Sustainable production and degradation of plastics using microbes

Impacts of different plastic residues on soil volatile profiles associated with microbiome dynamics

Plastic pollution poses a significant threat to soil ecosystems, yet the role of volatile organic compounds (VOCs) in plastic degradation is not well-studied. The present research focuses on the impact of polyethylene (PE), polylactic acid (PLA), and poly(butylene-adipate-co-terephthalate) (PBAT) residues on soil in a 12-week long lab-scale aerobic experiment. The study focused on the dynamics of VOC profiles, soil physicochemical properties, and microbial communities. PBAT, known for its biodegradability, produced a distinct VOC profile with hazardous compounds such as 1,3-butadiene, which is consistently associated with cardiovascular diseases and leukemia. Microbial analysis of PBAT revealed distinct bacterial and fungal diversity responses, along with unique KEGG pathway profiles compared to PE and PLA, suggesting its biodegradation process may involve biofilm formation and quorum sensing. Correlation analysis based on the relevant abundance of specific microbes exhibited strong positive correlations, such as Streptomyces with propyne emission and Hydrogenispora with ethylene emission. These results demonstrated distinct biodegradation patterns of various plastics in soil, identified through the combination of VOC detection and microbiome analysis.

Engineering Halomonas bluephagenesis for pilot production of terpolymers containing 3-hydroxybutyrate, 4-hydroxybutyrate and 3-hydroxyvalerate from glucose

Microbial poly(3-hydroxybutyrate-co-4-hydroxybutyrate-co-3-hydroxyvalerate), abbreviated as P(3HB-4HB-3HV) or P34HBHV, is a flexible polyhydroxyalkanoate (PHA) material ranging from softness to elasticity depending on the ratios of various monomers. Halomonas bluephagenesis, as the chassis of the next generation industrial biotechnology (NGIB) able to grow contamination free under open unsterile conditions. The resulting recombinants of H. bluephagenesis became capable of efficiently synthesizing P34HBHV utilizing glucose as the sole carbon source. Engineered H. bluephagenesis H1 (encoding ogdA, sucD, 4hbD, orfZ, scpA and scpB in chromosomes) transformed with a plasmid containing PHA synthesis genes phaC and phaA and its derivative H29 produced up to 92 % P(3HB-co-8.85 %4HB-co-8.47 %3HV) and 72 % P(3HB-co-13.21 %4HB-co-11.97 %3HV) in cell dry weight (CDW), respectively, in shake flasks. In bioreactor cultivation, H. bluephagenesis H39 constructed by integrating the 4hbD, phaC and phaA genes into the genome of H. bluephagenesis H1 achieved 95 g/L CDW with 69 % P(3HB-co-10.49 %4HB-co-3.54 %3HV), while H. bluephagenesis H43, further optimized with lpxM deletion, reached 73 g/L CDW with 78 % P(3HB-co-10.35 %4HB-co-4.54 %3HV) in a 100 L bioreactor. For the first time, H. bluephagenesis was successfully engineered to generate stable and hyperproductive derivative strains for pilot production of P(3HB-4HB-3HV) with customizable monomer ratios from glucose as the sole carbon source.

Marine plastic exposure triggers rapid recruitment of plastic-degrading bacteria and accelerates polymer-specific transformations

Plastic pollution in marine ecosystems is a growing concern, yet the degradation behavior of different plastic types and their interactions with microbial communities remain poorly understood. This study investigated the degradation kinetics and microbial colonization of four widely used plastic materials, surgical masks (most made of PP), PET bottles, PS foam, and PP cups, over 40 days of seawater exposure in the Central Atlantic of Morocco. Mass loss measurement revealed distinct degradation patterns, with PS foam showing the highest mass loss (13 %), followed by PET bottles (5 %), likely due to environmental stressors that promote mechanical fragmentation. Surgical masks and PP cups exhibited minimal degradation, retaining nearly all their original mass, as well as limited extent of biodegradation. Fourier Transform Infrared Spectroscopy (FTIR) and X-ray Diffraction (XRD) analyses showed the formation of oxidative functional groups on PP cups and significant structural changes in PS foam and PET, particularly in their crystalline structures, correlating with their higher mass reduction rates. SEM/EDX biofilm imaging confirmed extensive microbial colonization, particularly on PS and PET surfaces. Using 16S rRNA metabarcoding, we identified a striking enrichment of Exiguobacterium, followed by Pseudomonas, Acinetobacter and Bacillus genera, containing reported plastic degrading strains, which were strongly correlated with the accelerated breakdown of plastics. However, its role in accelerating plastic breakdown in this study remains unclear and may warrant further investigation. Co-occurrence network analysis revealed a progressive shift in microbial community structure, evolving from highly interconnected networks at day 0 to more specialized, modular clusters by day 40, dominated by Proteobacteria and Firmicutes. Atomic Absorption Spectrometry (AAS) demonstrated significant heavy metal accumulation on plastic surfaces, potentially influencing microbial colonization and activity. While the observed fragmentation of PS foam and PET highlights the susceptibility of certain plastics to environmental stressors, this study also positions microbial colonization as a potential contributor to plastic surface changes, providing novel insights into the interplay between microbial communities and plastic degradation in marine environments.

