DOCSLIB.ORG

Ideonella Sakaiensis Bacteria Pdf

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Ideonella sakaiensis bacteria pdf Continue Ideonella sakaiensis Scientific classification Domain: Bacteria Phylum: Proteobacteria Class: Betaproteobacteria Order: Burkholderiales Family: Comamonadaceae Genus: Ideonella Species: I. sakaiensis Binomial name Ideonella sakaiensisYoshida et al. 2016 (1) Ideonella sakaiensis is a bacterium from the genus Ideonella and the Comamonadaceae family, capable of breaking and consuming plastic polyethylene terephtalat (PET) as the sole source of carbon and energy. The bacterium was originally isolated from a sediment sample taken outside a plastic bottle processing plant in Sakai, Japan. Discovery Ideonella sakaiensis was first identified in 2016 by a team of researchers led by Kohei Oda of the Kyoto Institute of Technology and Kenji Miamoto of Keio University after collecting a sample of PET-contaminated sediment near a plastic bottle processing plant in Japan. The bacterium was isolated from a consortium of microorganisms in a sample of sediments, including protozoa and yeast cells. It has been shown that the entire microbial community mineralizes 75% of degraded PET into carbon dioxide after it has been initially degraded and assimilated by I. sakaiensis. The characteristic of Ideonella sakaiensis is gram-negative, aerobic and rod-shaped. It does not form disputes. The cells are mottled and have one flagellum. I. sakaiensis also tests positive for oxidase and catalase. The bacterium grows in the pH range from 5.5 to 9.0 (optimally at temperatures of 7 to 7.5) and temperature from 15 to 42 degrees Celsius (optimally at 30-37 degrees Celsius). Colonies I. sakaiensis are colorless, smooth and round. Its size ranges from 0.6-0.8 microns wide and 1.2-1.5 microns in length. It has been shown that the bacterium grows on PET surfaces in a community with other I. sakaiensis cells, adhering to PET and other cells with thin appendages. These appendages can also function to release PET-degrading enzymes on the PET surface. Thanks to phylogenetic analysis, the species was shown as part of the genus Ideonella, but possessed a much different genome than other known species in the genus, including Ideonella dechloratans and Ideonella azotifigens, thus justifying its classification as a new species. Degradation and assimilation of PET Ideonella sakaiensis cells stick to the PET surface and use secreted PET hydrolase, or PETase, to degrade PET into mono (2- hydroxyethyl)terephthalic acid (MHET), heteterodimer consisting of terephthalic acid (TPA) and ethylene glycolia. I. sakaiensis PETase operates by hydrolysing ester bonds present in PET with high specificity. As a result, MHET then degrades into two monomeric components of the lipid-anchor MHET hydrolase enzyme, or MHETase, on the outer cell membrane. Ethylene glycol is easily taken and used by I. sakaiensis and many other bacteria. Terephthal more recalcitrant connection, imported into the I. cell sakaiensis through the transporter protein terephtalic acid. Once in the cell, the molecule of aromatic terephthalic acid is oxidized by terephtalic acid-1.2-dioxygenase and 1.2-dihydroxy-3.5-cyclokhesadien-1.4-dicarboxylat dehydrogenase in catechol intermediate. The catechol ring is then splits by PCA 3.4-dioxygenase before the compound is integrated into other metabolic pathways (e.g. TCA cycle). As a result, both molecules derived from PET are used by the cell to produce energy and create the necessary biomolecules. After all, assimilated carbon can be mineralized for carbon dioxide and released into the atmosphere. The impact and application Discovery Of Ideonella sakaiensis has a potential value for the degradation of PET plastics. Prior to its discovery, the only known PET degradors were a small amount of bacteria and fungi, including Fusarium solani, and no organism was definitively known to degrade PET as a major source of carbon and energy. The discovery of I. sakaiensis spurred a discussion about BIO biodegradation as a method of recycling and biorecovery. The wild-type bacterium is able to colonize and break down a thin (0.2 mm thickness) low-crystal (soft) PET film in about six weeks, and the responsible PETase enzyme has been shown to degrade high-crystallity (hard) PET about 30 times slower than low-crystal PET. The large amount of PET produced is highly crystalline (e.g. plastic bottles), so it is believed that any potential use of the enzyme I. sakaiensis PETase in processing programs will need to be preceded by genetic optimization of the enzyme. The MHETase enzyme can also be optimized and used in recycling or biorecovery in combination with the PETase enzyme. It degrades MHET produced by PETase into ethylene glycol and terephthalic acid. Once formed, these two compounds can be additionally biodestruged into carbon