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Dassouki Dit Tahan M, Canbulat Özdemir M, Sanin FD, İmamoğlu İ. Bio-Aging of polyethylene during anaerobic and aerobic digestion. BIORESOURCE TECHNOLOGY 2025; 427:132395. [PMID: 40086698 DOI: 10.1016/j.biortech.2025.132395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 03/10/2025] [Accepted: 03/10/2025] [Indexed: 03/16/2025]
Abstract
Presence of microplastics (MPs) in wastewater treatment plants (WWTPs) require scrutiny from two perspectives: impact of MPs on treatment and on MPs themselves. Accordingly, this study investigates the impact of high-density polyethylene (HDPE) and low-density polyethylene (LDPE) on mesophilic aerobic and anaerobic digestion, with their concurrent characterization to discern MP biodegradation following digestion. HDPE having UV-stabilizer remains unchanged, whereas additive-free LDPE bio-ages, in both cases. On the flip side, HDPE negatively impacts anaerobic (i.e., 26 % reduction in methane) but not aerobic digestion, while LDPE affects neither. The very high LDPE doses used in our study (300 mg PE/g TS) yielding no negative impact on either aerobic or anaerobic digestion is notable. Lastly, bio-aging potential of PE is closely linked with amorphous/crystalline structure and presence/absence of additives. Such factors may affect microbial colonization, resulting in physical/chemical changes on the surface of PE and on digester operation.
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Affiliation(s)
- Maha Dassouki Dit Tahan
- Department of Environmental Engineering, Middle East Technical University, 06800 Ankara, Türkiye
| | - Melek Canbulat Özdemir
- Department of Environmental Engineering, Middle East Technical University, 06800 Ankara, Türkiye
| | - F Dilek Sanin
- Department of Environmental Engineering, Middle East Technical University, 06800 Ankara, Türkiye
| | - İpek İmamoğlu
- Department of Environmental Engineering, Middle East Technical University, 06800 Ankara, Türkiye.
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2
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Merchant M, Mande SS, Sar P. Microbial community enrichment and transition in landfill for the biotransformation of unpretreated low-density polyethylene (LDPE) under aerobic and anaerobic conditions. CHEMOSPHERE 2025; 382:144429. [PMID: 40413859 DOI: 10.1016/j.chemosphere.2025.144429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 04/13/2025] [Accepted: 04/15/2025] [Indexed: 05/27/2025]
Abstract
Low density polyethylene (LDPE), prevalent in single-use plastics, poses a significant environmental challenge due to its limited biodegradation. This study aims to enrich and characterize unpretreated LDPE degrading microorganisms from a nearly 50-year-old municipal landfill under aerobic and anaerobic conditions. Detailed analysis of the microbial communities through 16S rRNA gene based metataxonomy, whole genome metagenomics as well as thorough characterization of LDPE films exposed to the enriched microorganisms are done. Distinct shifts between plastisphere and bulk communities were observed. Shotgun metagenomics enabled reconstruction of thirty high-quality metagenome-assembled genomes (MAGs), revealing genes for plastic and hydrocarbon degradation, and biosurfactant production. Several plastic degradation-associated bacteria were identified, including Pseudomonas, Streptomyces, Burkholderia, Bacillus, Thermobifida, Saccharomonospora, Methylocaldum, Methylobacter, Ilumatobacter, Rubrivivax, and archaeal candidates like Methanosarcina and Nitrosarchaeum were observed. MAGs from Burkholderiales and Chlamydiales showed higher potential for LDPE degradation. Scanning electron microscopy showed biofilm formation on plastics, atomic force microscopy indicated surface topological changes, and Fourier transform infrared spectroscopy revealed increased carbonyl groups. Aerobic enrichments allowed up to 60% weight reduction of LDPE, with a degradation rate of 0.00766 mg/day and reaching half-life in nearly 90.49 days, confirming the biodegradation potential of the microbial community. From these observations, this study suggests two potential mechanisms of LDPE degradation under aerobic and anaerobic conditions by enriched communities. This study highlights role of landfill microbiomes in LDPE degradation, offering valuable insights into microbial succession of plastisphere and contributing to the development of effective plastic-degrading community. Future research could explore optimizing these for large-scale plastic waste management.
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Affiliation(s)
- Mitali Merchant
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India; TCS Research, Tata Consultancy Services Ltd., Pune, Maharashtra, India
| | - Sharmila S Mande
- TCS Research, Tata Consultancy Services Ltd., Pune, Maharashtra, India
| | - Pinaki Sar
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India.
