The persistence of polyethylene (PE) waste poses a major global environmental challenge due to its intrinsic resistance to biodegradation, which limits the application of engineered microorganisms in plastic waste treatment. In this study, an efficient low-density polyethylene (LDPE)-degrading system was developed using Yarrowia lipolytica Po1g as the chassis organism. Through screening of manganese peroxidases and laccases combined with a fluorescence-guided surface display system, we constructed two engineered strains, YME19 and YME20, exhibiting strong oxidative depolymerization activity. Synergistic enhancement of ultraviolet (UV)pretreated LDPE film degradation was achieved by Cu2+, 1-hydroxybenzotriazole (HBT), and tyrosol, with tyrosol showing the most prominent effect. After 7 days of treatment with YME20, the LDPE film exhibited a mass loss of 2.92% (equivalent to 5.84 mg). This was accompanied by pronounced surface erosion, including irregular deep pits, cracks, and increased pore density. Meanwhile, the surface hydrophilicity was significantly enhanced, as evidenced by a reduction of approximately 10.57 degrees in the water contact angle. ATR-FTIR analysis demonstrated extensive oxidative modification through the enrichment of oxygen-containing functional groups, while AFM and GC-MS analyses confirmed increased surface roughness and the formation of n-hexadecane, providing direct evidence of PE carbon-chain scission. Transcriptomic analysis elucidated the mechanism of tyrosol-enhanced degradation. Acting as a stress signal, tyrosol induces metabolic reprogramming that suppresses growth-associated metabolism while activating tolerance, DNA repair, and autophagy mechanisms. Furthermore, it strengthens biofilm formation through cell-wall remodeling and surface adhesion, collectively sustaining high degradation activity on the plastic surface. This study elucidates the pivotal role of tyrosol in LDPE biodegradation and provides a novel strategic framework for employing engineered yeast in the treatment of recalcitrant polymer wastes.

Microbial degradation of petroleum hydrocarbons is a cost-effective and eco-friendly strategy. However, it is often limited by nitrogen availability. In this study, engineered Saccharomyces cerevisiae strains were developed for efficient n-hexadecane degradation with enhanced tolerance to nitrogen starvation. The chassis strain SAH02 was initially modified by introducing alcohol dehydrogenase genes and laccase genes, followed by the over-expression of signal peptide genes to enhance laccase secretion. Among these engineered strains, SAH24 exhibited the highest degradation rate, achieving 51.95% for 10 g/L n-hexadecane under normal nitrogen condition after 96 h, which was significantly higher than that of SAH02 (19.68%). Under nitrogen starvation condition, although the degradation rate and final biomass of SAH24 decreased, its specific degradation rate increased significantly compared to that under normal nitrogen condition. Transcriptomic analysis of SAH24 under nitrogen starvation revealed upregulation of genes related to the tricarboxylic acid cycle, glyoxylate cycle, pyruvate dehydrogenase bypass, pentose phosphate pathway, n-hexadecane oxidation, and cell membrane transport. Based on these findings, nineteen candidate genes were selected for overexpression in SAH24 to further optimize its performance. The engineered strain SAH48 (co-overexpression of ACS1, ALD4, and HXT5) exhibited significantly improved n-hexadecane degradation rates of 57.52% under nitrogen starvation and 68.75% under normal nitrogen condition, compared with SAH24 (41.83% under nitrogen starvation and 51.95% under normal nitrogen).

Large-scale harmful algal blooms pose serious environmental and economic problems worldwide. Leptolyngbya boryana is a globally distributed filamentous cyanobacterium with physiological and ecological traits that favor bloom formation. However, its study and biotechnological use have been limited by the lack of effective genetic manipulation methods. In this work, we established a comprehensive genetic toolbox for L. boryana using strain FACHB-240 as a model. Genome analysis was first performed to define its genomic features, predict gene functions, and determine phylogenetic relationships. Based on this information, we developed practical engineering components, including suitable antibiotic markers, a set of promoters, inducible expression systems, identified genomic integration sites, and a conjugative DNA transfer method. To demonstrate the usefulness of the toolbox, a 26-kb fragment of a cyanophage genome that infects FACHB-240 was successfully integrated into the genome of host strain. Together, these tools provide a foundation for future synthetic biology studies and for developing green biotechnological applications involving L. boryana FACHB-240.

