DOCSLIB.ORG

Faculty of Agricultural Sciences

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Faculty of Agricultural Sciences FACULTY OF AGRICULTURAL SCIENCES Institute of Soil Science and Land Evaluation University of Hohenheim Soil Biology Prof. Dr. Ellen Kandeler Linking Microbial Abundance and Function to Understand Nitrogen Cycling in Grassland Soils Dissertation Submitted in fulfillment of the requirements for the degree “Doktor der Agrarwissenschaften” (Dr.sc.agr/Ph.D. in Agricultural Sciences) to the Faculty of Agricultural Sciences Presented by: Kathleen Marie Regan Tiffin, Ohio, USA 2016 ii This thesis was accepted as a doctoral thesis (Dissertation) in fulfillment of the regulations to acquire the doctoral degree "Doktor der Agrarwissenschaften” by the Faculty of Agricultural Sciences at University of Hohenheim on July 19, 2016. Date of oral examination: December 16, 2016 Examination Committee Chairperson: Prof. Dr. M. Rotehutscord Supervisor and reviewer: Prof. Dr. E. Kandeler Co-reviewer 1: Prof. Dr. F. Rasche Co-reviewer 2: Prof. Dr. Y. Oelmann (Universität Tübingen) I would like to dedicate this dissertation to my family, who have never questioned my pursuit of what have often appeared to be impossible goals. This includes my mother and my husband’s mother, who as women of a certain generation were both bold, each in her own way. They would be very proud. And especially this is for my granddaughters Samara and Dove, so that they grow up to know they can be or do anything they choose. It is always worthwhile to pursue a dream. iii Affidavit Pursuant to Sec. 8(2) of the University of Hohenheim’s doctoral degree regulations for Dr.sc.agr. 1. I hereby declare that I independently completed the doctoral thesis submitted on the topic “Linking Microbial Abundance and Function to Understand Nitrogen Cycling in Grassland Soils” 2. I only used the sources and aids documented and only made use of permissible assistance by third parties. In particular, I properly documented any contents which I used - either by directly quoting or paraphrasing - from other works. 3. I did not accept any assistance from a commercial doctoral agency or consulting firm. 4. I am aware of the meaning of this affidavit and the criminal penalties of an incorrect or incomplete affidavit. I hereby confirm the correctness of the above declaration. I hereby affirm in lieu of oath that I have, to the best of my knowledge, declared nothing but the truth and have not omitted any information. …………………………………………………………………………………………………... (Place, date) (Signature) iv Table of Contents List of Figures ......................................................................................................................... viii List of Tables ............................................................................................................................. ix List of Supplementary Figures ................................................................................................... x List of Supplementary Tables .................................................................................................... x 1 Summary ........................................................................................................................... 1 2 Zusammenfassung ............................................................................................................ 4 3 General Introduction ......................................................................................................... 7 3.1 Linking microbial abundance and function ................................................................. 7 3.2 Relevance of grasslands to linkages ............................................................................ 7 3.3 Scales and their relevance ............................................................................................ 7 3.3.1 Spatial scales ......................................................................................................... 7 Temporal scales ..................................................................................................... 8 3.4 Soil microbial community structure ............................................................................ 9 3.5 Nitrogen cycling community ..................................................................................... 10 Nitrogen fixation and ammonia oxidation – nitrification ................................... 10 Denitrification ..................................................................................................... 11 3.6 Potential enzyme activities ........................................................................................ 12 3.7 Phylogenetic analysis ................................................................................................ 12 4 Outline of the Thesis ....................................................................................................... 14 5 Seasonal controls on grassland microbial biogeography: are they governed by plants, abiotic properties or both? ................................................................................... 16 5.1 Abstract ...................................................................................................................... 17 5.2 Introduction ............................................................................................................... 17 5.3 Materials & Methods ................................................................................................. 19 Site description .................................................................................................... 19 Sample design ..................................................................................................... 20 Table of Content v Sampling – aboveground .................................................................................... 20 Sampling – belowground .................................................................................... 20 Physical, chemical, biological soil properties ..................................................... 21 Statistical analyses .............................................................................................. 22 5.4 Results ....................................................................................................................... 24 Temporal patterns ............................................................................................... 24 5.4.1.1 Plants and litter ........................................................................................... 24 5.4.1.2 Abiotic soil properties ................................................................................. 