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Mubayi V, Ahern CB, Calusinska M, O'Malley MA. Toward a Circular Bioeconomy: Designing Microbes and Polymers for Biodegradation. ACS Synth Biol 2024. [PMID: 38918080 DOI: 10.1021/acssynbio.4c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Polymer production is rapidly increasing, but there are no large-scale technologies available to effectively mitigate the massive accumulation of these recalcitrant materials. One potential solution is the development of a carbon-neutral polymer life cycle, where microorganisms convert plant biomass to chemicals, which are used to synthesize biodegradable materials that ultimately contribute to the growth of new plants. Realizing a circular carbon life cycle requires the integration of knowledge across microbiology, bioengineering, materials science, and organic chemistry, which itself has hindered large-scale industrial advances. This review addresses the biodegradation status of common synthetic polymers, identifying novel microbes and enzymes capable of metabolizing these recalcitrant materials and engineering approaches to enhance their biodegradation pathways. Design considerations for the next generation of biodegradable polymers are also reviewed, and finally, opportunities to apply findings from lignocellulosic biodegradation to the design and biodegradation of similarly recalcitrant synthetic polymers are discussed.
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Affiliation(s)
- Vikram Mubayi
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Colleen B Ahern
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Magdalena Calusinska
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, L-4422 Belvaux, Luxembourg
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Bioengineering, University of California, Santa Barbara, California 93106, United States
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
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2
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Blair EM, Brown JL, Li D, Holden PA, O'Malley MA. Metagenomics analysis yields assembled genomes from prokaryotic anaerobes with polymer-degrading potential. Biotechnol Prog 2024:e3484. [PMID: 38881311 DOI: 10.1002/btpr.3484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/18/2024]
Abstract
Anaerobic microbial communities are often highly degradative, such as those found in the herbivore rumen and large-scale anaerobic digesters. Since the microbial communities in these systems degrade recalcitrant organic polymers, we hypothesize that some microbes in anaerobic environments may be involved in man-made plastic association, deformation, or even breakdown. While efforts have been put toward characterizing microbial communities, many microbes remain unidentified until they can be sufficiently cultivated to generate enough genetic material to assemble high-quality metagenome assemblies and reference genomes. In this study, microbial consortia from goat fecal pellets and anaerobic digester sludge were cultivated for over 6 weeks to assemble metagenomes from novel anaerobic taxa with potential degradative activity. To select for microbes with potential plastic-degrading abilities, plastic strips were included in culture, though the presence of plastic did not appear to enrich for particularly degradative consortia, yet it did select for novel species that otherwise may not have been characterized. Whole-genome shotgun sequencing enabled assembly of 72 prokaryotic metagenome-assembled genomes (MAGs) with >90% completion, <5% contamination, and an N50 >10,000 bp; 17 of these MAGs are classified as novel species given their lack of similarity to publicly available genomes and MAGs. These 72 MAGs vary in predicted carbohydrate-degrading abilities, with genes predicted to encode fewer than 10 or up to nearly 400 carbohydrate-active enzymes. Overall, this enrichment strategy enables characterization of less abundant MAGs in a community, and the MAGs identified here can be further mined to advance understanding of degradative anaerobic microbial consortia.
