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Ruiz-Haddad L, Ali M, Pronk M, van Loosdrecht MC, Saikaly PE. Demystifying polyphosphate-accumulating organisms relevant to wastewater treatment: A review of their phylogeny, metabolism, and detection. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100387. [PMID: 38322240 PMCID: PMC10845257 DOI: 10.1016/j.ese.2024.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/31/2023] [Accepted: 12/31/2023] [Indexed: 02/08/2024]
Abstract
Currently, the most cost-effective and efficient method for phosphorus (P) removal from wastewater is enhanced biological P removal (EPBR) via polyphosphate-accumulating organisms (PAOs). This study integrates a literature review with genomic analysis to uncover the phylogenetic and metabolic diversity of the relevant PAOs for wastewater treatment. The findings highlight significant differences in the metabolic capabilities of PAOs relevant to wastewater treatment. Notably, Candidatus Dechloromonas and Candidatus Accumulibacter can synthesize polyhydroxyalkanoates, possess specific enzymes for ATP production from polyphosphate, and have electrochemical transporters for acetate and C4-dicarboxylates. In contrast, Tetrasphaera, Candidatus Phosphoribacter, Knoellia, and Phycicoccus possess PolyP-glucokinase and electrochemical transporters for sugars/amino acids. Additionally, this review explores various detection methods for polyphosphate and PAOs in activated sludge wastewater treatment plants. Notably, FISH-Raman spectroscopy emerges as one of the most advanced detection techniques. Overall, this review provides critical insights into PAO research, underscoring the need for enhanced strategies in biological phosphorus removal.
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Affiliation(s)
- Lucia Ruiz-Haddad
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Ali
- Department of Civil, Structural & Environmental Engineering, Trinity College Dublin, The University of Dublin, Dublin, 2, Ireland
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, Delft, 2629 HZ, the Netherlands
| | | | - Pascal E. Saikaly
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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2
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Di Gregorio S, Niccolini L, Seggiani M, Strangis G, Barbani N, Vitiello V, Becarelli S, Petroni G, Yan X, Buttino I. Marine copepod culture as a potential source of bioplastic-degrading microbiome: The case of poly(butylene succinate-co-adipate). CHEMOSPHERE 2024; 362:142603. [PMID: 38885765 DOI: 10.1016/j.chemosphere.2024.142603] [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: 10/12/2023] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
The poly(butylene succinate-co-adipate) (PBSA) is emerging as environmentally sustainable polyester for applications in marine environment. In this work the capacity of microbiome associated with marine plankton culture to degrade PBSA, was tested. A taxonomic and functional characterization of the microbiome associated with the copepod Acartia tonsa, reared in controlled conditions, was analysed by 16S rDNA metabarcoding, in newly-formed adult stages and after 7 d of incubation. A predictive functional metagenomic profile was inferred for hydrolytic activities involved in bioplastic degradation with a particular focus on PBSA. The copepod-microbiome was also characterized in newly-formed carcasses of A. tonsa, and after 7 and 33 d of incubation in the plankton culture medium. Copepod-microbiome showed hydrolytic activities at all developmental stages of the alive copepods and their carcasses, however, the evenness of the hydrolytic bacterial community significantly increased with the time of incubation in carcasses. Microbial genera, never described in association with copepods: Devosia, Kordia, Lentibacter, Methylotenera, Rheinheimera, Marinagarivorans, Paraglaciecola, Pseudophaeobacter, Gaiella, Streptomyces and Kribbella sps., were retrieved. Kribbella sp. showed carboxylesterase activity and Streptomyces sp. showed carboxylesterase, triacylglycerol lipase and cutinase activities, that might be involved in PBSA degradation. A culturomic approach, adopted to isolate bacterial specimen from carcasses, led to the isolation of the bacterial strain, Vibrio sp. 01 tested for the capacity to promote the hydrolysis of the ester bonds. Granules of PBSA, incubated 82 d at 20 °C with Vibrio sp. 01, were characterized by scanning electron microscopy, infrared spectroscopy, thermogravimetric analysis, and differential scanning calorimetry, showing fractures compared to the control sample, and hydrolysis of ester bonds. These preliminary results are encouraging for further investigation on the ability of the microbiome associated with plankton to biodegrade polyesters, such as PBSA, and increasing knowledge on microorganisms involved in bioplastic degradation in marine environment.
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Affiliation(s)
- Simona Di Gregorio
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy
| | - Luca Niccolini
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy; Functional Biology and Plankton Genomic Lab. ISPRA - Italian Institute for Environmental Protection and Research, Via del Cedro n.38, 57122, Livorno, Italy
| | - Maurizia Seggiani
- Department of Civil and Industrial Engineering, University of Pisa, Largo Lucio Lazzarino 1, 56122, Pisa, Italy
| | - Giovanna Strangis
- Department of Civil and Industrial Engineering, University of Pisa, Largo Lucio Lazzarino 1, 56122, Pisa, Italy
| | - Niccoletta Barbani
- Department of Civil and Industrial Engineering, University of Pisa, Largo Lucio Lazzarino 1, 56122, Pisa, Italy
| | - Valentina Vitiello
- Functional Biology and Plankton Genomic Lab. ISPRA - Italian Institute for Environmental Protection and Research, Via del Cedro n.38, 57122, Livorno, Italy; Sino-Italian Joint Laboratory Functional Biology of Marine Biota, ISPRA, 57122, Livorno, Italy
| | - Simone Becarelli
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy
| | - Giulio Petroni
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy
| | - Xiaojun Yan
- Sino-Italian Joint Laboratory Functional Biology of Marine Biota, ISPRA, 57122, Livorno, Italy; Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Isabella Buttino
- Functional Biology and Plankton Genomic Lab. ISPRA - Italian Institute for Environmental Protection and Research, Via del Cedro n.38, 57122, Livorno, Italy; Sino-Italian Joint Laboratory Functional Biology of Marine Biota, ISPRA, 57122, Livorno, Italy.
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Grzesiak J, Rogala MM, Gawor J, Kouřilová X, Obruča S. Polyhydroxyalkanoate involvement in stress-survival of two psychrophilic bacterial strains from the High Arctic. Appl Microbiol Biotechnol 2024; 108:273. [PMID: 38520566 PMCID: PMC10960890 DOI: 10.1007/s00253-024-13092-8] [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: 01/05/2024] [Revised: 02/19/2024] [Accepted: 02/25/2024] [Indexed: 03/25/2024]
Abstract
An ever-growing body of literature evidences the protective role of polyhydroxyalkanoates (PHAs) against a plethora of mostly physical stressors in prokaryotic cells. To date, most of the research done involved bacterial strains isolated from habitats not considered to be life-challenging or extremely impacted by abiotic environmental factors. Polar region microorganisms experience a multitude of damaging factors in combinations rarely seen in other of Earth's environments. Therefore, the main objective of this investigation was to examine the role of PHAs in the adaptation of psychrophilic, Arctic-derived bacteria to stress conditions. Arctic PHA producers: Acidovorax sp. A1169 and Collimonas sp. A2191, were chosen and their genes involved in PHB metabolism were deactivated making them unable to accumulate PHAs (ΔphaC) or to utilize them (Δi-phaZ) as a carbon source. Varying stressors were applied to the wild-type and the prepared mutant strains and their survival rates were assessed based on CFU count. Wild-type strains with a functional PHA metabolism were best suited to survive the freeze-thaw cycle - a common feature of polar region habitats. However, the majority of stresses were best survived by the ΔphaC mutants, suggesting that the biochemical imbalance caused by the lack of PHAs induced a permanent cell-wide stress response thus causing them to better withstand the stressor application. Δi-phaZ mutants were superior in surviving UV irradiation, hinting that PHA granule presence in bacterial cells is beneficial despite it being biologically inaccessible. Obtained data suggests that the ability to metabolize PHA although important for survival, probably is not the most crucial mechanism in the stress-resistance strategies arsenal of cold-loving bacteria. KEY POINTS: • PHA metabolism helps psychrophiles survive freezing • PHA-lacking psychrophile mutants cope better with oxidative and heat stresses • PHA granule presence enhances the UV resistance of psychrophiles.
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Affiliation(s)
- Jakub Grzesiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland.
| | - Małgorzata Marta Rogala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Xenie Kouřilová
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Stanislav Obruča
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
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Barbe V, Jacquin J, Bouzon M, Wolinski A, Derippe G, Cheng J, Cruaud C, Roche D, Fouteau S, Petit JL, Conan P, Pujo-Pay M, Bruzaud S, Ghiglione JF. Bioplastic degradation and assimilation processes by a novel bacterium isolated from the marine plastisphere. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133573. [PMID: 38306834 DOI: 10.1016/j.jhazmat.2024.133573] [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: 10/17/2023] [Revised: 11/23/2023] [Accepted: 01/17/2024] [Indexed: 02/04/2024]
Abstract
Biosourced and biodegradable plastics offer a promising solution to reduce environmental impacts of plastics for specific applications. Here, we report a novel bacterium named Alteromonas plasticoclasticus MED1 isolated from the marine plastisphere that forms biofilms on foils of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). Experiments of degradation halo, plastic matrix weight loss, bacterial oxygen consumption and heterotrophic biosynthetic activity showed that the bacterial isolate MED1 is able to degrade PHBV and to use it as carbon and energy source. The likely entire metabolic pathway specifically expressed by this bacterium grown on PHBV matrices was shown by further genomic and transcriptomic analysis. In addition to a gene coding for a probable secreted depolymerase, a gene cluster was located that encodes characteristic enzymes involved in the complete depolymerization of PHBV, the transport of oligomers, and in the conversion of the monomers into intermediates of central carbon metabolism. The transcriptomic experiments showed the activation of the glyoxylate shunt during PHBV degradation, setting the isocitrate dehydrogenase activity as regulated branching point of the carbon flow entering the tricarboxylic acid cycle. Our study also shows the potential of exploring the natural plastisphere to discover new bacteria with promising metabolic capabilities.
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Affiliation(s)
- Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Justine Jacquin
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France
| | - Madeleine Bouzon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Adèle Wolinski
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France
| | - Gabrielle Derippe
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France; Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne-Sud, UMR CNRS 6027, Rue Saint Maudé, Lorient, France
| | - Jingguang Cheng
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - David Roche
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Stéphanie Fouteau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Pascal Conan
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France
| | - Mireille Pujo-Pay
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France
| | - Stéphane Bruzaud
- Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne-Sud, UMR CNRS 6027, Rue Saint Maudé, Lorient, France
| | - Jean-François Ghiglione
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France.
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Choi SY, Lee Y, Yu HE, Cho IJ, Kang M, Lee SY. Sustainable production and degradation of plastics using microbes. Nat Microbiol 2023; 8:2253-2276. [PMID: 38030909 DOI: 10.1038/s41564-023-01529-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Plastics are indispensable in everyday life and industry, but the environmental impact of plastic waste on ecosystems and human health is a huge concern. Microbial biotechnology offers sustainable routes to plastic production and waste management. Bacteria and fungi can produce plastics, as well as their constituent monomers, from renewable biomass, such as crops, agricultural residues, wood and organic waste. Bacteria and fungi can also degrade plastics. We review state-of-the-art microbial technologies for sustainable production and degradation of bio-based plastics and highlight the potential contributions of microorganisms to a circular economy for plastics.