dioxide I. sakaiensis or other microbes, or they can be cleaned and used to produce a new PET in an industrial processing plant. The genetic engineering of the PET degrading enzyme Ideonella sakaiensis, PETase, has been genetically modified to break down PET faster as well as worsen PEF. See also See ideonella sakaiensis in Wiktionary, a free dictionary. Organisms break plastic pet bottles by recycling PETase, an enzyme produced by this bacterium. Pestalotiopsis microspora, an endophytic fungus species capable of destroying polyurethane. Inquiries - Yoshida, S.; Hiraga, K.; Takekhana, T.; Taniguchi, I.; Yamaji, H.; Maeda, J.; Toyohara, K.; Miamoto, K.; Kimura, Y.; Oda, K. (March 10, 2016). A bacterium that degrades and metabolizes poly (ethylene terephthalate). Science. 351 (6278): 1196–1199. Bibkod:2016Sci... 351.1196Y. PMID 26965627. a b c c e f g h i j k l m n Yoshida, Shosuke; Hiraga, Kazumi; Takehana, Toshihiko; Taniguchi, Ikuo; Yamaji, Chironao; Maeda, Yasuhito; Toyohara, Kiyotsuna; Miamoto, Kenji; Kimura, Yoshiharu (March 11, 2016). A bacterium that degrades and metabolizes poly (ethylene terephthalate). Science. 351 (6278): 1196–1199. Bibkod:2016Sci... 351.1196Y. doi:10.1126/science.aad6359. ISSN 1095-9203. PMID 26965627. Summary (PDF) (March 30, 2016). b Sombon Tanasupawat; Toshihiko Takehana; Shosuke Yoshida; Kazumi Hiraga; Kohei Oda (August 1, 2016). Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly (etien terephthalate). International Journal of Systematic and Evolutionary Microbiology. 66 (8): 2813–8. doi:10.1099/ijsem.0.001058. PMID 27045688. Pierce, BA; Heideman, M.T. (May 1, 1980). Metabolism di (ethylene glycol) (2-(2'-Hydroxyetoxy) ethanol and other short polys (ethylene glycol) with gram-negative bacteria. Microbiology. 118 (1): 21-27. doi:10.10.1099/0021287-118-1-21. ISSN 1350-0872. Coghlan, Andy. Bacteria found to eat pet plastics can help make recycling. A new scientist. Received on March 18, 2016. Al-Saba, 00:00; Ehiya, F.S.; Eshak, G.; Rabies, 00:00; ElMetwally, A.E. (March 2016). Green routes for the processing of polyethylene terephthalate. Egyptian Petroleum Journal. 25 (1): 53–64. doi:10.1016/j.ejpe.2015.03.001. Characteristics and design of plastic degrading aromatic polyesterase External references type of strain Ideonella sakaiensis on BacDive - Bacterial diversity metadata base extracted from This student page was not curated. Ideonella sakaiensis Introduction Discovery Of Bacteria, Ideonella sakaiensis 201-F6T, was published in the journal Science in March 2016. The new species was identified by microbiologists from the Kyoto Institute of Technology and Keio University when they tried to collect samples of sediment, soil and sewage that were contaminated with poly (ethylene terephthalate) (PET) near plastic recycling bottles in Sakai, Japan. An intriguing characteristic of this new bacterium is its ability to eat this type of plastic that was previously thought to be one of the most sadly resistant materials (1). The basic characteristic of Ideonella sakaiensis is Gram-negative, aerobic, non-spore formation, rod-shaped bacteria. It has a polar flagellum that allows mobility. In addition, the strain has been positive for both catalase and cytochrome oxidase tests. The bacterium grew best at 30-37 degrees Celsius and 7.0-7.5 pH, but was able to survive between 15 and 42 degrees Celsius and 5.5-9.0 pH. (2). Metabolism Although scientists initially discovered numerous different types of microbes that appear to be destroying PET, they eventually determine what sakaiensis was the only one that could consume plastic waste and assimilate it for growth. This strain can use plastic as both a carbon and an energy source by hydrolyzing PET. The intermediate reaction is formed in this process, the mono (2-hydroxyethyl) tereftalic acid is converted using two powerful enzymes, into two non-carbon monoxide called terthalic acid and ethylene glycol (1). After studying bacterial metabolism more closely, scientists now believe that the bacteria is first attached to the plastic with the help of some kind of short hand, like appendages. Next, it secretes one exoenzyme, which generates the aforementioned chemical intermediate. Once the PET is significantly degraded, the material can be taken into the cell, where the second enzyme catabolically breaks it down for metabolic use. Researchers found that the microbe consumed by PET comprehensively and after six months, the plastic was almost completely depleted at 30 degrees Celsius. Future applications Because PET is a plastic component found in most water bottles, polyester clothing and dinner trays, scientists hope that bacterial species can be used for widespread biodegradation. When used commercially, experts predict that the
Recommended publications
  • Marine Microorganisms: Evolution and Solution to Pollution Fu L Li1, Wang B1,2

