DOCSLIB.ORG

Characterization of the Key Enzymes Involved in Anaerobic Degradation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Characterization of the Key Enzymes Involved in Anaerobic Degradation Characterization of the key enzymes involved in anaerobic degradation of phthalate A dissertation submitted for the degree of Doctor of Natural Sciences (Dr. rer. nat.) at the University of Konstanz Faculty of Sciences Department of Biology Submitted by: Madan Junghare (M.Sc.) born on 3rd Nov. 1985 in Washim (MH), India Konstanz, 2016 Konstanzer Online-Publikations-System (KOPS) URL: http://nbn-resolving.de/urn:nbn:de:bsz:352-0-395942 Tag der mündlichen Prüfung: 2. Februar 2017 1. Gutachter: Prof. Dr. rer. nat. Bernhard Schink 2. Gutachter: Prof. Dr. Dieter Spiteller 3. Gutachter: Prof. Dr. Valentin Wittmann ACKNOWLEDGEMENTS First and foremost, I would like to express my sincere thanks to my supervisor Professor Bernhard Schink for giving me the opportunity to complete my Ph.D dissertation in his lab at the University of Konstanz on such an interesting project. You have provided me valuable guidance, support, and encouragements during my doctoral research, whenever it was needed. Secondly, I would like to thank my co-supervisor Professor Dieter Spiteller for his guidance, nurturing and offering me to use his lab facility for my research. You provided priceless aid for my research project. I wouldn’t have succeeded without your help. I really appreciate everything. Thanks to Professor Valentin Whitmann for acting as a third member of my thesis committee at the Graduate School of Chemical Biology. I am very thankful to Dr. David Schleheck for allowing me to use his proteomics lab facility for doing my research work. Thank you for your helpful discussion, suggestions, and for enriching my scientific knowledge during this period. I would like to thank everyone else in the Schink group for all their kindness, assistance, friendship and providing a great working environment, as well as enjoying coffee and cake time together. It has been a largely very enjoyable time. Vielen Vielen Danke nochmal an Alle! Many thanks to the friendly team at the Welcome Center, University of Konstanz for their support, advice and friendly cooperation in all bureaucratic matter. I like to acknowledge DAAD for providing me a PhD scholarship to begin my doctoral research and giving me an opportunity to study in Germany. A special thanks to my incredible family in India for their endless support, love and for all of the sacrifices that you’ve made on my behalf. You might not have known anything about my research, but you were always there for me. I dedicate this work to my father and mama, I know you would have been very happy and proud of me. Special thanks to my wife for her support, care and love. And also thank you for reading my thesis, feedback and for spending sleepless nights during the thesis writing. Lots of love to my sweet daughter Grishma. I hope my research work has advanced the knowledge in the field of anaerobic phthalate degradation. Enjoy! Table of contents Dissertation summary……………………………………………………………………………………….……………………………………………07 Dissertation Zusammenfassung….…………….…………………………………………………………...………………………………………09 Chapter 1. General introduction 1. Aromatic compounds in nature….…………………..………………………………………..………………………………………………...12 1.1 Aromaticity and stability 1.2 Occurrence and sources 2. Microbial degradation of aromatic compounds in nature………………………………………………….………………….…....13 2.1 Aerobic degradation 2.2 Anaerobic degradation 3. Phthalate esters, applications and biodegradation…………….……………………………..…………………………………………19 3.1 Phthalate esters as ‘plasticizers’ 3.2 ‘Man-made’ phthalate as pollutant 4. Microbial degradation of phthalate esters………………………………………………………………..…………………………………22 4.1 Importance of phthalate esters degradation 4.2 Initial steps in phthalate ester degradation 4.3 Aerobic phthalate degradation 4.4 Anaerobic phthalate degradation 5. Aims of the dissertation and objectives………………………………………………………………………………………….…………...28 6. Research co-authored but not included in the dissertation…………………………………….…………………………………..29 Chapter 2. Draft genome sequence of a nitrate-reducing, o-phthalate-degrading bacterium, Azoarcus sp. strain PA01 Abstract…………………………………………………………………..………………………………………………………………………………………31 Introduction…………………………………………………………………………..………………………………………………………………………..31 Organism information……………………………….………………………………..