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3
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Pereira S, Rubina M, Roga A, Selga T, Skinderskis E, Gudrā D, Kalniņa I, Vonda K, Fridmanis D, Muter O. Evaluation of functional capacity and plastic-degrading potential of Bacillus spp. and other bacteria derived from the Getliņi landfill (Latvia). ENVIRONMENTAL RESEARCH 2025; 279:121849. [PMID: 40373994 DOI: 10.1016/j.envres.2025.121849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2025] [Revised: 05/11/2025] [Accepted: 05/12/2025] [Indexed: 05/17/2025]
Abstract
The mechanisms of plastic biodegradation by microorganisms remain poorly understood because of high variability in environmental conditions. This study aimed to isolate, identify, and characterise bacteria with plastic-degrading potential derived from the Getliņi EKO landfill (Riga, Latvia). Among the bacteria selected, Bacillus was the predominant genus identified, whereas Pseudomonas dominated the metagenome. Comparative testing revealed the highest non-specific esterase activity in cultures of B. licheniformis and B. altitudinis. Following a 6-week batch experiment, a newly developed bacterial consortium biologically reduced the weight of untreated low-density polyethylene (LDPE), polyethylene terephthalate (PET), and high-density polyethylene (HDPE) by 19.44 %, 5.99 %, and 2.58 %, respectively. Thermally pre-treated PET and acid pre-treated HDPE resulted in greater weight losses than their respective untreated forms. Scanning electron microscopy primarily showed single cells and microcolonies attached to the granule surfaces. Microbial respiration and fluorescein diacetate hydrolysis tests suggested that the granules had a stimulating effect on the metabolic activity of planktonic cells. Cultures with untreated LDPE and PET exhibited the highest ecotoxicity for Thamnocephalus platyurus, reducing ingestion activity by 60.39 % and 71.25 % of the control, respectively. In conclusion, the Getliņi EKO landfill appears to be a promising sampling source for bacteria capable of biodegrading fossil-based polymers. Further refinement of methods for the isolation and evaluation of plastic degraders will provide new insights into the potential of microbial resources for plastic degradation.
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Affiliation(s)
- Sara Pereira
- Faculty of Medicine and Life Sciences, University of Latvia, 1 Jelgavas Str., Riga, LV-1004, Latvia; Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais 1, 1049-001, Lisbon, Portugal
| | - Marta Rubina
- Faculty of Medicine and Life Sciences, University of Latvia, 1 Jelgavas Str., Riga, LV-1004, Latvia
| | - Ance Roga
- Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., LV-1067, Riga, Latvia
| | - Tūrs Selga
- Faculty of Medicine and Life Sciences, University of Latvia, 1 Jelgavas Str., Riga, LV-1004, Latvia
| | - Edmunds Skinderskis
- Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., LV-1067, Riga, Latvia
| | - Dita Gudrā
- Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., LV-1067, Riga, Latvia
| | - Ineta Kalniņa
- Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., LV-1067, Riga, Latvia
| | - Kārlis Vonda
- Getliņi EKO Ltd., 57 Kaudzisu Str., Rumbula, LV-2121, Ropažu, Latvia
| | - Dāvids Fridmanis
- Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., LV-1067, Riga, Latvia
| | - Olga Muter
- Faculty of Medicine and Life Sciences, University of Latvia, 1 Jelgavas Str., Riga, LV-1004, Latvia.
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4
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Chen JQ, Rong Z, Zheng DQ, Wu YH, Xu XW. Degradation of polyethylene by three bacteria isolated from coastal beach. ENVIRONMENTAL RESEARCH 2025; 278:121603. [PMID: 40250591 DOI: 10.1016/j.envres.2025.121603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2025] [Revised: 04/10/2025] [Accepted: 04/11/2025] [Indexed: 04/20/2025]
Abstract
Polyethylene accumulates due to high production and slow degradation. Microbial degradation offers a promising solution for PE waste treatment. In this study, three bacterial strains, Alloalcanivorax sp. C16-1, Alloalcanivorax sp. C16-2, and Gordonia sp. R-1, were isolated from coastal plastic debris, each capable of utilizing polyethylene powder as the carbon source. After 30 days at 30 °C, low density polyethylene films showed modifications, including bacterial colonization, cracks, and holes as revealed by scanning electron microscopy. The water contact angle decreased, indicating increased hydrophilicity, while attenuated total reflection fourier transform infrared analysis confirmed surface oxidation with the formation of hydroxyl and carbonyl groups. High-temperature gel permeation chromatography showed decreases in the weight-average molecular weight of the films, indicating depolymerization. Nanoscale secondary ion mass spectrometry imaging demonstrated 13C assimilation from PE by the three strains at the single-cell level. Genomic analysis revealed that C16-1 and C16-2 were novel Alloalcanivorax species, with genes encoding potential PE-degrading enzymes, such as laccase and alkane hydroxylase, in all three isolates. These strains are widely distributed in marine environments, particularly in plastic accumulation hotspots, offering promising candidates for PE biodegradation research.
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Affiliation(s)
- Jun-Qing Chen
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China
| | - Zhen Rong
- State Key Laboratory of Submarine Geoscience, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, PR China
| | - Dao-Qiong Zheng
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China
| | - Yue-Hong Wu
- State Key Laboratory of Submarine Geoscience, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, PR China.
| | - Xue-Wei Xu
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China; National Deep Sea Center, Qingdao, 266000, PR China.
