DOCSLIB.ORG

Rapid Evolution of Plastic-Degrading Enzymes Prevalent in the Global Ocean

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Rapid Evolution of Plastic-Degrading Enzymes Prevalent in the Global Ocean bioRxiv preprint doi: https://doi.org/10.1101/2020.09.07.285692; this version posted September 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Title: Rapid Evolution of Plastic-degrading Enzymes Prevalent in the Global Ocean 2 3 Authors: Intikhab Alam1*, Nojood Aalismail2, Cecilia Martin2, Allan Kamau1, Francisco J. 4 Guzmán-Vega5, Tahira Jamil1, Afaque A. Momin5, Silvia G. Acinas3, Josep M. Gasol3, Stefan T. 5 Arold5,6, Takashi Gojobori1, Susana Agusti4 and Carlos M. Duarte1,2*. 6 Affiliations: 7 1Computational Bioscience Research Center (CBRC), King Abdullah University of Science and 8 Technology, Thuwal 23955, Saudi Arabia 9 2Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), 10 King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia 11 3Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC, Pg. 12 Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain 13 4Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), 14 King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia 15 5King Abdullah University of Science and Technology (KAUST), Computational Bioscience 16 Research Center (CBRC), Biological and Environmental Science and Engineering, Thuwal, 17 23955-6900, Saudi Arabia 18 6Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 19 Montpellier, France 20 . 21 *Correspondence to: [email protected], [email protected] 22 23 Short title: Plastic-degrading Enzymes Prevalent in the Global Ocean 24 25 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.07.285692; this version posted September 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 26 Abstract: 27 28 Estimates of marine plastic stocks, a major threat to marine life (1), are far lower than expected 29 from exponentially-increasing litter inputs, suggesting important loss factors (2, 3). These may 30 involve microbial degradation, as the plastic-degrading polyethylene terephthalate enzyme 31 (PETase) has been reported in marine microbial communities (4). An assessment of 416 32 metagenomes of planktonic communities across the global ocean identifies 68 oceanic PETase 33 variants (oPETase) that evolved from ancestral enzymes degrading polycyclic aromatic 34 hydrocarbons. Twenty oPETases show predicted efficiencies comparable to those of laboratory- 35 optimized PETases, suggesting strong selective pressures directing the evolution of these 36 enzymes. We found oPETases in 90.1% of samples across all oceans and depths, particularly 37 abundant at 1,000 m depth, with a strong dominance of Pseudomonadales containing putative 38 highly-efficient oPETase variants in the dark ocean. Enzymatic degradation may be removing 39 plastic from the marine environment while providing a carbon source for bathypelagic microbial 40 communities. 41 42 Exponential growth in plastic production along with poor waste management practices have led 43 to over 150 Tg plastic waste delivered to the ocean since 1950 (1), where it harms marine life, 44 from zooplankton to whales (5). Synthetic plastic polymers are derived from oil hydrocarbons 45 and designed to be durable in the environment (6, 7), being largely resistant to microbial 46 degradation. However, a newly-evolved plastic-degrading enzyme, polyethylene terephthalate 47 hydrolase (PETase), was recently discovered in a Japanese waste processing plant (8). This 48 PETase was inferred to have evolved since 1970, when the polyethylene terephthalate polymer 49 was introduced at industrial scale (9). The PETase catalyzes the hydrolysis of polyethylene 50 terephthalate (PET) plastic to monomeric mono-2-hydroxyethyl terephthalate (MHET), which is 51 ultimately broken down into non-hazardous monomers, terephthalate and ethylene glycol, by 52 MHETases. The efficiency of currently known PETases seems, however, to be low, and it has 53 been suggested that in the environment it only achieves a breakdown from micro- to 54 nanoplastics, rather than full degradation (10). 