…………………………………………………………………..32 Classification and features Chemotaxonomy Genome sequencing and information……………………………………………………………………………………………………………..36 Genome project history Growth conditions and genomic DNA preparation Genome sequencing and assembly Genome annotation Genome properties………………………………………………………………………………………………………………………………………….38 Insight from the genome sequence……………………………………..…………………………………………………………………….......41 I Chapter 3. Enzymes involved in the anaerobic degradation of ortho-phthalate by the nitrate-reducing bacterium Azoarcus sp. strain PA01 Abstract……………………………………………………………………………………………………………………….……………………………….…45 Introduction……………………………………………………………………………………………..……………………………………………………..45 Results………………………………………………………………………………………………………………………………………………..…………..47 Anaerobic growth with o-phthalate and physiological characteristics Differential proteome analysis of o-phthalate-grown cells versus benzoate-grown cells Characterization of the gene cluster involved in anaerobic o-phthalate degradation Enzyme activity measurements with cell-free extracts of Azoarcus sp. strain PA01 Discussion........…………………………………………………………………….…………………………………………………………….……………59 Experimental procedures…………………………………………………….………………………..………………………………………………..63 Bacterial strain and growth conditions Bacterial growth analysis Preparation of cell-free extracts Differential proteome analysis Protein identification by mass spectrometry Identification of gene clusters and phylogenetic analysis Determination of enzyme activities in cell-free extracts Synthesis of o-phthalyl-CoAs LC-MS/MS analysis of Coenzyme A esters Supporting information……………………………………………………………………………………………………………………………………70 Chapter 4. Cloning and over-expressions of genes involved in anaerobic o-phthalate decarboxylation to benzoate by the Azoarcus sp. strain PA01 Abstract……………………………………………………………………………………..……………………………………………………………………77 Introduction……………………………………………………..……………………………………………………………………………………………..77 Materials and methods…………………………………..……………………………………………………………………………………………….80 Materials and reagents Strains and cultivation conditions Gene amplifications, plasmid construction and sequencing Optimization of protein expression and purifications Molecular weight determination by SDS-PAGE Decarboxylase activity assays and cofactor identification Native protein PAGE analysis Sequence alignment and structure homology modelling Results………………………………………………………………………………………….………………….……………………………………………..86 Gene amplifications, cloning of PhtDa and PhtDb II 5 | P a g e Heterologous expression, purification and protein identification Enzyme activity, substrate specificity and cofactor requirement Phylogenetic position of PhtDa and PhtDb Multiple sequence alignment and homology-based structure modelling Native PAGE and protein identification by MS analysis Discussion……………………………………………………………………………………………………………..…………………………………………98 Chapter 5: Desulfoprunum benzoelyticum gen. nov., sp. nov., a Gram-stain-negative, benzoate-degrading, sulfate-reducing bacterium isolated from a wastewater treatment plant Abstract…………………………………………………………………………………………………………….…………………..........................103 Introduction………………………………………………………………………….………………………………….……………………………………104 Material and methods………………………………………..………………………………..……………………………………………………….104 Results and discussion……………….………………………………………………………….………………………………………………………107 Description of Desulfoprunum gen. nov. Description of Desulfoprunum benzoelyticum gen. nov., sp. nov. Chapter 6: Enrichment cultures degrading phthalate isomers under nitrate-reducing, sulfate-reducing and fermenting conditions Introduction…………………………………………………………………………………………………………………..………………………………115 Phthalate isomer degradation under denitrifying conditions Phthalate degradation under sulfate-reducing/fermenting conditions Partial characterization of enrichment culture KOPA Chapter 7: General discussion and concluding remarks General discussion…...…………………………………………………………………………………………………………………………………..121 Activation of o-phthalate by Azoarcus sp. strain PA01 Decarboxylation of activated o-phthalate by a two enzyme component system Concluding remarks and general outlook…………...………………………………………………............................................125 Personal record of achievements……………………………………………..…………………………………………………….126 List of publications……………………………………………………….………………….…………………………...127 Workshops and training courses attended……………………………….………………………………………………….128 References………………………………………………..………………………………..……………………………….129 Abbreviations………………………………………………………………….………………………………….