Effect of alkaline-thermal pretreatment on biodegradable plastics degradation and dissemination of antibiotic resistance genes in co-compost system

Biodegradable plastics (BDPs) are an eco-friendly alternative to traditional plastics in organic waste, but their microbial degradation and impact on antibiotic resistance genes (ARGs) transmission during co-composting remain poorly understood. This study examines how alkaline-thermal pretreatment enhances BDPs degradation and influences the fate of ARGs and mobile genetic elements (MGEs) in co-composting. Pretreatment with 0.1 mol/L NaOH at 100℃ for 40 minutes increased the surface roughness and hydrophilicity of BDPs while reducing their molecular weight and thermal stability. Incorporating pretreated BDPs film (8 g/kg-TS) into the compost reduced the molecular weight of the BDPs by 59.70 % during the maturation stage, facilitating compost heating and prolonging the thermophilic stage. However, incomplete degradation of BDPs releases numerous smaller-sized microplastics, which can act as carriers for microorganisms, facilitating the dissemination of ARGs across environments and posing significant ecological and public health risks. Metagenomic analysis revealed that pretreatment enriched plastic-degrading bacteria, such as Thermobifida fusca, on BDPs surfaces and accelerated microbial plastic degradation during the thermophilic stage, but also increased ARGs abundance. Although pretreatment significantly reduced MGEs abundance (tnpA, IS19), the risk of ARGs dissemination remained. Three plastic-degrading bacteria (Pigmentiphaga sp002188465, Bacillus clausii, and Bacillus altitudinis) were identified as ARGs hosts, underscoring the need to address the risk of horizontal gene transfer of ARGs associated with pretreatment in organic waste management.

The combination of microplastics and glyphosate affects the microbiome of soil inhabitant Enchytraeus crypticus

Microplastics and pesticides are emerging contaminants that threaten soil ecosystems, yet their combined effects on soil health and soil fauna remain poorly understood. In this study, we constructed a microcosm to assess the individual and combined effects of microplastics and glyphosate on soil physicochemical properties, microbial communities, and the gut microbiome of soil invertebrates (Enchytraeus crypticus). Biodegradable polylactic acid (PLA) and conventional polyethylene terephthalate (PET) were introduced at environmentally relevant concentrations. Our results revealed that PLA had a stronger disruptive effect on soil microbial communities than PET, altering microbial diversity and functional composition. Glyphosate, in contrast, primarily influenced the gut microbiome of E. crypticus, reducing microbial diversity and inducing oxidative stress. Combined exposure to microplastics and glyphosate significantly intensified oxidative stress but did not amplify microbial dysbiosis beyond the effects of microplastics alone. Compare to PET, PLA combined with glyphosate had the most pronounced effects on both soil and gut microbiomes, suggesting that biodegradable microplastics may pose greater ecological risks than conventional microplastics when used alongside pesticides. These findings underscore the need for a reassessment of biodegradable plastic use in agriculture and highlight the complex interactions between microplastics and pesticides in shaping soil ecosystem health.

Co-consumption for plastics upcycling: A perspective

The growing plastics end-of-life crisis threatens ecosystems and human health globally. Microbial plastic degradation and upcycling have emerged as potential solutions to this complex challenge, but their industrial feasibility and limitations thereon have not been fully characterized. In this perspective paper, we review literature describing both plastic degradation and transformation of plastic monomers into value-added products by microbes. We aim to understand the current feasibility of combining these into a single, closed-loop process. Our analysis shows that microbial plastic degradation is currently the rate-limiting step to "closing the loop", with reported rates that are orders of magnitude lower than those of pathways to upcycle plastic degradation products. We further find that neither degradation nor upcycling have been demonstrated at rates sufficiently high to justify industrialization at present. As a potential way to address these limitations, we suggest more investigation into mixotrophic approaches, showing that those which leverage the unique properties of plastic degradation products such as ethylene glycol might improve rates sufficiently to motivate industrial process development.

In Situ Synthesis of Plasticized Bacterial Cellulose Films for Daily Packaging Using Biobased Plasticizers

Bacterial cellulose (BC) naturally decomposes in the environment without releasing toxins or microplastics, making it a promising alternative to conventional plastics. However, its inherent brittleness after drying limits its broader application. This study investigates four biobased plasticizers─epoxy soybean oil, castor oil, tributyl citrate (TBC), and tributyl trans-aconitate (TBA)─to enhance the flexibility of BC through in situ modification. By combining a gel-assisted biosynthesis with an in situ spray plasticization method, biobased plasticizers are uniformly incorporated into the nanofiber network of BC, resulting in films with significantly improved flexibility and transparency. Among the biobased plasticizers, TBC and TBA showed the most effective plasticization, increasing the E% to 9.63 and 11.90%, respectively, corresponding to 6.3-fold and 7.5-fold enhancements compared to the control. This approach not only improves the mechanical properties of BC but also streamlines production by enabling a simplified processing method. The findings underscore the potential of plasticized BC biomaterials in replacing fossil-based plastics and advancing the development of sustainable materials.