24 5.4.1.3 Soil-microbial community variables ........................................................... 27 Univariate spatial patterns over time .................................................................. 27 Changes in spatial patterns of microbial and plant community structure and environmental profiles over time ........................................................................ 29 5.4.1.1 Mantel statistic – relationships among communities .................................. 29 5.4.1.2 PCA – distinctions within the microbial community .................................. 30 5.5 Discussion .................................................................................................................. 31 5.6 Conclusions ............................................................................................................... 34 5.7 Acknowledgments ..................................................................................................... 34 5.8 Supplementary material ............................................................................................. 36 6 Spatial and temporal dynamics of nitrogen fixing, nitrifying and denitrifying microbes in an unfertilized grassland soil ....................................................................... 42 6.1 Abstract ...................................................................................................................... 43 6.2 Introduction ............................................................................................................... 43 6.3 Materials and Methods .............................................................................................. 46 Site description .................................................................................................... 46 Sample design ..................................................................................................... 47 Sample collection ................................................................................................ 47 DNA extraction and quantification of marker genes .......................................... 47 Potential enzyme activities .................................................................................. 48 Table of Content vi Statistical analyses .............................................................................................. 49 6.4 Results ....................................................................................................................... 50 Temporal dynamics ............................................................................................. 50 Correlations between biotic and abiotic soil properties over time ...................... 53 Spatial structure................................................................................................... 57 Multivariate spatial relationships .......................................................................
Load more

Recommended publications
  • CUED Phd and Mphil Thesis Classes
    High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice.
    [Show full text]
  • Multiple Genome Sequences Reveal Adaptations of a Phototrophic Bacterium to Sediment Microenvironments
    Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments Yasuhiro Odaa, Frank W. Larimerb, Patrick S. G. Chainc,d,e, Stephanie Malfattic,d, Maria V. Shinc,d, Lisa M. Vergezc,d, Loren Hauserb, Miriam L. Landb, Stephan Braatschf, J. Thomas Beattyf, Dale A. Pelletierb, Amy L. Schaefera, and Caroline S. Harwooda,1 aDepartment of Microbiology, University of Washington, Seattle, WA 98195; bGenome Analysis and Systems Modeling, Oak Ridge National Laboratory, Oak Ridge, TN 37831; cJoint Genome Institute, Walnut Creek, CA 94598; dLawrence Livermore National Laboratory, Livermore, CA 94550; eDepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824; and fDepartment of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada Edited by Robert Haselkorn, University of Chicago, Chicago, IL, and approved October 14, 2008 (received for review September 13, 2008) The bacterial genus Rhodopseudomonas is comprised of photo- exist in soils and sediments, but on a microscale that is generally synthetic bacteria found widely distributed in aquatic sediments. too small for human observation. The genus Rhodopseudomonas Members of the genus catalyze hydrogen gas production, carbon consists of photosynthetic Alphaproteobacteria of extreme met- dioxide sequestration, and biomass turnover. The genome se- abolic versatility. Members of the genus are ubiquitous in quence of Rhodopseudomonas palustris CGA009 revealed a sur- temperate aquatic sediments (7–9), and isolates classified as prising richness of metabolic versatility that would seem to explain Rhodopseudomonas spp. can grow with or without light or its ability to live in a heterogeneous environment like sediment. oxygen, fix nitrogen, and have highly developed biodegradation However, there is considerable genotypic diversity among Rhodo- abilities.
    [Show full text]
  • Diversification and Niche Adaptations of Nitrospina-Like Bacteria in The
    The ISME Journal (2016) 10, 1383–1399 OPEN © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Diversification and niche adaptations of Nitrospina- like bacteria in the polyextreme interfaces of Red Sea brines David Kamanda Ngugi1, Jochen Blom2, Ramunas Stepanauskas3 and Ulrich Stingl1 1Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia; 2Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany and 3Bigelow Laboratories for Ocean Sciences, East Boothbay, ME 04544-0380, USA Nitrite-oxidizing bacteria (NOB) of the genus Nitrospina have exclusively been found in marine environments. In the brine–seawater interface layer of Atlantis II Deep (Red Sea), Nitrospina-like bacteria constitute up to one-third of the bacterial 16S ribosomal RNA (rRNA) gene sequences. This is much higher compared with that reported in other marine habitats (~10% of all bacteria), and was unexpected because no NOB culture has been observed to grow above 4.0% salinity, presumably due to the low net energy gained from their metabolism that is insufficient for both growth and osmoregulation. Using phylogenetics, single-cell genomics and metagenomic fragment recruitment approaches, we document here that these Nitrospina-like bacteria, designated as Candidatus Nitromaritima RS, are not only highly diverged from the type species Nitrospina gracilis (pairwise genome identity of 69%) but are also ubiquitous in the deeper, highly saline interface layers (up to 11.2% salinity) with temperatures of up to 52 °C. Comparative pan-genome analyses revealed that less than half of the predicted proteome of Ca. Nitromaritima RS is shared with N.
