylene terephthalate concentration. The microbiota were sampled from a landfill subject to decades-old plastic contamination and enriched through prolonged cultivation using these microplastics as the only carbon source. This approach aimed to select the microorganisms that best adapt to these specific substrates. As a result, we obtained simplified communities where multiple plastic metabolization pathways are widespread across abundant and rare microbial taxa. Major differences were found in terms of expression, which on average was higher in planktonic microbes than those firmly adhered to plastic, indicating complementary metabolic roles in potential microplastic assimilation. Moreover, metatranscriptomic patterns indicate a high transcriptional level of numerous genes in emerging taxa characterised by a marked accumulation of genomic variants, supporting the hypothesis that plastic metabolization requires an extensive rewiring in energy metabolism and thus provides a strong selective pressure. Altogether, our results provide an improved characterisation of the impact of microplastics derived from common plastics types on terrestrial microbial communities and suggest biotic responses investing contaminated sites as well as potential biotechnological targets for cooperative plastic upcycling.

Progress and Prospects of Microplastic Biodegradation Processes and Mechanisms: A Bibliometric Analysis

In order to visualize the content and development patterns of microplastic biodegradation research, the American Chemical Society (ACS), Elsevier, Springer Link, and American Society for Microbiology (ASM) were searched for the years 2012-2022 using Citespace and VOSvivewer for bibliometrics and visual analysis. The biodegradation processes and mechanisms of microplastics were reviewed on this basis. The results showed a sharp increase in the number of publications between 2012 and 2022, peaking in 2020-2021, with 62 more publications than the previous decade. The University of Chinese Academy of Sciences (UCAS), Northwest A&F University (NWAFU), and Chinese Academy of Agricultural Sciences (CAAS) are the top three research institutions in this field. Researchers are mainly located in China, The United States of America (USA), and India. Furthermore, the research in this field is primarily concerned with the screening of functional microorganisms, the determination of functional enzymes, and the analysis of microplastic biodegradation processes and mechanisms. These studies have revealed that the existing functional microorganisms for microplastic biodegradation are bacteria, predominantly Proteobacteria and Firmicutes; fungi, mainly Ascomycota; and some intestinal microorganisms. The main enzymes secreted in the process are hydrolase, oxidative, and depolymerization enzymes. Microorganisms degrade microplastics through the processes of colonization, biofilm retention, and bioenzymatic degradation. These studies have elucidated the current status of and problems in the microbial degradation of microplastics, and provide a direction for further research on the degradation process and molecular mechanism of functional microorganisms.

Catalytic and biocatalytic degradation of microplastics

In recent years, there has been a surge in annual plastic production, which has contributed to growing environmental challenges, particularly in the form of microplastics. Effective management of plastic and microplastic waste has become a critical concern, necessitating innovative strategies to address its impact on ecosystems and human health. In this context, catalytic degradation of microplastics emerges as a pivotal approach that holds significant promise for mitigating the persistent effects of plastic pollution. In this article, we critically explored the current state of catalytic degradation of microplastics and discussed the definition of degradation, characterization methods for degradation products, and the criteria for standard sample preparation. Moreover, the significance and effectiveness of various catalytic entities, including enzymes, transition metal ions (for the Fenton reaction), nanozymes, and microorganisms are summarized. Finally, a few key issues and future perspectives regarding the catalytic degradation of microplastics are proposed.

Bioprospecting the potential of the microbial community associated to Antarctic marine sediments for hydrocarbon bioremediation

Microorganisms that inhabit the cold Antarctic environment can produce ligninolytic enzymes potentially useful in bioremediation. Our study focused on characterizing Antarctic bacteria and fungi from marine sediment samples of King George and Deception Islands, maritime Antarctica, potentially affected by hydrocarbon influence, able to produce enzymes for use in bioremediation processes in environments impacted with petroleum derivatives. A total of 168 microorganism isolates were obtained: 56 from sediments of King George Island and 112 from Deception Island. Among them, five bacterial isolates were tolerant to cell growth in the presence of diesel oil and gasoline and seven fungal were able to discolor RBBR dye. In addition, 16 isolates (15 bacterial and one fungal) displayed enzymatic emulsifying activities. Two isolates were characterized taxonomically by showing better biotechnological results. Psychrobacter sp. BAD17 and Cladosporium sp. FAR18 showed pyrene tolerance (cell growth of 0.03 g mL-1 and 0.2 g mL-1) and laccase enzymatic activity (0.006 UL-1 and 0.10 UL-1), respectively. Our results indicate that bacteria and fungi living in sediments under potential effect of hydrocarbon pollution may represent a promising alternative to bioremediate cold environments contaminated with polluting compounds derived from petroleum such as polycyclic aromatic hydrocarbons and dyes.

Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics

BACKGROUND

Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype-phenotype linkages in the marine 'plastisphere', and these have revealed the dominance of photosynthetic microorganisms within warm climates. Advancing the functional representation of the marine plastisphere is vital for the development of specific databases cataloging the functional diversity of the associated microorganisms and their peptide and protein sequences, to fuel biotechnological discoveries. Here, we provide a comprehensive assessment for plastisphere metaproteomics, using multi-omics and data mining on thin plastic biofilms to provide unique insights into plastisphere metabolism. Our robust experimental design assessed DNA/protein co-extraction and cell lysis strategies, proteomics workflows, and diverse protein search databases, to resolve the active plastisphere taxa and their expressed functions from an understudied cold environment.

RESULTS

For the first time, we demonstrate the predominance and activity of hydrocarbonoclastic genera (Psychrobacter, Flavobacterium, Pseudomonas) within a primarily heterotrophic plastisphere. Correspondingly, oxidative phosphorylation, the citrate cycle, and carbohydrate metabolism were the dominant pathways expressed. Quorum sensing and toxin-associated proteins of Streptomyces were indicative of inter-community interactions. Stress response proteins expressed by Psychrobacter, Planococcus, and Pseudoalteromonas and proteins mediating xenobiotics degradation in Psychrobacter and Pseudoalteromonas suggested phenotypic adaptations to the toxic chemical microenvironment of the plastisphere. Interestingly, a targeted search strategy identified plastic biodegradation enzymes, including polyamidase, hydrolase, and depolymerase, expressed by rare taxa. The expression of virulence factors and mechanisms of antimicrobial resistance suggested pathogenic genera were active, despite representing a minor component of the plastisphere community.

CONCLUSION

Our study addresses a critical gap in understanding the functioning of the marine plastisphere, contributing new insights into the function and ecology of an emerging and important microbial niche. Our comprehensive multi-omics and comparative metaproteomics experimental design enhances biological interpretations to provide new perspectives on microorganisms of potential biotechnological significance beyond biodegradation and to improve the assessment of the risks associated with microorganisms colonizing marine plastic pollution. Video Abstract.

Study of the Bacterial, Fungal, and Archaeal Communities Structures near the Bulgarian Antarctic Research Base "St. Kliment Ohridski" on Livingston Island, Antarctica

As belonging to one of the most isolated continents on our planet, the microbial composition of different environments in Antarctica could hold a plethora of undiscovered species with the potential for biotechnological applications. This manuscript delineates our discoveries after an expedition to the Bulgarian Antarctic Base "St. Kliment Ohridski" situated on Livingston Island, Antarctica. Amplicon-based metagenomics targeting the 16S rRNA genes and ITS2 region were employed to assess the metagenomes of the bacterial, fungal, and archaeal communities across diverse sites within and proximal to the research station. The predominant bacterial assemblages identified included Oxyphotobacteria, Bacteroidia, Gammaprotobacteria, and Alphaprotobacteria. A substantial proportion of cyanobacteria reads were attributed to a singular uncultured taxon within the family Leptolyngbyaceae. The bacterial profile of a lagoon near the base exhibited indications of penguin activity, characterized by a higher abundance of Clostridia, similar to lithotelm samples from Hannah Pt. Although most fungal reads in the samples could not be identified at the species level, noteworthy genera, namely Betamyces and Tetracladium, were identified. Archaeal abundance was negligible, with prevalent groups including Woesearchaeales, Nitrosarchaeum, Candidatus Nitrosopumilus, and Marine Group II.

Psychrobacter species enrichment as potential microplastic degrader and the putative biodegradation mechanism in Shenzhen Bay sediment, China