Guidelines toward ecologically-informed bioprospecting for microbial plastic degradation

Biological degradation of plastics by microbial enzymes offers a sustainable alternative to traditional waste management methods that often pollute the environment. This review explores ecologically-informed bioprospecting for microorganisms possessing enzymes suitable for biological plastic waste treatment. Natural habitats enriched in plastic-like polymers, such as insect-derived polyesters, epicuticular microbial biofilms in the phyllosphere of plants in extreme environments, or aquatic ecosystems, are highlighted as promising reservoirs for bioprospecting. Anthropogenic habitats, including plastic-polluted soils and the plastisphere, have yielded potent enzymes such as PETases and cutinases, which are being exploited in biotechnology. However, bioprospecting in plastispheres and artificial environments frequently leads to the isolation of environmental opportunistic microorganisms, such as Pseudomonas aeruginosa, Aspergillus fumigatus, Parengyodontium album, or species of Fusarium, which are capable of becoming human and/or plant pathogens. These cases necessitate stringent biosecurity measures, including accurate molecular identification, ecological assessment, and containment protocols. Beyond advancing bioprospecting approaches toward a broader scope of relevant habitats, this review underscores the educational value of such screenings, specifically, in understudied natural habitats, emphasizing its potential to uncover novel enzymes and microorganisms and engage the next generation of researchers in interdisciplinary study integrating environmental microbiology, molecular biology, enzymology, polymer chemistry, and bioinformatics. Finally, we offer guidelines for microbial bioprospecting in various laboratory settings, ranging from standard environmental microbiology facilities to high-biosecurity facilities, thereby maximizing the diversity of scientists who may contribute to addressing urgent environmental challenges associated with plastic waste.

Cell-free biosensor with automated acoustic liquid handling for rapid and scalable characterization of cellobiohydrolases on microcrystalline cellulose

Engineering enzymes to degrade solid substrates, such as crystalline cellulose from paper sludge or microplastics in sewage sludge, presents challenges for high-throughput screening (HTS), as solid substrates are not readily accessible in cell-based biosensor systems. To address this challenge, we developed a cell-free cellobiose-detectable biosensor (CB-biosensor) for rapid characterization of cellobiohydrolase (CBH) activity, enabling direct detection of hydrolysis products without cellular constraints. The CB-biosensor demonstrates higher sensitivity than conventional assays and distinguishes between CBH subtypes (CBHI and CBHII) based on their modes of action. Integration with the Echo 525 liquid handler enables precise and reproducible sample processing, with fluorescence signals from automated preparations comparable to manual experiments. Furthermore, assay volumes can be reduced to just a few microlitres-impractical with manual methods. This cell-free CB-biosensor with Echo 525 minimizes reagent consumption, accelerates testing, and facilitates reliable large-scale screening. These findings highlight its potential to overcome current HTS limitations, advancing enzyme screening and accelerating the Design-Build-Test-Learn cycle for sustainable biomanufacturing.

Towards polyethylene terephthalate valorisation into PHB using an engineered Comamonas testosteroni strain

The abundant production of plastic materials, coupled with their recalcitrant nature, makes plastic waste a major challenge as a pollutant. Polyethylene terephthalate (PET) is a polyester formed by polycondensation of terephthalic acid (TPA) and ethylene glycol (EG). This plastic polymer can be completely depolymerized to its monomers using microbial enzymes. In this study, we verified in silico and in vivo that the bacterium Comamonas testosteroni RW31 is able to assimilate TPA and to produce the bioplastic polyhydroxybutyrate (PHB). This bacterium was engineered to heterologously express a fusion of the PET-degrading enzymes FAST-PETase and IsMHETase. We verified that our strain successfully secretes the enzymes and depolymerize PET both in vitro and in vivo, achieving a weight loss of 37.1 % and 0.83 %, respectively. We also studied its capacity to form biofilm. Furthermore, our strain can employ bis(2-hydroxyethyl) terephthalate (BHET), an intermediate of PET degradation, as feedstock to accumulate PHB up to 12.03 % of its dry weight in 14 h. Our findings highlight C. testosteroni RW31 as a promising chassis for synthetic biology strategies aimed at upcycling PET waste.

Microplastic induces microbial nitrogen limitation further alters microbial nitrogentransformation: Insights from metagenomic analysis

Microplastic has a significant impact on soil microbial communities, which play crucial roles in soil nitrogen (N) cycles. However, there is a limited understanding of their influences on genes associated with the entire N cycling pathways. Through a 120-day soil incubation using conventional (PE and PET) and biodegradable microplastics (PLA and PBAT), coupled with 16S rRNA and metagenomic sequencing, we investigated the responses of N-cycling genes to microplastics in two contrasting soils (i.e. black soil and loess soil). We found that biodegradable microplastics strongly altered microbial N functional profiles, and enhanced the abundance of numerous key genes involved in N fixation, organic N mineralization, N reduction, and denitrification. Furthermore, biodegradable microplastics significantly decreased net N mineralization (Nm) compared to control and conventional microplastic treatments, suggesting microbial N immobilization outweighed N mineralization. Analysis of the function-taxon bipartite network showed that the Nm was well predicted for the abundances and diversity of bacteria within specific modules, with Nm decreasing, the abundances of specific taxa in a given network modules increasing. These results indicated that biodegradable microplastics act as a carbon source to select specific taxa involved in enhancing N bioavailability (e.g., N fixation and organic N mineralization) to meet microbial N demand, which in turn filtered the bacterial community (decreased diversity but increased abundances) and gradually formed specific function-taxon modules. Comparing the two soils, microbes in the less fertile alkaline loess soil were more sensitive to biodegradable microplastics than those in the nutrient-rich acid black soil. Our study indicated that increasing usage of biodegradable plastics in the future may lead to accelerated soil microbial N limitation and transformation.