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Affiliation(s)
- So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea
- BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea
| | - Youngjoon Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea
- BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea
| | - Hye Eun Yu
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea
| | - In Jin Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea
- BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea
| | - Minju Kang
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea.
- BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea.
- BioInformatics Research Center, KAIST, Daejeon, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, Republic of Korea.
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Musilova J, Kourilova X, Hermankova K, Bezdicek M, Ieremenko A, Dvorak P, Obruca S, Sedlar K. Genomic and phenotypic comparison of polyhydroxyalkanoates producing strains of genus Caldimonas/ Schlegelella. Comput Struct Biotechnol J 2023; 21:5372-5381. [PMID: 37965057 PMCID: PMC10641440 DOI: 10.1016/j.csbj.2023.10.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs) have emerged as an environmentally friendly alternative to conventional polyesters. In this study, we present a comprehensive analysis of the genomic and phenotypic characteristics of three non-model thermophilic bacteria known for their ability to produce PHAs: Schlegelella aquatica LMG 23380T, Caldimonas thermodepolymerans DSM 15264, and C. thermodepolymerans LMG 21645 and the results were compared with the type strain C. thermodepolymerans DSM 15344T. We have assembled the first complete genomes of these three bacteria and performed the structural and functional annotation. This analysis has provided valuable insights into the biosynthesis of PHAs and has allowed us to propose a comprehensive scheme of carbohydrate metabolism in the studied bacteria. Through phylogenomic analysis, we have confirmed the synonymity between Caldimonas and Schlegelella genera, and further demonstrated that S. aquatica and S. koreensis, currently classified as orphan species, belong to the Caldimonas genus.
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Affiliation(s)
- Jana Musilova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Xenie Kourilova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Kristyna Hermankova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Matej Bezdicek
- Department of Internal Medicine – Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Anastasiia Ieremenko
- Department of Experimental Biology (Section of Microbiology, Microbial Bioengineering Laboratory), Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavel Dvorak
- Department of Experimental Biology (Section of Microbiology, Microbial Bioengineering Laboratory), Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Stanislav Obruca
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
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Chatonnet A, Perochon M, Velluet E, Marchot P. The ESTHER database on alpha/beta hydrolase fold proteins - An overview of recent developments. Chem Biol Interact 2023; 383:110671. [PMID: 37582413 DOI: 10.1016/j.cbi.2023.110671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/01/2023] [Accepted: 08/12/2023] [Indexed: 08/17/2023]
Abstract
The ESTHER database, dedicated to ESTerases and alpha/beta-Hydrolase Enzymes and Relatives (https://bioweb.supagro.inra.fr/ESTHER/general?what=index), offers online access to a continuously updated, sequence-based classification of proteins harboring the alpha/beta hydrolase fold into families and subfamilies. In particular, the database proposes links to the sequences, structures, ligands and huge diversity of functions of these proteins, and to the related literature and other databases. Taking advantage of the promiscuity of enzymatic function, many engineered esterases, lipases, epoxide-hydrolases, haloalkane dehalogenases are used for biotechnological applications. Finding means for detoxifying those protein members that are targeted by insecticides, herbicides, antibiotics, or for reactivating human cholinesterases when inhibited by nerve gas, are still active areas of research. Using or improving the capacity of some enzymes to breakdown plastics with the aim to recycle valuable material and reduce waste is an emerging challenge. Most hydrolases in the superfamily are water-soluble and act on or are inhibited by small organic compounds, yet in a few subfamilies some members interact with other, unrelated proteins to modulate activity or trigger functional partnerships. Recent development in 3D structure prediction brought by AI-based programs now permits analysis of enzymatic mechanisms for a variety of hydrolases with no experimental 3D structure available. Finally, mutations in as many as 34 of the 120 human genes compiled in the database are now linked to genetic diseases, a feature fueling research on early detection, metabolic pathways, pharmacological treatment or enzyme replacement therapy. Here we review those developments in the database that took place over the latest decade and discuss potential new applications and recent and future expected research in the field.
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Affiliation(s)
- Arnaud Chatonnet
- DMEM, Université de Montpellier, INRAE, 34000 Montpellier, France.
| | - Michel Perochon
- DMEM, Université de Montpellier, INRAE, 34000 Montpellier, France
| | - Eric Velluet
- INRAE-AgroM / UIC, Place Viala, 34060, Montpellier, France
| | - Pascale Marchot
- CNRS / Aix-Marseille Univ, lab Architecture et Fonction des Macromolécules Biologiques, Marseille, France
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8
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Grzesiak J, Gawor J, Rogala MM, Kouřilová X, Obruča S. Genetic engineering of low-temperature polyhydroxyalkanoate production by Acidovorax sp. A1169, a psychrophile isolated from a subglacial outflow. Extremophiles 2023; 27:25. [PMID: 37709928 PMCID: PMC10501959 DOI: 10.1007/s00792-023-01311-5] [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: 07/24/2023] [Accepted: 08/24/2023] [Indexed: 09/16/2023]
Abstract
In recent years, extremophilic microorganisms have been employed as producers of the microbial bioplastics polyhydroxyalkanoates (PHA), which are of great biotechnological value. Nevertheless, cold-loving or psychrophilic (cryophilic) bacteria have been neglected in this regard. Here, we present an investigation of the Arctic glacier-derived PHA producer Acidovorax sp. A1169. Biolog GEN III Microplates were used as a screening tool to identify the most suitable carbon substrate concerning PHA synthesis. The strain produced homopolymer poly(3-hydroxybutyrate) (PHB) most efficiently (2 g/L) at a temperature of 15 °C when supplied with fructose or mannitol as carbon sources with a substantial decrease of PHB biosynthesis at 17.5 °C. The PHB yield did not increase considerably or even decreased when carbon source concentration exceeded 10 g/L hinting that the strain is oligotrophic in nature. The strain was also capable of introducing 3-hydroxyvalerate (3HV) into the polymer structure, which is known to improve PHA thermoplastic properties. This is the first investigation providing insight into a PHA biosynthesis process by means of a true psychrophile, offering guidelines on polar-region bacteria cultivation, production of PHA and also on the methodology for genetic engineering of psychrophiles.
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Affiliation(s)
- Jakub Grzesiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland.
| | - Jan Gawor
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Małgorzata Marta Rogala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Xenie Kouřilová
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Stanislav Obruča
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
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9
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Kim SH, Cho JY, Hwang JH, Kim HJ, Oh SJ, Kim HJ, Bhatia SK, Yun J, Lee SH, Yang YH. Revealing the key gene involved in bioplastic degradation from superior bioplastic degrader Bacillus sp. JY35. Int J Biol Macromol 2023:125298. [PMID: 37315675 DOI: 10.1016/j.ijbiomac.2023.125298] [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: 03/15/2023] [Revised: 05/18/2023] [Accepted: 06/02/2023] [Indexed: 06/16/2023]
Abstract
The use of bioplastics, which can alleviate environmental pollution caused by non-degradable bioplastics, has received attention. As there are many types of bioplastics, method that can treat them simultaneously is important. Therefore, Bacillus sp. JY35 which can degrade different types of bioplastics, was screened in previous study. Most types of bioplastics, such as polyhydroxybutyrate (PHB), (P(3HB-co-4HB)), poly(butylene adipate-co-terephthalate) (PBAT), polybutylene succinate (PBS), and polycaprolactone (PCL), can be degraded by esterase family enzymes. To identify the genes that are involved in bioplastic degradation, analysis with whole-genome sequencing was performed. Among the many esterase enzymes, three carboxylesterase and one triacylglycerol lipase were identified and selected based on previous studies. Esterase activity using p-nitrophenyl substrates was measured, and the supernatant of JY35_02679 showed strong emulsion clarification activity compared with others. In addition, when recombinant E. coli was applied to the clear zone test, only the JY35_02679 gene showed activity in the clear zone test with bioplastic containing solid cultures. Further quantitative analysis showed 100 % PCL degradation at 7 days and 45.7 % PBS degradation at 10 days. We identified a gene encoding a bioplastic-degrading enzyme in Bacillus sp. JY35 and successfully expressed the gene in heterologous E. coli, which secreted esterases with broad specificity.
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Affiliation(s)
- Su Hyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jang Yeon Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jeong Hyeon Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Hyun Jin Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Suk Jin Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Hyun Joong Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul, Republic of Korea
| | - Jeonghee Yun
- Department of Forest Products and Biotechnology, Kookmin University, Seoul, Republic of Korea
| | - Sang-Ho Lee
- Department of Pharmacy, College of Pharmacy, Jeju National University, Jeju-si, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul, Republic of Korea.
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10
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Fransen KA, Av-Ron SHM, Buchanan TR, Walsh DJ, Rota DT, Van Note L, Olsen BD. High-throughput experimentation for discovery of biodegradable polyesters. Proc Natl Acad Sci U S A 2023; 120:e2220021120. [PMID: 37252959 PMCID: PMC10266013 DOI: 10.1073/pnas.2220021120] [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: 11/27/2022] [Accepted: 03/08/2023] [Indexed: 06/01/2023] Open
Abstract
The consistent rise of plastic pollution has stimulated interest in the development of biodegradable plastics. However, the study of polymer biodegradation has historically been limited to a small number of polymers due to costly and slow standard methods for measuring degradation, slowing new material innovation. High-throughput polymer synthesis and a high-throughput polymer biodegradation method are developed and applied to generate a biodegradation dataset for 642 chemically distinct polyesters and polycarbonates. The biodegradation assay was based on the clear-zone technique, using automation to optically observe the degradation of suspended polymer particles under the action of a single Pseudomonas lemoignei bacterial colony. Biodegradability was found to depend strongly on aliphatic repeat unit length, with chains less than 15 carbons and short side chains improving biodegradability. Aromatic backbone groups were generally detrimental to biodegradability; however, ortho- and para-substituted benzene rings in the backbone were more likely to be degradable than metasubstituted rings. Additionally, backbone ether groups improved biodegradability. While other heteroatoms did not show a clear improvement in biodegradability, they did demonstrate increases in biodegradation rates. Machine learning (ML) models were leveraged to predict biodegradability on this large dataset with accuracies over 82% using only chemical structure descriptors.
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Affiliation(s)
- Katharina A. Fransen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Sarah H. M. Av-Ron
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Tess R. Buchanan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Dylan J. Walsh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Dechen T. Rota
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Lana Van Note
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Bradley D. Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
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11
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Zhou W, Bergsma S, Colpa DI, Euverink GJW, Krooneman J. Polyhydroxyalkanoates (PHAs) synthesis and degradation by microbes and applications towards a circular economy. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 341:118033. [PMID: 37156023 DOI: 10.1016/j.jenvman.2023.118033] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/15/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
Overusing non-degradable plastics causes a series of environmental issues, inferring a switch to biodegradable plastics. Polyhydroxyalkanoates (PHAs) are promising biodegradable plastics that can be produced by many microbes using various substrates from waste feedstock. However, the cost of PHAs production is higher compared to fossil-based plastics, impeding further industrial production and applications. To provide a guideline for reducing costs, the potential cheap waste feedstock for PHAs production have been summarized in this work. Besides, to increase the competitiveness of PHAs in the mainstream plastics economy, the influencing parameters of PHAs production have been discussed. The PHAs degradation has been reviewed related to the type of bacteria, their metabolic pathways/enzymes, and environmental conditions. Finally, the applications of PHAs in different fields have been presented and discussed to induce comprehension on the practical potentials of PHAs.