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5
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Bruno D, Casartelli M, De Smet J, Gold M, Tettamanti G. Review: A journey into the black soldier fly digestive system: From current knowledge to applied perspectives. Animal 2025:101483. [PMID: 40222868 DOI: 10.1016/j.animal.2025.101483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 02/27/2025] [Accepted: 02/28/2025] [Indexed: 04/15/2025] Open
Abstract
Recent literature on the black soldier fly (BSF) confirms the deep interest in this species for the bioconversion of organic waste, including challenging substrates that contain recalcitrant macromolecules, and highlights the growing trend in new applications for this insect. While protein meal remains the most prominent use of BSF larvae, emerging research is increasingly exploring alternative applications of biomolecules derived from these larvae, including proteins, lipids, chitin, and antimicrobial peptides. Moreover, the high feeding versatility of this insect is being recognised in fields beyond animal feed, such as bioremediation, where its potential ability to degrade contaminants can present significant ecological benefits. Although there is now widespread agreement that a thorough understanding of BSF biology is essential to enlarge the range of applications in which this insect may offer new sustainable solutions, studies on the digestive system are still limited and we are far from having a whole comprehension of the functional features of this complex structure. In fact, the gut is not only the core of the bioconversion process but also represents the first defence barrier against ingested pathogens, and due to the presence of a highly versatile gut microbiota, it may be a potential source of novel microbes and enzymes that could find application in various biotechnological sectors. This review aims to provide a comprehensive overview of the current knowledge on the BSF midgut -the central region of the gut responsible for nutrient digestion and absorption- in both larvae and adults, together with information about mouthparts and the organisation of the alimentary canal. Moreover, starting from the most recent studies on the midgut and its microbiota, we discuss implications for improving larval production, exploiting challenging substrates, and mitigating pollutants in contaminated biomasses.
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Affiliation(s)
- D Bruno
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant, 3, 21100 Varese, Italy
| | - M Casartelli
- Department of Biosciences, University of Milano, via Celoria, 26, 20133 Milano, Italy; BAT Center-Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, Piazza Carlo di Borbone, 1, 80055 Portici, Italy
| | - J De Smet
- Department of Microbial and Molecular Systems, KU Leuven Campus Geel, Kleinhoefstraat, 4, 2440 Geel, Belgium
| | - M Gold
- Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse, 9, 8092 Zürich, Switzerland
| | - G Tettamanti
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant, 3, 21100 Varese, Italy; BAT Center-Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, Piazza Carlo di Borbone, 1, 80055 Portici, Italy.
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6
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Katnic SP, Gupta RK. From biofilms to biocatalysts: Innovations in plastic biodegradation for environmental sustainability. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2025; 374:124192. [PMID: 39842313 DOI: 10.1016/j.jenvman.2025.124192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 12/27/2024] [Accepted: 01/17/2025] [Indexed: 01/24/2025]
Abstract
The increase in plastic waste has evolved into a severe environmental crisis, which requires innovative recycling technologies to repurpose used plastic with adequate environmental protection. This review highlights the urgent need for innovative approaches to the treatment and degradation of post-use plastics. It investigates the promising role of biofilms in the biodegradation of polymers, especially for polymers such as polyethylene terephthalate (PET), polyurethane (PU), and polyethylene (PE). By examining biofilms, researchers can determine key enzymes involved in polymer degradation and improve their efficiency through genetic engineering. In addition, the review explores in detail the structure and development of biofilms on polymeric surfaces, elucidating the role of specific microbial strains necessary for biofilm formation and maintenance. Techniques for identifying enzymes within biofilms and improving their degradation ability are also discussed. The review concludes with recent discoveries in enzyme isolation and the key role of biofilms in the degradation and recycling of major plastic pollutants such as PET, PU, and PE. These findings highlight the potential of biofilm-derived enzymes to promote sustainable polymer recycling.
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Affiliation(s)
- Slavica Porobic Katnic
- National Institute for Materials Advancement, Pittsburg State University, Pittsburg, KS, 66762, USA; University of Belgrade, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, Belgrade, 11000, Serbia
| | - Ram K Gupta
- National Institute for Materials Advancement, Pittsburg State University, Pittsburg, KS, 66762, USA; Department of Chemistry, Pittsburg State University, Pittsburg, KS, 66762, USA.
