Biodegradation of polybutylene adipate-co-terephthalate by Priestia megaterium, Pseudomonas mendocina, and Pseudomonas pseudoalcaligenes following incubation in the soil

Enzymatic degradation of PET by hydrolase from Brucella intermedia IITR130 and its genomic insights

Plastic pollution, particularly from polyethylene terephthalate (PET), has become a significant environmental concern, necessitating innovative and sustainable degradation strategies. The present study provides valuable perspectives on the genomic and functional characteristics of Brucella intermedia IITR130, a bacterium capable of degrading PET. Hybrid genome sequencing of IITR130 resulted in identification of two chromosomes combining 4.59 Mbp size. Genomic annotation revealed occurrence of key enzymes involved in the PET sheet biodegradation pathway, including hydrolases, ring hydroxylating dioxygenases, protocatechuate 3,4 dioxygenases, genes for metabolism of several other natural and synthetic plastic. A hydrolase gene Hy1 of 24 kDa, was identified, expressed, and characterized, demonstrating an optimal catalytic activity at 37 °C and pH 8.5. Scanning electron microscopy (SEM) and fourier-transform infrared spectroscopy (FTIR) confirmed substantial degradation of PET surfaces treated with Hy1 protein, resulted in surface erosion, crack formation, and functional group modifications in the range 2150-2550 cm⁻1 and 2950-3350 cm⁻1 suggestive of O=C=O stretching and O-H stretching respectively. Monomethyl terephthalate (MMT) and terephthalic acid (TPA) were identified as PET degradation metabolites formed by strain IITR130. Fluorescence quenching showed higher substrate affinity for bis(2-hydroxyethyl) terephthalate (BHET) (Kd = 148.2) than terephthalic acid (TPA) (Kd = 674). Moreover, phylogenetic analysis of Hy1 protein revealed that Hy1 containing conserved catalytic triad (Ser108, His188, Asp155) belonging to the family III of hydrolase enzyme sharing a clade with PET degrading hydrolase PETase from Ideonella sakaiensis. These results demonstrate the potential of B. intermedia IITR130 as an efficient biocatalyst for PET biodegradation which could be exploited appropriately for plastic waste management.

Deep learning-enhanced hyperspectral imaging for rapid screening of Co-metabolic microplastic-degrading bacteria in environmental samples

Microbial biodegradation of microplastic (MP) emerges as an environmentally benign and highly promising strategy for alleviating MP pollution in the ecosystem. Conventional approaches for screening MP-degrading bacteria use pollutants as the sole carbon source. Co-metabolism plays an essential role in microbial screening, as it enables the discovery of additional degrading microorganisms. However, identifying co-metabolic degrading bacteria is challenging and time-intensive, as not all microorganisms on a co-metabolic medium exhibit degradation capability, increasing the need for refined screening methods. In this study, we propose a novel hyperspectral imaging (HSI) approach to rapidly screen polybutylene adipate terephthalate (PBAT) degrading bacteria directly from co-metabolic media. Hyperspectral images of solid media cultures were acquired, capturing both spatial (image) and spectral (chemical) information. Chemical components in the solid medium exhibit distinct changes under the influence of degrading and non-degrading bacteria. By analyzing the spectral information using machine and deep learning algorithms, it was possible to monitor the PBAT concentration changes in the solid medium, indirectly identifying degrading and non-degrading bacteria. This HSI-based model successfully screened out one kind of PBAT-degrading bacteria validated by traditional method, demonstrating potential for rapid screening of MP-degrading bacteria. With artificial intelligence (AI) technology attracting extensive attention across diverse fields, this study pioneers a new approach for the efficient screening of degrading microorganisms by combining AI algorithms with HSI. This innovative methodology is expected to display significant application potential, thus facilitating the research and development in related fields. SYNOPSIS: This study introduces a highly efficient method to screen co-metabolic MP-degrading bacteria. By combining HSI with deep learning, MP-degrading bacteria can be directly identified on co-metabolism solid media, greatly enhancing the efficiency of screening for MP-degrading microorganisms.