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Affiliation(s)
- Elaina M Blair
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Jennifer L Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Dong Li
- Bren School of Environmental Science & Management, University of California, Santa Barbara, California, USA
| | - Patricia A Holden
- Bren School of Environmental Science & Management, University of California, Santa Barbara, California, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
- Joint BioEnergy Institute (JBEI), Emeryville, California, USA
- Department of Bioengineering, University of California, Santa Barbara, California, USA
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3
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Álvarez-Méndez SJ, Díaz-Peña FJ, Gómez-Escabia S, González-Sálamo J, Hernández-Borges J. Tracking anthropogenic microparticles in wildlife of an alpine insular environment. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133291. [PMID: 38157812 DOI: 10.1016/j.jhazmat.2023.133291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/10/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Despite the isolation of remote natural regions, it has been discovered that they are experiencing the accumulation of anthropogenic microparticles (i.e., microplastics or natural or semisynthetic cellulosic particles). Teide National Park (Canary Islands, Spain) is a high-mountain protected area known for its rich biodiversity. This study aims to assess the occurrence of coloured anthropogenic particles in the faecal matter of wild mammals, specifically rabbits and mouflons, residing in the park. With this purpose, faeces were collected from 68 systematically distributed sampling points. A stereomicroscopy-guided grinding process allowed a chemical-free and quick visual inspection of 616 individual excreta, revealing that 96% were particle-free. However, 37 anthropogenic particles were found, which correspond to 0.79 ± 0.20 items per gram of dry faecal matter. The archetypical particle was a cellulosic blue microfibre of 2721 ± 407 µm, though poly(ethylene-vinyl acetate) and polypropylene were also identified via micro Fourier-transform infrared spectroscopic analysis. Atmospheric deposition and touristic pressure may be the sources of the anthropogenic particles, as they were randomly found in 36% of the sampling points. These findings represent the first evidence of anthropogenic particle ingestion by wild rabbits and mouflons, signifying the introduction of microplastics into terrestrial food chains in a remote high-mountain environment.
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Affiliation(s)
- Sergio J Álvarez-Méndez
- Departamento de Química Orgánica, Universidad de La Laguna (ULL), Avda. Astrofísico Francisco Sánchez, s/n, 38206 San Cristóbal de La Laguna, Spain; Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna (ULL), Avda. Astrofísico Francisco Sánchez, s/n, 38206 San Cristóbal de La Laguna, Spain
| | - Francisco J Díaz-Peña
- Departamento de Biología Animal, Edafología y Geología, Facultad de Ciencias, Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez, s/n, 38206 San Cristóbal de La Laguna, Spain.
| | - Santiago Gómez-Escabia
- Departamento de Biología Animal, Edafología y Geología, Facultad de Ciencias, Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez, s/n, 38206 San Cristóbal de La Laguna, Spain; Departamento de Química, Unidad Departamental de Química Analítica, Facultad de Ciencias, Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez, s/n, 38206 San Cristóbal de La Laguna, Spain
| | - Javier González-Sálamo
- Departamento de Química, Unidad Departamental de Química Analítica, Facultad de Ciencias, Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez, s/n, 38206 San Cristóbal de La Laguna, Spain; Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez, s/n, 38206 San Cristóbal de La Laguna, Spain
| | - Javier Hernández-Borges
- Departamento de Química, Unidad Departamental de Química Analítica, Facultad de Ciencias, Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez, s/n, 38206 San Cristóbal de La Laguna, Spain; Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez, s/n, 38206 San Cristóbal de La Laguna, Spain.
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4
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Díaz-García L, Chuvochina M, Feuerriegel G, Bunk B, Spröer C, Streit WR, Rodriguez-R LM, Overmann J, Jiménez DJ. Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes. Syst Appl Microbiol 2024; 47:126485. [PMID: 38211536 DOI: 10.1016/j.syapm.2023.126485] [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: 07/18/2023] [Revised: 10/19/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024]
Abstract
An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by A. colombiense. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.