Anaerobic co-biodegradation of polyhydroxyalkanoate and swine manure for volatile fatty acid production: The impact of C/N ratios and microbial dynamics

Polyhydroxyalkanoate (PHA) is the important biodegradable plastic, however, biodegradation of PHA waste in anaerobic environments emits more CH4, a potent greenhouse gas. Bioconversion of PHA waste to useful byproducts - volatile fatty acids (VFAs) is a practical method to upcycle carbon from PHA. In this study, PHA waste was anaerobically co-digested with swine manure (SM) (the typical high nitrogen waste) at different C/N ratios. The results indicate that co-digestion of PHA and SM with a C/N ratio of 32.1 achieved VFA production of 5488 mg COD/L and 0.20 g COD/g VS. No significant differences were found in terms of the highest VFA concentrations between treatments with C/N ratios of 43.4 and 32.1. VFA produciton of 3655 mg COD/L and 0.14 g COD/g VS was achieved at 19 days by adjusting the C/N ratio to 19.2. Four bacteria were identified as dominant microorganisms responsible for converting PHA and SM to VFA.

Polyhydroxykanoate-Assisted Photocatalytic TiO2 Films for Hydrogen Production

The photocatalytic production of hydrogen using biopolymer-immobilized titanium dioxide (TiO2) is an innovative and sustainable approach to renewable energy generation. TiO2, a well-known photocatalyst, benefits from immobilization on biopolymers due to its environmental friendliness, abundance, and biodegradability. In another way, to boost the efficiency of TiO2, its surface properties can be modified by incorporating co-catalysts like platinum (Pt) to improve charge separation. In this work, the surface of commercial TiO2 PC500 was modified with Pt nanoparticles (Pt1%@PC500) and then immobilized on glass surfaces using polyhydroxyalkanoate biopolymer poly(hydroxybutyrate-co-hydroxyhexanoate) (PHBH). The as-prepared immobilized Pt-modified TiO2 photocatalysts were fully characterized using various physicochemical techniques. The photocatalytic activity of the photocatalyst film was investigated for photocatalytic hydrogen production through water reduction using ethanol as a sacrificial donor. The impact of the film preparation conditions, e.g., PHBH concentration, PHBH:catalyst ratio, and temperature, on activity and stability was studied in detail. The application of biopolymer PHBH as a binder provides a green alternative to conventional immobilization methods, and with the application of PHBH, a stable and active photocatalyst film that showed lower activity compared to that of the suspended photocatalyst but good recyclability in six runs was prepared. A long-term photocatalytic hydrogen production experiment was carried out. In 98 h of operation, 12 mmol of hydrogen was produced in three consecutive runs with a PHBH/Pt1%@PC500 film having an area of ∼5.3 cm2. A significantly lower hydrogen productivity was observed after the first run, possibly due to a change in film structure, but thereafter, the productivity remained almost constant for the second and third runs. Hydrogen was the main product in the gas phase (90%), but carbon dioxide (4-5%) and methane (4-5%) were obtained as important byproducts. The byproducts are a consequence of the use of the sacrificial reagent ethanol. The results of the film performance are very promising, with regard to large-scale continuous hydrogen production.

Genetically encoded biosensors for the circular plastics bioeconomy

Current plastic production and consumption routes are unsustainable due to impact upon climate change and pollution, and therefore reform across the entire value chain is required. Biotechnology offers solutions for production from renewable feedstocks, and to aid end of life recycling/upcycling of plastics. Biology sequence/design space is complex requiring high-throughput analytical methods to facilitate the iterative optimisation, design-build, test-learn (DBTL), cycle of Synthetic Biology. Furthermore, genetic regulatory tools can enable harmonisation between biotechnological demands and the physiological constraints of the selected production host. Genetically encoded biosensors offer a solution for both requirements to facilitate the circular plastic bioeconomy. In this review we present a summary of biosensors developed to date reported to be responsive to plastic precursors/monomers. In addition, we provide a summary of the demonstrated and prospective applications of these biosensors for the construction and deconstruction of plastics. Collectively, this review provides a valuable resource of biosensor tools and enabled applications to support the development of the circular plastics bioeconomy.

The bifunctional impact of polylactic acid microplastics on composting processes and soil-plant systems: Dynamics of microbial communities and ecological niche competition

Although extensive research has been conducted on the environmental impact of microplastics (MPs), their effects on microorganisms during the composting process and on the compost-soil system remain unclear. Our research investigates the microbial response to polylactic acid microplastics (PLAMPs) during aerobic composting and examines how compost enriched with PLAMPs affects plants. Our findings reveal that PLAMPs play a dual role in the composting process, influencing microorganisms differently depending on the composting phase. PLAMPs reduce the relative abundance of sensitive bacterial ASVs, specifically those belonging to Limnochordaceae and Enterobacteriaceae, during composting, while increasing the relative abundance of ASVs belonging to Steroidobacteriaceae and Bacillaceae. The impact of PLAMPs on microbial community assembly and niche width was found to be phase-dependent. In the stabilization phase (S5), the presence of PLAMPs caused a shift in the core microbial network from bacterial dominance to fungal dominance, accompanied by heightened microbial antagonism. Additionally, these intricate microbial interactions can be transferred to the soil ecosystem. Our study indicates that composting, as a method of managing PLAMPs, is also influenced by PLAMPs. This influence is transferred to the soil through the use of compost, resulting in severe oxidative stress in plants. Our research is pivotal for devising future strategies for PLAMPs management and predicting the subsequent changes in compost quality and environmental equilibrium.