Microplastic (MP) pollution has emerged as a pressing environmental concern due to its ubiquity and longevity. Biodegradation of MPs has garnered significant attention in combatting global MP contamination. This study focused on MPs within sediments near the sewage outlet of Shenzhen Bay. The objective was to elucidate the microbial communities in sediments with varying MPs, particularly those with high MP loads, and to identify microorganisms associated with MP degradation. The results revealed varying MP abundance, ranging from 211 to 4140 items kg-1 dry weight (d. w.), with the highest concentration observed near the outfall. Metagenomic analysis confirmed the enrichment of Psychrobacter species in sediments with high MP content. Psychrobacter accounted for ∼16.71% of the total bacterial community and 41.71% of hydrocarbon degrading bacteria at the S3 site, exhibiting a higher abundance than at other sampling sites. Psychrobacter contributed significantly to bacterial function at S3, as evidenced by the Kyoto Encyclopedia of Genes and Genomes pathway and enzyme analysis. Notably, 28 enzymes involved in MP biodegradation were identified, predominantly comprising oxidoreductases, hydrolases, transferases, ligases, lyases, and isomerases. We propose a putative mechanism for MP biodegradation, involving the breakdown of long-chain plastic polymers and subsequent oxidation of short-chain oligomers, ultimately leading to thorough mineralization.

Biodegradation of Typical Plastics: From Microbial Diversity to Metabolic Mechanisms

Plastic production has increased dramatically, leading to accumulated plastic waste in the ocean. Marine plastics can be broken down into microplastics (<5 mm) by sunlight, machinery, and pressure. The accumulation of microplastics in organisms and the release of plastic additives can adversely affect the health of marine organisms. Biodegradation is one way to address plastic pollution in an environmentally friendly manner. Marine microorganisms can be more adapted to fluctuating environmental conditions such as salinity, temperature, pH, and pressure compared with terrestrial microorganisms, providing new opportunities to address plastic pollution. Pseudomonadota (Proteobacteria), Bacteroidota (Bacteroidetes), Bacillota (Firmicutes), and Cyanobacteria were frequently found on plastic biofilms and may degrade plastics. Currently, diverse plastic-degrading bacteria are being isolated from marine environments such as offshore and deep oceanic waters, especially Pseudomonas spp. Bacillus spp. Alcanivoras spp. and Actinomycetes. Some marine fungi and algae have also been revealed as plastic degraders. In this review, we focused on the advances in plastic biodegradation by marine microorganisms and their enzymes (esterase, cutinase, laccase, etc.) involved in the process of biodegradation of polyethylene terephthalate (PET), polystyrene (PS), polyethylene (PE), polyvinyl chloride (PVC), and polypropylene (PP) and highlighted the need to study plastic biodegradation in the deep sea.

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.

Heterologous expression, purification, and characterization of thermo- and alkali-tolerant laccase-like multicopper oxidase from Bacillus mojavensis TH309 and determination of its antibiotic removal potential

Laccases or laccase-like multicopper oxidases have great potential in bioremediation to oxidase phenolic or non-phenolic substrates. However, their inability to maintain stability in harsh environmental conditions and against non-substrate compounds is one of the main reasons for their limited use. The gene (mco) encoding multicopper oxidase from Bacillus mojavensis TH309 were cloned into pET14b( +), expressed in Escherichia coli, and purified as histidine tagged enzyme (BmLMCO). The molecular weight of the enzyme was about 60 kDa. The enzyme exhibited laccase-like activity toward 2,6-dimethoxyphenol (2,6-DMP), syringaldazine (SGZ), and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS). The highest enzyme activity was recorded at 80 °C and pH 8. BmLMCO showed a half-life of ~ 305, 99, 50, 46, 36, and 20 min at 40, 50, 60, 70, 80, and 90 °C, respectively. It retained more than 60% of its activity after pre-incubation in the range of pH 5-12 for 60 min. The enzyme activity significantly increased in the presence of 1 mM of Cu2+. Moreover, BmLMCO tolerated various chemicals and showed excellent compatibility with organic solvents. The Michaelis constant (Km) and the maximum velocity (Vmax) values of BmLMCO were 0.98 mM and 93.45 µmol/min, respectively, with 2,6-DMP as the substrate. BmLMCO reduced the antibacterial activity of cefprozil, gentamycin, and erythromycin by 72.3 ± 1.5%, 79.6 ± 6.4%, and 19.7 ± 4.1%, respectively. This is the first revealing shows the recombinant production of laccase-like multicopper oxidase from any B. mojavensis strains, its biochemical properties, and potential for use in bioremediation.