55 56 The discovery, and subsequent biotechnological improvement (11) of this spontaneously-evolved 57 plastic-degrading enzyme offers hope that plastic waste can be degraded in waste facilities, 58 thereby preventing it from entering the ocean (12). However, this still leaves the fate of the > 150 59 Tg plastic waste already delivered to the ocean unresolved. Recent estimates show that 99% of 60 the plastic that entered the oceans cannot be accounted for, since inventories of plastic floating 61 on the surface of the ocean account to ~ 1% of the expected load (2), pointing at the operation of 62 processes responsible for major losses of plastic at sea (3). One such process may involve the 63 microbial degradation of plastics. Microplastics, the numerically dominant marine debris, have 64 developed a characteristic microbial community, referred to as the marine plastisphere (10). If 65 the PETase enzyme evolved in waste treatment plants from ancestral Ideonella sakaiensis (I. 66 sakaiensis) genes (8), and provided the current prevalence of polyethylene terephthalate as debris 67 in the marine environment, it is possible that other PETases may have evolved independently in 68 plastisphere ocean microbes as well. The huge population of prokaryotes in the global ocean, 69 estimated to contribute 1029 cells distributed among 1010 different OTUs (13), provides enough bioRxiv preprint doi: https://doi.org/10.1101/2020.09.07.285692; this version posted September 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 70 population size, genetic diversity and rate of growth for mutations(14) to independently evolve 71 PETase activity, which would enable microorganisms to access a novel, widely available organic 72 substrate. Indeed, a recent assessment of PETase abundance in marine and terrestrial 73 environments, confirmed the presence of the PETase gene in 31 of the 108 environmental marine 74 samples examined, all from surface waters (4). However, a global assessment of the presence, 75 abundance and diversity of PETases in the whole ocean, extending to the deep ocean, the largest 76 microbial habitat in the biosphere (15), is yet to be conducted. 77 78 Results 79 Here we report the prevalence of PETases in the global ocean microbiome and provide a 80 phylogeny suggesting Oceanospirillales to be the parental clade leading to 68 identified variants 81 of marine PETase. We do so on the basis of a thorough exploration of PETase through gene 82 catalogs from two global-ocean expeditions, Tara Oceans (16) and Malaspina (17), delivering 83 416 metagenomes collected from 204 individual ocean locations across the Indian, Pacific and 84 Atlantic Oceans from surface to the deep sea (Fig. 1). 85 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.07.285692; this version posted September 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. PETase abundance (FPKM) ) log10(dat$Abundance + 0.1) h t −11.00-−1 0.510.0000.51.01011.5−1.0-−1 0.50.000.51.011.5−11.00-−1 0.510.0000.511.0011.5−11.00-−1 0.510.0000.511.0011.5−11.00-1−0.510.000 0.511.001 1.5−101.0-1−0.510.000 0.511.001 1.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5 p 10 10 10 e ) 100 D m ( 1 $ t 2 h 102 t a p 3 d 4 e 1( 04 Depth (m) 0 D 5 1 1 2 3 4 5 6 7 8 9 10 11 g 33 [] o 33 [] l 0 1000 2000 3000 4000 0 1000 2000 3000 4000 90˚S 90° N 9090° ˚NN Ocean Data View 0 m A B 60˚S 6060°˚NN 6060° ˚NN 1000 m 30˚S 3030° ˚NN 3030° N˚N 2000 m EQ e d u EQ t EQ 3000 m 0° i 0° t 30˚N a L 4000 m 3030° ˚SS 3030° ˚SS 60˚N w e i V 5000 m w 0 e i 60˚S a 90˚N 60° S 60˚S V t 60° S a a D t a D 32 [] n 33 a n 6000 m e a c e O c 90° S O 180˚W 90˚W0˚ 90˚E 180˚E 9090° ˚SS 180° W 90° W 0° 90° E 180° E 0 1000 2000 3000 4000 33 [] ) ) h h 60˚N t t 1 p p 1 2 3 4 5 6 71 8 2 9 3 10 4 11 5 6 7 8 9 10 11 ) s e e 100 0 0 e m 0.8 D l e D D ( s 1 1 p $ $ h 2 t t 30˚N a t 10 2 2 m a a 0.6 T p 3 3 a d d s E e 4 ( ( 4 140 D P n 0 0 5 5 0.4 o 1 1 i h t t EQ-1 0 1 -1 0 1 i g -1 0 1 -1 0 1 -1 0 1 g −1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−−11.00 −0.510.00.00 0.50.511.001.01.5−11.51.00−1.0−0.5−0.510.00 0.00.50.511.00 1.01.5−11.001.5−−0.51.010.0−00.50.50.011.000.51.5−11.01.00 −1.50.5−11.00.00−0.510.01.00 1.50.5−101.01.0−0.51.510.0−01.00.5−0.511.000.01.50.51.01.5c −1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5−1.0−0.50.00.51.01.5 w o o 0.2 a l l log10(dat$Abundance + 0.1) log10(dat$Abr undance + 0.1) F PETase abundance (FPKM) 0 30˚S 8 w e 1 2 i M E V 6 K 60˚S a 3 4 t P 0 a 0 F D 5 6 n E 4 a e 7 8 S c ± O C 180˚W 90˚W0˚ 90˚E n 180˚2E a e 20200000 M 0 8 ) m ( AM3 M F h t 6 K BM4 p P e 40400000 F CM5 D E 4 S ± n w 2 a e i e V a M 60600000 t a 0 D n 0 0 0 0 0 0 a 0 0 0 Seafloor depth (m) e 0 0 0 c 1 5 0 0 0 0 O - - 1 2 3 3 - - - 180˚W 90˚W0˚ 90˚E 180˚E 0 0 > 0° 0 0 0 0 180° W 90° W 90° E 180° E 1 0 0 0 5 0 0 1 2 33 [] Longitude Depth (m) 86 87 88 Fig.