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7
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Mendoza JE, Tineo D, Chuquibala-Checan B, Atalaya-Marin N, Taboada-Mitma VH, Tafur-Culqui J, Tarrillo E, Gómez-Fernández D, Goñas M, Reyes-Reyes MA. Global perspectives on the biodegradation of LDPE in agricultural systems. Front Microbiol 2025; 15:1510817. [PMID: 39839104 PMCID: PMC11748793 DOI: 10.3389/fmicb.2024.1510817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Accepted: 12/19/2024] [Indexed: 01/23/2025] Open
Abstract
The increasing use of plastics globally has generated serious environmental and human health problems, particularly in the agricultural sector where low-density polyethylene (LDPE) and other plastics are widely used. Due to its low recycling rate and slow degradation process, LDPE is a major source of pollution. This paper addresses the problem of plastic accumulation in agriculture, focusing on LDPE biodegradation strategies. The studies reviewed include recent data and the methodologies used include state-of-the-art technologies and others that have been used for decades, to monitor and measure the degree of biodegradation that each treatment applied can have, including SEM, GCMS, HPLC, and microscopy. The countries investigating these biodegradation methodologies are identified, and while some countries have been developing them for some years, others have only begun to address this problem in recent years. The use of microorganisms such as bacteria, fungi, algae, and insect larvae that influence its decomposition is highlighted. A workflow is proposed to carry out this type of research. Despite the advances, challenges remain, such as optimizing environmental conditions to accelerate the process and the need for further research that delves into microbial interactions in various environmental contexts.
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Affiliation(s)
- Jani E. Mendoza
- Centro Experimental Yanayacu, Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias (DSME), Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Daniel Tineo
- Centro Experimental Yanayacu, Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias (DSME), Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Beimer Chuquibala-Checan
- Centro Experimental Yanayacu, Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias (DSME), Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Nilton Atalaya-Marin
- Centro Experimental Yanayacu, Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias (DSME), Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Victor H. Taboada-Mitma
- Centro Experimental Yanayacu, Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias (DSME), Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Josué Tafur-Culqui
- Centro Experimental Yanayacu, Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias (DSME), Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Ever Tarrillo
- Centro Experimental Yanayacu, Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias (DSME), Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Darwin Gómez-Fernández
- Centro Experimental Yanayacu, Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias (DSME), Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Malluri Goñas
- Centro Experimental Yanayacu, Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias (DSME), Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - María Andrea Reyes-Reyes
- Corporación para la Investigación de la Corrosión (CIC), Piedecuesta, Colombia
- Grupo de Investigación en Compuestos Orgánicos de Interés Medicinal (CODEIM), Universidad Industrial de Santander (UIS), Bucaramanga, Colombia
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8
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Jiménez DJ, Chaparro D, Sierra F, Custer GF, Feuerriegel G, Chuvochina M, Diaz-Garcia L, Mendes LW, Ortega Santiago YP, Rubiano-Labrador C, Salcedo Galan F, Streit WR, Dini-Andreote F, Reyes A, Rosado AS. Engineering the mangrove soil microbiome for selection of polyethylene terephthalate-transforming bacterial consortia. Trends Biotechnol 2025; 43:162-183. [PMID: 39304351 DOI: 10.1016/j.tibtech.2024.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 08/23/2024] [Accepted: 08/28/2024] [Indexed: 09/22/2024]
Abstract
Mangroves are impacted by multiple environmental stressors, including sea level rise, erosion, and plastic pollution. Thus, mangrove soil may be an excellent source of as yet unknown plastic-transforming microorganisms. Here, we assess the impact of polyethylene terephthalate (PET) particles and seawater intrusion on the mangrove soil microbiome and report an enrichment culture experiment to artificially select PET-transforming microbial consortia. The analysis of metagenome-assembled genomes of two bacterial consortia revealed that PET catabolism can be performed by multiple taxa, of which particular species harbored putative novel PET-active hydrolases. A key member of these consortia (Mangrovimarina plasticivorans gen. nov., sp. nov.) was found to contain two genes encoding monohydroxyethyl terephthalate hydrolases. This study provides insights into the development of strategies for harnessing soil microbiomes, thereby advancing our understanding of the ecology and enzymology involved in microbial-mediated PET transformations in marine-associated systems.