    [Show full text]
  • From Genotype to Phenotype: Inferring Relationships Between Microbial Traits and Genomic Components
    From genotype to phenotype: inferring relationships between microbial traits and genomic components Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Heinrich-Heine-Universit¨atD¨usseldorf vorgelegt von Aaron Weimann aus Oberhausen D¨usseldorf,29.08.16 aus dem Institut f¨urInformatik der Heinrich-Heine-Universit¨atD¨usseldorf Gedruckt mit der Genehmigung der Mathemathisch-Naturwissenschaftlichen Fakult¨atder Heinrich-Heine-Universit¨atD¨usseldorf Referent: Prof. Dr. Alice C. McHardy Koreferent: Prof. Dr. Martin J. Lercher Tag der m¨undlichen Pr¨ufung: 24.02.17 Selbststandigkeitserkl¨ arung¨ Hiermit erkl¨areich, dass ich die vorliegende Dissertation eigenst¨andigund ohne fremde Hilfe angefertig habe. Arbeiten Dritter wurden entsprechend zitiert. Diese Dissertation wurde bisher in dieser oder ¨ahnlicher Form noch bei keiner anderen Institution eingereicht. Ich habe bisher keine erfolglosen Promotionsversuche un- ternommen. D¨usseldorf,den . ... ... ... (Aaron Weimann) Statement of authorship I hereby certify that this dissertation is the result of my own work. No other person's work has been used without due acknowledgement. This dissertation has not been submitted in the same or similar form to other institutions. I have not previously failed a doctoral examination procedure. Summary Bacteria live in almost any imaginable environment, from the most extreme envi- ronments (e.g. in hydrothermal vents) to the bovine and human gastrointestinal tract. By adapting to such diverse environments, they have developed a large arsenal of enzymes involved in a wide variety of biochemical reactions. While some such enzymes support our digestion or can be used for the optimization of biotechnological processes, others may be harmful { e.g. mediating the roles of bacteria in human diseases.
    [Show full text]
  • Activity and Ecophysiology of Nitrite-Oxidizing Bacteria in Natural
    Activity and ecophysiology of nitrite-oxidizing bacteria in natural and engineered habitats Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften im Department Biologie der Universität Hamburg vorgelegt von Boris Nowka aus Bremen Hamburg 2014 Contents List of abbreviations 2 Chapter I Introduction 4 Chapter II Natural distribution of Nitrospira lineage I and II 16 and differentiation of two new isolates from activated sludge by morphological and physiological features Chapter III Comparative oxidation kinetics of nitrite-oxidizing 40 bacteria: nitrite availability as key factor for niche differentiation Chapter IV Summary 61 References 66 Appendix List of publications 81 Supplementary information 82 Acknowledgments 85 List of abbreviations °C degree Celsius % percentage µl microliter µm micrometer AOA ammonia-oxidizing archaea AOB ammonia-oxidizing bacteria BCA bicinchoninic acid BLAST Basic Local Alignment Search Tool bp base pairs CDS coding sequence cm centimeter DAPI 4',6-diamidino-2-phenylindole DGGE denaturing gradient gel electrophoresis DNA deoxyribonucleic acid DO dissolved oxygen EM electron microscopy EPS extracellular polymeric substances Fig. figure FISH fluorescence in situ hybridization fmol femtomole g gram h hour HPLC high-performance liquid chromatography l liter mM millimolar min minute nm nanometer NOB nitrite-oxidizing bacteria NXR nitrite oxidoreductase PCR polymerase chain reaction RAS recirculation aquaculture system 2 RFLP restriction fragment length polymorphism rpm revolutions per minute rRNA ribosomal ribonucleic acid s second SEM scanning electron microscope SMP soluble microbial products Tab. table TEM transmission electron microscope v volume WWTP wastewater treatment plant 3 Chapter I Introduction The nitrogen cycle The nitrogen cycle (Fig. 1.1) is a key process for life on earth. In the atmosphere and in natural waters nitrogen (N) exists mainly as dinitrogen gas (N2).