Polyethylene (PE) poses a persistent challenge to global environmental pollution. In this study, a bacterial strain, Arthrobacter sp. PE01, was isolated from landfill leachate and found to be capable of degrading low-density polyethylene (LDPE). A weight loss of 3.23% was observed over 49 d of incubation. Multi-technique characterization, including Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and atomic force microscopy (AFM), confirmed surface erosion and oxidation. Quantitative analyses further revealed that after 30 d of treatment, the water contact angle (WCA) on unwashed films decreased from 102.66 degrees to 57.73 degrees, and energy-dispersive X-ray spectroscopy (EDX) showed a decrease in surface carbon from 96.92% to 69.03% with corresponding increases in oxygen (to 19.16%) and nitrogen (to 11.81%) within 30 d. Gas chromatographymass spectrometry (GC-MS) identified n-hexadecane and n-eicosane as degradation intermediates, and the strain degraded these alkanes by 46.35% and 42.28% within 7 d. Biofilm formation was shown to be a critical initial step that modifies surface hydrophobicity and facilitates subsequent enzymatic attack. Whole-genome sequencing further elucidated a four-stage pathway potentially involved in this process, including quorumsensing-mediated biofilm formation, multi-enzyme depolymerization, assimilation by beta-oxidation, and mineralization via the TCA cycle. These findings contribute to a mechanistic understanding of polymer-microbe interactions and may inform the development of biofilm-mediated processes for plastic waste management.

BackgroundArtificial microbial consortium has been widely employed to improve the production of fengycin, a natural lipopeptide. Kinetic models are essential for understanding and predicting the dynamic behavior of metabolic systems, especially microbial consortia. Since the time evolution of metabolite concentrations and biomass is continuous and dynamic, systems of ordinary differential equations (ODEs) provide a natural and effective framework for capturing such interactions. In this work, a kinetic model based on ODEs was established to describe a multi-strain artificial consortium for fengycin synthesis, utilizing Bacillus subtilis, Yarrowia lipolytica, and Corynebacterium glutamicum as target strains.ResultsThe model captures microbial growth, intermediate metabolite formation, final product synthesis, and substrate consumption. It was successfully applied to analyze and interpret the cultivation data of target strains on various substrates. The model explicitly incorporates the accumulation of amino acids synthesized by C. glutamicum, the accumulation of fatty acids synthesized by Y. lipolytica, and the process in which B. subtilis utilized amino acids and fatty acids as partial precursors for fengycin production. The mathematical model ended up as a nonlinear ordinary differential system, which was solved with an adaptive step-size Runge-Kutta method, coupled with a genetic algorithm to roughly estimate the optimal model parameters associated with cellular growth, substrate consumption, and product level in fermentation broths.ConclusionsThe numerical results of the kinetic model agreed well with experimental data, and all seven sets of experimental conditions were fitted with overall relative errors ranging from 7.4 to 15.1%. This kinetic modeling provided a meaningful tool for the rational design and construction of further artificial consortia.

Polyethylene terephthalate (PET) is one of the most widely used plastic materials, and its large-scale application has caused severe environmental pollution. Compared to traditional physical and chemical degradation methods, biological degradation is considered the most promising approach. In this context, this review starts with the current research status of PET plastic microbial degradation. Then, it summarizes the construction of strains for heterologous expression of PET-degrading enzymes, the development status of whole-cell catalysts, the innovative ideas of microbial consortia and microorganism-enzyme systems, and the application development of microorganism-functional material systems. In addition, this review includes the use of multiple characterization methods to monitor the degradation effects of PET and changes in strain characteristics, providing theoretical evidence for PET degradation research. Finally, the researches on valorization of PET degradation monomers through synthetic biology are discussed, underscoring the potential of microbial degradation in PET waste upcycling.