Computer-aided discovery of a novel thermophilic laccase for low-density polyethylene degradation

Polyethylene (PE) and industrial dyes are recalcitrant pollutants calling for the development of sustainable solutions for their degradation. Laccases have been explored for removal of contaminants and pollutants, including dye decolorization and plastic degradation. Here, a novel thermophilic laccase from PE-degrading Lysinibaccillus fusiformis (LfLAC3) was identified through a computer-aided and activity-based screening. Biochemical studies of LfLAC3 indicated its high robustness and catalytic promiscuity. Dye decolorization experiments showed that LfLAC3 was able to degrade all the tested dyes with decolorization percentage from 39% to 70% without the use of a mediator. LfLAC3 was also demonstrated to degrade low-density polyethylene (LDPE) films after eight weeks of incubation with either crude cell lysate or purified enzyme. The formation of a variety of functional groups was detected using Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). Damage on the surfaces of PE films was observed via scanning electron microscopy (SEM). The potential catalytic mechanism of LfLAC3 was disclosed by structure and substrate-binding modes analysis. These findings demonstrated that LfLAC3 is a promiscuous enzyme that has promising potential for dye decolorization and PE degradation.

Characterization of 17β-estradiol-degrading enzyme from Microbacterium sp. MZT7 and its function on E2 biodegradation in wastewater

BACKGROUND

17β-estradiol (E2) residues exhibit harmful effects both for human and animals and have got global attention of the scientific community. Microbial enzymes are considered as one of the effective strategies having great potential for removal E2 residues from the environment. However, limited literature is available on the removal of E2 from wastewater using short-chain dehydrogenase.

RESULTS

In this study, 17β-estradiol degrading enzyme (17β-HSD-0095) was expressed and purified from Microbacterium sp. MZT7. The optimal pH and temperature for reaction was 7 and 40 °C, respectively. Molecular docking studies have shown that the ARG215 residue form a hydrogen bond with oxygen atom of the substrate E2. Likewise, the point mutation results have revealed that the ARG215 residue play an important role in the E2 degradation by 17β-HSD-0095. In addition, 17β-HSD-0095 could remediate E2 contamination in synthetic livestock wastewater.

CONCLUSIONS

These findings offer some fresh perspectives on the molecular process of E2 degradation and the creation of enzyme preparations that can degrade E2.

Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules

Climate change and the induced environmental disturbances is one of the major threats that have a strong impact on bacterial communities in the Antarctic environment. To cope with the persistent extreme environment and inhospitable conditions, psychrophilic bacteria are thriving and displaying striking adaptive characteristics towards severe external factors including freezing temperature, sea ice, high radiation and salinity which indicates their potential in regulating climate change's environmental impacts. The review illustrates the different adaptation strategies of Antarctic microbes to changing climate factors at the structural, physiological and molecular level. Moreover, we discuss the recent developments in "omics" approaches to reveal polar "blackbox" of psychrophiles in order to gain a comprehensive picture of bacterial communities. The psychrophilic bacteria synthesize distinctive cold-adapted enzymes and molecules that have many more industrial applications than mesophilic ones in biotechnological industries. Hence, the review also emphasizes on the biotechnological potential of psychrophilic enzymes in different sectors and suggests the machine learning approach to study cold-adapted bacteria and engineering the industrially important enzymes for sustainable bioeconomy.

Highly efficient low-temperature biodegradation of polyethylene microplastics by using cold-active laccase cell-surface display system

To eliminate efficiency restriction of polyethylene microplastics low-temperature biodegradation, a novel InaKN-mediated Escherichia coli surface display platform for cold-active degrading laccase PsLAC production was developed. Display efficiency of 88.0% for engineering bacteria BL21/pET-InaKN-PsLAC was verified via subcellular extraction and protease accessibility, exhibiting an activity load of 29.6 U/mg. Cell growth and membrane integrity revealed BL21/pET-InaKN-PsLAC maintained stable growth and intact membrane structure during the display process. The favorable applicability was confirmed, with 50.0% activity remaining in 4 days at 15 °C, and 39.0% activity recovery retention after 15 batches of activity substrate oxidation reactions. Moreover, BL21/pET-InaKN-PsLAC possessed high polyethylene low-temperature depolymerizing capacity. Bioremediation experiments proved that the degradation rate was 48.0% within 48 h at 15 °C, and reached 66.0% after 144 h. Collectively, cold-active PsLAC functional surface display technology and its significant contributions to polyethylene microplastics low-temperature degradation constitute an effective improvement strategy for biomanufacturing and microplastics cold remediation.