…………146 III 6 | P a g e Dissertation summary Anaerobic phthalate degradation was assumed to proceed through initial decarboxylation of phthalate (ortho) to benzoate. However, the intermediates and enzymes involved in anaerobic phthalate decarboxylation were largely unknown. The aim of this dissertation was to investigate the biochemistry of anaerobic phthalate degradation, especially the steps and enzymes involved in the decarboxylation of phthalate to benzoate. In particular, the study focused on the enrichment and isolation of anaerobic phthalate-degrading bacteria under nitrate-reducing, sulfate-reducing and fermenting conditions. Strain PA01 was isolated and purified from an enrichment culture that degrades phthalate coupled to nitrate reduction. 16S rRNA
Load more

Recommended publications
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Assessment of Bacterial Species Present in Pasig River and Marikina River Soil Using 16S Rdna Phylogenetic Analysis
    International Journal of Philippine Science and Technology, Vol. 08, No. 2, 2015 !73 SHORT COMMUNICATION Assessment of bacterial species present in Pasig River and Marikina River soil using 16S rDNA phylogenetic analysis Maria Constancia O. Carrillo*, Paul Kenny L. Ko, Arvin S. Marasigan, and Arlou Kristina J. Angeles Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Padre Faura St., Ermita, Manila Philippines 1000 Abstract—The Pasig River system, which includes its major tributaries, the Marikina, Taguig-Pateros, and San Juan Rivers, is the most important river system in Metro Manila. It is known to be heavily polluted due to the dumping of domestic, industrial and solid wastes. Identification of microbial species present in the riverbed may be used to assess water and soil quality, and can help in assessing the river’s capability of supporting other flora and fauna. In this study, 16S rRNA gene or 16S rDNA sequences obtained from community bacterial DNA extracted from riverbed soil of Napindan (an upstream site along the Pasig River) and Vargas (which is along the Marikina River) were used to obtain a snapshot of the types of bacteria populating these sites. The 16S rDNA sequences of amplicons produced in PCR with total DNA extracted from soil samples as template were used to build clone libraries. Four positive clones were identified from each site and were sequenced. BLAST analysis revealed that none of the contiguous sequences obtained had complete sequence similarity to any known cultured bacterial species. Using the classification output of the Ribosomal Database Project (RDP) Classifier and DECIPHER programs, 16S rDNA sequences of closely related species were collated and used to construct a neighbor-joining phylogenetic tree using MEGA6.
    [Show full text]
  • Optimization and Characterization of the Growth Of
    OPTIMIZATION AND CHARACTERIZATION OF THE GROWTH OF THE PHOTOSYNTHETIC BACTERIUM BLASTOCHLORIS VIRIDIS AND A BRIEF SURVEY OF ITS POTENTIAL AS A REMEDIATIVE TOOL A Dissertation Submitted to the Graduate School of the University of Notre Dame in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Darcy Danielle LaClair, B.S. ___________________________________ Agnes E. Ostafin, Director Graduate Program in Chemical and Biomolecular Engineering Notre Dame, Indiana April 2006 OPTIMIZATION AND CHARACTERIZATION OF THE GROWTH OF THE PHOTOSYNTHETIC BACTERIUM BLASTOCHLORIS VIRIDIS AND A BRIEF SURVEY OF THEIR POTENTIAL AS A REMEDIATIVE TOOL Abstract by Darcy Danielle LaClair The growth of B. viridis was characterized in an undefined rich medium and a well-defined medium, which was later selected for further experimentation to insure repeatability. This medium presented a significant problem in obtaining either multigenerational or vigorous growth because of metabolic limitations; therefore optimization of the medium was undertaken. A primary requirement to obtain good growth was a shift in the pH of the medium from 6.9 to 5.9. Once this shift was made, it was possible to obtain growth in subsequent generations, and the media formulation was optimized. A response curve suggested optimum concentrations of 75 mM carbon, supplemented as sodium malate, 12.5 mM nitrogen, supplemented as ammonium sulfate, Darcy Danielle LaClair and 12.7 mM phosphate buffer. In addition, the vitamins p-Aminobenzoic acid, Thiamine, Biotin, B12, and Pantothenate were important to achieving good growth and good pigment formation. Exogenous carbon dioxide, added as 2.5 g sodium bicarbonate per liter media also enhanced growth and reduced the lag time.