Seasonal and height dynamics of volatile organic compounds in rubber plantation: Impacts on ozone and secondary organic aerosol formation

Rubber trees emit a range of volatile organic compounds (VOCs), including isoprene, monoterpenes, and sesquiterpenes, as part of their natural metabolism. These VOCs can significantly influence air quality through photochemical reactions that produce ozone and secondary organic aerosols (SOAs). This study examines the impact of VOCs detected in a rubber tree plantation in Northeastern Thailand on air quality, highlighting their role in atmospheric reactions that lead to the formation of ozone and SOAs. VOCs were collected at varying heights and seasons using Tenax-TA tubes paired with an atmospheric sampler pump and identified by gas chromatography-mass spectrometry. In total, 100 VOCs were identified, including alkanes, alkenes, terpenes, aromatics, and oxygenated VOCs. Principal Coordinate Analysis (PCoA) revealed distinct seasonal VOC profiles, with hydrocarbons, peaking in summer and terpenes in the rainy season. The Linear Mixed-Effects (LME) model indicates that VOC concentrations are more influenced by seasonal changes than by sampling heights. Secondary organic aerosol potential (SOAP) and ozone formation potential (OFP) of selected VOC species were also determined. The total SOAP ranged from 67.24 μg/m3 in summer to 17.87 μg/m3 in winter, while the total OFP ranged from 377.87 μg/m3 in summer to 139.39 μg/m3 in winter. Additionally, positive matrix factorization (PMF) analysis identified four main VOC sources: gasoline combustion (18.3 %), microbial activity (38.6 %), monoterpene emissions during latex production (15.0 %), and industrial sources (28.1 %). These findings provide essential information for managing air pollution in rubber tree plantations. By adopting focused air quality management strategies, plantation operators can mitigate the adverse effects of VOCs, promoting a healthier and more sustainable future.

Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals

Microorganisms, including bacteria, archaea, viruses, fungi, and protists, are essential to life on Earth and the functioning of the biosphere. Here, we discuss the key roles of microorganisms in achieving the United Nations Sustainable Development Goals (SDGs), highlighting recent and emerging advances in microbial research and technology that can facilitate our transition toward a sustainable future. Given the central role of microorganisms in the biochemical processing of elements, synthesizing new materials, supporting human health, and facilitating life in managed and natural landscapes, microbial research and technologies are directly or indirectly relevant for achieving each of the SDGs. More importantly, the ubiquitous and global role of microbes means that they present new opportunities for synergistically accelerating progress toward multiple sustainability goals. By effectively managing microbial health, we can achieve solutions that address multiple sustainability targets ranging from climate and human health to food and energy production. Emerging international policy frameworks should reflect the vital importance of microorganisms in achieving a sustainable future.

BhrPETase catalyzed polyethylene terephthalate depolymerization: A quantum mechanics/molecular mechanics approach

Polyethylene terephthalate (PET) is a widely used material in our daily life, particularly in areas such as packaging, fibers, and engineering plastics. However, PET waste can accumulate in the environment and pose a great threat to our ecosystem. Recently enzymatic conversion has emerged as an efficient and green strategy to address the PET crisis. Here, using a theoretical approach combining molecular dynamics simulation and quantum mechanics/molecular mechanics calculations, the depolymerization mechanism of the thermophilic cutinase BhrPETase was fully deciphered. Surprisingly, unlike the previously studied cutinase LCCICCG, our results indicate that the first step, catalytic triad assisted nucleophilic attack, is the rate-determining step. The corresponding Boltzmann weighted average energy barrier is 18.2 kcal/mol. Through extensive comparison between BhrPETase and LCCICCG, we evidence that key features like charge CHis@N1 and angle APET@C1-Ser@O1-His@H1 significantly impact the depolymerization efficiency of BhrPETase. Non-covalent bond interaction and distortion/interaction analysis inform new insights on enzyme engineer and may aid the recycling of enzymatic PET waste. This study will aid the advancement of the plastic bio-recycling economy and promote resource conservation and reuse.

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.

In situ real-time pathway to study the polyethylene long-term degradation process by a marine fungus through confocal Raman quantitative imaging

Since plastic waste has become a worldwide pollution problem, studying the ability of marine microorganisms to degrade plastic waste is important. However, conventional methods are unable to in situ real-time study the ability of microorganisms to biodegrade plastics. In recent years, Raman spectroscopy has been widely used in the characterization of plastics as well as in the study of biological metabolism due to its low cost, rapidity, label-free, non-destructive, and water-independent features, which provides us with new ideas to address the above limitations. Here, we have established a method to study the degradation ability of microorganisms on plastics using confocal Raman imaging. Alternaria alternata FB1, a recently reported polyethylene (PE) degrading marine fungus, is used as a model to perform a long-term (up to 274 days) in situ real-time nondestructive inspection of its degradation process. We can prove the degradation of PE plastics from the following two aspects, visualization and analysis of the degradation process based on depth imaging and quantification of the degradation rate by crystallinity calculations. The findings also reveal unprecedented degradation details. The method is important for realizing high-throughput screening of microorganisms with potential to degrade plastics and studying the degradation process of plastics in the future.

Effects of agricultural mulch film on swine manure composting: Film degradation and nitrogen transformation

The utilization of biodegradable mulch films (bio-MFs) is essential for agricultural safety. This study explored the effects of no MF (CK), aging bio-MF (BM), non-aging bio-MF (NBM), and aging polyethylene (PE)-MF (PEM) on swine manure composting. The results demonstrated that outdoor aging (45 days) accelerated the macroscopic degradation of bio-MF in the BM. A reduction in NH4+-N and NH3 emissions in the initial composting was observed owing to an increase in the carbon source or the bulking effect provided by the MFs. N2O emissions from days 9 to 21 were higher in the PEM than other treatments because of the formation of anaerobic zone in the MF-based aggregates. An obvious increase of amoA in PEM indicated a promoted nitrification during the maturation phase, meanwhile the increase of NO2--N and aggregate promoted denitrification. Altogether, MF influenced composting through the synergistic effects of increasing the carbon source, bulking effect, and aggregates.

