DOCSLIB.ORG

The Handbook of Environmental Chemistry

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

The Handbook of Environmental Chemistry Editor-in-Chief: O. Hutzinger Volume 5 Water Pollution Part R Advisory Board: D. Barceló · P. Fabian · H. Fiedler · H. Frank · J. P. Giesy · R. A. Hites M. A. K. Khalil · D. Mackay · A. H. Neilson · J. Paasivirta · H. Parlar S. H. Safe · P.J. Wangersky The Handbook of Environmental Chemistry Recently Published and Forthcoming Volumes Environmental Specimen Banking Emerging Contaminants from Industrial and Volume Editors: S. A. Wise and P.P.R. Becker Municipal Waste Vol. 3/S Volume Editors: D. Barceló and M. Petrovic Vol. 5/S Polymers: Chances and Risks Volume Editors: P. Eyerer, M. Weller Marine Organic Matter: Biomarkers, and C. Hübner Isotopes and DNA Vol. 3/V Volume Editor: J. K. Volkman Vol. 2/N, 2005 The Rhine Volume Editor: T.P. Knepper Environmental Photochemistry Part II Vol. 5/L, 03.2006 Volume Editors: P. Boule, D. Bahnemann and P. Robertson Persistent Organic Pollutants Vol. 2/M, 2005 in the Great Lakes Volume Editor: R. A. Hites Air Quality in Airplane Cabins Vol. 5/N, 2006 and Similar Enclosed Spaces VolumeEditor:M.B.Hocking Antifouling Paint Biocides Vol. 4/H, 2005 VolumeEditor:I.Konstantinou Vol. 5/O, 2006 Environmental Effects of Marine Finfish Aquaculture Estuaries VolumeEditor:B.T.Hargrave VolumeEditor:P.J.Wangersky Vol. 5/M, 2005 Vol. 5/H, 2006 The Mediterranean Sea The Caspian Sea Environment Volume Editor: A. Saliot Volume Editors: A. Kostianoy and A. Kosarev Vol. 5/K, 2005 Vol. 5/P, 2005 Environmental Impact Assessment of Recycled The Black Sea Environment Wastes on Surface and Ground Waters Volume Editors: A. Kostianoy and A. Kosarev Engineering Modeling and Sustainability Vol. 5/Q Volume Editor: T.A. Kassim Vol. 5/F (3 Vols.), 2005 Oxidants and Antioxidant Defense Systems Volume Editor : T. Gr une Vol. 2/O, 2005 Fuel Oxygenates Volume Editor: Damià Barceló With contributions by E.Arvin·A.Babé·D.Barceló·L.Bastiaens·C.Baus·H.-J.Brauch L. Debor · J. Fawell · F. Fayolle-Guichard · A. Fischer · C. W. Greer M.M.Häggblom·M.A.Jochmann·D.Labbé·S.Lacorte M. Martienssen · D. McGregor · F. Monot · M. Moran · C. Oehm H.-H.Richnow·M.Rosell·M.Schirmer·J.E.Schmidt T. C. Schmidt · C. Stefan · H. D. Stupp · P. Werner · C. K. Waul 123 Environmental chemistry is a rather young and interdisciplinary field of science. Its aim is a complete description of the environment and of transformations occurring on a local or global scale. Environ- mental chemistry also gives an account of the impact of man’s activities on the natural environment by describing observed changes. The Handbook of Environmental Chemistry provides the compilation of today’s knowledge. Contribu- tions are written by leading experts with practical experience in their fields. The Handbook will grow with the increase in our scientific understanding and should provide a valuable source not only for scientists, but also for environmental managers and decision-makers. The Handbook of Environmental Chemistry is published in a series of five volumes: Volume 1: The Natural Environment and the Biogeochemical Cycles Volume 2: Reactions and Processes Volume 3: Anthropogenic Compounds Volume 4: Air Pollution Volume 5: Water Pollution The series Volume 1 The Natural Environment and the Biogeochemical Cycles describes the natural environment and gives an account of the global cycles for elements and classes of natural compounds. The series Volume 2 Reactions and Processes is an account of physical transport, and chemical and biological transformations of chemicals in the environment. The series Volume 3 Anthropogenic Compounds describes synthetic compounds, and compound classes as well as elements and naturally occurring chemical entities which are mobilized by man’s activities. The series Volume 4 Air Pollution and Volume 5 Water Pollution deal with the description of civilization’s effects on the atmosphere and hydrosphere. Within the individual series articles do not appear in a predetermined sequence. Instead, we invite contributors as our knowledge matures enough to warrant a handbook article. Suggestions for new topics from the scientific community to members of the Advisory Board or to the Publisher are very welcome. Library of Congress Control Number: 2007927987 ISSN 1433-6863 ISBN 978-3-540-72640-1 Springer Berlin Heidelberg New York DOI 10.1007/978-3-540-72641-8 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broad- casting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable for prosecution under the German