Microbial degradation of petroleum hydrocarbons plays an essential role in mitigating petroleum contamination. However, high-salt stress in petroleum-contaminated environments can significantly reduce the efficiency of microbial degradation. In this study, transcriptome analysis was carried out on Yarrowia lipolytica (YAH13) to elucidate the osmoprotective mechanism of erythritol under high-salt stress (1.5 M NaCl), revealing its multifaceted role in maintaining intracellular energy homeostasis and lipid metabolism during high-salinity stress. Thus, YAH13 was engineered to enhance the alkane degradation rate under high-salt stress. Among the obtained strains, YAO09, which enhanced the lipid droplet synthesis and fatty acid metabolism pathways, exhibited a significantly enhanced alkane degradation rate of 83.2% under nonstress and 77.2% under high-salt stress conditions over YAH13 (72.1% under nonstress and 65.2% under high-salt stress). YAO10, which enhanced the erythritol synthesis pathway, was virtually unaffected by high-salt stress. It showed a degradation rate of 76.7% under high-salt stress, which was similar to that under nonstress conditions (77.7%). This study offers new possibilities for the effective degradation of petroleum pollutants and the enhancement of tolerance to high-salt stress in the bioremediation process.

Petroleum hydrocarbon pollution has become one of the global environmental problems, posing a serious threat to the environment and human health. Microbial remediation plays an important role in the remediation of petroleum hydrocarbon-contaminated environment. Nevertheless, the stress factors present in the environment polluted by petroleum hydrocarbons limit the effectiveness of microbial remediation. This paper reviews the common stress factors in petroleum hydrocarbon-polluted environment and the response mechanisms of microorganisms to these factors. Furthermore, we introduce the methods to improve microbial tolerance, such as irrational modification, rational modification based on systems biology tools or tolerance mechanisms, and the construction of microbial consortia. The application of these methods is expected to improve the viability and remediation efficiency of microorganisms in petroleum hydrocarbon-contaminated environment and provide new perspectives and technical support for environmental remediation.

The current extensive production and widespread use of polyethylene (PE) has resulted in the accumulation of its waste in the environment, posing a significant threat to the global ecosystem and human health. Biodegradation is regarded as an environmentally sustainable approach for plastic waste treatment. However, achieving high biodegradation efficiency of PE is primary challenge. In this study, the engineered Yarrowia lipolytica strains, expressing heterologous PE-degrading enzymes, were successfully constructed for enhancing degradation of pretreated low-density polyethylene (LDPE) at room temperature. SEM results showed significant changes in surface roughness and erosion of pretreated samples after incubation with the engineered strains of alkane hydroxylase-secreting YPE04 and laccase-secreting YPE10. Notably, YPE04 and YPE10 reduced the weight of LDPE films by 8.9 +/- 0.9 % and 11.8 +/- 0.7 %, respectively, within 7 days. It was further clarified by GC-MS that the main degradation products of LDPE films by the aforementioned two engineered strains were 9-octadecenoic acid and n-dodecyl methacrylate, respectively. Overall, two strains, YPE04 and YPE10, were obtained with great potential for LDPE degradation. This study not only provides a reference for the construction of efficient PE- degrading strains but also offers new ideas for the application of bioremediation technology in plastic waste management.