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Affiliation(s)
- Wen Zhou
- Products and Processes for Biotechnology, Engineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands
| | - Simon Bergsma
- Products and Processes for Biotechnology, Engineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands
| | - Dana Irene Colpa
- Products and Processes for Biotechnology, Engineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands
| | - Gert-Jan Willem Euverink
- Products and Processes for Biotechnology, Engineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands
| | - Janneke Krooneman
- Products and Processes for Biotechnology, Engineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands; Bioconversion and Fermentation Technology, Research Centre Biobased Economy, Hanze University of Applied Sciences, Groningen, the Netherlands.
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12
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Mohanan N, Wong MCH, Budisa N, Levin DB. Polymer-Degrading Enzymes of Pseudomonas chloroaphis PA23 Display Broad Substrate Preferences. Int J Mol Sci 2023; 24:ijms24054501. [PMID: 36901931 PMCID: PMC10003648 DOI: 10.3390/ijms24054501] [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: 01/02/2023] [Revised: 01/27/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
Although many bacterial lipases and PHA depolymerases have been identified, cloned, and characterized, there is very little information on the potential application of lipases and PHA depolymerases, especially intracellular enzymes, for the degradation of polyester polymers/plastics. We identified genes encoding an intracellular lipase (LIP3), an extracellular lipase (LIP4), and an intracellular PHA depolymerase (PhaZ) in the genome of the bacterium Pseudomonas chlororaphis PA23. We cloned these genes into Escherichia coli and then expressed, purified, and characterized the biochemistry and substrate preferences of the enzymes they encode. Our data suggest that the LIP3, LIP4, and PhaZ enzymes differ significantly in their biochemical and biophysical properties, structural-folding characteristics, and the absence or presence of a lid domain. Despite their different properties, the enzymes exhibited broad substrate specificity and were able to hydrolyze both short- and medium-chain length polyhydroxyalkanoates (PHAs), para-nitrophenyl (pNP) alkanoates, and polylactic acid (PLA). Gel Permeation Chromatography (GPC) analyses of the polymers treated with LIP3, LIP4, and PhaZ revealed significant degradation of both the biodegradable as well as the synthetic polymers poly(ε-caprolactone) (PCL) and polyethylene succinate (PES).
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Affiliation(s)
- Nisha Mohanan
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Michael C.-H. Wong
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, MB R3T 2N2, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, MB R3T 2N2, Canada
- Biocatalysis Group, Technical University of Berlin, Müller-Breslau-Str. 10, D-10623 Berlin, Germany
- Correspondence: or (N.B.); (D.B.L.); Tel.: +1-204-474-7429
| | - David B. Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
- Correspondence: or (N.B.); (D.B.L.); Tel.: +1-204-474-7429
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13
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Cazaudehore G, Monlau F, Gassie C, Lallement A, Guyoneaud R. Active microbial communities during biodegradation of biodegradable plastics by mesophilic and thermophilic anaerobic digestion. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130208. [PMID: 36308937 DOI: 10.1016/j.jhazmat.2022.130208] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/14/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Biodegradable plastics, if they are not properly managed at their end-of-life, can have the same hazardous environmental consequences as conventional plastics. This study investigates the treatment of the main biodegradable plastics under mesophilic and thermophilic anaerobic digestion using biochemical methane potential test and the microorganisms involved in the process using amplicon sequencing of the 16 S rRNA. Here we showed that, only PHB and TPS undergone important and rapid biodegradation under mesophilic condition (38 °C). By contrast, PCL and PLA exhibited very low biodegradation rate as 500 days were required to reach the ultimate methane yield. Little or no degradation occurred for PBAT and PBS at 38 °C. Under thermophilic conditions (58 °C), TPS, PHB, and PLA reached high levels of biodegradation in a relatively short period (< 100 d). While PBS, PBAT, and PCL could not be converted into methane at 58 °C. PHB degraders (Enterobacter and Cupriavidus) and lactate-utilizing bacteria (Moorella and Tepidimicrobium) appeared to play an important role in the PHB and PLA degradation, respectively. This work not only provides crucial data on the anaerobic digestion of the main biodegradable plastics but also enriches the understanding of the microorganisms involved in this process, which are of great importance for future development of the treatment of biodegradable plastics in anaerobic digestion systems.
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Affiliation(s)
- G Cazaudehore
- APESA, Pôle Valorisation, 64121 Montardon, France; Université de Pau et des Pays de l'Adour / E2S UPPA / CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000, Pau, France.
| | - F Monlau
- APESA, Pôle Valorisation, 64121 Montardon, France
| | - C Gassie
- Université de Pau et des Pays de l'Adour / E2S UPPA / CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000, Pau, France
| | - A Lallement
- APESA, Pôle Valorisation, 64121 Montardon, France
| | - R Guyoneaud
- Université de Pau et des Pays de l'Adour / E2S UPPA / CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000, Pau, France
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14
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Qin R, Zhu Y, Ai M, Jia X. Reconstruction and optimization of a Pseudomonas putida-Escherichia coli microbial consortium for mcl-PHA production from lignocellulosic biomass. Front Bioeng Biotechnol 2022; 10:1023325. [PMID: 36338139 PMCID: PMC9626825 DOI: 10.3389/fbioe.2022.1023325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
The demand for non-petroleum-based, especially biodegradable plastics has been on the rise in the last decades. Medium-chain-length polyhydroxyalkanoate (mcl-PHA) is a biopolymer composed of 6–14 carbon atoms produced from renewable feedstocks and has become the focus of research. In recent years, researchers aimed to overcome the disadvantages of single strains, and artificial microbial consortia have been developed into efficient platforms. In this work, we reconstructed the previously developed microbial consortium composed of engineered Pseudomonas putida KT∆ABZF (p2-a-J) and Escherichia coli ∆4D (ACP-SCLAC). The maximum titer of mcl-PHA reached 3.98 g/L using 10 g/L glucose, 5 g/L octanoic acid as substrates by the engineered P. putida KT∆ABZF (p2-a-J). On the other hand, the maximum synthesis capacity of the engineered E. coli ∆4D (ACP-SCLAC) was enhanced to 3.38 g/L acetic acid and 0.67 g/L free fatty acids (FFAs) using 10 g/L xylose as substrate. Based on the concept of “nutrient supply-detoxification,” the engineered E. coli ∆4D (ACP-SCLAC) provided nutrient for the engineered P. putida KT∆ABZF (p2-a-J) and it acted to detoxify the substrates. Through this functional division and rational design of the metabolic pathways, the engineered P. putida-E. coli microbial consortium could produce 1.30 g/L of mcl-PHA from 10 g/L glucose and xylose. Finally, the consortium produced 1.02 g/L of mcl-PHA using lignocellulosic hydrolysate containing 10.50 g/L glucose and 10.21 g/L xylose as the substrate. The consortium developed in this study has good potential for mcl-PHA production and provides a valuable reference for the production of high-value biological products using inexpensive carbon sources.
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Affiliation(s)
- Ruolin Qin
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yinzhuang Zhu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Mingmei Ai
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- *Correspondence: Xiaoqiang Jia,
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15
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Díaz Rodríguez CA, Díaz-García L, Bunk B, Spröer C, Herrera K, Tarazona NA, Rodriguez-R LM, Overmann J, Jiménez DJ. Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation. ISME COMMUNICATIONS 2022; 2:89. [PMID: 37938754 PMCID: PMC9723784 DOI: 10.1038/s43705-022-00176-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2023]
Abstract
The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.
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Affiliation(s)
- Carlos Andrés Díaz Rodríguez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Chemical and Biological Engineering, Advanced Biomanufacturing Centre, University of Sheffield, Sheffield, UK
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Katherine Herrera
- Department of Civil and Environmental Engineering, Universidad de los Andes, Bogotá, Colombia
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig University of Technology, Braunschweig, Germany
| | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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16
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Awasthi SK, Kumar M, Kumar V, Sarsaiya S, Anerao P, Ghosh P, Singh L, Liu H, Zhang Z, Awasthi MK. A comprehensive review on recent advancements in biodegradation and sustainable management of biopolymers. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119600. [PMID: 35691442 DOI: 10.1016/j.envpol.2022.119600] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/26/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Recent years have seen upsurge in plastic manufacturing and its utilization in various fields, such as, packaging, household goods, medical applications, and beauty products. Due to various adverse impacts imposed by synthetic plastics on the health of living well-being and the environment, the biopolymers have been emerged out an alternative. Although, the biopolymers such as polyhydroxyalkanoates (PHA) are entirely degradable. However, the other polymers, such as poly (lactic acid) (PLA) are only partially degradable and often not biosynthesized. Biodegradation of the polymers using microorganisms is considered an effective bioremediation approach. Biodegradation can be performed in aerobic and anaerobic environments. In this context, the present review discusses the biopolymer production, their persistence in the environment, aerobic biodegradation, anaerobic biodegradation, challenges associated with biodegradation and future perspectives. In addition, this review discusses the advancement in the technologies associated with biopolymer production, biodegradation, and their biodegradation standard in different environmental settings. Furthermore, differences in the degradation condition in the laboratory as well as on-site are discussed.
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Affiliation(s)
- Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Manish Kumar
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Vinay Kumar
- Department of Biotechnology, Indian Institute of Technology (IIT) Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Prathmesh Anerao
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Pooja Ghosh
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Hong Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
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17
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Kankonkar HT, Khandeparker RS. Microplastics a Novel Substratum for Polyhydroxyalkanoate (PHA)-Producing Bacteria in Aquatic Environments. Curr Microbiol 2022; 79:258. [PMID: 35852610 PMCID: PMC9295092 DOI: 10.1007/s00284-022-02929-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/08/2022] [Indexed: 12/02/2022]
Abstract
Polyhydroxyalkanoates (PHA) being biological polymers have attracted great attention. PHA have similar properties to that of synthetic plastic and are biodegradable. To discourage plastic pollution in the environment alternative solutions to the plastic pollution has to be readily available. High cost in production of PHA limits the production of these polymers at industrial scale. Bacteria are screened for PHA from diverse niches to meet the current requirements of cheap PHA production at industrial level. The microbial biofilm formed on the surface of microplastic could be a potential source in providing bacteria of economic importance. This paper is an attempt to search microplastic niche for potential PHA producers. PHA production variation was observed with different parameters such as type of carbon source, nitrogen source concentration and also time of incubation. Bacillus sp. CM27 showed maximum PHA yield up to 32.1% among other isolates at 48 h with 2% glucose as carbon source. Optimization of media leads to increase in PHA yield (37.69%) of CDW in Bacillus sp. CM27. Amino acid sequence of Bacillus sp.CM27 showed the presence of PhaC box with sequence, G-Y-C-M-G-G having cysteine in the middle of the box. The extracted polymer was confirmed by FTIR spectroscopy.
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Affiliation(s)
- Harshada T Kankonkar
- Microbial Ecology Laboratory, Biological Oceanography Division, CSIR-National Institute of Oceanography, Raj Bhavan Road, Dona Paula, Goa, 403004, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rakhee S Khandeparker
- Microbial Ecology Laboratory, Biological Oceanography Division, CSIR-National Institute of Oceanography, Raj Bhavan Road, Dona Paula, Goa, 403004, India.