Copyright Law. Springer is a part of Springer Science+Business Media springer.com c Springer-Verlag Berlin Heidelberg 2007 The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Cover design: WMXDesign GmbH, Heidelberg Typesetting and Production: LE-TEXJelonek,Schmidt&VöcklerGbR,Leipzig Printed on acid-free paper 02/3180 YL – 5 4 3 2 1 0 Editor-in-Chief Prof. em. Dr. Otto Hutzinger Universität Bayreuth c/o Bad Ischl Office Grenzweg 22 5351 Aigen-Vogelhub, Austria [email protected] Volume Editor Prof. Dr. Damià Barceló Dept. of Environmental Chemistry IIQAB-CSIC JordiGirona, 18–26 08034 Barcelona, Spain [email protected] Advisory Board Prof. Dr. D. Barceló Prof. Dr. J. P. Giesy Dept. of Environmental Chemistry Department of Zoology IIQAB-CSIC Michigan State University JordiGirona, 18–26 East Lansing, MI 48824-1115, USA 08034 Barcelona, Spain [email protected] [email protected] Prof. Dr. R. A. Hites Prof. Dr. P. Fabian Indiana University Lehrstuhl für Bioklimatologie School of Public und Immissionsforschung and Environmental Affairs der Universität München Bloomington, IN 47405, USA Hohenbachernstraße 22 [email protected] 85354 Freising-Weihenstephan, Germany Prof. Dr. M. A. K. Khalil Dr.H.Fiedler Department of Physics Scientific Affairs Office Portland State University UNEP Chemicals Science Building II, Room 410 11–13, chemin des Anémones P.O. Box 751 1219 Châteleine (GE), Switzerland Portland, OR 97207-0751, USA hfi[email protected] [email protected] Prof. Dr. H. Frank Prof. Dr. D. Mackay Lehrstuhl für Umwelttechnik Department of Chemical Engineering und Ökotoxikologie and Applied Chemistry Universität Bayreuth University of Toronto Postfach 10 12 51 Toronto, ON, M5S 1A4, Canada 95440 Bayreuth, Germany VI Prof. Dr. A. H. Neilson Prof. Dr. S. H. Safe Swedish Environmental Research Institute Department of Veterinary P.O. Box 21060 Physiology and Pharmacology 10031 Stockholm, Sweden College of Veterinary Medicine [email protected] Texas A & M Universit y College Station, TX 77843-4466, USA Prof. Dr. J. Paasivirta [email protected] Department of Chemistry University of Jyväskylä Prof.P.J.Wangersky Survontie 9 University of Victoria P.O. Box 3 5 Centre for Earth and Ocean Research 40351 Jyväskylä, Finland P.O. Box 1700 Victoria, BC, V8W 3P6, Canada Prof.Dr.Dr.H.Parlar wangers@telus. net Institut für Lebensmitteltechnologie und Analytische Chemie Technische Universität München 85350 Freising-Weihenstephan, Germany The Handbook of Environmental Chemistry Also Available Electronically For all customers who have a standing order to The Handbook of Environmen- talChemistry,weoffertheelectronicversionviaSpringerLinkfreeofcharge. Please contact your librarian who can receive a password or free access to the full articles by registering at: springerlink.com If you do not have a subscription, you can still view the tables of contents of the volumes and the abstract of each article by going to the SpringerLink Home- page, clicking on “Browse by Online Libraries”, then “Chemical Sciences”, and finally choose The Handbook of Environmental Chemistry. You will find information about the – Editorial Board –AimsandScope – Instructions for Authors –SampleContribution at springer.com using the search function. Preface Environmental Chemistry is a relatively young science. Interest in this subject, however, is growing very rapidly and, although no agreement has been reached as yet about the exact content and limits of this interdisciplinary discipline, there appears to be increasing interest in seeing environmental topics which are based on chemistry embodied in this subject. One of the first objectives of Environmental Chemistry must be the study of the environment and of natural chemical processes which occur in the environment. A major purpose of this series on Environmental Chemistry, therefore, is to present a reasonably uniform view of various aspects of the chemistry of the environment and chemical reactions occurring in the environment. The industrial activities of man have given a new dimension to Environ- mental Chemistry. We have now synthesized and described over five million chemical compounds and chemical industry produces about hundred and fifty million tons of synthetic chemicals annually. We ship billions of tons of oil per year and through mining operations and other geophysical modifications, large quantities of inorganic and organic materials are released from their natural deposits. Cities and metropolitan areas of up to
Recommended publications
  • Rpon (Σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola Tertiaricarbonis Strain