Fungal biodegradation of poly(butylene adipate-co-terephthalate)-polylactic acid-thermoplastic starch based commercial bio-plastic film at ambient conditions

Microbial biodegradation of commercially available poly(butylene adipate-co-terephthalate)-polylactic acid-thermoplastic starch based bio-plastic has been pursued at high temperatures exceeding 55 °C. Herein, we first reported three newly isolated fungal strains from farmland soil samples of Republic of Korea namely, Pyrenochaetopsis sp. strain K2, Staphylotrichum sp. S2-1, and Humicola sp. strain S2-3 were capable of degrading a commercial bio-plastic film with degradation rates of 9.5, 8.6, and 12.2%, respectively after 3 months incubation at ambient conditions. Scanning electron microscopy (SEM) analyses showed that bio-plastic film was extensively fragmented with severe cracking on the surface structure after incubation with isolated fungal strains. X-ray diffraction (XRD) analysis also revealed that high crystallinity of the commercial bio-plastic film was significantly decreased after degradation by fungal strains. Liquid chromatography-mass spectrometry (LC-MS) analyses of the fungal culture supernatants containing the bio-plastic film showed the peaks for adipic acid, terephthalic acid (TPA), and terephthalate-butylene (TB) as major metabolites, suggesting cleavage of ester bonds and accumulation of TPA. Furthermore, a consortium of fungal strain K2 with TPA degrading bacterium Pigmentiphaga sp. strain P3-2 isolated from the same sampling site exhibited faster degradation rate of the bio-plastic film within 1 month of incubation with achieving complete biodegradation of accumulated TPA. We assume that the extracellular lipase activity presented in the fungal cultures could hydrolyze the ester bonds of PBAT component of bio-plastic film. Taken together, the fungal and bacterial consortium investigated herein could be beneficial for efficient biodegradation of the commercial bio-plastic film at ambient conditions.

Metagenomic exploration of microbial and enzymatic traits involved in microplastic biodegradation

Agricultural mulch films are frequently applied to achieve high yield, resulting in large quantities of microplastic (MP) pollution in agroecosystem. However, studies focusing specifically on the diversity of MP-degrading enzymes and related microbial communities have yet to be conducted. Here, we established a soil microcosmic incubation with addition of 5% (w/w) conventional (low-density polyethylene (LDPE)) and biodegradable (blend of polylactic acid (PLA) and polybutylene adipate terephthalate (PBAT)) MPs for incubation 90 days. The DNA samples extracted from soils and plastisphere of MPs were examined by metagenomics and genome binning methods, specifically targeting carbohydrate-active enzymes (CAZymes) and plastic-degrading enzymes (PDZymes). The results revealed that plastisphere of MPs exhibited significantly distinct patterns of CAZymes and PDZymes from soils, and abundances of all examined exoenzymes were higher in plastisphere than those in soils. Plastisphere of LDPE-MPs selectively enriched proteases and alkane monooxygenase (alkB), and required families of carbohydrate-binding module (CBM) to increase the binding of CAZymes with MPs. Dissimilarly, diverse CAZymes with high abundances were observed in the plastisphere of PBAT-PLA MPs and esterases were important indicative PDZymes for PBAT-PLA degradation. The enriched exoenzymes in plastisphere of LDPE-MPs were mainly assigned to Actinobacteria while Proteobacteria with higher abundance in plastisphere of PBAT-PLA MPs containing most indicative exoenzymes. Moreover, a high-quality genome classified as Amycolatopsis japonica was reconstructed and found to contain one or more gene copies of indicative exoenzymes for polyethylene. Two novel genomes classified as Sphingomonas were selectively enriched in plastisphere of PBAT-PLA MPs and contained diverse genes encoding degrading exoenzymes. Taken together, our study highlighted the CAZymes and PDZymes can be exploited as potent microbial strategies for solving MPs pollution in croplands.