Hierarchically-structured laccase@Ni3(PO4)2 hybrid nanoflowers for antibiotic degradation: Application in real wastewater effluent and toxicity evaluation

Laccase@Ni₃(PO₄)₂ hybrid nanoflowers (HNFs) were prepared by the anisotropic growth of biomineralized nickel phosphate. The immobilization yield was 77.5 ± 3.6 %, and the immobilized enzyme retained 50 % of its initial activity after 18 reusability cycles. The immobilized and free enzymes lost 80 % of their activity after 18 and 6 h incubation in municipal wastewater effluent (MWWE), respectively. The increase in α-helix content (8 %) following immobilization led to a more rigid enzyme structure, potentially contributing to its improved stability. The removal of ciprofloxacin from MWWE by laccase@Ni₃(PO₄)₂·HNFs/p-coumaric acid oxidation system was optimized using a Box-Behnken design. Under the optimized conditions [initial laccase activity (0.05 U mL^-1), the concentration of p-coumaric acid (2.9 mM), and treatment time (4.9 h)], the biocatalyst removed 90 % of ciprofloxacin (10 mg L^-1) from MWWE. The toxicity of ciprofloxacin against some G⁺ and G^- bacteria was reduced by 35-70 %, depending on their strain. The EC₅₀ of ciprofloxacin for the alga Raphidocelis subcapitata reduced from 3.08 to 1.07 mg L^-1 (p-value <0.05) after the bioremoval. Also, the acute and chronic toxicity of identified biodegradation products was lower than ciprofloxacin at three trophic levels, as predicted by ECOSAR software.

Gross Negligence: Impacts of Microplastics and Plastic Leachates on Phytoplankton Community and Ecosystem Dynamics

Plastic debris is an established environmental menace affecting aquatic systems globally. Recently, microplastics (MP) and plastic leachates (PL) have been detected in vital human organs, the vascular system, and in vitro animal studies positing severe health hazards. MP and PL have been found in every conceivable aquatic ecosystem─from open oceans and deep sea floors to supposedly pristine glacier lakes and snow covered mountain catchment sites. Many studies have documented the MP and PL impacts on a variety of aquatic organisms, whereby some exclusively focus on aquatic microorganisms. Yet, the specific MP and PL impacts on primary producers have not been systematically analyzed. Therefore, this review focuses on the threats posed by MP, PL, and associated chemicals on phytoplankton, their comprehensive impacts at organismal, community, and ecosystem scales, and their endogenous amelioration. Studies on MP- and PL-impacted individual phytoplankton species reveal the production of reactive oxygen species, lipid peroxidation, physical damage of thylakoids, and other physiological and metabolic changes, followed by homo- and heteroaggregations, ultimately eventuating in decreased photosynthesis and primary productivity. Likewise, analyses of the microbial community in the plastisphere show a radically different profile compared to the surrounding planktonic diversity. The plastisphere also enriches multidrug-resistant bacteria, cyanotoxins, and pollutants, accelerating microbial succession, changing the microbiome, and thus, affecting phytoplankton diversity and evolution. These impacts on cellular and community scales manifest in changed ecosystem dynamics with widespread bottom-up and top-down effects on aquatic biodiversity and food web interactions. These adverse effects─through altered nutrient cycling─have "knock-on" impacts on biogeochemical cycles and greenhouse gases. Consequently, these impacts affect provisioning and regulating ecosystem services. Our citation network analyses (CNA) further demonstrate dire effects of MP and PL on all trophic levels, thereby unsettling ecosystem stability and services. CNA points to several emerging nodes indicating combined toxicity of MP, PL, and their associated hazards on phytoplankton. Taken together, our study shows that ecotoxicity of plastic particles and their leachates have placed primary producers and some aquatic ecosystems in peril.

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.

Screening of Polyethylene-Degrading Bacteria from Rhyzopertha Dominica and Evaluation of Its Key Enzymes Degrading Polyethylene

Polyethylene (PE) is widely used, and it has caused serious environmental problems due to its difficult degradation. At present, the mechanism of PE degradation by microorganisms is not clear, and the related enzymes of PE degradation need to be further explored. In this study, Acinetobacter baumannii Rd-H2 was obtained from Rhizopertha dominica, which had certain degradation effect on PE plastic. The degradation performance of the strains was evaluated by weight loss rate, SEM, ATR/FTIR, WCA, and GPC. The multi-copper oxidase gene abMco, which may be one of the key genes for PE degradation, was analyzed and successfully expressed in E. coli. The laccase activity of the gene was determined, and the enzyme activity was up to 159.82 U/L. The optimum temperature and pH of the enzyme are 45 °C and 4.5 respectively. It shows good stability at 30-45 °C. Cu²⁺ can activate the enzyme. The abMCO was used to degrade polyethylene film, showing a good degradation effect, proving that the enzyme could be the key to degrading PE.