    [Show full text]
  • Phylogenomics and Signature Proteins for the Alpha Proteobacteria and Its Main Groups Radhey S Gupta* and Amy Mok
    BMC Microbiology BioMed Central Research article Open Access Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups Radhey S Gupta* and Amy Mok Address: Department of Biochemistry and Biomedical Science, McMaster University, Hamilton L8N3Z5, Canada Email: Radhey S Gupta* - [email protected]; Amy Mok - [email protected] * Corresponding author Published: 28 November 2007 Received: 20 July 2007 Accepted: 28 November 2007 BMC Microbiology 2007, 7:106 doi:10.1186/1471-2180-7-106 This article is available from: http://www.biomedcentral.com/1471-2180/7/106 © 2007 Gupta and Mok; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales), very few or no distinctive molecular or biochemical characteristics are known. Results: We have carried out comprehensive phylogenomic analyses by means of Blastp and PSI- Blast searches on the open reading frames in the genomes of several α-proteobacteria (viz. Bradyrhizobium japonicum, Brucella suis, Caulobacter crescentus, Gluconobacter oxydans, Mesorhizobium loti, Nitrobacter winogradskyi, Novosphingobium aromaticivorans, Rhodobacter sphaeroides 2.4.1, Silicibacter sp. TM1040, Rhodospirillum rubrum and Wolbachia (Drosophila) endosymbiont). These studies have identified several proteins that are distinctive characteristics of all α-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz.
    [Show full text]
  • Phylogenomics and Signature Proteins for the Alpha Proteobacteria and Its Main Groups Radhey S Gupta* and Amy Mok
    BMC Microbiology BioMed Central Research article Open Access Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups Radhey S Gupta* and Amy Mok Address: Department of Biochemistry and Biomedical Science, McMaster University, Hamilton L8N3Z5, Canada Email: Radhey S Gupta* - [email protected]; Amy Mok - [email protected] * Corresponding author Published: 28 November 2007 Received: 20 July 2007 Accepted: 28 November 2007 BMC Microbiology 2007, 7:106 doi:10.1186/1471-2180-7-106 This article is available from: http://www.biomedcentral.com/1471-2180/7/106 © 2007 Gupta and Mok; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales), very few or no distinctive molecular or biochemical characteristics are known. Results: We have carried out comprehensive phylogenomic analyses by means of Blastp and PSI- Blast searches on the open reading frames in the genomes of several α-proteobacteria (viz. Bradyrhizobium japonicum, Brucella suis, Caulobacter crescentus, Gluconobacter oxydans, Mesorhizobium loti, Nitrobacter winogradskyi, Novosphingobium aromaticivorans, Rhodobacter sphaeroides 2.4.1, Silicibacter sp. TM1040, Rhodospirillum rubrum and Wolbachia (Drosophila) endosymbiont). These studies have identified several proteins that are distinctive characteristics of all α-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz.
    [Show full text]
  • An Investigation of Carbon and Nitrogen Metabolism Through a Genomic Analysis of the Genus Nitrobacter
    AN ABSTRACT OF THE DISSERTATION OF Shawn R. Starkenburg for the degree of Doctor of Philosophy in Microbiology presented on December 18, 2007 Title: An Investigation of Carbon and Nitrogen Metabolism through a Genomic Analysis of the Genus Nitrobacter Abstract approved: ___________________________________________________________ Peter J. Bottomley The chemolithoautotrophic nitrite oxidizing bacteria (NOB) participate in the biogeochemical cycling of nitrogen by catalyzing and conserving energy from the - - oxidation of nitrite (NO2 ) to nitrate (NO3 ) via a nitrite oxidoreductase (NXR). The main objective of this work was to comparatively annotate and analyze the genome sequences of Nitrobacter winogradskyi NB255 and Nitrobacter hamburgensis X14 and use this information to extend our understanding of nitrogen and carbon metabolism in NOB. Through the analysis of the N. winogradskyi genome, genes encoding pathways for known modes of lithotrophic and heterotrophic growth were identified, including multiple enzymes involved in anapleurotic reactions centered on C2 to C4 metabolism. N. winogradskyi lacked genes encoding a complete glycolysis pathway and for the active transport of sugars. The N. hamburgensis genome harbored many genes not found in N. winogradskyi, including a complete glycolysis pathway, unique electron transport components, and putative pathways for the catabolism of aromatic, organic and one-carbon compounds. FAD-dependent oxidases were identified in the genome of N. hamburgensis which suggested that lactate could be metabolized, providing reductant and carbon to the cell. Indeed, D-lactate enhanced the growth rate and yield of - N. hamburgensis in the presence of NO2 and served as a sole energy and carbon source - in the absence of NO2 . Although lactate consumption occurred constitutively in lithoautotrophically grown cells, evidence was obtained for physiological adaptation to - lactate.