As a lipopeptide, fengycin exhibits environmentally friendly, safe, and long-lasting biocontrol efficacy. However, due to its complex structure and the challenges in chemical synthesis, it is primarily produced through biosynthesis. This study reports an improvement in fengycin production in Bacillus subtilis by engineering the central carbon metabolic pathway and blocking the carbon overflow pathway. The highest production achieved 1290.31 mg/L, representing a 2.05-fold increase compared to the original strain. Additionally, a coculture system was established in which Corynebacterium glutamicum supplied proline to strain CGF-PA, achieving a further increase in production to 2491.97 mg/L. The fengycin homologues were characterized using IMS-MS and separated by preparative liquid chromatography. The antifungal activities of fengycin homologues were quantitatively evaluated against Fusarium graminearum, Botrytis cinerea, Pyricularia oryzae, and Rhizoctonia solani, and their morphological changes were observed. The study also investigated the differences in antifungal activity among the fengycin variants. Components 4, 5, 6, and 7 exhibited relatively strong antifungal activity, and the various components of fengycin were found to work synergistically.

Biodegradation of Polyethylene Terephthalate (PET) offer a strategic avenue for addressing the global plastic pollution crisis. However, the degradation performance of PET hydrolases remains a technological bottleneck for the industrial realization of plastic biodegradation. In this study, we employed an integrated strategy combining semi-rational design and directed evolution to discover new mutation sites (N114, N205, N233 and S269) that enhance the catalytic activity and thermostability of Ideonella sakaiensis PETase (IsPETase). Subsequently, through the combined design of newly discovered mutation sites, we screened the novel quadruple mutant (N114I/N205K/N233K/S269V, named QM-PETase-2), which exhibited a 4.9-fold increase in catalytic efficiency and a ΔTm of +12.4 °C. Interestingly, the four newly discovered mutation sites are all located in the loop region of the enzyme structure, which might play a crucial role on the structural stability of enzyme. Also, molecular dynamics simulations revealed that the QM-PETase-2 exhibited a more stable structure and an expanded substrate-binding cleft, which would facilitate the binding of the polymer PET substrate. Especially, the newly quadruple mutation sites were introduced into three reported high-performance PETase mutants FAST-PETase, PA-PETase, and DepoPETase. The obtained combined mutants, named QMFAST-PETase, QMPA-PETase, and QM-DepoPETase, demonstrated higher activity and thermal stability, indicating that the newly discovered mutations are universal for improving the performance of PETase. This research would be helpful in guiding the optimization and development of PETase.

Due to their bacteriostatic or bactericidal effects, antibiotics are widely used in the prevention and treatment of human and animal diseases. However, their irrational utilization has caused severe environmental pollution and threatened human health and safety through food chain. Given the critical limitations of traditional antibiotic detection methods, such as high costs, technical complexity, and time-consuming operations, it is essential to develop robust, accurate, sensitive, and field-deployable technologies for antibiotic detection. In recent years, biosensors have emerged as powerful tools for antibiotic detection, owing to their advantages of fast response, high accuracy, excellent sensitivity, and cost-effectiveness. This review systematically summarizes the working principles of biosensors based on different biological recognition elements (enzymes, antibodies, cells, and aptamers), and comprehensively discusses their specific applications in the field of antibiotic detection. Additionally, the article elaborates on the critical roles of signal amplification technologies and artificial intelligence in optimizing biosensor performance, accelerating the discovery of novel antimicrobial drugs, and enabling rapid data processing. It is worth mentioning that we analyzed the potential drawbacks of each recognition element, as well as the practical challenges faced by integrating various signal amplification technologies and artificial intelligence into different types of biosensors. Finally, the future challenges and development directions of biosensors is outlined to provide valuable insights and references for researchers in this field.

Ethylene glycol, a pivotal monomer from polyethylene terephthalate (PET) degradation, is crucial for transforming into high-value products to support a circular economy in plastics. However, the metabolic complexities and suboptimal fermentation results impede its efficient conversion to glycolic acid. In this study, the cell factory of Escherichia coli was successfully constructed for converting ethylene glycol into glycolic acid, advancing its application as a sustainable feedstock alternative in bioprocess. Based on transcriptomic data and metabolic engineering, 15 identified genes led to an obvious boost in production, up to 12.8 %. Adopting pH-controlled fermentation, strains YF2G*GA3 and YF2G*GA23 achieved unprecedented glycolic acid titers utilizing ethylene glycol in Escherichia coli. YF2G*GA3, in particular, attained a yield of 1.13 g/g with a yield of 91.87 %, greatly outperforming the original YFGA strain's 0.67 g/g yield. In conclusion, the power of metabolic engineering guided by transcriptomic data was exemplified. It not only provides new strategies for microbial platform of glycolic acid production, but also supports the circular plastic economy.