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Affiliation(s)
- Laura Díaz-García
- Department of Chemical and Biological Engineering, Advanced Biomanufacturing Centre, University of Sheffield, UK
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | - Golo Feuerriegel
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - 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
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - 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
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia; Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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5
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Quartinello F, Subagia R, Zitzenbacher S, Reich J, Vielnascher R, Becher E, Hall M, Ribitsch D, Guebitz GM. Dihydropyrimidinase from Saccharomyces kluyveri can hydrolyse polyamides. Front Bioeng Biotechnol 2023; 11:1158226. [PMID: 37180040 PMCID: PMC10169691 DOI: 10.3389/fbioe.2023.1158226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023] Open
Abstract
In Saccharomyces kluyveri, dihydropyrimidinase (DHPaseSK) is involved in the pyrimidine degradation pathway, which includes the reversible ring cleavage between nitrogen 3 and carbon 4 of 5,6-dihydrouracil. In this study, DPHaseSK was successfully cloned and expressed in E. coli BL-21 Gold (DE3) with and without affinity tags. Thereby, the Strep-tag enabled fastest purification and highest specific activity (9.5 ± 0.5 U/mg). The biochemically characterized DHPaseSK_Strep had similar kinetic parameters (Kcat/Km) on 5,6-dihydrouracil (DHU) and para-nitroacetanilide respectively, with 7,229 and 4060 M-1 s-1. The hydrolytic ability of DHPaseSK_Strep to polyamides (PA) was tested on PA consisting of monomers with different chain length (PA-6, PA-6,6, PA-4,6, PA-4,10 and PA-12). According to LC-MS/TOF analysis, DHPaseSK_Strep showed a preference for films containing the shorter chain monomers (e.g., PA-4,6). In contrast, an amidase from Nocardia farcinica (NFpolyA) showed some preference for PA consisting of longer chain monomers. In conclusion, in this work DHPaseSK_Strep was demonstrated to be able to cleave amide bonds in synthetic polymers, which can be an important basis for development of functionalization and recycling processes for polyamide containing materials.
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Affiliation(s)
- Felice Quartinello
- Austrian Centre of Industrial Biotechnology, Tulln an der Donau, Austria
- Department of Agrobiotechnology, Institute of Environmental Biotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Raditya Subagia
- Austrian Centre of Industrial Biotechnology, Tulln an der Donau, Austria
| | | | - Johanna Reich
- Austrian Centre of Industrial Biotechnology, Tulln an der Donau, Austria
| | - Robert Vielnascher
- Austrian Centre of Industrial Biotechnology, Tulln an der Donau, Austria
| | - Erik Becher
- Institute of Chemistry, University of Graz, Graz, Austria
| | - Mélanie Hall
- Institute of Chemistry, University of Graz, Graz, Austria
- BioHealth, University of Graz, Graz, Austria
| | - Doris Ribitsch
- Austrian Centre of Industrial Biotechnology, Tulln an der Donau, Austria
- Department of Agrobiotechnology, Institute of Environmental Biotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Georg M. Guebitz
- Austrian Centre of Industrial Biotechnology, Tulln an der Donau, Austria
- Department of Agrobiotechnology, Institute of Environmental Biotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Austria
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6
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Microplastics in Terrestrial Domestic Animals and Human Health: Implications for Food Security and Food Safety and Their Role as Sentinels. Animals (Basel) 2023; 13:ani13040661. [PMID: 36830448 PMCID: PMC9951732 DOI: 10.3390/ani13040661] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Terrestrial domestic animals are exposed to microplastics, therefore, contaminating the food chain, in the case of livestock, or acting as sentinels for human exposure, in the case of companion animals. The aim of this review was to address the importance of terrestrial domestic animals on human exposure to microplastics. Animal products may already show some microplastics contamination, which may occur during their lifetime, possibly also compromising productivity, and during processing, originating from equipment and packaging. Moreover, release of microplastics in animal feces (or manure) leads to the contamination of agricultural fields, with possible impacts and internalization in plants. Therefore, microplastics pose a threat to food security, compromising food productivity, and food safety, by being a foreign material found in animal products. Conversely, in urban environments, companion animals (cats and dogs) may be relevant sentinels for human exposure. While oral exposure may vary in pets compared to humans, due to indiscriminate ingestion and chewing or licking behaviors, airborne exposure is likely to be a good indicator for human exposure. Therefore, future studies should address the importance of terrestrial domestic animals for human exposure of microplastics, both in the food chain and as sentinels for environmental exposure.