Blue valorization of lignin-derived monomers via reprogramming marine bacterium Roseovarius nubinhibens

Biological valorization of lignin, the second most abundant biopolymer on Earth, is an indispensable sector to build a circular economy and net-zero future. However, lignin is recalcitrant to bioupcycling, demanding innovative solutions. We report here the biological valorization of lignin-derived aromatic carbon to value-added chemicals without requesting extra organic carbon and freshwater via reprogramming the marine Roseobacter clade bacterium Roseovarius nubinhibens. We discovered the unusual advantages of this strain for the oxidation of lignin monomers and implemented a CRISPR interference (CRISPRi) system with the lacI-Ptrc inducible module, nuclease-deactivated Cas9, and programmable gRNAs. This is the first CRISPR-based regulatory system in R. nubinhibens, enabling precise and efficient repression of genes of interest. By deploying the customized CRISPRi, we reprogrammed the carbon flux from a lignin monomer, 4-hydroxybenzoate, to achieve the maximum production of protocatechuate, a pharmaceutical compound with antibacterial, antioxidant, and anticancer properties, with minimal carbon to maintain cell growth and drive biocatalysis. As a result, we achieved a 4.89-fold increase in protocatechuate yield with a dual-targeting CRISPRi system, and the system was demonstrated with real seawater. Our work underscores the power of CRISPRi in exploiting novel microbial chassis and will accelerate the development of marine synthetic biology. Meanwhile, the introduction of a new-to-the-field lineage of marine bacteria unveils the potential of blue biotechnology leveraging resources from the ocean.IMPORTANCEOne often overlooked sector in carbon-conservative biotechnology is the water resource that sustains these enabling technologies. Similar to the "food-versus-fuel" debate, the competition of freshwater between human demands and bioproduction is another controversial issue, especially under global water scarcity. Here, we bring a new-to-the-field lineage of marine bacteria with unusual advantages to the stage of engineering biology for simultaneous carbon and water conservation. We report the valorization of lignin monomers to pharmaceutical compounds without requesting extra organic substrate (e.g., glucose) or freshwater by reprogramming the marine bacterium Roseovarius nubinhibens with a multiplex CRISPR interference system. Beyond the blue lignin valorization, we present a proof-of-principle of leveraging marine bacteria and engineering biology for a sustainable future.

Engineered plastic-associated bacteria for biodegradation and bioremediation

The global plastic waste crisis has triggered the development of novel methods for removal of recalcitrant polymers from the environment. Biotechnological approaches have received particular attention due to their potential for enabling sustainable, low-intensity bioprocesses which could also be interfaced with microbial upcycling pathways to support the emerging circular bioeconomy. However, low biodegradation efficiency of solid plastic materials remains a bottleneck, especially at mesophilic conditions required for one-pot degradation and upcycling. A promising strategy used in nature to address this is localisation of plastic-degrading microbes to the plastic surface via biofilm-mediated surface association. This review highlights progress and opportunities in leveraging these naturally occurring mechanisms of biofilm formation and other cell-surface adhesion biotechnologies to co-localise engineered cells to plastic surfaces. We further discuss examples of combining these approaches with extracellular expression of plastic-degrading enzymes to accelerate plastic degradation. Additionally, we review this topic in the context of nano- and microplastics bioremediation and their removal from wastewater and finally propose future research directions for this nascent field.

Utilization of orange peel waste for sustainable amino acid production by Corynebacterium glutamicum

Oranges are the most processed fruit in the world-it is therefore apparent that the industrial production of orange juice generates large quantities of orange peel as a by-product. Unfortunately, the management of the orange peel waste leads to economic and environmental problems. Meanwhile, the use of sustainable raw materials for the production of bulk chemicals, such as amino acids, is becoming increasingly attractive. To address both issues, this study focused on the use of orange peel waste as a raw material for media preparation for the production of amino acids by engineered Corynebacterium glutamicum. C. glutamicum grew on pure orange peel hydrolysate (OPH) and growth was enhanced by the addition of a nitrogen source and a pH buffer. Inhibitory effects by the combination of high concentrations of OPH, (NH4)2SO4, and MOPS buffer in the wild-type strain (WT), were overcome in the tyrosine-producing engineered C. glutamicum strain AROM3. Genetic modifications that we identified to allow for improved growth rates under these conditions included the deletions of the vanillin dehydrogenase gene vdh, the ʟ-lactate dehydrogenase gene ldhA and the 19 genes comprising cluster cg2663-cg2686. A growth inhibiting compound present in high concentrations in the OPH is 5-(hydroxymethyl)furfural (HMF). We identified vdh as being primarily responsible for the oxidation of HMF to its acid 5-hydroxymethyl-2-furancarboxylic acid (HMFCA), as the formation of HMFCA was reduced by 97% upon deletion of vdh in C. glutamicum WT. In addition, we showed that growth limitations could be overcome by adjusting the media preparation, using a combination of cheap ammonia water and KOH for pH neutralization after acidic hydrolysis. Overall, we developed a sustainable medium based on orange peel waste for the cultivation of C. glutamicum and demonstrated the successful production of the exemplary amino acids ʟ-arginine, ʟ-lysine, ʟ-serine, ʟ-valine and ʟ-tyrosine.