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18
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Musilova J, Kourilova X, Pernicova I, Bezdicek M, Lengerova M, Obruca S, Sedlar K. Novel thermophilic polyhydroxyalkanoates producing strain Aneurinibacillus thermoaerophilus CCM 8960. Appl Microbiol Biotechnol 2022; 106:4669-4681. [PMID: 35759037 DOI: 10.1007/s00253-022-12039-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/26/2022]
Abstract
Aneurinibacillus thermoaerophilus CCM 8960 is a thermophilic bacterium isolated from compost in Brno. The bacterium accumulates polyhydroxyalkanoates (PHAs), a biodegradable and renewable alternative to petrochemical polymers. The bacterium reveals several features that make it a very interesting candidate for the industrial production of PHA. At first, due to its thermophilic character, the bacterium can be utilized in agreement with the concept of next-generation industrial biotechnology (NGIB), which relies on extremophiles. Second, the bacterium is capable of producing PHA copolymers containing a very high portion of 4-hydroxybutyrate (4HB). Such materials possess unique properties and can be advantageously used in multiple applications, including but not limited to medicine and healthcare. Therefore, this work focuses on the in-depth characterization of A. thermoaerophilus CCM 8960. In particular, we sequenced and assembled the genome of the bacterium and identified its most important genetic features, such as the presence of plasmids, prophages, CRISPR arrays, antibiotic-resistant genes, and restriction-modification (R-M) systems, which might be crucial for the development of genome editing tools. Furthermore, we focused on genes directly involved in PHA metabolism. We also experimentally studied the kinetics of glycerol and 1,4-butanediol (1,4BD) utilization as well as biomass growth and PHA production during cultivation. Based on these data, we constructed a metabolic model to reveal metabolic fluxes and nodes of glycerol and 1,4BD concerning their incorporation into the poly(3-hydroxybutyrate-co-4-hydroxybutyrate (P(3HB-co-4HB)) structure. KEY POINTS: • Aneurinibacillus sp. H1 was identified as Aneurinibacillus thermoaerophilus. • PHA metabolism pathway with associated genes was presented. • Unique monomer composition of produced PHAs was reported.
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Affiliation(s)
- Jana Musilova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Xenie Kourilova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Iva Pernicova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Matej Bezdicek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Martina Lengerova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Stanislav Obruca
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic.
- Department of Informatics, Institute of Bioinformatics, Ludwig-Maximilians-Universität München, Munich, Germany.
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19
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Strain-specific predation of Bdellovibrio bacteriovorus on Pseudomonas aeruginosa with a higher range for cystic fibrosis than for bacteremia isolates. Sci Rep 2022; 12:10523. [PMID: 35732651 PMCID: PMC9217795 DOI: 10.1038/s41598-022-14378-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/06/2022] [Indexed: 12/23/2022] Open
Abstract
This work aimed to evaluate the predatory activity of Bdellovibrio bacteriovorus 109J on clinical isolates of Pseudomonas aeruginosa selected from well-characterized collections of cystic fibrosis (CF) lung colonization (n = 30) and bloodstream infections (BSI) (n = 48) including strains selected by genetic lineage (frequent and rare sequence types), antibiotic resistance phenotype (susceptible and multidrug-resistant isolates), and colony phenotype (mucoid and non-mucoid isolates). The intraspecies predation range (I-PR) was defined as the proportion of susceptible strains within the entire collection. In contrast, the predation efficiency (PE) is the ratio of viable prey cells remaining after predation compared to the initial inoculum. I-PR was significantly higher for CF (67%) than for BSI P. aeruginosa isolates (35%) probably related to an environmental origin of CF strains whereas invasive strains are more adapted to humans. I-PR correlation with bacterial features such as mucoid morphotype, genetic background, or antibiotic susceptibility profile was not detected. To test the possibility of increasing I-PR of BSI isolates, a polyhydroxyalkanoate depolymerase deficient B. bacteriovorus bd2637 mutant was used. Global median I-PR and PE values remained constant for both predators, but 31.2% of 109J-resistant isolates were susceptible to the mutant, and 22.9% of 109J-susceptible isolates showed resistance to predation by the mutant, pointing to a predator–prey specificity process. The potential use of predators in the clinical setting should be based on the determination of the I-PR for each species, and the PE of each particular target strain.
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20
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Mohanan N, Wong CH, Budisa N, Levin DB. Characterization of Polymer Degrading Lipases, LIP1 and LIP2 From Pseudomonas chlororaphis PA23. Front Bioeng Biotechnol 2022; 10:854298. [PMID: 35519608 PMCID: PMC9065602 DOI: 10.3389/fbioe.2022.854298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022] Open
Abstract
The outstanding metabolic and bioprotective properties of the bacterial genus Pseudomonas make these species a potentially interesting source for the search of hydrolytic activities that could be useful for the degradation of plastics. We identified two genes encoding the intracellular lipases LIP1 and LIP2 of the biocontrol bacterium Pseudomonas chlororaphis PA23 and subsequently performed cloning and expression in Escherichia coli. The lip1 gene has an open reading frame of 828 bp and encodes a protein of 29.7 kDa whereas the lip2 consists of 834 bp and has a protein of 30.2 kDa. Although secondary structure analyses of LIP1 and LIP2 indicate a dominant α/β-hydrolase-fold, the two proteins differ widely in their amino acid sequences (15.39% identity), substrate specificities, and hydrolysis rates. Homology modeling indicates the catalytic serine in both enzymes located in a GXSXG sequence motif (lipase box). However, LIP1 has a catalytic triad of Ser152-His253-Glu221 with a GGX-type oxyanion pocket, whereas LIP2 has Ser138-His249-Asp221 in its active site and a GX-type of oxyanion hole residues. However, LIP1 has a catalytic triad of Ser152-His253-Glu221 with an oxyanion pocket of GGX-type, whereas LIP2 has Ser138-His249-Asp221 in its active site and a GX-type of oxyanion hole residues. Our three-dimensional models of LIP1 and LIP2 complexed with a 3-hydroxyoctanoate dimer revealed the core α/β hydrolase-type domain with an exposed substrate binding pocket in LIP1 and an active-site capped with a closing lid domain in LIP2. The recombinant LIP1 was optimally active at 45°C and pH 9.0, and the activity improved in the presence of Ca2+. LIP2 exhibited maximum activity at 40°C and pH 8.0, and was unaffected by Ca2+. Despite different properties, the enzymes exhibited broadsubstrate specificity and were able to hydrolyze short chain length and medium chain length polyhydroxyalkanoates (PHAs), polylactic acid (PLA), and para-nitrophenyl (pNP) alkanoates. Gel Permeation Chromatography (GPC) analysis showed a decrease in the molecular weight of the polymers after incubation with LIP1 and LIP2. The enzymes also manifested some polymer-degrading activity on petroleum-based polymers such as poly(ε-caprolactone) (PCL) and polyethylene succinate (PES), suggesting that these enzymes could be useful for biodegradation of synthetic polyester plastics. The study will be the first report of the complete characterization of intracellular lipases from bacterial and/or Pseudomonas species. The lipases, LIP1 and LIP2 are different from other bacterial lipases/esterases in having broad substrate specificity for polyesters.
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Affiliation(s)
- Nisha Mohanan
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Chun Hin Wong
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - David B. Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada
- *Correspondence: David B. Levin,
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Gomes M, Rondelez Y, Leibler L. Lessons from Biomass Valorization for Improving Plastic-Recycling Enzymes. Annu Rev Chem Biomol Eng 2022; 13:457-479. [PMID: 35378043 DOI: 10.1146/annurev-chembioeng-092120-091054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Synthetic polymers such as plastics exhibit numerous advantageous properties that have made them essential components of our daily lives, with plastic production doubling every 15 years. The relatively low cost of petroleum-based polymers encourages their single use and overconsumption. Synthetic plastics are recalcitrant to biodegradation, and mismanagement of plastic waste leads to their accumulation in the ecosystem, resulting in a disastrous environmental footprint. Enzymes capable of depolymerizing plastics have been reported recently that may provide a starting point for eco-friendly plastic recycling routes. However, some questions remain about the mechanisms by which enzymes can digest insoluble solid substrates. We review the characterization and engineering of plastic-eating enzymes and provide some comparisons with the field of lignocellulosic biomass valorization. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Margarida Gomes
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Yannick Rondelez
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Ludwik Leibler
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
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22
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Characterization of Streptomyces nymphaeiformis sp. nov., and its taxonomic relatedness to other polyhydroxybutyrate-degrading streptomycetes. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005266] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyhydroxybutyrate (PHB)-degrading actinomycete, strain SFB5AT, was identified as a species of
Streptomyces
based on its membrane fatty acid profile and the presence of ll-diaminopimelic acid in the cell wall. It formed sporulating mycelia on most agar media, but flat or wrinkled, moist colonies on trypticase soy agar. Spores were smooth, cylindrical, and borne on long, straight to flexuous chains. It produced a light brown diffusible pigment, but not melanin. Comparison of genomic digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values indicated that strain SFB5AT was related to
Streptomyces litmocidini
JCM 4394T,
Streptomyces vietnamensis
GIMV4.0001T,
Streptomyces nashvillensis
JCM 4498T and
Streptomyces tanashiensis
JCM 4086T, plus 11 other species. However, the dDDH and ANI values were well below the species differentiation thresholds of <70 and <95 %, respectively; also, multilocus sequence analysis distances exceeded the species threshold of 0.007. Moreover, strain SFB5AT differed from the other species in pigmentation and its ability to catabolize arabinose. Strain SFB5AT and 11 of its 15 closest relatives degraded PHB and have genes for extracellular, short-chain-length denatured polyhydroxyalkanoate depolymerases. These enzymes from strain SFB5AT and its closest relatives had a type 1 catalytic domain structure, while those from other relatives had a type 2 structure, which differs from type one in the position of a consensus histidine in the active site. Thus, phenotypic and genotypic differences suggest that strain SFB5AT represents a new species of Streptomyces, for which we propose the name Streptomyces nymphaeiformis sp. nov. The type strain is SFB5AT (=NRRL B-65520T=DSM 112030T).
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El-Malek FA, Steinbüchel A. Post-Synthetic Enzymatic and Chemical Modifications for Novel Sustainable Polyesters. Front Bioeng Biotechnol 2022; 9:817023. [PMID: 35071219 PMCID: PMC8766639 DOI: 10.3389/fbioe.2021.817023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Because of their biodegradability, compostability, compatibility and flexible structures, biodegradable polymers such as polyhydroxyalkanoates (PHA) are an important class of biopolymers with various industrial and biological uses. PHAs are thermoplastic polyesters with a limited processability due to their low heat resistance. Furthermore, due to their high crystallinity, some PHAs are stiff and brittle. These features result sometimes in very poor mechanical characteristics with low extension at break values which limit the application range of some natural PHAs. Several in vivo approaches for PHA copolymer modifications range from polymer production to enhance PHA-based material performance after synthesis. The methods for enzymatic and chemical polymer modifications are aiming at modifying the structures of the polyesters and thereby their characteristics while retaining the biodegradability. This survey illustrates the efficient use of enzymes and chemicals in post-synthetic PHA modifications, offering insights on these green techniques for modifying and improving polymer performance. Important studies in this sector will be reviewed, as well as chances and obstacles for their stability and hyper-production.