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7
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Dong X, Liu X, Hou Q, Wang Z. From natural environment to animal tissues: A review of microplastics(nanoplastics) translocation and hazards studies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 855:158686. [PMID: 36099943 DOI: 10.1016/j.scitotenv.2022.158686] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/24/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Microplastics (MPs) and nanoplastic (NPs) pollution is a global concern due to the massive use of plastic products. Although there have been many studies on the treatments of animals with MPs/NPs, there are few systematic summaries of MPs/NPs translocation and hazards in animals. This review comprehensively summarizes the pathways by which animals are exposed to MPs/NPs in the environment, in particular, to summarize in detail their translocation and hazards in vivo. Studies have shown that MPs/NPs enter the animals' body through water, food, breath and even skin, enter the blood circulation through the lungs and digestive tract, and eventually accumulate in various tissues. After a summary of the studies, we found a high correlation between the tissue accumulation of MPs/NPs and their particle size, with 4-20 μm MPs appearing to be more prone to accumulate in tissues. These MPs/NPs accumulated in animal tissues may be transferred to humans through the food chain. Thus, we summarized the studies on the accumulation of MPs/NPs in livestock and poultry products, showing that MPs/NPs in livestock and poultry products gradually increased with the complexity of processing and packaging processes. There are few reports related to direct contamination of livestock products by MPs/NPs, we hope that this review will bring together the growing body of evidence that MPs/NPs can directly harm human health through the food chain.
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Affiliation(s)
- Xusheng Dong
- Ruminant Nutrition and Physiology Laboratory, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, PR China
| | - Xinbei Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai'an, PR China
| | - Qiuling Hou
- Ruminant Nutrition and Physiology Laboratory, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, PR China
| | - Zhonghua Wang
- Ruminant Nutrition and Physiology Laboratory, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, PR China.
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8
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Al-Tohamy R, Ali SS, Zhang M, Elsamahy T, Abdelkarim EA, Jiao H, Sun S, Sun J. Environmental and Human Health Impact of Disposable Face Masks During the COVID-19 Pandemic: Wood-Feeding Termites as a Model for Plastic Biodegradation. Appl Biochem Biotechnol 2023; 195:2093-2113. [PMID: 36370247 PMCID: PMC9652579 DOI: 10.1007/s12010-022-04216-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 11/14/2022]
Abstract
The ongoing COVID-19 pandemic has resulted in an unprecedented form of plastic pollution: personal protective equipment (PPE). On the eve of the COVID-19 pandemic, there is a tremendous increase in the production of plastic-based PPE. To control the spread of the virus, face masks (FMs) are used as primary PPE. Thus, the production and usage of FM significantly increased as the COVID-19 pandemic was still escalating. The primary raw materials for the manufacturing of FMs are non-biodegradable synthetic polymers derived from petrochemicals. This calls for an urgent need to develop novel strategies for the efficient degradation of plastics. Furthermore, most of these masks contain plastic or other derivatives of plastic. The extensive usage of FM generates millions of tons of plastic waste for the environment in a short span of time. However, their degradation in the environment and consequences are poorly understood. Therefore, the potential impacts of disposable FM on the environment and human health during the COVID-19 pandemic are clarified in the present study. Despite structural and recalcitrance variations, lignocellulose and plastic polymers have physicochemical features, including carbon skeletons with comparable chemical bonds as well as hydrophobic properties in amorphous and crystalline regions. In this review, we argue that there is much to be learned from termites by transferring knowledge from research on lignocellulose degradation by termites to that on plastic waste.