    Rpon (Σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola Tertiaricarbonis Strain

    Lawrence Berkeley National Laboratory Recent Work Title RpoN (σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain. Permalink https://escholarship.org/uc/item/9f26h2cp Journal Applied and environmental microbiology, 83(14) ISSN 0099-2240 Authors Yu, Dianzhen Xia, Ming Zhang, Liping et al. Publication Date 2017-07-01 DOI 10.1128/aem.00709-17 Peer reviewed eScholarship.org Powered by the California Digital Library University of California RpoN (σσ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain Dianzhen Yu,a,b Ming Xia,a,b Liping Zhang,a Yulong Song,a You Duan,a,b Tong Yuan,d,f Minjie Yao,c Liyou Wu,d Chunyuan Tian,e Zhenbin Wu,a Xiangzhen Li,c Jizhong Zhou,d Dongru Qiua Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Chinaa ; University of Chinese Academy of Sciences, Beijing, Chinab; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Chinac ; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USAd; School of Life Sciences and Technology, Hubei Engineering University, Xiaogan, Chinae; College of Life Science, Henan Agricultural University, Zhengzhou, Chinaf ABSTRACT Some bacteria are capable of forming flocs, in which bacterial cells become self-flocculated by secreted extracellular polysaccharides and other biopolymers. The floc-forming bacteria play a central role in activated sludge, which has been widely utilized for the treatment of municipal sewage and industrial wastewater. Here, we use a floc-forming bacterium, Aquincola tertiaricarbonis RN12, as a model to explore the biosynthesis of extracellular polysaccharides and the regulation of floc formation.
  • Biosynthesis of 2-Hydroxyisobutyric Acid (2-HIBA) from Renewable Carbon Thore Rohwerder*, Roland H Müller

    Biosynthesis of 2-Hydroxyisobutyric Acid (2-HIBA) from Renewable Carbon Thore Rohwerder*, Roland H Müller