Novel polyurethane-degrading cutinase BaCut1 from Blastobotrys sp. G-9 with potential role in plastic bio-recycling

Environmental pollution caused by plastic waste has become global problem that needs to be considered urgently. In the pursuit of a circular plastic economy, biodegradation provides an attractive strategy for managing plastic wastes, whereas effective plastic-degrading microbes and enzymes are required. In this study, we report that Blastobotrys sp. G-9 isolated from discarded plastic in landfills is capable of depolymerizing polyurethanes (PU) and poly (butylene adipate-co-terephthalate) (PBAT). Strain G-9 degrades up to 60% of PU foam after 21 days of incubation at 28 ℃ by breaking down carbonyl groups via secretory hydrolase as confirmed by structural characterization of plastics and degradation products identification. Within the supernatant of strain G-9, we identify a novel cutinase BaCut1, belonging to the esterase family, that can reproduce the same effect. BaCut1 demonstrates efficient degradation toward commercial polyester plastics PU foam (0.5 mg enzyme/25 mg plastic) and agricultural film PBAT (0.5 mg enzyme/10 mg plastic) with 50% and 18% weight loss at 37 ℃ for 48 h, respectively. BaCut1 hydrolyzes PU into adipic acid as a major end-product with 42.9% recovery via ester bond cleavage, and visible biodegradation is also identified from PBAT, which is a beneficial feature for future recycling economy. Molecular docking, along with products distribution, elucidates a special substrate-binding modes of BaCut1 with plastic substrate analogue. BaCut1-mediated polyester plastic degradation offers an alternative approach for managing PU plastic wastes through possible bio-recycling.

Dietary lipid supplementation alleviated the impacts of polystyrene nanoplastic exposure in Litopenaeus vannamei

The widespread occurrence of nanoplastic (NP) pollution in the environment is a growing concern, and its presence poses a potential threat to cultured aquatic animals. Previously, we found that NPs can significantly affect the lipid metabolism of shrimp. However, relevant reports about the effects of increasing dietary lipid levels on NP toxicity are lacking. Therefore, we explored the effects of dietary supplementation with different lipid levels on the growth and lipid metabolism of Pacific white shrimp (Litopenaeus vannamei). We cultured L. vannamei at three dietary lipid levels (3 %, 6 %, and 9 %) and three NP concentrations (0, 1, and 3 mg/L) for 2 months. We evaluated the effects of lipid levels on growth indexes, hepatopancreas morphological structure, lipid metabolism-related enzyme activity, and gene expression of the shrimp. The results showed that as lipid intake increased, the survival rate, body weight growth rate, and hepatosomatic ratio of the shrimp increased while the feed conversion rate decreased. Additionally, the crude protein and crude lipid contents increased, whereas the moisture and ash contents did not change much. We found that the morphological structure of the hepatopancreas was seriously damaged in the 3 mg/L NPs and 3 % dietary lipid group. Finally, lipid metabolism-related enzyme activities and gene expression levels increased with increased dietary lipid levels. Together, these results suggest that increasing dietary lipid content can improve shrimp growth and alleviate lipid metabolism disorders caused by NPs. This study is the first to show that nutrition regulation can alleviate the toxicity of NPs, and it provides a theoretical basis for the green and healthy culture of L. vannamei.

Mechanisms and high-value applications of phthalate isomers degradation pathways in bacteria

Phthalate isomers are key intermediates in the biodegradation of pollutants including waste polyethylene terephthalate (PET) plastics and plasticizers. So far, an increasing number of phthalate isomer-degrading strains have been isolated, and their degradation pathways show significant diversity. In this paper, we comprehensively review the current status of research on the degrading bacteria, degradation characteristics, aerobic and anaerobic degradation pathways, and degradation genes (clusters) of phthalate isomers, and discuss the current shortcomings and challenges. Moreover, the degradation process of phthalate isomers produces many important aromatic precursor molecules, which can be used to produce higher-value derivative chemicals, and the modification of their degradation pathways holds good prospects. Therefore, this review also highlights the current progress made in modifying the phthalate isomer degradation pathway and explores its potential for high-value applications.

Biosynthesis of Polyhydroxyalkanoates in Cupriavidus necator B-10646 on Saturated Fatty Acids

It has been established that the wild-type Cupriavidus necator B-10646 strain uses saturated fatty acids (SFAs) for growth and polyhydroxyalkanoate (PHA) synthesis. It uses lauric (12:0), myristic (14:0), palmitic (16:0) and stearic (18:0) acids as carbon sources; moreover, the elongation of the C-chain negatively affects the biomass and PHA yields. When bacteria grow on C12 and C14 fatty acids, the total biomass and PHA yields are comparable up to 7.5 g/L and 75%, respectively, which twice exceed the values that occur on longer C16 and C18 acids. Regardless of the type of SFAs, bacteria synthesize poly(3-hydroxybutyrate), which have a reduced crystallinity (Cx from 40 to 57%) and a molecular weight typical for poly(3-hydroxybutyrate) (P(3HB)) (Mw from 289 to 465 kDa), and obtained polymer samples demonstrate melting and degradation temperatures with a gap of about 100 °C. The ability of bacteria to assimilate SFAs opens up the possibility of attracting the synthesis of PHAs on complex fat-containing substrates, including waste.