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Affiliation(s)
- Rania Al-Tohamy
- grid.440785.a0000 0001 0743 511XBiofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013 China
| | - Sameh Samir Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China. .,Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Meng Zhang
- grid.440785.a0000 0001 0743 511XBiofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013 China
| | - Tamer Elsamahy
- grid.440785.a0000 0001 0743 511XBiofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013 China
| | - Esraa A. Abdelkarim
- grid.440785.a0000 0001 0743 511XBiofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013 China
| | - Haixin Jiao
- grid.440785.a0000 0001 0743 511XBiofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013 China
| | - Sarina Sun
- Institute of Textiles and Clothing, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
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Król B, Słupczyńska M, Wilk M, Asghar M, Cwynar P. Anaerobic rumen fungi and fungal direct-fed microbials
in ruminant feeding. JOURNAL OF ANIMAL AND FEED SCIENCES 2022. [DOI: 10.22358/jafs/153961/2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Biochemical characterization of a thermally stable, acidophilic and surfactant-tolerant xylanase from Aspergillus awamori AFE1 and hydrolytic efficiency of its immobilized form. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Abstract
In the Anthropocene, plastic pollution is a worldwide concern that must be tackled from different viewpoints, bringing together different areas of science. Microbial transformation of polymers is a broad-spectrum research topic that has become a keystone in the circular economy of fossil-based and biobased plastics. To have an open discussion about these themes, experts in the synthesis of polymers and biodegradation of lignocellulose and plastics convened within the framework of The Transnational Network for Research and Innovation in Microbial Biodiversity, Enzymes Technology and Polymer Science (MENZYPOL-NET), which was recently created by early-stage scientists from Colombia and Germany. In this context, the international workshop “Microbial Synthesis and Degradation of Polymers: Toward a Sustainable Bioeconomy” was held on 27 September 2021 via Zoom. The workshop was divided into two sections, and questions were raised for discussion with panelists and expert guests. Several key points and relevant perspectives were delivered, mainly related to (i) the microbial evolution driven by plastic pollution; (ii) the relevance of and interplay between polymer structure/composition, enzymatic mechanisms, and assessment methods in plastic biodegradation; (iii) the recycling and valorization of plastic waste; (iv) engineered plastic-degrading enzymes; (v) the impact of (micro)plastics on environmental microbiomes; (vi) the isolation of plastic-degrading (PD) microbes and design of PD microbial consortia; and (vii) the synthesis and applications of biobased plastics. Finally, research priorities from these key points were identified within the microbial, enzyme, and polymer sciences.
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12
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Dearing MD, Weinstein SB. Metabolic Enabling and Detoxification by Mammalian Gut Microbes. Annu Rev Microbiol 2022; 76:579-596. [PMID: 35671535 DOI: 10.1146/annurev-micro-111121-085333] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The longstanding interactions between mammals and their symbionts enable thousands of mammal species to consume herbivorous diets. The microbial communities in mammals degrade both plant fiber and toxins. Microbial toxin degradation has been repeatedly documented in domestic ruminants, but similar work in wild mammals is more limited due to constraints on sampling and manipulating the microbial communities in these species. In this review, we briefly describe the toxins commonly encountered in mammalian diets, major classes of biotransformation enzymes in microbes and mammals, and the gut chambers that house symbiotic microbes. We next examine evidence for microbial detoxification in domestic ruminants before providing case studies on microbial toxin degradation in both foregut- and hindgut-fermenting wild mammals. We end by discussing species that may be promising for future investigations, and the advantages and limitations of approaches currently available for studying degradation of toxins by mammalian gut microbes. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- M Denise Dearing
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA;
| | - Sara B Weinstein
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA;
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13
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Barcoto MO, Rodrigues A. Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation. Front Microbiol 2022; 13:812143. [PMID: 35685924 PMCID: PMC9171207 DOI: 10.3389/fmicb.2022.812143] [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: 11/09/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.
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Affiliation(s)
- Mariana O. Barcoto
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Andre Rodrigues
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
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14
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Du Y, Liu X, Dong X, Yin Z. A review on marine plastisphere: biodiversity, formation, and role in degradation. Comput Struct Biotechnol J 2022; 20:975-988. [PMID: 35242288 PMCID: PMC8861569 DOI: 10.1016/j.csbj.2022.02.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 12/20/2022] Open
Abstract
The pollution of plastic waste has become an increasingly serious environmental crisis. Recently, plastic has been detected in various kinds of environments, even in human tissues, which is an increasing threat to the ecosystems and humans. In the ocean, the plastic waste is eventually fragmentized into microplastics (MPs) under the disruption of physical and chemical processes. MPs are colonized by microbial communities such as fungi, diatoms, and bacteria, which form biofilms on the surface of the plastic called “plastisphere”. In this review, we summarize the studies related to microorganisms in the plastisphere in recent years and describe the microbial species in the plastisphere, mainly including bacteria, fungi, and autotrophs. Secondly, we explore the interactions between MPs and the plastisphere. The depth of MPs in the ocean and the nutrients in the surrounding seawater can have a great impact on the community structure of microorganisms in the plastisphere. Finally, we discuss the types of MP-degrading bacteria in the ocean, and use the “seed bank” theory to speculate on the potential sources of MP-degrading microorganisms. Challenges and future research prospects are also discussed.