    Rohwerder and Müller Microbial Cell Factories 2010, 9:13 http://www.microbialcellfactories.com/content/9/1/13 RESEARCH Open Access Biosynthesis of 2-hydroxyisobutyric acid (2-HIBA) from renewable carbon Thore Rohwerder*, Roland H Müller Abstract Nowadays a growing demand for green chemicals and cleantech solutions is motivating the industry to strive for bio- based building blocks. We have identified the tertiary carbon atom-containing 2-hydroxyisobutyric acid (2-HIBA) as an interesting building block for polymer synthesis. Starting from this carboxylic acid, practically all compounds posses- sing the isobutane structure are accessible by simple chemical conversions, e. g. the commodity methacrylic acid as well as isobutylene glycol and oxide. During recent years, biotechnological routes to 2-HIBA acid have been proposed and significant progress in elucidating the underlying biochemistry has been made. Besides biohydrolysis and biooxi- dation, now a bioisomerization reaction can be employed, converting the common metabolite 3-hydroxybutyric acid to 2-HIBA by a novel cobalamin-dependent CoA-carbonyl mutase. The latter reaction has recently been discovered in the course of elucidating the degradation pathway of the groundwater pollutant methyl tert-butyl ether (MTBE) in the new bacterial species Aquincola tertiaricarbonis. This discovery opens the ground for developing a completely bio- technological process for producing 2-HIBA. The mutase enzyme has to be active in a suitable biological system pro- ducing 3-hydroxybutyryl-CoA, which is the precursor of the well-known bacterial bioplastic polyhydroxybutyrate (PHB). This connection to the PHB metabolism is a great advantage as its underlying biochemistry and physiology is well understood and can easily be adopted towards producing 2-HIBA.
  • Aquabacterium Limnoticum Sp. Nov., Isolated from a Freshwater Spring

    Aquabacterium Limnoticum Sp. Nov., Isolated from a Freshwater Spring

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by National Chung Hsing University Institutional Repository International Journal of Systematic and Evolutionary Microbiology (2012), 62, 698–704 DOI 10.1099/ijs.0.030635-0 Aquabacterium limnoticum sp. nov., isolated from a freshwater spring Wen-Ming Chen,1 Nian-Tsz Cho,1 Shwu-Harn Yang,2 A. B. Arun,3 Chiu-Chung Young4 and Shih-Yi Sheu2 Correspondence 1Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine Shih-Yi Sheu University, no. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC [email protected] 2Department of Marine Biotechnology, National Kaohsiung Marine University, no. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC 3Yenepoya Research Center, Yenepoya University, University Rd, Deralakatee, Mangalore, Karnataka State, India 4College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC A Gram-negative, facultatively anaerobic, short-rod-shaped, non-motile and non-spore-forming bacterial strain, designated ABP-4T, was isolated from a freshwater spring in Taiwan and was characterized using the polyphasic taxonomy approach. Growth occurred at 20–40 6C (optimum, 30–37 6C), at pH 7.0–10.0 (optimum, pH 7.0–9.0) and with 0–3 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ABP-4T, together with Aquabacterium fontiphilum CS-6T (96.4 % sequence similarity), Aquabacterium commune B8T (96.1 %), Aquabacterium citratiphilum B4T (95.5 %) and Aquabacterium parvum B6T (94.7 %), formed a deep line within the order Burkholderiales.
  • Rhizobacterial Community Structure in Response to Nitrogen Addition