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Affiliation(s)
- Fady Abd El-Malek
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)-International Research Agenda, Lodz University of Technology, Lodz, Poland
| | - Alexander Steinbüchel
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)-International Research Agenda, Lodz University of Technology, Lodz, Poland
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24
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Viljakainen VR, Hug LA. New approaches for the characterization of plastic-associated microbial communities and the discovery of plastic-degrading microorganisms and enzymes. Comput Struct Biotechnol J 2021; 19:6191-6200. [PMID: 34900132 PMCID: PMC8632723 DOI: 10.1016/j.csbj.2021.11.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/14/2021] [Accepted: 11/14/2021] [Indexed: 12/04/2022] Open
Abstract
Plastics in the environment represent new substrates for microbial colonization, and recent methodological advances allow for in-depth characterization of plastic-associated microbial communities (PAMCs). Over the past several decades, discovery of plastic degrading enzymes (PDEs) and plastic degrading microorganisms (PDMs) has been driven by efforts to understand microbially-mediated plastic degradation in the environment and to discover biocatalysts for plastic processing. In this review, we discuss the evolution of methodology in plastic microbiology and highlight major advancements in the field stemming from computational microbiology. Initial research relied largely on culture-based approaches like clear-zone assays to screen for PDMs and microscopy to characterize PAMCs. New computational tools and sequencing technologies are accelerating discoveries in the field through culture-independent and multi-omic approaches, rapidly generating targets for protein engineering and improving the potential for plastic-waste management.
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Affiliation(s)
- V R Viljakainen
- University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
| | - L A Hug
- University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
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25
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Qin ZH, Mou JH, Chao CYH, Chopra SS, Daoud W, Leu SY, Ning Z, Tso CY, Chan CK, Tang S, Hathi ZJ, Haque MA, Wang X, Lin CSK. Biotechnology of Plastic Waste Degradation, Recycling, and Valorization: Current Advances and Future Perspectives. CHEMSUSCHEM 2021; 14:4103-4114. [PMID: 34137191 DOI: 10.1002/cssc.202100752] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/12/2021] [Indexed: 06/12/2023]
Abstract
Although fossil-based plastic products have many attractive characteristics, their production has led to severe environmental burdens that require immediate solutions. Despite these plastics being non-natural chemical compounds, they can be degraded and metabolized by some microorganisms, which suggests the potential application of biotechnologies based on the mechanism of plastic biodegradation. In this context, microbe-based strategies for the degradation, recycling, and valorization of plastic waste offer a feasible approach for alleviating environmental challenges created by the accumulation of plastic waste. This Minireview highlights recent advances in the biotechnology-based biodegradation of both traditional polymers and bio-based plastics, focusing on the mechanisms of biodegradation. From an application perspective, this Minireview also summarizes recent progress in the recycling and valorization of plastic waste, which are feasible solutions for tackling the plastic waste dilemma.
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Affiliation(s)
- Zi-Hao Qin
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Jin-Hua Mou
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | | | | | - Walid Daoud
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Shao-Yuan Leu
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong
| | - Zhi Ning
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Hong Kong
| | - Chi Yan Tso
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Chak Keung Chan
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Shixing Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510632, P. R. China
| | | | - Md Ariful Haque
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Xiang Wang
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, P. R. China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Hong Kong
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26
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Kawai F. Emerging Strategies in Polyethylene Terephthalate Hydrolase Research for Biorecycling. CHEMSUSCHEM 2021; 14:4115-4122. [PMID: 33949146 DOI: 10.1002/cssc.202100740] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/02/2021] [Indexed: 06/12/2023]
Abstract
The research on polyethylene terephthalate (PET) hydrolyzing enzymes started in 2005; several studies are now nearing the objective of their application in biorecycling of PET, which is an urgent environmental issue. The thermostability of PET hydrolases must be higher than 70 °C, which has already been established by several thermophilic cutinases, as higher thermostability results in higher activity. Additionally, pretreatment of waste PET to more enzyme-attackable forms is necessary for PET biorecycling. This Minireview summarizes research on enzymatic PET hydrolysis from two viewpoints: 1) improvement of PET hydrolases by focusing on their thermostabilities by mutation of enzyme genes, their expression in several hosts, and their modifications; and 2) processing of waste PET to readily biodegradable forms. Finally, the outlook of PET biorecycling is described.
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Affiliation(s)
- Fusako Kawai
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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27
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Attallah OA, Mojicevic M, Garcia EL, Azeem M, Chen Y, Asmawi S, Brenan Fournet M. Macro and Micro Routes to High Performance Bioplastics: Bioplastic Biodegradability and Mechanical and Barrier Properties. Polymers (Basel) 2021; 13:2155. [PMID: 34208796 PMCID: PMC8271944 DOI: 10.3390/polym13132155] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 01/23/2023] Open
Abstract
On a score sheet for plastics, bioplastics have a medium score for combined mechanical performance and a high score for biodegradability with respect to counterpart petroleum-based plastics. Analysis quickly confirms that endeavours to increase the mechanical performance score for bioplastics would be far more achievable than delivering adequate biodegradability for the recalcitrant plastics, while preserving their impressive mechanical performances. Key architectural features of both bioplastics and petroleum-based plastics, namely, molecular weight (Mw) and crystallinity, which underpin mechanical performance, typically have an inversely dependent relationship with biodegradability. In the case of bioplastics, both macro and micro strategies with dual positive correlation on mechanical and biodegradability performance, are available to address this dilemma. Regarding the macro approach, processing using selected fillers, plasticisers and compatibilisers have been shown to enhance both targeted mechanical properties and biodegradability within bioplastics. Whereas, regarding the micro approach, a whole host of bio and chemical synthetic routes are uniquely available, to produce improved bioplastics. In this review, the main characteristics of bioplastics in terms of mechanical and barrier performances, as well as biodegradability, have been assessed-identifying both macro and micro routes promoting favourable bioplastics' production, processability and performance.
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Affiliation(s)
- Olivia A. Attallah
- Materials Research Institute, Athlone Institute of Technology, N37 HD68 Athlone, Ireland; (O.A.A.); (E.L.G.); (M.A.); (Y.C.); (M.B.F.)
| | - Marija Mojicevic
- Materials Research Institute, Athlone Institute of Technology, N37 HD68 Athlone, Ireland; (O.A.A.); (E.L.G.); (M.A.); (Y.C.); (M.B.F.)
| | - Eduardo Lanzagorta Garcia
- Materials Research Institute, Athlone Institute of Technology, N37 HD68 Athlone, Ireland; (O.A.A.); (E.L.G.); (M.A.); (Y.C.); (M.B.F.)
| | - Muhammad Azeem
- Materials Research Institute, Athlone Institute of Technology, N37 HD68 Athlone, Ireland; (O.A.A.); (E.L.G.); (M.A.); (Y.C.); (M.B.F.)
| | - Yuanyuan Chen
- Materials Research Institute, Athlone Institute of Technology, N37 HD68 Athlone, Ireland; (O.A.A.); (E.L.G.); (M.A.); (Y.C.); (M.B.F.)
| | - Shumayl Asmawi
- Fundamental and Applied Science Department, Universiti Teknologi PETRONAS, Bandar Seri Iskandar 32610, Perak Darul Ridzuan, Malaysia;
| | - Margaret Brenan Fournet
- Materials Research Institute, Athlone Institute of Technology, N37 HD68 Athlone, Ireland; (O.A.A.); (E.L.G.); (M.A.); (Y.C.); (M.B.F.)
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28
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Nikolaivits E, Pantelic B, Azeem M, Taxeidis G, Babu R, Topakas E, Brennan Fournet M, Nikodinovic-Runic J. Progressing Plastics Circularity: A Review of Mechano-Biocatalytic Approaches for Waste Plastic (Re)valorization. Front Bioeng Biotechnol 2021; 9:696040. [PMID: 34239864 PMCID: PMC8260098 DOI: 10.3389/fbioe.2021.696040] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/28/2021] [Indexed: 01/10/2023] Open
Abstract
Inspirational concepts, and the transfer of analogs from natural biology to science and engineering, has produced many excellent technologies to date, spanning vaccines to modern architectural feats. This review highlights that answers to the pressing global petroleum-based plastic waste challenges, can be found within the mechanics and mechanisms natural ecosystems. Here, a suite of technological and engineering approaches, which can be implemented to operate in tandem with nature's prescription for regenerative material circularity, is presented as a route to plastics sustainability. A number of mechanical/green chemical (pre)treatment methodologies, which simulate natural weathering and arthropodal dismantling activities are reviewed, including: mechanical milling, reactive extrusion, ultrasonic-, UV- and degradation using supercritical CO2. Akin to natural mechanical degradation, the purpose of the pretreatments is to render the plastic materials more amenable to microbial and biocatalytic activities, to yield effective depolymerization and (re)valorization. While biotechnological based degradation and depolymerization of both recalcitrant and bioplastics are at a relatively early stage of development, the potential for acceleration and expedition of valuable output monomers and oligomers yields is considerable. To date a limited number of independent mechano-green chemical approaches and a considerable and growing number of standalone enzymatic and microbial degradation studies have been reported. A convergent strategy, one which forges mechano-green chemical treatments together with the enzymatic and microbial actions, is largely lacking at this time. An overview of the reported microbial and enzymatic degradations of petroleum-based synthetic polymer plastics, specifically: low-density polyethylene (LDPE), high-density polyethylene (HDPE), polystyrene (PS), polyethylene terephthalate (PET), polyurethanes (PU) and polycaprolactone (PCL) and selected prevalent bio-based or bio-polymers [polylactic acid (PLA), polyhydroxyalkanoates (PHAs) and polybutylene succinate (PBS)], is detailed. The harvesting of depolymerization products to produce new materials and higher-value products is also a key endeavor in effectively completing the circle for plastics. Our challenge is now to effectively combine and conjugate the requisite cross disciplinary approaches and progress the essential science and engineering technologies to categorically complete the life-cycle for plastics.
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Affiliation(s)
- Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Brana Pantelic
- Eco-Biotechnology & Drug Development Group, Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - George Taxeidis
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Ramesh Babu
- AMBER Centre, CRANN Institute, School of Chemistry, Trinity College Dublin, Dublin, Ireland
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | | | - Jasmina Nikodinovic-Runic
- Eco-Biotechnology & Drug Development Group, Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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29
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Microbial cell factories for the production of polyhydroxyalkanoates. Essays Biochem 2021; 65:337-353. [PMID: 34132340 DOI: 10.1042/ebc20200142] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/14/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022]
Abstract
Pollution caused by persistent petro-plastics is the most pressing problem currently, with 8 million tons of plastic waste dumped annually in the oceans. Plastic waste management is not systematized in many countries, because it is laborious and expensive with secondary pollution hazards. Bioplastics, synthesized by microorganisms, are viable alternatives to petrochemical-based thermoplastics due to their biodegradable nature. Polyhydroxyalkanoates (PHAs) are a structurally and functionally diverse group of storage polymers synthesized by many microorganisms, including bacteria and Archaea. Some of the most important PHA accumulating bacteria include Cupriavidus necator, Burkholderia sacchari, Pseudomonas sp., Bacillus sp., recombinant Escherichia coli, and certain halophilic extremophiles. PHAs are synthesized by specialized PHA polymerases with assorted monomers derived from the cellular metabolite pool. In the natural cycle of cellular growth, PHAs are depolymerized by the native host for carbon and energy. The presence of these microbial PHA depolymerases in natural niches is responsible for the degradation of bioplastics. Polyhydroxybutyrate (PHB) is the most common PHA with desirable thermoplastic-like properties. PHAs have widespread applications in various industries including biomedicine, fine chemicals production, drug delivery, packaging, and agriculture. This review provides the updated knowledge on the metabolic pathways for PHAs synthesis in bacteria, and the major microbial hosts for PHAs production. Yeasts are presented as a potential candidate for industrial PHAs production, with their high amenability to genetic engineering and the availability of industrial-scale technology. The major bottlenecks in the commercialization of PHAs as an alternative for plastics and future perspectives are also critically discussed.