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Affiliation(s)
- Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, PR China
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, PR China
| | - Xinbei Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai’an, PR China
| | - Xusheng Dong
- Ruminant Nutrition and Physiology Laboratory, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, PR China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai’an, PR China
- Corresponding author.
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15
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Rapid synthesis of sustainable poly(ethylene 2,5-furandicarboxylate)-block-poly(tetramethylene oxide) multiblock copolymers with tailor-made properties via a cascade polymerization route. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.124313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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16
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Blair EM, Dickson KL, O'Malley MA. Microbial communities and their enzymes facilitate degradation of recalcitrant polymers in anaerobic digestion. Curr Opin Microbiol 2021; 64:100-108. [PMID: 34700124 DOI: 10.1016/j.mib.2021.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 11/15/2022]
Abstract
Microbial consortia efficiently degrade complex biopolymers found in the organic fraction of municipal solid waste (OFMSW). Through enzyme production and division of labor during anaerobic digestion, microbial communities break down recalcitrant polymers and make fermentation products, including methane. However, microbial communities remain underutilized for waste degradation as it remains difficult to characterize and predict microbial interactions during waste breakdown, especially as cultivation conditions change drastically throughout anaerobic digestion. This review discusses recent progress and opportunities in cultivating natural and engineered consortia for OFMSW hydrolysis, including how recalcitrant substrates are degraded by enzymes as well as the critical factors that govern microbial interactions and culture stability. Methods to measure substrate degradation are also reviewed, and we demonstrate the need for increased standardization to enable comparisons across different environments.
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Affiliation(s)
- Elaina M Blair
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Katharine L Dickson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA, 94608, USA.
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17
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Shiels PG, Painer J, Natterson-Horowitz B, Johnson RJ, Miranda JJ, Stenvinkel P. Manipulating the exposome to enable better ageing. Biochem J 2021; 478:2889-2898. [PMID: 34319404 PMCID: PMC8331090 DOI: 10.1042/bcj20200958] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/03/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023]
Abstract
The sum total of life course exposures creates an exposome that has a significant impact on age-related health. Understanding the interplay between exposome factors and the (epi) genome, offers pertinent insights into the ageing process and its relationship with the accumulation of allostatic load. We propose to exploit this to develop a biomimetic approach that will provide insight into how evolution through natural selection in other species has solved many age related human health issues. In particular, we will emphasise the need to reconnect a more mechanistic approach to medical science with a broader natural sciences approach, using biomimetics to mitigate the global burden of age related ill health. In particular, we will discuss how such an approach indicates leverage of the activities of the Nrf 2 gene to enhance health span via reintroduction of the classical 'Food as Medicine' concept, including modulation of the microbiome and the creation of more salutogenic and biophilic environments. Additionally, we will discuss how this approach integrates with novel and developing senotherapies.
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Affiliation(s)
- Paul G. Shiels
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, U.K
| | - Johanna Painer
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine, Savoyenstreet 1, 1160 Vienna, Austria
| | - Barbara Natterson-Horowitz
- Department of Human Evolutionary Biology, UCLA Division of Cardiology, Co-Director, Evolutionary Medicine Program at UCLA, Harvard University, California, U.S.A
| | - Richard J. Johnson
- Division of Renal Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, U.S.A
| | - Jaime J. Miranda
- CRONICAS Centre of Excellence in Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Campus Flemingsberg, Stockholm, Sweden
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