Mining strategies for isolating plastic-degrading microorganisms

Plastic waste is a growing global pollutant. Plastic degradation by microorganisms has captured attention as an earth-friendly tactic. Although the mechanisms of plastic degradation by bacteria, fungi, and algae have been explored over the past decade, a large knowledge gap still exists regarding the identification, sorting, and cultivation of efficient plastic degraders, primarily because of their uncultivability. Advances in sequencing techniques and bioinformatics have enabled the identification of microbial degraders and related enzymes and genes involved in plastic biodegradation. In this review, we provide an outline of the situation of plastic degradation and summarize the methods for effective microbial identification using multidisciplinary techniques such as multiomics, meta-analysis, and spectroscopy. This review introduces new strategies for controlling plastic pollution in an environmentally friendly manner. Using this information, highly efficient and colonizing plastic degraders can be mined via targeted sorting and cultivation. In addition, based on the recognized rules and plastic degraders, we can perform an in-depth analysis of the associated degradation mechanism, metabolic features, and interactions.

Potential synergy of microplastics and nitrogen enrichment on plant holobionts in wetland ecosystems

Wetland ecosystems are global hotspots for environmental contaminants, including microplastics (MPs) and nutrients such as nitrogen (N) and phosphorus (P). While MP and nutrient effects on host plants and their associated microbial communities at the individual level have been studied, their synergistic effects on a plant holobiont (i.e., a plant host plus its microbiota, such as bacteria and fungi) in wetland ecosystems are nearly unknown. As an ecological entity, plant holobionts play pivotal roles in biological nitrogen fixation, promote plant resilience and defense chemistry against pathogens, and enhance biogeochemical processes. We summarize evidence based on recent literature to elaborate on the potential synergy of MPs and nutrient enrichment on plant holobionts in wetland ecosystems. We provide a conceptual framework to explain the interplay of MPs, nutrients, and plant holobionts and discuss major pathways of MPs and nutrients into the wetland milieu. Moreover, we highlight the ecological consequences of loss of plant holobionts in wetland ecosystems and conclude with recommendations for pending questions that warrant urgent research. We found that nutrient enrichment promotes the recruitment of MPs-degraded microorganisms and accelerates microbially mediated degradation of MPs, modifying their distribution and toxicity impacts on plant holobionts in wetland ecosystems. Moreover, a loss of wetland plant holobionts via long-term MP-nutrient interactions may likely exacerbate the disruption of wetland ecosystems' capacity to offer nature-based solutions for climate change mitigation through soil organic C sequestration. In conclusion, MP and nutrient enrichment interactions represent a severe ecological risk that can disorganize plant holobionts and their taxonomic roles, leading to dysbiosis (i.e., the disintegration of a stable plant microbiome) and diminishing wetland ecosystems' integrity and multifunctionality.

Extraction Methods Determine the Quality of Soil Microbiota Acquisition

The soil microbiome plays a key role in plant health. Native soil microbiome inoculation, metagenomic profiling, and high-throughput cultivation require efficient microbe extraction. Sonication and oscillation are the most common methods used to extract soil microbiomes. However, the extraction efficiency of these methods has not been investigated in full. In this study, we compared the culturable microbe numbers, community structures, and alpha diversities among the different methods, including sonication, oscillation, and centrifugation, and their processing times. The study results showed that sonication significantly increases the culturable colony number compared with oscillation and centrifugation. Furthermore, the sonication strategy was found to be the main factor influencing extraction efficiency, but increased sonication time can aid in recovery from this impact. Finally, the extraction processing times were found to have a significant negative relationship with α-diversity among the extracted microbiota. In conclusion, sonication is the main factor for enriching in situ microbiota, and increased extraction time significantly decreases the α-diversity of the extracted microbiota. The results of this study provide insights into the isolation and utilization of different microorganism sources.

Ductile Copolyesters Prepared Using Succinic Acid, 1,4-Butanediol, and Bis(2-hydroxyethyl) Terephthalate with Minimizing Generation of Tetrahydrofuran

Poly(1,4-butylene succinate) (PBS) is a promising sustainable and biodegradable synthetic polyester. In this study, we synthesized PBS-based copolyesters by incorporating 5-20 mol% of -O2CC6H4CO2- and -OCH2CH2O- units through the polycondensation of succinic acid (SA) with 1,4-butanediol (BD) and bis(2-hydroxyethyl) terephthalate (BHET). Two different catalysts, H3PO4 and the conventional catalyst (nBuO)4Ti, were used comparatively in the synthesis process. The copolyesters produced using the former were treated with M(2-ethylhexanoate)2 (M = Mg, Zn, Mn) to connect the chains through ionic interactions between M2+ ions and either -CH2OP(O)(OH)O- or (-CH2O)2P(O)O- groups. By incorporating BHET units (i.e., -O2CC6H4CO2- and -OCH2CH2O-), the resulting copolyesters exhibited improved ductile properties with enhanced elongation at break, albeit with reduced tensile strength. The copolyesters prepared with H3PO4/M(2-ethylhexanoate)2 displayed a less random distribution of -O2CC6H4CO2- and -OCH2CH2O- units, leading to a faster crystallization rate, higher Tm value, and higher yield strength compared to those prepared with (nBuO)4Ti using the same amount of BHET. Furthermore, they displayed substantial shear-thinning behavior in their rheological properties due to the presence of long-chain branches of (-CH2O)3P=O units. Unfortunately, the copolyesters prepared with H3PO4/M(2-ethylhexanoate)2, and hence containing M2+, -CH2OP(O)(OH)O-, (-CH2O)2P(O)O- groups, did not exhibit enhanced biodegradability under ambient soil conditions.