Load more

Recommended publications
  • Marine Microorganisms: Evolution and Solution to Pollution Fu L Li1, Wang B1,2
    COMMENTARY Marine microorganisms: Evolution and solution to pollution Fu L Li1, Wang B1,2 Li FL, Wang B. Marine microorganisms: Evolution and solution to pollution. J Mar Microbiol. 2018;2(1):4-5. nce ocean nurtured life, now she needs our care. Marine microorganism will be an opportunity to further understand ourselves and to seek for new Ois the host of ocean in all ages. We should learn from them humbly. methods of fighting old infections. Marine microorganism is tightly bond with human during the history of evolution and nowadays’ environment pollution. Along with industrial revolution, our marine ecosystem suffered serious pollutions. Microplastics are tiny plastic particles (<5 mm) (Figure 1B), Although the topic is still in debate, life is probably originated from which poison marine lives. Because these microplastics are very hard to be submarine in hydrothermal vent systems (1). In the journey of evolution, our degraded, it is predicted that there will be more microplastics than fish in biosphere was completely dominated by microbes for a very long time (Figure ocean by the year 2050 (7). Since marine sediments are considered as the sink 1A). Human being evolves with those microorganisms. Consequently, of microplastics and marine microbes are key dwellers of marine sediments, the influences of microorganisms can be found in all aspects of human more attention should be paid on the interactions between microplastics biology. More than 65% of our genes originated with bacteria, archaea, and and marine microbes. Actually, a call for this has been published in 2011 unicellular eukaryotes, including those genes responsible for host-microbe (8).
    [Show full text]
  • Recent Advances in Biocatalysts Engineering for Polyethylene Terephthalate Plastic Waste Green Recycling
    Environment International 145 (2020) 106144 Contents lists available at ScienceDirect Environment International journal homepage: www.elsevier.com/locate/envint Review article Recent advances in biocatalysts engineering for polyethylene terephthalate plastic waste green recycling Nadia A. Samak a,b,c,1, Yunpu Jia a,b,1, Moustafa M. Sharshar a,b, Tingzhen Mu a, Maohua Yang a, Sumit Peh a,b, Jianmin Xing a,b,* a CAS Key Laboratory of Green Process and Engineering & State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China b College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China c Processes Design and Development Department, Egyptian Petroleum Research Institute, Nasr City, 11727 Cairo, Egypt ARTICLE INFO ABSTRACT Handling Editor: Guo-ping Sheng The massive waste of poly(ethylene terephthalate) (PET) that ends up in the landfills and oceans and needs hundreds of years for degradation has attracted global concern. The poor stability and productivity of the Keywords: available PET biocatalysts hinder their industrial applications. Active PET biocatalysts can provide a promising Plastic waste avenue for PET bioconversion and recycling. Therefore, there is an urgent need to develop new strategies that Poly(ethylene terephthalate) could enhance the stability, catalytic activity, solubility, productivity, and re-usability of these PET biocatalysts Recycling under harsh conditions such as high temperatures, pH, and salinity. This has raised great attention in using Biocatalysts ’ Bioengineering bioengineering strategies to improve PET biocatalysts robustness and catalytic behavior. Herein, historical and forecasting data of plastic production and disposal were critically reviewed.