    Rhizobacterial Community Structure in Response to Nitrogen Addition

    University of Massachusetts Amherst ScholarWorks@UMass Amherst Stockbridge Faculty Publication Series Stockbridge School of Agriculture 2018 Rhizobacterial community structure in response to nitrogen addition varied between two Mollisols differing in soil organic carbon Tengxiang Lian Chinese Academy of Sciences Zhenhua Yu Chinese Academy of Sciences Junjie Liu Chinese Academy of Sciences Yangsheng li Chinese Academy of Sciences Guanghua Wang Chinese Academy of Sciences See next page for additional authors Follow this and additional works at: https://scholarworks.umass.edu/stockbridge_faculty_pubs Lian, Tengxiang; Yu, Zhenhua; Liu, Junjie; li, Yangsheng; Wang, Guanghua; Liu, Xiaobing; Herbert, Stephen J.; Wu, Junjiang; and Jin, Jian, "Rhizobacterial community structure in response to nitrogen addition varied between two Mollisols differing in soil organic carbon" (2018). Scientific Reports. 2. https://doi.org/10.1038/s41598-018-30769-z This Article is brought to you for free and open access by the Stockbridge School of Agriculture at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Stockbridge Faculty Publication Series by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. Authors Tengxiang Lian, Zhenhua Yu, Junjie Liu, Yangsheng li, Guanghua Wang, Xiaobing Liu, Stephen J. Herbert, Junjiang Wu, and Jian Jin This article is available at ScholarWorks@UMass Amherst: https://scholarworks.umass.edu/stockbridge_faculty_pubs/2 www.nature.com/scientificreports OPEN Rhizobacterial community structure in response to nitrogen addition varied between two Received: 2 February 2018 Accepted: 5 July 2018 Mollisols difering in soil organic Published: xx xx xxxx carbon Tengxiang Lian1,2, Zhenhua Yu1, Junjie Liu1, Yansheng Li1, Guanghua Wang 1, Xiaobing Liu1, Stephen J.
  • Multiple Thresholds and Trajectories of Microbial Biodiversity Predicted Across Browning Gradients by Neural Networks and Decision Tree Learning

    Multiple Thresholds and Trajectories of Microbial Biodiversity Predicted Across Browning Gradients by Neural Networks and Decision Tree Learning

    www.nature.com/ismecomms ARTICLE OPEN Multiple thresholds and trajectories of microbial biodiversity predicted across browning gradients by neural networks and decision tree learning 1,2,5 1,3,5 1,2 1,2 4 3 Laurent Fontaine ✉, Maryia Khomich , Tom Andersen , Dag O. Hessen , Serena Rasconi , Marie L. Davey and Alexander Eiler 1,2 © The Author(s) 2021 Ecological association studies often assume monotonicity such as between biodiversity and environmental properties although there is growing evidence that nonmonotonic relations dominate in nature. Here, we apply machine-learning algorithms to reveal the nonmonotonic association between microbial diversity and an anthropogenic-induced large-scale change, the browning of freshwaters, along a longitudinal gradient covering 70 boreal lakes in Scandinavia. Measures of bacterial richness and evenness (alpha-diversity) showed nonmonotonic trends in relation to environmental gradients, peaking at intermediate levels of browning. Depending on the statistical methods, variables indicative for browning could explain 5% of the variance in bacterial community composition (beta-diversity) when applying standard methods assuming monotonic relations and up to 45% with machine- learning methods taking non-monotonicity into account. This non-monotonicity observed at the community level was explained by the complex interchangeable nature of individual taxa responses as shown by a high degree of nonmonotonic responses of individual bacterial sequence variants to browning. Furthermore, the nonmonotonic models
  • Appendix 1. Validly Published Names, Conserved and Rejected Names, And