    [Show full text]
  • FISH Handbook for Biological Wastewater Treatment
    ©2019 The Author(s) This is an Open Access book distributed under the terms of the Creative Commons Attribution Licence (CC BY 4.0), which permits copying and redistribution for non- commercial purposes, provided the original work is properly cited and that any new works are made available on the same conditions (http://creativecommons.org/licenses/by/4.0/). This does not affect the rights licensed or assigned from any third party in this book. This title was made available Open Access through a partnership with Knowledge Unlatched. IWA Publishing would like to thank all of the libraries for pledging to support the transition of this title to Open Access through the KU Select 2018 program. Downloaded from http://iwaponline.com/ebooks/book-pdf/521273/wio9781780401775.pdf by guest on 25 September 2021 Identification and quantification of microorganisms in activated sludge and biofilms by FISH and biofilms by sludge in activated Identification and quantification of microorganisms Treatment Wastewater Biological for Handbook FISH The FISH Handbook for Biological Wastewater Treatment provides all the required information for the user to be able to identify and quantify important microorganisms in activated sludge and biofilms by using fluorescence in situ hybridization (FISH) and epifluorescence microscopy. It has for some years been clear that most microorganisms in biological wastewater systems cannot be reliably identified and quantified by conventional microscopy or by traditional culture-dependent methods such as plate counts. Therefore, molecular FISH Handbook biological methods are vital and must be introduced instead of, or in addition to, conventional methods. At present, FISH is the most widely used and best tested of these methods.
    [Show full text]
  • Syntrophic Butyrate and Propionate Oxidation Processes 491
    Environmental Microbiology Reports (2010) 2(4), 489–499 doi:10.1111/j.1758-2229.2010.00147.x Minireview Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanismsemi4_147 489..499 Nicolai Müller,1† Petra Worm,2† Bernhard Schink,1* a cytoplasmic fumarate reductase to drive energy- Alfons J. M. Stams2 and Caroline M. Plugge2 dependent succinate oxidation. Furthermore, we 1Faculty for Biology, University of Konstanz, D-78457 propose that homologues of the Thermotoga mar- Konstanz, Germany. itima bifurcating [FeFe]-hydrogenase are involved 2Laboratory of Microbiology, Wageningen University, in NADH oxidation by S. wolfei and S. fumaroxidans Dreijenplein 10, 6703 HB Wageningen, the Netherlands. to form hydrogen. Summary Introduction In anoxic environments such as swamps, rice fields In anoxic environments such as swamps, rice paddy fields and sludge digestors, syntrophic microbial communi- and intestines of higher animals, methanogenic commu- ties are important for decomposition of organic nities are important for decomposition of organic matter to matter to CO2 and CH4. The most difficult step is the CO2 and CH4 (Schink and Stams, 2006; Mcinerney et al., fermentative degradation of short-chain fatty acids 2008; Stams and Plugge, 2009). Moreover, they are the such as propionate and butyrate. Conversion of these key biocatalysts in anaerobic bioreactors that are used metabolites to acetate, CO2, formate and hydrogen is worldwide to treat industrial wastewaters and solid endergonic under standard conditions and occurs wastes. Different types of anaerobes have specified only if methanogens keep the concentrations of these metabolic functions in the degradation pathway and intermediate products low. Butyrate and propionate depend on metabolite transfer which is called syntrophy degradation pathways include oxidation steps of (Schink and Stams, 2006).