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Affiliation(s)
- Diego Javier Jiménez
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
| | - Dayanne Chaparro
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia; Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Felipe Sierra
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia; Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Gordon F Custer
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA; The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Golo Feuerriegel
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | - Laura Diaz-Garcia
- Department of Chemical and Biological Engineering, Advanced Biomanufacturing Centre, University of Sheffield, Sheffield, UK
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil
| | - Yina Paola Ortega Santiago
- Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia; Research Management, Agroindustrial Production and Transformation Research Group (GIPTA), Department of Agroindustrial Sciences, Universidad Popular del Cesar, Aguachica, Cesar, Colombia
| | - Carolina Rubiano-Labrador
- Chemical and Biological Studies Group, Basic Sciences Faculty, Universidad Tecnológica de Bolívar, Cartagena de Indias, Colombia
| | - Felipe Salcedo Galan
- Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA; The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Alexandre Soares Rosado
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
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9
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Kumar A, Lakhawat SS, Singh K, Kumar V, Verma KS, Dwivedi UK, Kothari SL, Malik N, Sharma PK. Metagenomic analysis of soil from landfill site reveals a diverse microbial community involved in plastic degradation. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:135804. [PMID: 39276741 DOI: 10.1016/j.jhazmat.2024.135804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/23/2024] [Accepted: 09/09/2024] [Indexed: 09/17/2024]
Abstract
In this study, we have investigated microbial communities structure and function using high throughput amplicon sequencing and whole metagenomic sequencing of DNA extracted from different depths of a plastic-laden landfill site. With diverse taxonomic groups inhabiting the plastic-rich soil, our study demonstrates the remarkable adaptability of microbes to use this new substrate as a carbon source. FTIR spectroscopic analysis of soil indicated degradation of plastic as perceived from the carbonyl index of 0.16, 0.72, and 0.44 at 0.6, 0.9 and 1.2 m depth, respectively. Similarly, water contact angles of 108.7 degree, 99.7 degree, 62.7 degree, and 77.8 degree of plastic pieces collected at 0.3, 0.6, 0.9, and 1.2 m depths respectively showed increased wettability and hydrophilicity of the plastic. Amplicon analysis of 16S and 18 S rRNA revealed a high abundance of several plastic-degrading bacterial groups, including Pseudomonas, Rhizobiales, Micrococcaceae, Chaetomium, Methylocaldum, Micromonosporaceae, Rhodothermaceae and fungi, including Trichoderma, Aspergillus, Candida at 0.9 m. The co-existence of specific microbial groups at different depths of landfill site indicates importance of bacterial and fungal interactions for plastic. Whole metagenome analysis of soil sample at 0.9 m depth revealed a high abundance of genes encoding enzymes that participate in the biodegradation of PVC, polyethylene, PET, and polyurethane. Curation of the pathways related to the degradation of these materials provided a blueprint for plastic biodegradation in this ecosystem. Altogether, our study has highlighted the importance of microbial cooperation for the biodegradation of pollutants. Our metagenome-based investigation supports the current perception that consortia of fungi-bacteria are preferable to axenic cultures for effective bioremediation of the environment.
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Affiliation(s)
- Akhilesh Kumar
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | | | - Kashmir Singh
- Department of Biotechnology, Panjab University Chandigarh, India
| | - Vikram Kumar
- Amity Institute of Pharmacy, Amity University Rajasthan, Jaipur, Rajasthan, India
| | | | | | - S L Kothari
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Naveen Malik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India.
| | - Pushpender Kumar Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India; Amity Centre for Nanobiotechnology and Nanomedicine, Amity University Rajasthan, Jaipur, India.
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10
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Saeng-Kla K, Mhuantong W, Termsaithong T, Pinyakong O, Sonthiphand P. Biodegradation of Di-2-Ethylhexyl Phthalate by Mangrove Sediment Microbiome Impacted by Chronic Plastic Waste. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 27:19. [PMID: 39625614 DOI: 10.1007/s10126-024-10399-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Accepted: 11/27/2024] [Indexed: 02/26/2025]
Abstract
Plastic pollution through the leaching of di(2-ethylhexyl) phthalate (DEHP), a widely used plasticizer, has led to the emergence of mangrove pollution. This study aimed to assess the DEHP removal efficiency of indigenous mangrove sediment microbiomes and identify key DEHP degraders using microcosm construction and metagenomic analysis. During the 35-day incubation period, the indigenous mangrove sediment microbiome, affected by chronic plastic pollution, demonstrated a 99% degradation efficiency of 200 mg/kg DEHP. Spearman's correlation analysis suggested that Myxococcales, Methyloligellaceae, Mycobacterium, and Micromonospora were potentially responsible for DEHP degradation. Based on PICRUSt2, the DEHP-degrading pathway in the sediment was predicted to be an anaerobic process involving catechol metabolism through catC, pcaD, pcaI, pcaF, and fadA. Efficient bacterial isolates from the mangrove sediment, identified as Gordonia sp. and Gordonia polyisoprenivorans, were able to degrade DEHP (65-97%) within 7 days and showed the ability to degrade other phthalate esters (PAEs).
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Affiliation(s)
- Kanphorn Saeng-Kla
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, 12120, Thailand
| | - Teerasit Termsaithong
- Learning Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
- Theoretical and Computational Physics (TCP) Group, Center of Excellence in Theoretical and Computational Science (TaCS-CoE), King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Onruthai Pinyakong
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Bangkok, 10330, Thailand
| | - Prinpida Sonthiphand
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand.