    [Show full text]
  • Characteristics of Newly Isolated Nitrifying Bacteria from Rhizoplane of Paddy Rice
    Vol. 16, No. 2, 101–108, 2001 Characteristics of Newly Isolated Nitrifying Bacteria from Rhizoplane of Paddy Rice HIROFUMI TOMIYAMA1, MIFUYU OHSHIMA1, SATOKO ISHII1, KAZUO SATOH1, REIJI TAKAHASHI1, KATSUNORI ISOBE1, HIDETOSHI IWANO1 and TATSUAKI TOKUYAMA1* 1 College of Bioresource Sciences, Nihon University, Kameino, Fujisawa, Kanagawa 252–8510, Japan (Received October 15, 2000—Accepted February 19, 2001) An ammonia-oxidizing bacterium, strain NRS527 and nitrite-oxidizing bacterium, strain NRB 5220 were new- ly isolated from rhizoplane of paddy rice. The cells of strain NRS527 are spiral (0.2–0.3 mm wide, with 3–6 turns), gram negative, obligately aerobic, and chemolithotrophic. Intracytoplasmic membranes, a characteristic of ammmonia-oxidizing bacteria are absent. The optimum concentration of ammonium sulfate (substrate) in the medium is 38 mM. The G+C content of the total DNA is 59.18 mol%. The similarity of 16S rRNA (%) to Nitrosospira briensis C-128 is 94.71. The supplemental effect of organic compounds could not be recognized. The cells of strain NRB5220 are rod shaped (0.5–0.8´1.0–2.0 mm), gram negative, and obligately aerobic. The G+C content is 60.37 mol%. The similarity of 16S rRNA (%) to Nitrobacter agilis ATCC14123 is 97.38. The optimum concentration of sodium nitrite (substrate) in the medium is 22 mM. Growth of strain NRB5220 is hastened when peptone and yeast extract are added to the medium as nutrients. Both strains were resistant to tetracycline at 33 mg/ml. The new nitrifying bacteria isolated from rhizoplane of paddy rice were identified as Nitrosospira sp. NRS527 and Nitrobacter sp.
    [Show full text]
  • Bacterial Genomes, a Tale of Gene Transfer, Recombination and Cladogenesis Florent Lassalle
    Bacterial genomes, a tale of gene transfer, recombination and cladogenesis Florent Lassalle To cite this version: Florent Lassalle. Bacterial genomes, a tale of gene transfer, recombination and cladogenesis. Pop- ulations and Evolution [q-bio.PE]. Université Claude Bernard - Lyon I, 2013. English. NNT : 2013LYO10234. tel-01214968 HAL Id: tel-01214968 https://tel.archives-ouvertes.fr/tel-01214968 Submitted on 13 Oct 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. No 234-2013 Année 2013 These` de l’universitede´ Lyon Présentée devant L’UNIVERSITÉ CLAUDE BERNARD LYON 1 pour l’obtention du Diplomeˆ de doctorat (arrêté du 7 août 2006) soutenue publiquement le 26 novembre 2013 par Florent Lassalle Les génomes bactériens, une histoire de transfert de gènes, de recombinaison et de cladogénèse. Directeurs de thèse : Xavier Nesme Vincent Daubin Jury : Céline Brochier-Armanet Examinateur Vincent Daubin Directeur de thèse Xavier Nesme Directeur de thèse Cécile Neuveglise´ Rapporteur Eduardo P. C. Rocha Examinateur J. Peter W. Young Rapporteur 2 UNIVERSITE CLAUDE BERNARD - LYON 1 Président de l’Université M. François-Noël GILLY Vice-président du Conseil d’Administration M. le Professeur Hamda BEN HADID Vice-président du Conseil des Etudes et de la Vie Univer- M.