    [Show full text]
  • Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris
    RESEARCH ARTICLE Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris Sonja Oberbeckmann1,2,3☯, A. Mark Osborn1,2,4, Melissa B. Duhaime5☯* 1 Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, United Kingdom, a11111 2 School of Life Sciences, University of Lincoln, Brayford Pool Lincoln LN6 7TS, United Kingdom, 3 Environmental Microbiology Working Group, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany, 4 School of Applied Sciences, Royal Melbourne Institute of Technology University, PO Box 77, Bundoora, VIC3083, Australia, 5 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America ☯ These authors contributed equally to this work. * [email protected] OPEN ACCESS Citation: Oberbeckmann S, Osborn AM, Duhaime MB (2016) Microbes on a Bottle: Substrate, Season Abstract and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris. PLoS Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem- ONE 11(8): e0159289. doi:10.1371/journal. level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize pone.0159289 aquatic plastic debris and members of these biofilm communities are speculated to include Editor: Dee A. Carter, University of Sydney, pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing AUSTRALIA microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in Received: May 11, 2015 selecting for unique microbial communities. This work aimed to characterize microbial bio- Accepted: April 26, 2016 film communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communi- Published: August 3, 2016 ties, and identify seasonal and geographical influences on the communities.
    [Show full text]
  • Structure of the Plastic-Degrading Ideonella Sakaiensis Mhetase Bound to a Substrate
    ARTICLE https://doi.org/10.1038/s41467-019-09326-3 OPEN Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate Gottfried J. Palm 1, Lukas Reisky 2, Dominique Böttcher2, Henrik Müller2, Emil A.P. Michels1, Miriam C. Walczak2, Leona Berndt1, Manfred S. Weiss3, Uwe T. Bornscheuer 2 & Gert Weber 1,4 The extreme durability of polyethylene terephthalate (PET) debris has rendered it a long-term environmental burden. At the same time, current recycling efforts still lack sustainability. Two 1234567890():,; recently discovered bacterial enzymes that specifically degrade PET represent a promising solution. First, Ideonella sakaiensis PETase, a structurally well-characterized consensus α/β-hydrolase fold enzyme, converts PET to mono-(2-hydroxyethyl) terephthalate (MHET). MHETase, the second key enzyme, hydrolyzes MHET to the PET educts terephthalate and ethylene glycol. Here, we report the crystal structures of active ligand-free MHETase and MHETase bound to a nonhydrolyzable MHET analog. MHETase, which is reminiscent of feruloyl esterases, possesses a classic α/β-hydrolase domain and a lid domain conferring substrate specificity. In the light of structure-based mapping of the active site, activity assays, mutagenesis studies and a first structure-guided alteration of substrate specificity towards bis-(2-hydroxyethyl) terephthalate (BHET) reported here, we anticipate MHETase to be a valuable resource to further advance enzymatic plastic degradation. 1 Molecular Structural Biology, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany. 2 Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany. 3 Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße15, 12489 Berlin, Germany.