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11
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Chen Z, Sun W, Wang S, Yang J, Huang W, Huang D, Jiang K, Zhang X, Sun X. Interactions between microplastics and organic contaminants: The microbial mechanisms for priming effects of organic compounds on microplastic biodegradation. WATER RESEARCH 2024; 267:122523. [PMID: 39353345 DOI: 10.1016/j.watres.2024.122523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 09/15/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]
Abstract
The co-presence of plastics and other organic contaminants is pervasive in various ecosystems, particularly in areas with intensive anthropogenic activities. Their interactions inevitably impact the composition and functions of the plastisphere microbiome, which in turn determines the trajectory of these contaminants. Antibiotics are a group of organic contaminants that warrant particular attention due to their wide presence in environments and significant potential to disseminate antibiotic resistance genes (ARGs) within the plastisphere. Therefore, this study investigated the impacts of sulfadiazine (SDZ), a prevalent environmental antibiotic, on the composition and function of the plastisphere microbial community inhabiting micro-polyethylene (mPE), one of the most common microplastic contaminants. Our findings indicated that the presence of SDZ increased the overall plastisphere microbial abundance and enriched populations that are capable of degrading both SDZ and mPE. The abundance of Aquabacterium, a dominant plastisphere population that is capable of degrading both SDZ and mPE, increased over the course of SDZ exposure, while another abundant mPE-degrading population, Ketobacter, remained stable. Accordingly, the removal of SDZ was enhanced in the presence of mPE. Moreover, the results further revealed that not only SDZ but also other labile organic contaminants (e.g., aniline and hexane) could accelerate mPE biodegradation through a priming effect. This investigation underscores the complex dynamics among microplastics, organic contaminants, and the plastisphere microbiome, offering insights into the environmental fate of plastic and antibiotic pollutants.
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Affiliation(s)
- Zhenyu Chen
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.
| | - Shuni Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Jinchan Yang
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Wei Huang
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Duanyi Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Kai Jiang
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China
| | - Xin Zhang
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China.
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.
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12
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MacLean J, Bartholomäus A, Blukis R, Liebner S, Wagner D. Metatranscriptomics of microbial biofilm succession on HDPE foil: uncovering plastic-degrading potential in soil communities. ENVIRONMENTAL MICROBIOME 2024; 19:95. [PMID: 39574143 PMCID: PMC11583400 DOI: 10.1186/s40793-024-00621-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 09/27/2024] [Indexed: 11/24/2024]
Abstract
BACKGROUND Although plastic pollution is increasing worldwide, very little is known about the microbial processes that take place once plastic debris is incorporated into the soil matrix. In this study, we conducted the first metatranscriptome analysis of polyethylene (PE)-associated biofilm communities in highly polluted landfill soil and compared their gene expression to that of a forest soil community within a 53-day period. RESULTS Our findings indicate that the microbial population present in soil contaminated with plastic debris is predisposed to both inhabit and degrade plastic surfaces. Surprisingly, the microbial community from undisturbed forest soil contained a diverse array of plastic-associated genes (PETase, alkB, etc.), indicating the presence of an enzymatic machinery capable of plastic degradation. Plastic-degrading taxa were upregulated in the early stages of biofilm formation. During the maturation of the biofilm, the alkB1/alkM transcripts, which encode PE-degrading enzymes, and transporters such as fadL, livG, livF, livH, and livM were upregulated, along with transcripts associated with the fatty acid β-oxidation pathway. CONCLUSIONS In this study, we address the underlying patterns of gene expression during biofilm development in a PE-associated plastisphere in soil and address the pressing question of whether natural microbial communities have the potential to biodegrade petrochemical-based plastic in the soil environment.
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Affiliation(s)
- Joana MacLean
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany.
| | - Alexander Bartholomäus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany
| | - Roberts Blukis
- GFZ German Research Centre for Geosciences, Section Interface Geochemistry, 14473, Potsdam, Germany
- Leibniz-Institut für Kristallzüchtung, Max-Born-Str. 2, 12489, Berlin, Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, 14476, Potsdam, Germany
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13
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Shafana Farveen M, Narayanan R. Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review. Arch Microbiol 2024; 206:441. [PMID: 39432094 DOI: 10.1007/s00203-024-04165-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 09/28/2024] [Accepted: 10/10/2024] [Indexed: 10/22/2024]
Abstract
Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.
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Affiliation(s)
- Mohamed Shafana Farveen
- Department of Genetic Engineering, College of Engineering and Technology (CET), SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai, Tamil Nadu, 603 203, India
| | - Rajnish Narayanan
- Department of Genetic Engineering, College of Engineering and Technology (CET), SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai, Tamil Nadu, 603 203, India.
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14
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Ridley RS, Conrad RE, Lindner BG, Woo S, Konstantinidis KT. Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes. Sci Rep 2024; 14:8798. [PMID: 38627476 PMCID: PMC11021508 DOI: 10.1038/s41598-024-59279-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.