    [Show full text]
  • Regulación De La Expresión De La Ruta De Degradación De Compuestos Dihidroxilados En Azoarcus Anaerobius Y Thauera Aromatica AR-1
    Consejo Superior de Investigaciones Científicas Estación Experimental del Zaidín Regulación de la expresión de la ruta de degradación de compuestos dihidroxilados en Azoarcus anaerobius y Thauera aromatica AR-1 Tesis Doctoral Daniel Pacheco Sánchez 2018 III Editor: Editorial de la Universidad de Granada Autor: Daniel Pacheco Sánchez Dibujo de la portada: María Pacheco García Impreso en mayo de 2018 IV Regulación de la expresión de la ruta de degradación de compuestos dihidroxilados en Azoarcus anaerobius y Thauera aromatica AR-1 Memoria que presenta el Licenciado en Biología Daniel Pacheco Sánchez para aspirar al Título de Doctor Fdo. Daniel Pacheco Sánchez VºBº de la Directora Fdo.: Silvia Marqués Martín Doctora en Biología Investigadora Científica CSIC EEZ-CSIC/Universidad de Granada 2018 V Editor: Universidad de Granada. Tesis Doctorales Autor: Daniel Pacheco Sánchez ISBN: 978-84-9163-909-1 URI: http://hdl.handle.net/10481/52300 VI Esta tesis doctoral ha sido realizada en el Grupo de Microbiología Ambiental y Biodegradación perteneciente al Departamento de Protección Ambiental de la Estación Experimental del Zaidín (CSIC), por Daniel Pacheco Sánchez, cuya Investigación ha sido financiada por los proyectos BIO-2011-23615 del MICINN y P08-CVI03591 de la Junta de Andalucía. Parte de los resultados obtenidos durante esta tesis doctoral sido presentados en los siguientes congresos y publicaciones: Publicaciones RedR1 and RedR2, Transcripcional regulators of the anaerobic degradation pathways in Azoarcus anaerobius. Molina-Fuentes, A, Pacheco, D., Marqués, S. FEBS Journal 279: 492-493 (2012). The Azoarcus anaerobius 1,3-Dihydroxybenzene (Resorcinol) Anaerobic Degradation Pathway Is Controlled by the Coordinated Activity of Two Enhancer- Binding Proteins.
    [Show full text]
  • Identification of N2-Fixing Plant-And Fungus-Associated Azoarcus
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Nov. 1997, p. 4331–4339 Vol. 63, No. 11 0099-2240/97/$04.0010 Copyright © 1997, American Society for Microbiology Identification of N2-Fixing Plant- and Fungus-Associated Azoarcus Species by PCR-Based Genomic Fingerprints THOMAS HUREK, BIANCA WAGNER, AND BARBARA REINHOLD-HUREK* Max-Planck-Institut fu¨r Terrestrische Mikrobiologie, Arbeitsgruppe Symbioseforschung, D-35043 Marburg, Germany Received 14 February 1997/Accepted 30 August 1997 Most species of the diazotrophic Proteobacteria Azoarcus spp. occur in association with grass roots, while A. tolulyticus and A. evansii are soil bacteria not associated with a plant host. To facilitate species identification and strain comparison, we developed a protocol for PCR-generated genomic fingerprints, using an automated sequencer for fragment analysis. Commonly used primers targeted to REP (repetitive extragenic palindromic) and ERIC (enterobacterial repetitive intergenic consensus) sequence elements failed to amplify fragments from the two species tested. In contrast, the BOX-PCR assay (targeted to repetitive intergenic sequence elements of Streptococcus) yielded species-specific genomic fingerprints with some strain-specific differences. PCR profiles of an additional PCR assay using primers targeted to tRNA genes (tDNA-PCR, for tRNAIle) were more discriminative, allowing differentiation at species-specific (for two species) or infraspecies-specific level. Our protocol of several consecutive PCR assays consisted of 16S ribosomal DNA (rDNA)-targeted, genus- specific
    [Show full text]
  • Propionic Acid Degradation by Syntrophic Bacteria During Anaerobic Biowaste Digestion Propionic Acid Degradation Propionic WIREŁŁO