High-salt content in food waste (FW) affects its resource utilization during biotransformation. In this study, adaptive laboratory evolution (ALE), gene editing, and artificial consortia were performed out to improve the salt-tolerance of Bacillus amyloliquefaciens for producing lipopeptide under FW and seawater. High-salt stress significantly decreased lipopeptide production in the B. amyloliquefaciens HM618 and ALE strains. The total lipopeptide production in the recombinant B. amyloliquefaciens HM-4KSMSO after overexpressing the ion transportor gene ktrA and proline transporter gene opuE and replacing the promoter of gene mrp was 1.34 times higher than that in the strain HM618 in medium containing 30 g/L NaCl. Lipopeptide production under salttolerant consortia containing two strains (HM-4KSMSO and Corynebacterium glutamicum) and three-strains (HM-4KSMSO, salt-tolerant C. glutamicum, and Yarrowia lipolytica) was 1.81- and 2.28-fold higher than that under pure culture in a medium containing FW or both FW and seawater, respectively. These findings provide a new strategy for using high-salt FW and seawater to produce value-added chemicals.

Fengycin has great potential for applications in biological control because of its biosafety and degradability. In this study, the addition of exogenous precursors increased fengycin production by Bacillus subtilis. Corynebacterium glutamicum was engineered to produce high levels of precursors (Thr, Pro, Val, and Ile) to promote the biosynthesis of fengycin. Furthermore, recombinant C. glutamicum and Yarrowia lipolytica providing amino acid and fatty acid precursors were co-cultured to improve fengycin production by B. subtilis in a three-strain artificial consortium, in which fengycin production was 2100 mg·L-1. In addition, fengycin production by the consortium in a 5 L bioreactor reached 3290 mg·L-1. Fengycin had a significant antifungal effect on Rhizoctonia solani, which illustrates its potential as a food preservative. Taken together, this work provides a new strategy for improving fengycin production by a microbial consortium and metabolic engineering.

Iturin A biosynthesis has garnered considerable interest, yet bottlenecks persist in its low productivity in wild strains and the ability to engineer Bacillus amyloliquefaciens producers. This study reveals that deleting the endogenous plasmid, plas1, from the wild-type B. amyloliquefaciens HM618 notably enhances iturin A synthesis, likely related to the effect of the Rap phosphatase gene within plas1. Furthermore, inactivating Rap phosphatase-related genes (rapC, rapF, and rapH) in the genome of the strain also improved the iturin A level and specific productivity while reducing cell growth. Strategic rap genes and plasmid elimination achieved a synergistic balance between cell growth and iturin A production. Engineered strain HM-DR13 exhibited an increase in iturin A level to 849.9 mg/L within 48 h, significantly shortening the production period. These insights underscore the critical roles of endogenous plasmids and Rap phosphatases in iturin A biosynthesis, presenting a novel engineering strategy to optimize iturin A production in B. amyloliquefaciens.