    Appendix 1. Validly Published Names, Conserved and Rejected Names, And

    Appendix 1. Validly published names, conserved and rejected names, and taxonomic opinions cited in the International Journal of Systematic and Evolutionary Microbiology since publication of Volume 2 of the Second Edition of the Systematics* JEAN P. EUZÉBY New phyla Alteromonadales Bowman and McMeekin 2005, 2235VP – Valid publication: Validation List no. 106 – Effective publication: Names above the rank of class are not covered by the Rules of Bowman and McMeekin (2005) the Bacteriological Code (1990 Revision), and the names of phyla are not to be regarded as having been validly published. These Anaerolineales Yamada et al. 2006, 1338VP names are listed for completeness. Bdellovibrionales Garrity et al. 2006, 1VP – Valid publication: Lentisphaerae Cho et al. 2004 – Valid publication: Validation List Validation List no. 107 – Effective publication: Garrity et al. no. 98 – Effective publication: J.C. Cho et al. (2004) (2005xxxvi) Proteobacteria Garrity et al. 2005 – Valid publication: Validation Burkholderiales Garrity et al. 2006, 1VP – Valid publication: Vali- List no. 106 – Effective publication: Garrity et al. (2005i) dation List no. 107 – Effective publication: Garrity et al. (2005xxiii) New classes Caldilineales Yamada et al. 2006, 1339VP VP Alphaproteobacteria Garrity et al. 2006, 1 – Valid publication: Campylobacterales Garrity et al. 2006, 1VP – Valid publication: Validation List no. 107 – Effective publication: Garrity et al. Validation List no. 107 – Effective publication: Garrity et al. (2005xv) (2005xxxixi) VP Anaerolineae Yamada et al. 2006, 1336 Cardiobacteriales Garrity et al. 2005, 2235VP – Valid publica- Betaproteobacteria Garrity et al. 2006, 1VP – Valid publication: tion: Validation List no. 106 – Effective publication: Garrity Validation List no. 107 – Effective publication: Garrity et al.
  • Contents Topic 1. Introduction to Microbiology. the Subject and Tasks

    Contents Topic 1. Introduction to Microbiology. the Subject and Tasks

    Contents Topic 1. Introduction to microbiology. The subject and tasks of microbiology. A short historical essay………………………………………………………………5 Topic 2. Systematics and nomenclature of microorganisms……………………. 10 Topic 3. General characteristics of prokaryotic cells. Gram’s method ………...45 Topic 4. Principles of health protection and safety rules in the microbiological laboratory. Design, equipment, and working regimen of a microbiological laboratory………………………………………………………………………….162 Topic 5. Physiology of bacteria, fungi, viruses, mycoplasmas, rickettsia……...185 TOPIC 1. INTRODUCTION TO MICROBIOLOGY. THE SUBJECT AND TASKS OF MICROBIOLOGY. A SHORT HISTORICAL ESSAY. Contents 1. Subject, tasks and achievements of modern microbiology. 2. The role of microorganisms in human life. 3. Differentiation of microbiology in the industry. 4. Communication of microbiology with other sciences. 5. Periods in the development of microbiology. 6. The contribution of domestic scientists in the development of microbiology. 7. The value of microbiology in the system of training veterinarians. 8. Methods of studying microorganisms. Microbiology is a science, which study most shallow living creatures - microorganisms. Before inventing of microscope humanity was in dark about their existence. But during the centuries people could make use of processes vital activity of microbes for its needs. They could prepare a koumiss, alcohol, wine, vinegar, bread, and other products. During many centuries the nature of fermentations remained incomprehensible. Microbiology learns morphology, physiology, genetics and microorganisms systematization, their ecology and the other life forms. Specific Classes of Microorganisms Algae Protozoa Fungi (yeasts and molds) Bacteria Rickettsiae Viruses Prions The Microorganisms are extraordinarily widely spread in nature. They literally ubiquitous forward us from birth to our death. Daily, hourly we eat up thousands and thousands of microbes together with air, water, food.
  • Soil Characteristics Constrain the Response of Bacterial and Fungal Communities And

    Soil Characteristics Constrain the Response of Bacterial and Fungal Communities And

    bioRxiv preprint doi: https://doi.org/10.1101/2020.09.04.284042; this version posted September 6, 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-NC 4.0 International license. 1 Soil characteristics constrain the response of bacterial and fungal communities and 2 hydrocarbon degradation genes to phenanthrene soil contamination and 3 phytoremediation with poplars. 4 5 Sara Correa-Garcíaa,b, Karelle Rheaultb, Julien Tremblayc, Armand Séguinb, and 6 Etienne Yergeaua# 7 8 a Centre Armand Frappier Santé Biotechnologie, Institut national de la recherche 9 scientifique, Université du Québec, Laval, QC, Canada 10 b Laurentian Forest Center, Natural Resources Canada, Québec City, QC, Canada 11 c Energy, Mining and Environment, National Research Council Canada, Montréal, QC, 12 Canada 13 14 Running Head: effect of soil on microbial response to phenanthrene 15 16 # Address correspondence to prof. Etienne Yergeau: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.04.284042; this version posted September 6, 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-NC 4.0 International license. 17 Abstract 18 19 Rhizodegradation is a promising cleanup technology where microorganisms degrade 20 soil contaminants in the rhizosphere. A symbiotic relationship is expected to occur 21 between plant roots and soil microorganisms in contaminated soils that enhance natural 22 microbial degradation in soils.