    [Show full text]
  • A Bacterium That Degrades and Assimilates Poly(Ethylene Terephthalate)
    1 Title: A bacterium that degrades and assimilates poly(ethylene terephthalate) 2 † 3 Authors: Shosuke Yoshida1,2 , Kazumi Hiraga1, Toshihiko Takehana3, Ikuo Taniguchi4, 4 Hironao Yamaji1, Yasuhito Maeda5, Kiyotsuna Toyohara5, Kenji Miyamoto2*, Yoshiharu 5 Kimura4, & Kohei Oda1* 6 Affiliations: 7 1Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, 8 Matsugasaki, Sakyo-ku, Kyoto .0.-0 0 , 1apan 9 2Department of Biosciences and Informatics, Keio 2ni3ersity, 3-14-1 Hiyoshi, Kohoku-ku, 10 Yokohama, Kanagawa 223-0 22, 1apan 11 35ife Science Materials 5aboratory, ADEKA Corporation, 7-2-34 Higashiogu, Arakawa-ku, 12 Tokyo 11.-0 3, 1apan 13 4Department of Polymer Science, Faculty of Te,tile Science, Kyoto Institute of Technology, 14 Matsugasaki, Sakyo-ku, Kyoto .0.-0 0 , 1apan 15 Ecology-Related Material Group Inno3ation Research Institute, Teijin 5td., Hinode-cho 2-1, 16 Iwakuni, Yamaguchi 740-0 11, 1apan 17 Current address: Department of Polymer Chemistry, Graduate School of Engineering, Kyoto 18 2ni3ersity, Nishikyo-ku, Kyoto .1 -0 30, 1apan 19 "Correspondence to: K.M. (kmiyamotoAbio.keio.ac.jp) or K.O. (bikaAkit.ac.jp). 20 21 1 22 Abstract: Poly(ethylene terephthalate) (PET) is used e,tensi3ely worldwide in plastic products, 23 and its accumulation in the en3ironment has become a global concern. Because the ability to 24 enzymatically degrade PET for microbial growth has been limited to a few fungal species, 25 biodegradation is not yet a 3iable remediation or recycling strategy. By screening natural 26 microbial communities e,posed to PET in the en3ironment, we isolated a no3el bacterium, 27 Ideonella sakaiensis 201-F., that is able to utilize PET as its major energy and carbon source.
    [Show full text]
  • Enzymatic PET Degradation
    GREEN AND SUSTAINABLE CHEMISTRY CHIMIA 2019, 73, No. 9 743 doi:10.2533/chimia.2019.743 Chimia 73 (2019) 743–749 © Swiss Chemical Society Enzymatic PET Degradation Athena Papadopoulou§, Katrin Hecht§, and Rebecca Buller* Abstract: Plastic, in the form of packaging material, disposables, clothing and other articles with a short lifespan, has become an indispensable part of our everyday life. The increased production and use of plastic, however, accelerates the accumulation of plastic waste and poses an increasing burden on the environment with negative effects on biodiversity and human health. PET, a common thermoplastic, is recycled in many countries via ther- mal, mechanical and chemical means. Recently, several enzymes have been identified capable of degrading this recalcitrant plastic, opening possibilities for the biological recycling of the omnipresent material. In this review, we analyze the current knowledge of enzymatic PET degradation and discuss advances in improving the involved enzymes via protein engineering. Looking forward, the use of plastic degrading enzymes may facilitate sustain- able plastic waste management and become an important tool for the realization of a circular plastic economy. Keywords: Biocatalysis · Biodegradation · Enzyme engineering · Plastic recycling · PET Dr. Athena Papadopoulou studied Biology 1. Introduction and received her BSc from the University Plastic has become an omnipresent material in our daily life of Ioannina. She completed her MSc in and, as a consequence, the plastic industry has become the seventh Chemistry with a focus on Chemical and most important industry in Europe, employing more than 1.5 mil- Biochemical Technologies. In 2013 she lion people with a turnover of 355 billion Euros in 2017.[1] Plastic moved to Biotechnology group at the production is cheap and the generated plastic items are durable University of Ioannina to pursue her PhD and versatile.
    [Show full text]
  • Bacteria – Friend Or Foe?