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Affiliation(s)
- Rodney S Ridley
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Roth E Conrad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Seongwook Woo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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15
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Kim H, Yoo K. Marine plastisphere selectively enriches microbial assemblages and antibiotic resistance genes during long-term cultivation periods. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123450. [PMID: 38280464 DOI: 10.1016/j.envpol.2024.123450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/07/2024] [Accepted: 01/24/2024] [Indexed: 01/29/2024]
Abstract
Several studies have focused on identifying and quantifying suspended plastics in surface and subsurface seawater. Microplastics (MPs) have attracted attention as carriers of antibiotic resistance genes (ARGs) in the marine environment. Plastispheres, specific biofilms on MP, can provide an ideal niche to spread more widely through horizontal gene transfer (HGT), thereby increasing risks to ecosystems and human health. However, the microbial communities formed on different plastic types and ARG abundances during exposure time in natural marine environments remain unclear. Four types of commonly used MPs (polyethylene (PE), polypropylene (PP), polystyrene (PS), and polyvinyl chloride (PVC)) were periodically cultured (46, 63, and 102 d) in a field-based marine environment to study the co-selection of ARGs and microbial communities in marine plastispheres. After the first 63 d of incubation (p < 0.05), the initial 16S rRNA gene abundance of microorganisms in the plastisphere increased significantly, and the biomass subsequently decreased. These results suggest that MPs can serve as vehicles for various microorganisms to travel to different environments and eventually provide a niche for a variety of microorganisms. Additionally, the qPCR results showed that MPs selectively enriched ARGs. In particular, tetA, tetQ, sul1, and qnrS were selectively enriched in the PVC-MPs. The abundances of intl1, a mobile genetic element, was measured in all MP types for 46 d (5.22 × 10-5 ± 8.21 × 10-6 copies/16s rRNA gene copies), 63 d (5.90 × 10-5 ± 2.49 × 10-6 copies/16s rRNA gene copies), and 102 d (4.00 × 10-5 ± 5.11 × 10-6 copies/16s rRNA gene copies). Network analysis indicated that ARG profiles co-occurred with key biofilm-forming bacteria. This study suggests that the selection of ARGs and their co-occurring bacteria in MPs could potentially accelerate their transmission through HGT in natural marine plastics.
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Affiliation(s)
- Hyunsu Kim
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea
| | - Keunje Yoo
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea.
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16
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Rong Z, Ding ZH, Wu YH, Xu XW. Degradation of low-density polyethylene by the bacterium Rhodococcus sp. C-2 isolated from seawater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167993. [PMID: 37866604 DOI: 10.1016/j.scitotenv.2023.167993] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/04/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Low-density polyethylene (LDPE), which accounts for 20% of the global plastic production, is discharged in great quantities into the ocean, threatening marine life and ecosystems. Marine microorganisms have previously been reported to degrade LDPE plastics; however, the exploration of strains and enzymes that degrade LDPE is still limited. Here, an LDPE-degrading bacterium was isolated from seawater of the Changjiang Estuary, China and identified as Rhodococcus sp. C-2, the relative abundance of which was dramatically enhanced during PE-degrading microbial enrichment. The strain C-2 exhibited the degradation of LDPE films, leading to their morphological deterioration, reduced hydrophobicity and tensile strength, weight loss, as well as the formation of oxygen-containing functional groups in short-chain products. Sixteen bacterial enzymes potentially involved in LDPE degradation were screened using genomic, transcriptomic, and degradation product analyses. Thereinto, the glutathione peroxidase GPx with exposed active sites catalyzed the LDPE depolymerization with the cooperation of its dissociated superoxide anion radicals. Furthermore, an LDPE degradation model involving multiple enzymes was proposed. The present study identifies a novel PE-degrading enzyme (PEase) for polyethylene bioremediation and promotes the understanding of LDPE degradation.
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Affiliation(s)
- Zhen Rong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China; Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Zhi-Hao Ding
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China; Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Yue-Hong Wu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China; Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China.
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China; Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China.
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17
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Hu X, Gu H, Sun X, Wang Y, Liu J, Yu Z, Li Y, Jin J, Wang G. Metagenomic exploration of microbial and enzymatic traits involved in microplastic biodegradation. CHEMOSPHERE 2024; 348:140762. [PMID: 38006912 DOI: 10.1016/j.chemosphere.2023.140762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/08/2023] [Accepted: 11/17/2023] [Indexed: 11/27/2023]
Abstract
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.
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Affiliation(s)
- Xiaojing Hu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Haidong Gu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Xiangxin Sun
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongbin Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Junjie Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Yansheng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
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18
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Singleton SL, Davis EW, Arnold HK, Daniels AMY, Brander SM, Parsons RJ, Sharpton TJ, Giovannoni SJ. Identification of rare microbial colonizers of plastic materials incubated in a coral reef environment. Front Microbiol 2023; 14:1259014. [PMID: 37869676 PMCID: PMC10585116 DOI: 10.3389/fmicb.2023.1259014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/15/2023] [Indexed: 10/24/2023] Open
Abstract
Plastic waste accumulation in marine environments has complex, unintended impacts on ecology that cross levels of community organization. To measure succession in polyolefin-colonizing marine bacterial communities, an in situ time-series experiment was conducted in the oligotrophic coastal waters of the Bermuda Platform. Our goals were to identify polyolefin colonizing taxa and isolate bacterial cultures for future studies of the biochemistry of microbe-plastic interactions. HDPE, LDPE, PP, and glass coupons were incubated in surface seawater for 11 weeks and sampled at two-week intervals. 16S rDNA sequencing and ATR-FTIR/HIM were used to assess biofilm community structure and chemical changes in polymer surfaces. The dominant colonizing taxa were previously reported cosmopolitan colonizers of surfaces in marine environments, which were highly similar among the different plastic types. However, significant differences in rare community composition were observed between plastic types, potentially indicating specific interactions based on surface chemistry. Unexpectedly, a major transition in community composition occurred in all material treatments between days 42 and 56 (p < 0.01). Before the transition, Alteromonadaceae, Marinomonadaceae, Saccharospirillaceae, Vibrionaceae, Thalassospiraceae, and Flavobacteriaceae were the dominant colonizers. Following the transition, the relative abundance of these taxa declined, while Hyphomonadaceae, Rhodobacteraceae and Saprospiraceae increased. Over the course of the incubation, 8,641 colonizing taxa were observed, of which 25 were significantly enriched on specific polyolefins. Seven enriched taxa from families known to include hydrocarbon degraders (Hyphomonadaceae, Parvularculaceae and Rhodobacteraceae) and one n-alkane degrader (Ketobacter sp.). The ASVs that exhibited associations with specific polyolefins are targets of ongoing investigations aimed at retrieving plastic-degrading microbes in culture.