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30
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Hong K, Beld J, Davis TD, Burkart MD, Palenik B. Screening and characterization of polyhydroxyalkanoate granules, and phylogenetic analysis of polyhydroxyalkanoate synthase gene PhaC in cyanobacteria. JOURNAL OF PHYCOLOGY 2021; 57:754-765. [PMID: 33350471 DOI: 10.1111/jpy.13123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 09/06/2020] [Accepted: 10/13/2020] [Indexed: 06/12/2023]
Abstract
Using Nile Red and BODIPY 493/503 dye-staining and fluorescence microscopy, twenty cyanobacterial strains, including ten commercially available strains and ten environmental isolates from estuaries, freshwater ponds, and lagoons, were screened for the accumulation of ecologically important and potentially biotechnologically significant carbon storage granules such as polyhydroxyalkanoates (PHA). Dye-staining granules were observed in six strains. Three Synechocystis, spp. strains WHSYN, LSNM, and CGF-1, and a Phormidium-like sp. CGFILA were isolated from environmental sources and found to produce granules of polyhydroxyalkanoate (PHA) according to PHA synthase gene (phaC) PCR screening and 1 H NMR analyses. The environmental isolate, Nodularia sp. Las Olas and commercially available Phormidium cf. iriguum CCALA 759 displayed granules but screened negative for PHA according to phaC PCR and 1 H NMR analyses. Partial polyhydroxyalkanoate synthase subunit C (phaC) and 16S rRNA gene sequences obtained from the PHA-accumulating strains and analyzed alongside publicly available phaC, phaE, 16S rRNA, and 23S rRNA data help in understanding the distribution and evolutionary history of PHA biosynthesis within the phylum Cyanobacteria. The data show that the presence of phaC is highly conserved within the genus Synechocystis, and present in at least one isolate of Phormidium. Maximum likelihood analyses and cophylogenetic modeling of PHA synthase gene sequences provide evidence of a recent horizontal gene transfer event between distant genera of cyanobacteria related to Pleurocapsa sp. PCC 7327 and Phormidium-like sp. CGFILA. These findings will help guide additional screening for PHA producers, and may explain why some Phormidium species produce PHAs, while others do not.
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Affiliation(s)
- Karl Hong
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, 92093-0202, USA
| | - Joris Beld
- Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92093-0202, USA
- Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Tony D Davis
- Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92093-0202, USA
| | - Michael D Burkart
- Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92093-0202, USA
| | - Brian Palenik
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, 92093-0202, USA
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31
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Boey JY, Mohamad L, Khok YS, Tay GS, Baidurah S. A Review of the Applications and Biodegradation of Polyhydroxyalkanoates and Poly(lactic acid) and Its Composites. Polymers (Basel) 2021; 13:1544. [PMID: 34065779 PMCID: PMC8150976 DOI: 10.3390/polym13101544] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Overconsumption of plastic goods and improper handling of petroleum-derived plastic waste have brought a plethora of negative impacts to the environment, ecosystem and human health due to its recalcitrance to degradation. These drawbacks become the main driving force behind finding biopolymers with the degradable properties. With the advancement in biopolymer research, polyhydroxyalkanoate (PHA) and poly(lacyic acid) (PLA) and its composites have been alluded to as a potential alternative to replace the petrochemical counterpart. This review highlights the current synthesis process and application of PHAs and PLA and its composites for food packaging materials and coatings. These biopolymers can be further ameliorated to enhance their applicability and are discussed by including the current commercially available packaging products. Factors influencing biodegradation are outlined in the latter part of this review. The main aim of this review article is to organize the scattered available information on various aspects of PHAs and PLA, and its composites for packaging application purposes. It is evident from a literature survey of about 140 recently published papers from the past 15 years that PLA and PHA show excellent physical properties as potential food packaging materials.
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Affiliation(s)
| | | | | | | | - Siti Baidurah
- School of Industrial Technology, Universiti Sains Malaysia, Minden 11800, Malaysia; (J.Y.B.); (L.M.); (Y.S.K.); (G.S.T.)
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Kouřilová X, Schwarzerová J, Pernicová I, Sedlář K, Mrázová K, Krzyžánek V, Nebesářová J, Obruča S. The First Insight into Polyhydroxyalkanoates Accumulation in Multi-Extremophilic Rubrobacter xylanophilus and Rubrobacter spartanus. Microorganisms 2021; 9:909. [PMID: 33923216 PMCID: PMC8146576 DOI: 10.3390/microorganisms9050909] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/27/2022] Open
Abstract
Actinobacteria belonging to the genus Rubrobacter are known for their multi-extremophilic growth conditions-they are highly radiation-resistant, halotolerant, thermotolerant or even thermophilic. This work demonstrates that the members of the genus are capable of accumulating polyhydroxyalkanoates (PHA) since PHA-related genes are widely distributed among Rubrobacter spp. whose complete genome sequences are available in public databases. Interestingly, all Rubrobacter strains possess both class I and class III synthases (PhaC). We have experimentally investigated the PHA accumulation in two thermophilic species, R. xylanophilus and R. spartanus. The PHA content in both strains reached up to 50% of the cell dry mass, both bacteria were able to accumulate PHA consisting of 3-hydroxybutyrate and 3-hydroxyvalerate monomeric units, none other monomers were incorporated into the polymer chain. The capability of PHA accumulation likely contributes to the multi-extremophilic characteristics since it is known that PHA substantially enhances the stress robustness of bacteria. Hence, PHA can be considered as extremolytes enabling adaptation to extreme conditions. Furthermore, due to the high PHA content in biomass, a wide range of utilizable substrates, Gram-stain positivity, and thermophilic features, the Rubrobacter species, in particular Rubrobacter xylanophilus, could be also interesting candidates for industrial production of PHA within the concept of Next-Generation Industrial Biotechnology.
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Affiliation(s)
- Xenie Kouřilová
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (X.K.); (I.P.)
| | - Jana Schwarzerová
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic; (J.S.); (K.S.)
| | - Iva Pernicová
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (X.K.); (I.P.)
| | - Karel Sedlář
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic; (J.S.); (K.S.)
| | - Kateřina Mrázová
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Kralovopolska 147, 612 64 Brno, Czech Republic; (K.M.); (V.K.)
| | - Vladislav Krzyžánek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Kralovopolska 147, 612 64 Brno, Czech Republic; (K.M.); (V.K.)
| | - Jana Nebesářová
- Biology Centre, The Czech Academy of Sciences, v.v.i., Branisovska 31, 370 05 Ceske Budejovice, Czech Republic;
- Faculty of Science, Charles University, Vinicna 7, 128 44 Prague 2, Czech Republic
| | - Stanislav Obruča
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (X.K.); (I.P.)
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Vannini C, Rossi A, Vallerini F, Menicagli V, Seggiani M, Cinelli P, Lardicci C, Balestri E. Microbial communities of polyhydroxyalkanoate (PHA)-based biodegradable composites plastisphere and of surrounding environmental matrix: a comparison between marine (seabed) and coastal sediments (dune sand) over a long-time scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142814. [PMID: 33129544 DOI: 10.1016/j.scitotenv.2020.142814] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/30/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Most researches on the plastisphere in coastal environments deal with plastics floating in seawater. Comparatively smaller attention has been devoted to the plastisphere of plastics buried in marine sediments, and very little is known on that of plastics on coastal sand dunes. Yet, limited information is available on the impact of plastics, especially biodegradable plastics, on microbial organisms in their surroundings. Nevertheless, a large amount of plastics sink on the seabed or is deposited on beach-dune systems. We investigated the succession of plastisphere microbial community on two biodegradable composites based on poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV) and seagrass fibres (PHBV/PO), buried in seabed and dune sediments over a 27 months period in mesocosm. PHBV is regarded as a valuable alternative to conventional plastics and PHBV/PO has recently been designed for applications in coastal habitat restoration. We also examined the degradation rate and impact of these plastics on the microbial communities of surrounding sediments. Microbial communities of the surface of PHBV and PHBV/PO in seabed and dune sand differ from those of surrounding sediments, displaying a lower richness. Plastics colonization occurs largely from bacteria present in surrounding sediments, although the contribution from the water column bacterial pool could be not negligible for plastics in the seabed. No significant differences were detected between the communities of the two plastics and no significant impact of plastics on microbial community of the surrounding sediments was detected. The exceptional long duration of this study allowed to gain information on the succession of a plastisphere community over a previously unexplored time scale. Succession appears highly dynamic in dune sand even after two years, while the community structure in seabed seems to reach stability after one year. These findings highlight the importance of performing long-term studies when trying to characterize composition and dynamics of plastisphere bacterial communities.
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Affiliation(s)
- Claudia Vannini
- Department of Biology, University of Pisa, Pisa I-56126, Italy; CIME, Centro Interdipartimentale di Microscopia Elettronica, University of Pisa, Pisa I-56126, Italy.
| | - Alessia Rossi
- Department of Biology, University of Pisa, Pisa I-56126, Italy.
| | | | | | - Maurizia Seggiani
- Department of Civil and Industrial Engineering, University of Pisa, Pisa I-56126, Italy.
| | - Patrizia Cinelli
- Department of Civil and Industrial Engineering, University of Pisa, Pisa I-56126, Italy.
| | - Claudio Lardicci
- Department of Biology, University of Pisa, Pisa I-56126, Italy; Department of Earth Sciences, University of Pisa, Pisa I-56126, Italy.
| | - Elena Balestri
- Department of Biology, University of Pisa, Pisa I-56126, Italy.
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Lascu I, Mereuță I, Chiciudean I, Hansen H, Avramescu SM, Tănase A, Stoica I. Complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate. Microbiologyopen 2021; 10:e1182. [PMID: 33970538 PMCID: PMC8087987 DOI: 10.1002/mbo3.1182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/30/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are biodegradable bioplastics that can be manufactured sustainably and represent a promising green alternative to petrochemical-based plastics. Here, we describe the complete genome of a new marine PHA-producing bacterium-Photobacterium ganghwense (strain C2.2), which we have isolated from the Black Sea seashore. This new isolate is psychrotolerant and accumulates PHA when glycerol is provided as the main carbon source. Transmission electron microscopy, specific staining with Nile Red visualized via epifluorescence microscopy and gas chromatography analysis confirmed the accumulation of PHA. This is the only PHA-producing Photobacterium for which we now have a complete genome sequence, allowing us to investigate the pathways for PHA production and other secondary metabolite synthesis pathways. The de novo assembly genome, obtained using open-source tools, comprises two chromosomes (3.5, 2 Mbp) and a megaplasmid (202 kbp). We identify the entire PHA synthesis gene cluster that encodes a class I PHA synthase, a phasin, a 3-ketothiolase, and an acetoacetyl-CoA reductase. No conventional PHA depolymerase was identified in strain C2.2, but a putative lipase with extracellular amorphous PHA depolymerase activity was annotated, suggesting that C2.2 is unable to degrade intracellular PHA. A complete pathway for the conversion of glycerol to acetyl-CoA was annotated, in accordance with its ability to convert glycerol to PHA. Several secondary metabolite biosynthetic gene clusters and a low number of genes involved in antibiotic resistance and virulence were also identified, indicating the strain's suitability for biotechnological applications.