  • Bchb D Bacteria P Cyanobacteria C Cyanobacteriia O Synechococcales F Prochlorotrichaceae G Prochlorothrix S Prochlorothrix Hollandica WGS ID ANKN01 1/1-488

    Tree scale: 0.1 bchZ d Bacteria p Eremiobacterota c Eremiobacteria o UBP12 f UBA5184 g BOG-1502 s BOG-1502 sp003134035 WGS ID PLAE01 1/1-377 0.84 bchZ GCA 000019165.1 ASM1916v1 protein ABZ83897.1 chlorophyllide reductase subunit z Heliobacterium modesticaldum Ice1 /1-442 0.89 bchZ d Bacteria p Acidobacteriota c Blastocatellia o Chloracidobacteriales f Chloracidobacteriaceae g Chloracidobacterium s Chloracidobacterium thermophilum A WGS ID LMXM01 1/3-449 1.00 bchZ GCA 000226295.1 ASM22629v1 protein AEP12277.1 chlorophyllide reductase subunit Z Chloracidobacterium thermophilum B /3-448 bchZ d Bacteria p Chloroflexota c Chloroflexia o Chloroflexales f Roseiflexaceae g Kouleothrix s Kouleothrix aurantiaca WGS ID LJCR01 1/3-438 1.00 bchZ d Bacteria p Chloroflexota c Chloroflexia o Chloroflexales f Roseiflexaceae g UBA965 s UBA965 sp002292925 WGS ID DBCF01 1/3-464 0.79 bchZ GCA 000017805.1 ASM1780v1 protein ABU59783.1 chlorophyllide reductase subunit Z Roseiflexus castenholzii DSM 13941 /3-462 1.00 bchZ GCA 000016665.1 ASM1666v1 protein ABQ91617.1 chlorophyllide reductase subunit Z Roseiflexus sp. RS-1 /3-455 0.98 0.90 bchZ d Bacteria p Chloroflexota c Chloroflexia o Chloroflexales f Chloroflexaceae g UBA1466 s UBA1466 sp002325605 WGS ID DCSM01 1/1-455 bchZ GCA 000022185.1 ASM2218v1 protein ACM55469.1 chlorophyllide reductase subunit Z Chloroflexus sp. Y-400-fl /3-458 1.00 0.52 bchZ GCA 000018865.1 ASM1886v1 protein ABY36984.1 chlorophyllide reductase subunit Z Chloroflexus aurantiacus J-10-fl /3-460 0.99 bchZ d Bacteria p Chloroflexota c Chloroflexia