    KARLSRUHERBERICHTE ZUR INGENIEURBIOLOGIE . MONIKA FELCHNER-Z WIREŁŁO Propionic Acid Degradation by Syntrophic Bacteria During Anaerobic Biowaste Digestion Propionic Acid Degradation Propionic WIREŁŁO . MONIKA FELCHNER-Z 49 . Monika Felchner-Z wirełło Propionic Acid Degradation by Syntrophic Bacteria During Anaerobic Biowaste Digestion Karlsruher Berichte zur Ingenieurbiologie Band 49 Institut für Ingenieurbiologie und Biotechnologie des Abwassers Karlsruher Institut für Technologie Herausgeber: Prof. Dr. rer. nat. J. Winter Propionic Acid Degradation by Syntrophic Bacteria During Anaerobic Biowaste Digestion by . Monika Felchner-Z wirełło Dissertation, Karlsruher Institut für Technologie (KIT) Fakultät für Fakultät für Bauingenieur-, Geo- und Umweltwissenschaften Tag der mündlichen Prüfung: 08. Februar 2013 Referenten: Prof. Dr. rer. nat. habil. Josef Winter Korreferenten: Prof. Dr.-Ing. E.h. Hermann H. Hahn, Ph.D. Prof. Dr hab. in˙z . Jacek Namie´snik Impressum Karlsruher Institut für Technologie (KIT) KIT Scientific Publishing Straße am Forum 2 D-76131 Karlsruhe KIT Scientific Publishing is a registered trademark of Karlsruhe Institute of Technology. Reprint using the book cover is not allowed. www.ksp.kit.edu This document – excluding the cover – is licensed under the Creative Commons Attribution-Share Alike 3.0 DE License (CC BY-SA 3.0 DE): http://creativecommons.org/licenses/by-sa/3.0/de/ The cover page is licensed under the Creative Commons Attribution-No Derivatives 3.0 DE License (CC BY-ND 3.0 DE): http://creativecommons.org/licenses/by-nd/3.0/de/ Print on Demand 2014 ISSN 1614-5267 ISBN 978-3-7315-0159-6 DOI: 10.5445/KSP/1000037825 Propionic Acid Degradation by Syntrophic Bacteria During Anaerobic Biowaste Digestion Zur Erlangung des akademischen Grades eines DOKTOR-INGENIEURS von der Fakult¨at f¨ur Bauingenieur-, Geo- und Umweltwissenschaften des Karlsruher Instituts f¨ur Technologie (KIT) genehmigte DISSERTATION von Dipl.-Ing.
    [Show full text]
  • 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.
    [Show full text]
  • Isotope Array Analysis of Rhodocyclales Uncovers Functional Redundancy and Versatility in an Activated Sludge
    The ISME Journal (2009) 3, 1349–1364 & 2009 International Society for Microbial Ecology All rights reserved 1751-7362/09 $32.00 www.nature.com/ismej ORIGINAL ARTICLE Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge Martin Hesselsoe1, Stephanie Fu¨ reder2, Michael Schloter3, Levente Bodrossy4, Niels Iversen1, Peter Roslev1, Per Halkjær Nielsen1, Michael Wagner2 and Alexander Loy2 1Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark; 2Department of Microbial Ecology, University of Vienna, Wien, Austria; 3Department of Terrestrial Ecogenetics, Helmholtz Zentrum Mu¨nchen—National Research Center for Environmental Health, Neuherberg, Germany and 4Department of Bioresources/Microbiology, ARC Seibersdorf Research GmbH, Seibersdorf, Austria Extensive physiological analyses of different microbial community members in many samples are difficult because of the restricted number of target populations that can be investigated in reasonable time by standard substrate-mediated isotope-labeling techniques. The diversity and ecophysiology of Rhodocyclales in activated sludge from a full-scale wastewater treatment plant were analyzed following a holistic strategy based on the isotope array approach, which allows for a parallel functional probing of different phylogenetic groups. Initial diagnostic microarray, comparative 16S rRNA gene sequence, and quantitative fluorescence in situ hybridization surveys indicated the presence of a diverse community, consisting of an estimated number of 27 operational taxonomic units that grouped in at least seven main Rhodocyclales lineages. Substrate utilization profiles of probe-defined populations were determined by radioactive isotope array analysis and microautoradiography-fluorescence in situ hybridization of activated sludge samples that were briefly exposed to different substrates under oxic and anoxic, nitrate-reducing conditions.