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Affiliation(s)
- Irina Lascu
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Ioana Mereuță
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Iulia Chiciudean
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Hilde Hansen
- Department of ChemistryFaculty of Science and TechnologyUiT The Arctic University of NorwayTromsøNorway
| | - Sorin Marius Avramescu
- Department of Organic Chemistry, Biochemistry and CatalysisFaculty of ChemistryUniversity of BucharestBucharestRomania
| | - Ana‐Maria Tănase
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Ileana Stoica
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
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Viljakainen VR, Hug LA. The phylogenetic and global distribution of bacterial polyhydroxyalkanoate bioplastic-degrading genes. Environ Microbiol 2021; 23:1717-1731. [PMID: 33496062 DOI: 10.1111/1462-2920.15409] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 01/04/2021] [Accepted: 01/18/2021] [Indexed: 11/30/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are a family of microbially made polyesters commercialized as biodegradable plastics. PHA production rates are predicted to increase as concerns around environmental plastic contamination and limited fossil fuel resources have increased the importance of biodegradable and bio-based plastic alternatives. Microbially produced PHA depolymerases are the key enzymes mediating PHA biodegradation, but only a few PHA depolymerases have been well-characterized and screens employing metagenomic sequence data are lacking. Here, we used 3078 metagenomes to analyse the distribution of PHA depolymerases in microbial communities from diverse aquatic, terrestrial and waste management systems. We significantly expand the recognized diversity of this protein family by screening 1914 Gb of sequence data and identifying 13 869 putative PHA depolymerases in 1295 metagenomes. Our results indicate that PHA depolymerases are unevenly distributed across environments. We predicted the highest frequency of PHA depolymerases in wastewater systems and the lowest in marine and thermal springs. In tandem, we screened 5290 metagenome-assembled genomes to describe the phylogenetic distribution of PHA depolymerases, which is substantially broader compared with current cultured representatives. The Proteobacteria and Bacteroidota are key lineages encoding PHA depolymerases, but PHA depolymerases were predicted from members of the Bdellovibrionota, Methylomirabilota, Actinobacteriota, Firmicutes, Spirochaetota, Desulfobacterota, Myxococcota and Planctomycetota.
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Affiliation(s)
- V R Viljakainen
- University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada
| | - L A Hug
- University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada
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de Vogel FA, Schlundt C, Stote RE, Ratto JA, Amaral-Zettler LA. Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates. Microorganisms 2021; 9:186. [PMID: 33467086 PMCID: PMC7830162 DOI: 10.3390/microorganisms9010186] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
Biodegradable and compostable plastics are getting more attention as the environmental impacts of fossil-fuel-based plastics are revealed. Microbes can consume these plastics and biodegrade them within weeks to months under the proper conditions. The biobased polyhydroxyalkanoate (PHA) polymer family is an attractive alternative due to its physicochemical properties and biodegradability in soil, aquatic, and composting environments. Standard test methods are available for biodegradation that employ either natural inocula or defined communities, the latter being preferred for standardization and comparability. The original marine biodegradation standard test method ASTM D6691 employed such a defined consortium for testing PHA biodegradation. However, the taxonomic composition and metabolic potential of this consortium have never been confirmed using DNA sequencing technologies. To this end, we revived available members of this consortium and determined their phylogenetic placement, genomic sequence content, and metabolic potential. The revived members belonged to the Bacillaceae, Rhodobacteraceae, and Vibrionaceae families. Using a comparative genomics approach, we found all the necessary enzymes for both PHA production and utilization in most of the members. In a clearing-zone assay, three isolates also showed extracellular depolymerase activity. However, we did not find classical PHA depolymerases, but identified two potentially new extracellular depolymerases that resemble triacylglycerol lipases.
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Affiliation(s)
- Fons A. de Vogel
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, The Netherlands;
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.115, 3508 TC Utrecht, The Netherlands
| | - Cathleen Schlundt
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA;
| | - Robert E. Stote
- U.S. Army Combat Capabilities Development Command Soldier Center, 10 General Greene Avenue, Natick, MA 01760, USA; (R.E.S.); (J.A.R.)
| | - Jo Ann Ratto
- U.S. Army Combat Capabilities Development Command Soldier Center, 10 General Greene Avenue, Natick, MA 01760, USA; (R.E.S.); (J.A.R.)
| | - Linda A. Amaral-Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, The Netherlands;
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA;
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, The Netherlands
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Fernandes M, Salvador A, Alves MM, Vicente AA. Factors affecting polyhydroxyalkanoates biodegradation in soil. Polym Degrad Stab 2020. [DOI: 10.1016/j.polymdegradstab.2020.109408] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Choi SY, Cho IJ, Lee Y, Kim YJ, Kim KJ, Lee SY. Microbial Polyhydroxyalkanoates and Nonnatural Polyesters. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1907138. [PMID: 32249983 DOI: 10.1002/adma.201907138] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/20/2020] [Indexed: 06/11/2023]
Abstract
Microorganisms produce diverse polymers for various purposes such as storing genetic information, energy, and reducing power, and serving as structural materials and scaffolds. Among these polymers, polyhydroxyalkanoates (PHAs) are microbial polyesters synthesized and accumulated intracellularly as a storage material of carbon, energy, and reducing power under unfavorable growth conditions in the presence of excess carbon source. PHAs have attracted considerable attention for their wide range of applications in industrial and medical fields. Since the first discovery of PHA accumulating bacteria about 100 years ago, remarkable advances have been made in the understanding of PHA biosynthesis and metabolic engineering of microorganisms toward developing efficient PHA producers. Recently, nonnatural polyesters have also been synthesized by metabolically engineered microorganisms, which opened a new avenue toward sustainable production of more diverse plastics. Herein, the current state of PHAs and nonnatural polyesters is reviewed, covering mechanisms of microbial polyester biosynthesis, metabolic pathways, and enzymes involved in biosynthesis of short-chain-length PHAs, medium-chain-length PHAs, and nonnatural polyesters, especially 2-hydroxyacid-containing polyesters, metabolic engineering strategies to produce novel polymers and enhance production capabilities and fermentation, and downstream processing strategies for cost-effective production of these microbial polyesters. In addition, the applications of PHAs and prospects are discussed.
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Affiliation(s)
- So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - In Jin Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Youngjoon Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yeo-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- BioProcess Engineering Research Center and Bioinformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
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Hori C, Sugiyama T, Watanabe K, Sun J, Kamada Y, Ooi T, Isono T, Satoh T, Sato SI, Taguchi S, Matsumoto K. Isolation of poly[d-lactate (LA)-co-3-hydroxybutyrate)]-degrading bacteria from soil and characterization of d-LA homo-oligomer degradation by the isolated strains. Polym Degrad Stab 2020. [DOI: 10.1016/j.polymdegradstab.2020.109231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Identification and characterization of a novel extracellular polyhydroxyalkanoate depolymerase in the complete genome sequence of Undibacterium sp. KW1 and YM2 strains. PLoS One 2020; 15:e0232698. [PMID: 32369496 PMCID: PMC7199957 DOI: 10.1371/journal.pone.0232698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 04/19/2020] [Indexed: 12/02/2022] Open
Abstract
Polyhydroxyalkanoate (PHA) is a biodegradable polymer that is synthesized by a wide range of microorganisms. One of the derivatives of PHA, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH) has flexible material properties and low melting temperature. We have previously demonstrated that PHBH is degradable in a freshwater environment via the formation of biofilm on the surface of the PHBH film. Undibacterium sp. KW1 and YM2, which were isolated from the biofilm present on the PHBH film in the freshwater sample, were shown to have PHBH-degrading activity. In this study, the complete genome sequence of KW1 and YM2 revealed that the extracellular PHA depolymerase gene, designated as phaZUD, was present in their chromosomes. Sequence analysis revealed that PhaZUD contained four domains: a signal peptide, catalytic domain, linker domain, and substrate-binding domain. Escherichia coli harboring a PhaZUD-expressing plasmid showed PHBH-degrading activity in LB medium containing 1 wt% PHBH powder. The recombinant His-tagged PhaZUD from KW1 and YM2 was purified from the culture supernatant and shown to have PHBH-degrading activity at the optimum temperature of 35 and 40°C, respectively. When the degradation product in the PHBH solution was treated with PhaZUD and assayed by LC-TOF-MS, we detected various oligomer structures, but no more than pentamers, which consist of 3-hydroxybutyrate and 3-hydroxyhexanoate. These results demonstrated that PhaZUD may have an endo-type extracellular PHA depolymerase activity.
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Characterization of an intracellular poly(3-hydroxyalkanoate) depolymerase from the soil bacterium, Pseudomonas putida LS46. Polym Degrad Stab 2020. [DOI: 10.1016/j.polymdegradstab.2020.109127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Yañez L, Conejeros R, Vergara-Fernández A, Scott F. Beyond Intracellular Accumulation of Polyhydroxyalkanoates: Chiral Hydroxyalkanoic Acids and Polymer Secretion. Front Bioeng Biotechnol 2020; 8:248. [PMID: 32318553 PMCID: PMC7147478 DOI: 10.3389/fbioe.2020.00248] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/10/2020] [Indexed: 01/05/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs) are ubiquitous prokaryotic storage compounds of carbon and energy, acting as sinks for reducing power during periods of surplus of carbon source relative to other nutrients. With close to 150 different hydroxyalkanoate monomers identified, the structure and properties of these polyesters can be adjusted to serve applications ranging from food packaging to biomedical uses. Despite its versatility and the intensive research in the area over the last three decades, the market share of PHAs is still low. While considerable rich literature has accumulated concerning biochemical, physiological, and genetic aspects of PHAs intracellular accumulation, the costs of substrates and processing costs, including the extraction of the polymer accumulated in intracellular granules, still hampers a more widespread use of this family of polymers. This review presents a comprehensive survey and critical analysis of the process engineering and metabolic engineering strategies reported in literature aimed at the production of chiral (R)-hydroxycarboxylic acids (RHAs), either from the accumulated polymer or by bypassing the accumulation of PHAs using metabolically engineered bacteria, and the strategies developed to recover the accumulated polymer without using conventional downstream separations processes. Each of these topics, that have received less attention compared to PHAs accumulation, could potentially improve the economy of PHAs production and use. (R)-hydroxycarboxylic acids can be used as chiral precursors, thanks to its easily modifiable functional groups, and can be either produced de-novo or be obtained from recycled PHA products. On the other hand, efficient mechanisms of PHAs release from bacterial cells, including controlled cell lysis and PHA excretion, could reduce downstream costs and simplify the polymer recovery process.