    Bacteria – Friend or Foe? By Rachel L. Dittmar & Rosa M. Santana Carrero [email protected], [email protected] April 2020 Danger! Sick! Gross! Vaccine! Disease! Medicine! Dirty! MRSA! Eww! E. coli! What is the first thing that comes to mind when you hear “bacteria”? Science! Microscope! MRSA! Salmonella! Hospital! Germs! Staph! Food! Small! 2 Introduction to Bacteria 3 Bacterial nomenclature • Bacteria are referred to by their genus and species, with genus coming first and species coming last: Escherichia coli Escherichia: genus Species: coli Bacteria names are ALWAYS italicized. Genus names are capitalized and species names are not. Sometimes, the genus is abbreviated by its first initial: E. coli 4 Bacteria are prokaryotes. 5 What are prokaryotes? • Plasma membrane separates the cell from its surrounding environment • Cytoplasm contains organelles • Contain DNA consisting of a single large, circular chromosome • Ribosomes make proteins 6 Prokaryotes v. Eukaryotes 7 Image from: https://www.difference.wiki/prokaryotic-cell-vs-eukaryotic-cell/ How do these organisms differ? Prokaryotes Eukaryotes - circular DNA - linear DNA (found in nucleus) - no nucleus - nucleus - no membrane bound organelles - membrane bound organelles - small- less than 10μm - larger than 10μm - unicellular - can be unicellular and multicellular 8 Bacteria are very small. 9 How big are bacteria? Bacteria are very small: 0.1 – 5.0 micrometers. A micrometer (μm) is 0.000001 meters or 0.001 millimeters (mm) For comparison, a human hair is 30 – 100 μm Image from: https://www.khanacademy.org/science/high-school-biology/hs-cells/hs-prokaryotes-and-eukaryotes/a/prokaryotic-cells 10 Bacteria are classified by phenotype or genotype.
    [Show full text]
  • Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris
    RESEARCH ARTICLE Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris Sonja Oberbeckmann1,2,3☯, A. Mark Osborn1,2,4, Melissa B. Duhaime5☯* 1 Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, United Kingdom, a11111 2 School of Life Sciences, University of Lincoln, Brayford Pool Lincoln LN6 7TS, United Kingdom, 3 Environmental Microbiology Working Group, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany, 4 School of Applied Sciences, Royal Melbourne Institute of Technology University, PO Box 77, Bundoora, VIC3083, Australia, 5 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America ☯ These authors contributed equally to this work. * [email protected] OPEN ACCESS Citation: Oberbeckmann S, Osborn AM, Duhaime MB (2016) Microbes on a Bottle: Substrate, Season Abstract and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris. PLoS Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem- ONE 11(8): e0159289. doi:10.1371/journal. level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize pone.0159289 aquatic plastic debris and members of these biofilm communities are speculated to include Editor: Dee A. Carter, University of Sydney, pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing AUSTRALIA microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in Received: May 11, 2015 selecting for unique microbial communities. This work aimed to characterize microbial bio- Accepted: April 26, 2016 film communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communi- Published: August 3, 2016 ties, and identify seasonal and geographical influences on the communities.
    [Show full text]
  • Enhancing Biodegradation Capabilities of the Ideonella
    Enhancing Biodegradation Capabilities of the Ideonella sakaiensis Plasmid Using mutD Escherichia coli: A Case Study in the Use of Directed Microbial Evolution and Bioengineering Faiferlick, Nicholas (School: Camdenton High School) Polyethylene terephthalate (PET) is the most produced plastic globally, composing single-use plastic bottles, shopping bags, and more. Consequently, the environment suffers from its production and disposal. Recently, scientists discovered a species of bacteria, Ideonella sakaiensis, the ester bonds of PET as a carbon source, disposing of PET microplastics and macroplastics. The bacterium was immediately considered for PET plastic disposal, although the degradation rate of the bacteria was found to be less than adequate for large scale disposal. The purpose of this experiment was to increase the efficiency of biodegradation. In doing so, a rapidly mutating strain of bacteria, mutD Escherichia coli, was transformed with the plasmid DNA of I. sakaiensis. The transformed E. coli adopted the degradation abilities of I. sakaiensis, as well as the mutagenic properties of the E. coli. It was hypothesized that the transformed bacteria would degrade PET, as well as mutate to achieve a higher rate of degradation, with more efficient strains of bacteria outcompeting less efficient strains in a natural selection process. It was found that the transformed and mutated E. coli could degrade PET 400% more efficiently than I. sakaiensis as a result of this directed evolution. The results’ support of the hypotheses presents several universal applications: bacteria is a viable solution for PET disposal. Furthermore, other species of bacteria, such as those naturally occurring in lakes and oceans, can be transformed to degrade PET, efficiently and cleanly ridding the environment of most single-use plastic pollution, which was not thought possible before..