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Affiliation(s)
| | - Edward W. Davis
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Holly K. Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | | - Susanne M. Brander
- Department of Fisheries, Wildlife, and Conservation Sciences, Coastal Oregon Marine Experiment Station, Oregon State University, Newport, OR, United States
| | | | - Thomas J. Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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19
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Ali S, Bukhari DA, Rehman A. Call for biotechnological approach to degrade plastic in the era of COVID-19 pandemic. Saudi J Biol Sci 2023; 30:103583. [PMID: 36748033 PMCID: PMC9893805 DOI: 10.1016/j.sjbs.2023.103583] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/09/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Plastic pollution is a global issue and has become a major concern since Coronavirus disease (COVID)-19. In developing nations, landfilling and illegal waste disposal are typical ways to dispose of COVID-19-infected material. These technologies worsen plastic pollution and other human and animal health problems. Plastic degrades in light and heat, generating hazardous primary and secondary micro-plastic. Certain bacteria can degrade artificial polymers using genes, enzymes, and metabolic pathways. Microorganisms including bacteria degrade petrochemical plastics slowly. High molecular weight, strong chemical bonds, and excessive hydrophobicity reduce plastic biodegradation. There is not enough study on genes, enzymes, and bacteria-plastic interactions. Synthetic biology, metabolic engineering, and bioinformatics methods have been created to biodegrade synthetic polymers. This review will focus on how microorganisms' degrading capacity can be increased using recent biotechnological techniques.
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Key Words
- BHET, bis(2-hydroxyethyl
- Bacteria
- COVID-19
- COVID-19, Coronavirus disease-19
- FTIR, Fourier-transform infrared
- HDPE, High-density polyethene
- LDPE, Low-density polyethene
- MHET, Mono(2-hydroxyethyl
- MP, Microplastics
- Microorganisms
- NP, Nanoplastics
- PE, Polyethene
- PES, Polyethylene succinate
- PET, Polyethylene terephthalate
- PP, Polypropylene
- PPE, Personal protective equipment
- PS, Polystyrene
- PVC, Polyvinyl chloride
- Plastic degradation
- Plastic pollution
- TCA, Tricarboxylic acid
- TPA, Terephthalic acid
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Affiliation(s)
- Shakir Ali
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Dilara A. Bukhari
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Abdul Rehman
- Institute of Microbiology and Molecular Genetics, University of the Punjab, New Campus, Lahore 54590, Pakistan
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20
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Zhang C, Mu Y, Li T, Jin FJ, Jin CZ, Oh HM, Lee HG, Jin L. Assembly strategies for polyethylene-degrading microbial consortia based on the combination of omics tools and the "Plastisphere". Front Microbiol 2023; 14:1181967. [PMID: 37138608 PMCID: PMC10150012 DOI: 10.3389/fmicb.2023.1181967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
Numerous microorganisms and other invertebrates that are able to degrade polyethylene (PE) have been reported. However, studies on PE biodegradation are still limited due to its extreme stability and the lack of explicit insights into the mechanisms and efficient enzymes involved in its metabolism by microorganisms. In this review, current studies of PE biodegradation, including the fundamental stages, important microorganisms and enzymes, and functional microbial consortia, were examined. Considering the bottlenecks in the construction of PE-degrading consortia, a combination of top-down and bottom-up approaches is proposed to identify the mechanisms and metabolites of PE degradation, related enzymes, and efficient synthetic microbial consortia. In addition, the exploration of the plastisphere based on omics tools is proposed as a future principal research direction for the construction of synthetic microbial consortia for PE degradation. Combining chemical and biological upcycling processes for PE waste could be widely applied in various fields to promote a sustainable environment.
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Affiliation(s)
- Chengxiao Zhang
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yulin Mu
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Taihua Li
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Feng-Jie Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Chun-Zhi Jin
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
- Hyung-Gwan Lee,
| | - Long Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Long Jin,
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