Although fengycin exhibits broad-spectrum antifungal properties, its application is hindered due to its low biosynthesis level and the co-existence of iturin A and surfactin in Bacillus amyloliquefaciens HM618, a probiotic strain. In this study, transcriptome analysis and gene editing were used to explore the potential mechanisms regulating fengycin production in B. amyloliquefaciens. The fengycin level of B. amyloliquefacien HM-3 (∆itu-ΔsrfAA) was 88.41 mg/L after simultaneously inhibiting the biosyntheses of iturin A and surfactin. The knockout of gene eps associated with biofilm formation significantly increased the fengycin level of the strain HM618, whereas the fengycin level decreased 32.05

Microbial degradation of petroleum hydrocarbons plays a vital role in mitigating petroleum contamination and heavy oil extraction. In this study, a Saccharomyces cerevisiae capable of degrading hexadecane has been successfully engineered, achieving a maximum degradation rate of up to 20.42%. However, the degradation ability of this strain decreased under various pressure conditions such as high temperature, high osmotic pressure, and acidity conditions. Therefore, a S. cerevisiae with high tolerance to these conditions has been constructed. And then, we constructed an “anti-stress hydrocarbon-degrading” consortium comprising engineered yeast strain SAH03, which degrades hexadecane, and glutathione synthetic yeast YGSH10, which provides stress resistance. This consortium was able to restore the degradation ability of SAH03 under various pressure conditions, particularly exhibiting a significant increase in degradation rate from 5.04% to 17.04% under high osmotic pressure. This study offers a novel approach for improving microbial degradation of petroleum hydrocarbons.

There has been extensive research on the biological recycling of PET waste to address the issue of plastic waste pollution, with ethylene glycol (EG) being one of the main components recovered from this process. Therefore, finding ways to convert PET monomer EG into high-value products is crucial for effective PET waste recycling. In this study, we successfully engineered Escherichia coli to utilize EG and produce glycolic acid (GA), expecting to facilitate the biological recycling of PET waste. The engineered E. coli, able to utilize 10 g/L EG to produce 1.38 g/L GA within 96 h, was initially constructed. Subsequently, strategies based on overexpression of key enzymes and knock-out of the competing pathways are employed to enhance EG utilization along with GA biosynthesis. An engineered E. coli, characterized by the highest GA production titer and substrate conversion rate, was obtained. The GA titer increased to 5.1 g/L with a yield of 0.75 g/g EG, which is the highest level in the shake flake experiments. Transcriptional level analysis and metabolomic analysis were then conducted, revealing that overexpression of key enzymes and knock-out of the competing pathways improved the metabolic flow in the EG utilization. The improved metabolic flow also leads to accelerated synthesis and metabolism of amino acids.

Lipopeptides possess significant antifungal activity and serve as eco-friendly biopesticides. However, their widespread application is limited by exorbitant production costs and low yields. Food waste emerges as a promising substrate for lipopeptide production. To efficiently harness the starch in food waste during bioconversion it into lipopeptides, the engineered Bacillus amyloliquefaciens HM618, constructed by knocking out multiple extracellular proteolytic enzyme genes (aprE, nprE, vpr, and epr) and overexpressing gene amyA with Phag promoter, capable of producing both high-level extracellular amylase and lipopeptides. It was found that the recombinant B. amyloliquefaciens HM3-5 in the pure culture containing starch exhibited notable amylase activity about 17046.37U/mL, a total of 2530.72mg/L lipopeptides, and 80.02% degradation rate of starch. Considering the crucial roles of fatty acids and amino acids precursors in lipopeptide synthesis, these engineered B. amyloliquefaciens producing higher-level extracellular amylase, Y. lipolytica producing fatty acids, and C. glutamicum releasing proline and serine were integrated to construct an artificial consortium for efficiently bio-converting food waste into lipopeptides. After optimized inoculation times and ratios of these engineered strains, the levels of surfactin, fengycin, and iturin A in the four-strains artificial consortium during food waste bioconversion reached 8690.67, 635.83, and 74.19mg/L, respectively. The total lipopeptides in the four-strains artificial consortium reached 9400.69mg/L, 2.38-fold increase compared to that in the pure culture of strain HM3-5. Furthermore, the degradation efficiencies of starch and oil in food waste were 96.41% and 98.35%, respectively. This work provides a new strategy for efficiently bio-transforming food waste into lipopeptides.