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Affiliation(s)
- Luz Yañez
- Green Technology Research Group, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de los Andes, Santiago, Chile
| | - Raúl Conejeros
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Alberto Vergara-Fernández
- Green Technology Research Group, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de los Andes, Santiago, Chile
| | - Felipe Scott
- Green Technology Research Group, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de los Andes, Santiago, Chile
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Yang Y, Daims H, Liu Y, Herbold CW, Pjevac P, Lin JG, Li M, Gu JD. Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems. mBio 2020; 11:e03175-19. [PMID: 32184251 PMCID: PMC7078480 DOI: 10.1128/mbio.03175-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/06/2020] [Indexed: 11/20/2022] Open
Abstract
The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions.IMPORTANCE The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.
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Affiliation(s)
- Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong, People's Republic of China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Holger Daims
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China
| | - Craig W Herbold
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Petra Pjevac
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, Hsinchu City, Taiwan
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong, People's Republic of China
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Zadjelovic V, Chhun A, Quareshy M, Silvano E, Hernandez-Fernaud JR, Aguilo-Ferretjans MM, Bosch R, Dorador C, Gibson MI, Christie-Oleza JA. Beyond oil degradation: enzymatic potential of Alcanivorax to degrade natural and synthetic polyesters. Environ Microbiol 2020; 22:1356-1369. [PMID: 32079039 PMCID: PMC7187450 DOI: 10.1111/1462-2920.14947] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022]
Abstract
Pristine marine environments are highly oligotrophic ecosystems populated by well‐established specialized microbial communities. Nevertheless, during oil spills, low‐abundant hydrocarbonoclastic bacteria bloom and rapidly prevail over the marine microbiota. The genus Alcanivorax is one of the most abundant and well‐studied organisms for oil degradation. While highly successful under polluted conditions due to its specialized oil‐degrading metabolism, it is unknown how they persist in these environments during pristine conditions. Here, we show that part of the Alcanivorax genus, as well as oils, has an enormous potential for biodegrading aliphatic polyesters thanks to a unique and abundantly secreted alpha/beta hydrolase. The heterologous overexpression of this esterase proved a remarkable ability to hydrolyse both natural and synthetic polyesters. Our findings contribute to (i) better understand the ecology of Alcanivorax in its natural environment, where natural polyesters such as polyhydroxyalkanoates (PHA) are produced by a large fraction of the community and, hence, an accessible source of carbon and energy used by the organism in order to persist, (ii) highlight the potential of Alcanivorax to clear marine environments from polyester materials of anthropogenic origin as well as oils, and (iii) the discovery of a new versatile esterase with a high biotechnological potential.
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Affiliation(s)
| | - Audam Chhun
- School of Life Sciences, University of Warwick, Warwick, UK
| | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Warwick, UK
| | | | - Juan R Hernandez-Fernaud
- School of Life Sciences, University of Warwick, Warwick, UK.,Unidad de investigación-HUC, La Laguna-Tenerife, Spain
| | - María M Aguilo-Ferretjans
- School of Life Sciences, University of Warwick, Warwick, UK.,Department of Biology, University of the Balearic Islands, Spain
| | - Rafael Bosch
- Department of Biology, University of the Balearic Islands, Spain.,IMEDEA (CSIC-UIB), Esporles, Spain
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Warwick, UK.,Warwick Medical School, University of Warwick, Warwick, UK
| | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Warwick, UK.,Department of Biology, University of the Balearic Islands, Spain.,IMEDEA (CSIC-UIB), Esporles, Spain
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Martínez-Tobón DI, Waters B, Elias AL, Sauvageau D. Streamlined production, purification, and characterization of recombinant extracellular polyhydroxybutyrate depolymerases. Microbiologyopen 2020; 9:e1001. [PMID: 32087608 PMCID: PMC7142370 DOI: 10.1002/mbo3.1001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 01/06/2023] Open
Abstract
Heterologous production of extracellular polyhydroxybutyrate (PHB) depolymerases (PhaZs) has been of interest for over 30 years, but implementation is sometimes difficult and can limit the scope of research. With the constant development of tools to improve recombinant protein production in Escherichia coli, we propose a method that takes characteristics of PhaZs from different bacterial strains into account. Recombinant His‐tagged versions of PhaZs (rPhaZ) from Comamonas testosteroni 31A, Cupriavidus sp. T1, Marinobacter algicola DG893, Pseudomonas stutzeri, and Ralstonia sp. were successfully produced with varying expression, solubility, and purity levels. PhaZs from C. testosteroni and P. stutzeri were more amenable to heterologous expression in all aspects; however, using the E. coli Rosetta‐gami B(DE3) expression strain and establishing optimal conditions for expression and purification (variation of IPTG concentration and use of size exclusion columns) helped circumvent low expression and purity for the other PhaZs. Degradation activity of the rPhaZs was compared using a simple PHB plate‐based method, adapted to test for various pH and temperatures. rPhaZ from M. algicola presented the highest activity at 15°C, and rPhaZs from Cupriavidus sp. T1 and Ralstonia sp. had the highest activity at pH 5.4. The methods proposed herein can be used to test the production of soluble recombinant PhaZs and to perform preliminary evaluation for applications that require PHB degradation.
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Affiliation(s)
- Diana I Martínez-Tobón
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Brennan Waters
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Anastasia L Elias
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
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Biochemical properties and biotechnological applications of microbial enzymes involved in the degradation of polyester-type plastics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140315. [DOI: 10.1016/j.bbapap.2019.140315] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/07/2019] [Accepted: 10/22/2019] [Indexed: 01/03/2023]
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Nambu Y, Ishii-Hyakutake M, Harada K, Mizuno S, Tsuge T. Expanded amino acid sequence of the PhaC box in the active center of polyhydroxyalkanoate synthases. FEBS Lett 2019; 594:710-716. [PMID: 31665820 DOI: 10.1002/1873-3468.13651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/27/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022]
Abstract
Polyhydroxyalkanoate (PHA) synthases catalyze the polymerization reaction of the acyl moiety of hydroxyacyl-coenzyme A into polyester. The catalytic subunit PhaC of PHA synthase has the PhaC box sequence at the active site that is typically described as G-X-C-X-G-G (X is an arbitrary amino acid), and cysteine is an active center. In this study, an amino acid replacement was introduced into the PhaC box of the PHA synthase derived from Ralstonia eutropha (PhaCRe ) to investigate the importance of highly conserved residues in polymerizing activity. Point mutagenesis revealed that PhaCRe mutants with the expanded PhaC box sequence ([GAST]-X-C-X-[GASV]-[GA]) are functional PHA synthases. These findings highlight the low mutational robustness of the last glycine residue in the PhaC box as well as that of the active center cysteine.
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Affiliation(s)
- Yuka Nambu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Manami Ishii-Hyakutake
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan.,Bioplastic Research Team, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Ken Harada
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Shoji Mizuno
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Takeharu Tsuge
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
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Coordinated Regulation of the Size and Number of Polyhydroxybutyrate Granules by Core and Accessory Phasins in the Facultative Microsymbiont Sinorhizobium fredii NGR234. Appl Environ Microbiol 2019; 85:AEM.00717-19. [PMID: 31375484 DOI: 10.1128/aem.00717-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/23/2019] [Indexed: 12/15/2022] Open
Abstract
The exact roles of various granule-associated proteins (GAPs) of polyhydroxybutyrate (PHB) are poorly investigated, particularly for bacteria associated with plants. In this study, four structural GAPs, named phasins PhaP1 to PhaP4, were identified and demonstrated as true phasins colocalized with PHB granules in Sinorhizobium fredii NGR234, a facultative microsymbiont of Vigna unguiculata and many other legumes. The conserved PhaP2 dominated in regulation of granule size under both free-living and symbiotic conditions. PhaP1, another conserved phasin, made a higher contribution than accessory phasins PhaP4 and PhaP3 to PHB biosynthesis at stationary phase. PhaP3, with limited phyletic distribution on the symbiosis plasmid of Sinorhizobium, was more important than PhaP1 in regulating PHB biosynthesis in V. unguiculata nodules. Under the test conditions, no significant symbiotic defects were observed for mutants lacking individual or multiple phaP genes. The mutant lacking two PHB synthases showed impaired symbiotic performance, while mutations in individual PHB synthases or a PHB depolymerase yielded no symbiotic defects. This phenomenon is not related to either the number or size of PHB granules in test mutants within nodules. Distinct metabolic profiles and cocktail pools of GAPs of different phaP mutants imply that core and accessory phasins can be differentially involved in regulating other cellular processes in the facultative microsymbiont S. fredii NGR234.IMPORTANCE Polyhydroxybutyrate (PHB) granules are a store of carbon and energy in bacteria and archaea and play an important role in stress adaptation. Recent studies have highlighted distinct roles of several granule-associated proteins (GAPs) in regulating the size, number, and localization of PHB granules in free-living bacteria, though our knowledge of the role of GAPs in bacteria associated with plants is still limited. Here we report distinct roles of core and accessory phasins associated with PHB granules of Sinorhizobium fredii NGR234, a broad-host-range microsymbiont of diverse legumes. Core phasins PhaP2 and PhaP1 are conserved major phasins in free-living cells. PhaP2 and accessory phasin PhaP3, encoded by an auxiliary gene on the symbiosis plasmid, are major phasins in nitrogen-fixing bacteroids in cowpea nodules. GAPs and metabolic profiles can vary in different phaP mutants. Contrasting symbiotic performances between mutants lacking PHB synthases, depolymerase, or phasins were revealed.
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Venkiteshwaran K, Benn N, Seyedi S, Zitomer D. Methane yield and lag correlate with bacterial community shift following bioplastic anaerobic co-digestion. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2019.100198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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50
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Current knowledge on enzymatic PET degradation and its possible application to waste stream management and other fields. Appl Microbiol Biotechnol 2019; 103:4253-4268. [PMID: 30957199 PMCID: PMC6505623 DOI: 10.1007/s00253-019-09717-y] [Citation(s) in RCA: 235] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/20/2019] [Accepted: 02/22/2019] [Indexed: 11/21/2022]
Abstract
Enzymatic hydrolysis of polyethylene terephthalate (PET) has been the subject of extensive previous research that can be grouped into two categories, viz. enzymatic surface modification of polyester fibers and management of PET waste by enzymatic hydrolysis. Different enzymes with rather specific properties are required for these two processes. Enzymatic surface modification is possible with several hydrolases, such as lipases, carboxylesterases, cutinases, and proteases. These enzymes should be designated as PET surface–modifying enzymes and should not degrade the building blocks of PET but should hydrolyze the surface polymer chain so that the intensity of PET is not weakened. Conversely, management of PET waste requires substantial degradation of the building blocks of PET; therefore, only a limited number of cutinases have been recognized as PET hydrolases since the first PET hydrolase was discovered by Müller et al. (Macromol Rapid Commun 26:1400–1405, 2005). Here, we introduce current knowledge on enzymatic degradation of PET with a focus on the key class of enzymes, PET hydrolases, pertaining to the definition of enzymatic requirements for PET hydrolysis, structural analyses of PET hydrolases, and the reaction mechanisms. This review gives a deep insight into the structural basis and dynamics of PET hydrolases based on the recent progress in X-ray crystallography. Based on the knowledge accumulated to date, we discuss the potential for PET hydrolysis applications, such as in designing waste stream management.
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