    [Show full text]
  • “Candidatus Propionivibrio Aalborgensis”: a Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants
    Aalborg Universitet “Candidatus Propionivibrio aalborgensis” A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants Albertsen, Mads; McIlroy, Simon Jon; Stokholm-Bjerregaard, Mikkel; Karst, Søren Michael; Nielsen, Per Halkjær Published in: Frontiers in Microbiology DOI (link to publication from Publisher): 10.3389/fmicb.2016.01033 Creative Commons License CC BY 4.0 Publication date: 2016 Document Version Publisher's PDF, also known as Version of record Link to publication from Aalborg University Citation for published version (APA): Albertsen, M., McIlroy, S. J., Stokholm-Bjerregaard, M., Karst, S. M., & Nielsen, P. H. (2016). “Candidatus Propionivibrio aalborgensis”: A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants. Frontiers in Microbiology, 7, [1033]. https://doi.org/10.3389/fmicb.2016.01033 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. ? Users may download and print one copy of any publication from the public portal for the purpose of private study or research. ? You may not further distribute the material or use it for any profit-making activity or commercial gain ? You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us at [email protected] providing details, and we will remove access to the work immediately and investigate your claim. fmicb-07-01033 June 30, 2016 Time: 16:42 # 1 ORIGINAL RESEARCH published: 04 July 2016 doi: 10.3389/fmicb.2016.01033 “Candidatus Propionivibrio aalborgensis”: A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants Mads Albertsen1†, Simon J.
    [Show full text]
  • Anaerobic Mineralization of Quaternary Carbon Atoms: Isolation of Denitrifying Bacteria on Pivalic Acid (2,2-Dimethylpropionic Acid)
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Mar. 2003, p. 1866–1870 Vol. 69, No. 3 0099-2240/03/$08.00ϩ0 DOI: 10.1128/AEM.69.3.1866–1870.2003 Copyright © 2003, American Society for Microbiology. All Rights Reserved. Anaerobic Mineralization of Quaternary Carbon Atoms: Isolation of Denitrifying Bacteria on Pivalic Acid (2,2-Dimethylpropionic Acid) Christina Probian, Annika Wu¨lfing, and Jens Harder* Downloaded from Department of Microbiology, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany Received 22 August 2002/Accepted 26 November 2002 The degradability of pivalic acid was established by the isolation of several facultative denitrifying strains belonging to Zoogloea resiniphila,toThauera and Herbaspirillum, and to Comamonadaceae, related to [Aquaspi- rillum] and Acidovorax, and of a nitrate-reducing bacterium affiliated with Moraxella osloensis. Pivalic acid was completely mineralized to carbon dioxide. The catabolic pathways may involve an oxidation to dimethyl- malonate or a carbon skeleton rearrangement, a putative 2,2-dimethylpropionyl coenzyme A mutase. http://aem.asm.org/ Quaternary carbon atoms bind with all four single ␴ bonds unable to respire oxygen (21). Our isolation strategy with pi- to carbon atoms. This structural motif is present in natural valic acid as sole electron donor and carbon source aimed at compounds as well as in xenobiotic substances. Resin acids, this physiology in order to obtain many strains quickly: enrich- tricyclic diterpenes, are present in cell walls and are discharged ment of an anaerobic nitrate-reducing population in liquid during the pulping process, yielding toxic wastewaters. Aerobic culture was followed by repeated aerobic growth on oxic plates growth of bacteria on defined resin acids has been studied to to obtain single colonies.
    [Show full text]