    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).
  • Recent Advances in Biocatalysts Engineering for Polyethylene Terephthalate Plastic Waste Green Recycling

    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.
  • Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris

    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.
  • Structure of the Plastic-Degrading Ideonella Sakaiensis Mhetase Bound to a Substrate

    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.
  • A Bacterium That Degrades and Assimilates Poly(Ethylene Terephthalate)

    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.
  • Enzymatic PET Degradation

    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.
  • Bacteria – Friend Or Foe?

    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.

  • Cluster 1 Cluster 3 Cluster 2

    5 9 Luteibacter yeojuensis strain SU11 (Ga0078639_1004, 2640590121) 7 0 Luteibacter rhizovicinus DSM 16549 (Ga0078601_1039, 2631914223) 4 7 Luteibacter sp. UNCMF366Tsu5.1 (FG06DRAFT_scaffold00001.1, 2595447474) 5 5 Dyella japonica UNC79MFTsu3.2 (N515DRAFT_scaffold00003.3, 2558296041) 4 8 100 Rhodanobacter sp. Root179 (Ga0124815_151, 2699823700) 9 4 Rhodanobacter sp. OR87 (RhoOR87DRAFT_scaffold_21.22, 2510416040) Dyella japonica DSM 16301 (Ga0078600_1041, 2640844523) Dyella sp. OK004 (Ga0066746_17, 2609553531) 9 9 9 3 Xanthomonas fuscans (007972314) 100 Xanthomonas axonopodis (078563083) 4 9 Xanthomonas oryzae pv. oryzae KACC10331 (NC_006834, 637633170) 100 100 Xanthomonas albilineans USA048 (Ga0078502_15, 2651125062) 5 6 Xanthomonas translucens XT123 (Ga0113452_1085, 2663222128) 6 5 Lysobacter enzymogenes ATCC 29487 (Ga0111606_103, 2678972498) 100 Rhizobacter sp. Root1221 (056656680) Rhizobacter sp. Root1221 (Ga0102088_103, 2644243628) 100 Aquabacterium sp. NJ1 (052162038) Aquabacterium sp. NJ1 (Ga0077486_101, 2634019136) Uliginosibacterium gangwonense DSM 18521 (B145DRAFT_scaffold_15.16, 2515877853) 9 6 9 7 Derxia lacustris (085315679) 8 7 Derxia gummosa DSM 723 (H566DRAFT_scaffold00003.3, 2529306053) 7 2 Ideonella sp. B508-1 (I73DRAFT_BADL01000387_1.387, 2553574224) Zoogloea sp. LCSB751 (079432982) PHB-accumulating bacterium (PHBDraf_Contig14, 2502333272) Thiobacillus sp. 65-1059 (OJW46643.1) 8 4 Dechloromonas aromatica RCB (NC_007298, 637680051) 8 4 7 7 Dechloromonas sp. JJ (JJ_JJcontig4, 2506671179) Dechloromonas RCB 100 Azoarcus
  • Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor

    Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor

    Invitation for the public defense of my thesis Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic and biochemistry Physiology bacteria that use chlorate and/or nitrate as electron acceptor as electron nitrate and/or use chlorate that bacteria Physiology and biochemistry Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic hydrocarbon- degrading bacteria that bacteria that use chlorate and/or nitrate as electron acceptor use chlorate and/or nitrate as electron acceptor The public defense of my thesis will take place in the Aula of Wageningen University (Generall Faulkesweg 1, Wageningen) on December 18 2013 at 4:00 pm. This defense is followed by a reception in Café Carré (Vijzelstraat 2, Wageningen). Margreet J. Oosterkamp J. Margreet Paranimphs Ton van Gelder ([email protected]) Aura Widjaja Margreet J. Oosterkamp ([email protected]) Marjet Oosterkamp (911 W Springfield Ave Apt 19, Urbana, IL 61801, USA; [email protected]) Omslag met flap_MJOosterkamp.indd 1 25-11-2013 5:58:31 Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor Margreet J. Oosterkamp Thesis-MJOosterkamp.indd 1 25-11-2013 6:42:09 Thesis committee Thesis supervisor Prof. dr. ir. A. J. M. Stams Personal Chair at the Laboratory of Microbiology Wageningen University Thesis co-supervisors Dr. C. M. Plugge Assistant Professor at the Laboratory of Microbiology Wageningen University Dr. P. J. Schaap Assistant Professor at the Laboratory of Systems and Synthetic Biology Wageningen University Other members Prof. dr. L. Dijkhuizen, University of Groningen Prof. dr. H. J. Laanbroek, University of Utrecht Prof.
  • Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris

    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.
  • Structure and Evolution of Chlorate Reduction Composite Transposons

    Structure and Evolution of Chlorate Reduction Composite Transposons

    RESEARCH ARTICLE Structure and Evolution of Chlorate Reduction Composite Transposons Iain C. Clark,a Ryan A. Melnyk,b Anna Engelbrektson,b John D. Coatesb Department of Civil and Environmental Engineeringa and Department of Plant and Microbial Biology,b University of California, Berkeley, California, USA ABSTRACT The genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechlora- tans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualiza- tion. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobi- lized at least once from a perchlorate reducer to build chlorate respiration.
  • Rapid Evolution of Plastic-Degrading Enzymes Prevalent in the Global Ocean

    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.