    [Show full text]
  • Microorganismos, Enzimas Y Perspectivas Futuras
    Biodegradación de tereftalato de polietileno: microorganismos, enzimas y perspectivas futuras Biodegradation of polyethylene terephthalate: microorganisms, enzymes and future prospects https://www.genengnews.com/news/molecular-scissors-for-plastic- waste/ Trabajo de Fin de Grado Jorge Pérez Parrilla Tutorizado por Ana María Rodríguez Pérez y Samuel Rodríguez Martín Grado en Biología. Julio 2020 ÍNDICE Resumen.................................................................................................................................1 Abstract ..................................................................................................................................1 1. Introducción ....................................................................................................................2 1.1 Los plásticos, relevancia y peligros que suponen ......................................................2 1.2 Estrategias para el tratamiento de los residuos plásticos ............................................3 1.2.1 Plásticos biodegradables .........................................................................................3 1.2.2 Reciclaje .................................................................................................................4 1.2.3 Incineración y métodos químicos de reciclaje .........................................................5 1.2.4 Biodegradación .......................................................................................................5 1.3 Biodegradación de plásticos: El
    [Show full text]
  • 1/4 Discovery of a Bacterium That Degrades and Assimilates Poly(Ethylene Terephthalate)
    Press Release March 30, 2016 Keio University Kyoto Institute of Technology Discovery of a Bacterium that Degrades and Assimilates Poly(ethylene terephthalate) could Serve as a Degradation and/or Fermentation Platform for Biological Recycling of PET Waste Products A group of researchers comprising Keio University Faculty of Science and Technology Assistant Professor Shosuke Yoshida (currently a researcher for the ERATO Akiyoshi Bio-Nanotransporter Project at the Graduate School of Engineering, Kyoto University), Keio University Associate Professor Kenji Miyamoto, Kyoto Institute of Technology Professor Emeritus Kohei Oda, and Professor Emeritus Yoshiharu Kimura, conducted a collaborative research project with Teijin Limited and ADEKA Corporation and discovered a bacterium that degrades and assimilates poly(ethylene terephthalate) (PET) and were able to identify the decomposition mechanism. PET is used extensively throughout the world, commonly in clothing and plastic bottles. Most PET products simply end up in landfills, never entering a recycling process, and it was generally believed that PET is resistant to microbial degradation. However, the present research overturns certain aspects of this commonly accepted theory, and the findings are expected to contribute greatly to the development of bio-recycling technology of PET waste products. The results were published in the American science journal, Science, on March 10, 2016 (Eastern Standard Time). 1. Main Research Findings ・ Researchers have discovered a novel bacterium Ideonella sakaiensis 201-F6 that is able to degrade and assimilate PET. ・ Researchers have discovered two types of enzymes* (PETase and MHETase), which are produced by the 201-F6 strain and are capable of hydrolyzing PET. ・ Based on the properties of PETase and MHETase, it is now understood that the 201-F6 strain is able to use PET as its major energy source and exist in the natural environment.
    [Show full text]
  • Science Journals
    RESEARCH | REPORTS BIODEGRADATION bers of the filamentous fungi Fusarium oxy- sporum and F. solani, which have been shown to grow on a mineral medium containing PET yarns [although no growth levels were speci- A bacterium that degrades and fied (5, 6)]. Once identified, microorganisms with the enzymatic machinery needed to degrade PET assimilates poly(ethylene terephthalate) could serve as an environmental remediation strategy as well as a degradation and/or fermen- Shosuke Yoshida,1,2* Kazumi Hiraga,1 Toshihiko Takehana,3 Ikuo Taniguchi,4 tation platform for biological recycling of PET Hironao Yamaji,1 Yasuhito Maeda,5 Kiyotsuna Toyohara,5 Kenji Miyamoto,2† waste products. Yoshiharu Kimura,4 Kohei Oda1† We collected 250 PET debris–contaminated en- vironmental samples including sediment, soil, Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its wastewater, and activated sludge from a PET accumulation in the environment has become a global concern. Because the ability to bottle recycling site (7). Using these samples, enzymatically degrade PET has been thought to be limited to a few fungal species, we screened for microorganisms that could use biodegradation is not yet a viable remediation or recycling strategy. By screening natural low-crystallinity (1.9%) PET film as the major microbial communities exposed to PET in the environment, we isolated a novel bacterium, carbon source for growth. One sediment sample Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. contained a distinct microbial consortium that When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the formed on the PET film upon culturing (Fig.
    [Show full text]