    [Show full text]
  • Complete Genome Sequence of Nitrobacter Hamburgensis X14 and Comparative Genomic Analysis of Species Within the Genus Nitrobacterᰔ† Shawn R
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, May 2008, p. 2852–2863 Vol. 74, No. 9 0099-2240/08/$08.00ϩ0 doi:10.1128/AEM.02311-07 Copyright © 2008, American Society for Microbiology. All Rights Reserved. Complete Genome Sequence of Nitrobacter hamburgensis X14 and Comparative Genomic Analysis of Species within the Genus Nitrobacterᰔ† Shawn R. Starkenburg,1* Frank W. Larimer,2 Lisa Y. Stein,3 Martin G. Klotz,4,5 Patrick S. G. Chain,6,7,8 Luis A. Sayavedra-Soto,1 Amisha T. Poret-Peterson,4 Mira E. Gentry,4 Daniel J. Arp,1 Bess Ward,9 and Peter J. Bottomley1 Oregon State University, Corvallis, Oregon 973311; Oak Ridge National Laboratory, Oak Ridge, Tennessee 378312; University of California, Riverside, California 925213; Department of Biology4 and Department of Microbiology and Immunology,5 University of Louisville, Louisville, Kentucky 40292; Lawrence Livermore National Laboratory, Livermore, California 945506; Joint Genome Institute, Walnut Creek, California 945987; Michigan State University, East Lansing, Michigan 488248; and Princeton University, Princeton, New Jersey 085449 Received 12 October 2007/Accepted 15 February 2008 The alphaproteobacterium Nitrobacter hamburgensis X14 is a gram-negative facultative chemolithoautotroph that conserves energy from the oxidation of nitrite to nitrate. Sequencing and analysis of the Nitrobacter hamburgensis X14 genome revealed four replicons comprised of one chromosome (4.4 Mbp) and three plasmids (294, 188, and 121 kbp). Over 20% of the genome is composed of pseudogenes and paralogs. Whole-genome comparisons were conducted between N. hamburgensis and the finished and draft genome sequences of Nitrobacter winogradskyi and Nitrobacter sp. strain Nb-311A, respectively. Most of the plasmid-borne genes were unique to N.
    [Show full text]
  • Housekeeping Genes Essential for Pantothenate Biosynthesis Are
    Villaseñor et al. BMC Microbiology 2011, 11:66 http://www.biomedcentral.com/1471-2180/11/66 RESEARCHARTICLE Open Access Housekeeping genes essential for pantothenate biosynthesis are plasmid-encoded in Rhizobium etli and Rhizobium leguminosarum Tomás Villaseñor1, Susana Brom1, Araceli Dávalos1, Luis Lozano2, David Romero1 and Alejandro García-de los Santos1* Abstract Background: A traditional concept in bacterial genetics states that housekeeping genes, those involved in basic metabolic functions needed for maintenance of the cell, are encoded in the chromosome, whereas genes required for dealing with challenging environmental conditions are located in plasmids. Exceptions to this rule have emerged from genomic sequence data of bacteria with multipartite genomes. The genome sequence of R. etli CFN42 predicts the presence of panC and panB genes clustered together on the 642 kb plasmid p42f and a second copy of panB on plasmid p42e. They encode putative pantothenate biosynthesis enzymes (pantoate-b-alanine ligase and 3-methyl-2- oxobutanoate hydroxymethyltransferase, respectively). Due to their ubiquitous distribution and relevance in the central metabolism of the cell, these genes are considered part of the core genome; thus, their occurrence in a plasmid is noteworthy. In this study we investigate the contribution of these genes to pantothenate biosynthesis, examine whether their presence in plasmids is a prevalent characteristic of the Rhizobiales with multipartite genomes, and assess the possibility that the panCB genes may have reached plasmids by horizontal gene transfer. Results: Analysis of mutants confirmed that the panC and panB genes located on plasmid p42f are indispensable for the synthesis of pantothenate. A screening of the location of panCB genes among members of the Rhizobiales showed that only R.
    [Show full text]