Microorganisms that produce enzymes active on biodegradable polyesters are ubiquitous

Biodegradability standards measure ultimate biodegradation of polymers by exposing the material under test to a natural microbial inoculum. Available tests developed by the International Organization for Standardization (ISO) use inoculums sampled from different environments e.g. soil, marine sediments, seawater. Understanding whether each inoculum is to be considered as microbially unique or not can be relevant for the interpretation of tests results. In this review, we address this question by consideration of the following: (i) the chemical nature of biodegradable plastics (virtually all biodegradable plastics are polyesters) (ii) the diffusion of ester bonds in nature both in simple molecules and in polymers (ubiquitous); (iii) the diffusion of decomposers capable of producing enzymes, called esterases, which accelerate the hydrolysis of esters, including polyesters (ubiquitous); (iv) the evidence showing that synthetic polyesters can be depolymerized by esterases (large and growing); (v) the evidence showing that these esterases are ubiquitous (growing and confirmed by bioinformatics studies). By combining the relevant available facts it can be concluded that if a certain polyester shows ultimate biodegradation when exposed to a natural inoculum, it can be considered biodegradable and need not be retested using other inoculums. Obviously, if the polymer does not show ultimate biodegradation it must be considered recalcitrant, until proven otherwise.

Enhancing biodegradation of PBAT through bio-stimulation using Pseudozyma jejuensis for effective plastic waste reduction

Polybutylene adipate-co-terephthalate (PBAT) is a flexible and biodegradable material that finds applications in mulching film and the food packaging industry. In this study, we aimed to address the global plastic waste problem by developing an improved biodegradation system for PBAT. Our focus was on utilizing the biodegradation capabilities of Pseudozyma jejuensis, a microorganism known for its ability to decompose Polycaprolactam (PCL). Through bio-stimulation, we aimed to enhance the growth mechanism of P. jejuensis and optimize PBAT biodegradation. Our results demonstrated significant structural changes in the PBAT film, as revealed by FT-IR analysis. Moreover, FE-SEM imaging exhibited evident surface erosion and pitting, indicating physical alterations due to biodegradation. These findings provide strong evidence for the efficiency of our developed biodegradation system. To fully harness the potential of this system and enable its practical implementation, further research is warranted to optimize and scale up the process. Our work contributes to the ongoing efforts to combat the global plastic waste crisis, offering a valuable solution for the efficient biodegradation of PBAT.

Microorganisms and Biochar Improve the Remediation Efficiency of Paspalum vaginatum and Pennisetum alopecuroides on Cadmium-Contaminated Soil

Phytoremediation can help remediate potential toxic elements (PTE) in soil. Microorganisms and soil amendments are effective means to improve the efficiency of phytoremediation. This study selected three microorganisms that may promote phytoremediation, including bacteria (Ceratobasidium), fungi (Pseudomonas mendocina), and arbuscular-mycorrhizal fungi (AMF, Funneliformis caledonium). The effects of single or mixed inoculation of three microorganisms on the phytoremediation efficiency of Paspalum vaginatum and Pennisetum alopecuroides were tested under three different degrees of cadmium-contaminated soil (low 10 mg/kg, medium 50 mg/kg, and high 100 mg/kg). The results showed that single inoculation of AMF or Pseudomonas mendocina could significantly increase the biomass of two plants under three different degrees of cadmium-contaminated soil, and the growth-promoting effect of AMF was better than Pseudomonas mendocina. However, simultaneous inoculation of these two microorganisms did not show a better effect than the inoculation of one. Inoculation of Ceratobasidium reduced the biomass of the two plants under high concentrations of cadmium-contaminated soil. Among all treatments, the remediation ability of the two plants was the strongest when inoculated with AMF alone. On this basis, this study explored the effect of AMF combined with corn-straw-biochar on the phytoremediation efficiency of Paspalum vaginatum and Pennisetum alopecuroides. The results showed that biochar could affect plant biomass and Cd concentration in plants by reducing Cd concentration in soil. The combined use of biochar and AMF increased the biomass of Paspalum vaginatum by 8.9-48.6% and the biomass of Pennisetum alopecuroides by 8.04-32.92%. Compared with the single use of AMF or biochar, the combination of the two is better, which greatly improves the efficiency of phytoremediation.