  • The Role of Photoheterotrophic and Chemoautotrophic

    The role of photoheterotrophic and chemoautotrophic prokaryotes in the microbial food web in terrestrial Antarctica: a cultivation approach combined with functional analysis Guillaume Tahon Promotor Prof. Dr. Anne Willems Dissertation submitted in fulfillment of the requirements for the degree of Doctor (Ph.D.) of Science: Biotechnology (Ghent University) Tahon Guillaume | The role of photoheterotrophic and chemoautotrophic prokaryotes in the microbial food web in terrestrial Antarctica: a cultivation approach combined with functional analysis Copyright © 2017, Tahon Guillaume ISBN-number: 978-94-6197-523-2 All rights are reserved. No part of this thesis protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording or by any information storage or retrieval system without written permission of the author and promotor. Printed by University Press | http://www.universitypress.be Ph.D. thesis, Faculty of Sciences, Ghent University, Ghent, Belgium This Ph.D. work was supported by the Fund for Scientific Research – Flanders (project G.0146.12) Publically defended in Ghent, Belgium, May 5th, 2017 Examination committee Prof. Dr. Savvas Savvides (Chairman) L-Probe: Laboratory for protein Biochemistry and Biomolecular Engineering Faculty of Sciences, Ghent University, Belgium VIB Inflammation Research Center VIB, Ghent, Belgium Prof. Dr. Anne Willems (Promotor) LM-UGent: Laboratory of Microbiology Faculty of Sciences, Ghent University, Belgium Prof. Dr. Elie Verleyen (Secretary) Laboratory of Protistology and Aquatic Ecology Faculty of Sciences, Ghent University, Belgium Em. Prof. Dr. Paul De Vos LM-UGent: Laboratory of Microbiology Faculty of Sciences, Ghent University, Belgium Dr. Natalie Leys SCK·CEN: Environment, Health and Safety Belgian Nuclear Research Centre, Mol, Belgium Dr.
  • Bacterial Contributions to Delignification and Lignocellulose

    Bacterial Contributions to Delignification and Lignocellulose

    The ISME Journal (2019) 13:413–429 https://doi.org/10.1038/s41396-018-0279-6 ARTICLE Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing 1 1 1 1 Roland C. Wilhelm ● Rahul Singh ● Lindsay D. Eltis ● William W. Mohn Received: 8 January 2018 / Revised: 20 May 2018 / Accepted: 11 August 2018 / Published online: 26 September 2018 © The Author(s) 2018. This article is published with open access Abstract Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin, cellulose and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa 1234567890();,: 1234567890();,: or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of 13C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose- degradation. Very few taxa incorporated 13C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation.
  • Distinct Bacterial Consortia Established in ETBE-Degrading Enrichments from a Polluted Aquifer

    Distinct Bacterial Consortia Established in ETBE-Degrading Enrichments from a Polluted Aquifer

    applied sciences Article Distinct Bacterial Consortia Established in ETBE-Degrading Enrichments from a Polluted Aquifer Martina Kyselková 1,2,*, Joana Falcão Salles 1,3 , Alain Dumestre 4, Yves Benoit 5 and Geneviève L. Grundmann 1 1 Université Lyon1, CNRS, UMR5557, Ecologie Microbienne, INRA, 69622 Villeurbanne CEDEX, France; [email protected] (J.F.S.); [email protected] (G.L.G.) 2 Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology, 37005 Ceskˇ é Budˇejovice,Czech Republic 3 University of Groningen, Groningen Institute for Evolutionary Life Sciences, 9747 AG Groningen, The Netherlands 4 SERPOL, 69200 Vénissieux, France; [email protected] 5 IFP Energies Nouvelles, 92852 Rueil-Malmaison, France; [email protected] * Correspondence: [email protected]; Tel.: +33-387-775-770 Received: 16 August 2019; Accepted: 2 October 2019; Published: 11 October 2019 Abstract: Ethyl tert-butyl ether (ETBE) is a gasoline additive that became an important aquifer pollutant. The information about natural bacterial consortia with a capacity for complete ETBE degradation is limited. Here we assess the taxonomical composition of bacterial communities and diversity of the ethB gene (involved in ETBE biodegradation) in ETBE-enrichment cultures that were established from a gasoline-polluted aquifer, either from anoxic ETBE-polluted plume water (PW), or from an upstream non-polluted water (UW). We used a 16S rRNA microarray, and 16S rRNA and ethB gene sequencing. Despite the dissimilar initial chemical conditions and microbial composition, ETBE-degrading consortia were obtained from both PW and UW. The composition of ETBE-enrichment cultures was distinct from their initial water samples, reflecting the importance of the rare biosphere as a reservoir of potential ETBE degraders.