Nitrogen Fixation in Pure Culture by Rhizobia Isolated from Stem Nodules
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Azorhizobium Doebereinerae Sp. Nov
ARTICLE IN PRESS Systematic and Applied Microbiology 29 (2006) 197–206 www.elsevier.de/syapm Azorhizobium doebereinerae sp. Nov. Microsymbiont of Sesbania virgata (Caz.) Pers.$ Fa´tima Maria de Souza Moreiraa,Ã, Leonardo Cruzb,Se´rgio Miana de Fariac, Terence Marshd, Esperanza Martı´nez-Romeroe,Fa´bio de Oliveira Pedrosab, Rosa Maria Pitardc, J. Peter W. Youngf aDepto. Cieˆncia do solo, Universidade Federal de Lavras, C.P. 3037 , 37 200–000, Lavras, MG, Brazil bUniversidade Federal do Parana´, C.P. 19046, 81513-990, PR, Brazil cEmbrapa Agrobiologia, antiga estrada Rio, Sa˜o Paulo km 47, 23 851-970, Serope´dica, RJ, Brazil dCenter for Microbial Ecology, Michigan State University, MI 48824, USA eCentro de Investigacio´n sobre Fijacio´n de Nitro´geno, Universidad Nacional Auto´noma de Mexico, Apdo Postal 565-A, Cuernavaca, Mor, Me´xico fDepartment of Biology, University of York, PO Box 373, York YO10 5YW, UK Received 18 August 2005 Abstract Thirty-four rhizobium strains were isolated from root nodules of the fast-growing woody native species Sesbania virgata in different regions of southeast Brazil (Minas Gerais and Rio de Janeiro States). These isolates had cultural characteristics on YMA quite similar to Azorhizobium caulinodans (alkalinization, scant extracellular polysaccharide production, fast or intermediate growth rate). They exhibited a high similarity of phenotypic and genotypic characteristics among themselves and to a lesser extent with A. caulinodans. DNA:DNA hybridization and 16SrRNA sequences support their inclusion in the genus Azorhizobium, but not in the species A. caulinodans. The name A. doebereinerae is proposed, with isolate UFLA1-100 ( ¼ BR5401, ¼ LMG9993 ¼ SEMIA 6401) as the type strain. -
Revised Taxonomy of the Family Rhizobiaceae, and Phylogeny of Mesorhizobia Nodulating Glycyrrhiza Spp
Division of Microbiology and Biotechnology Department of Food and Environmental Sciences University of Helsinki Finland Revised taxonomy of the family Rhizobiaceae, and phylogeny of mesorhizobia nodulating Glycyrrhiza spp. Seyed Abdollah Mousavi Academic Dissertation To be presented, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, for public examination in lecture hall 3, Viikki building B, Latokartanonkaari 7, on the 20th of May 2016, at 12 o’clock noon. Helsinki 2016 Supervisor: Professor Kristina Lindström Department of Environmental Sciences University of Helsinki, Finland Pre-examiners: Professor Jaakko Hyvönen Department of Biosciences University of Helsinki, Finland Associate Professor Chang Fu Tian State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University, China Opponent: Professor J. Peter W. Young Department of Biology University of York, England Cover photo by Kristina Lindström Dissertationes Schola Doctoralis Scientiae Circumiectalis, Alimentariae, Biologicae ISSN 2342-5423 (print) ISSN 2342-5431 (online) ISBN 978-951-51-2111-0 (paperback) ISBN 978-951-51-2112-7 (PDF) Electronic version available at http://ethesis.helsinki.fi/ Unigrafia Helsinki 2016 2 ABSTRACT Studies of the taxonomy of bacteria were initiated in the last quarter of the 19th century when bacteria were classified in six genera placed in four tribes based on their morphological appearance. Since then the taxonomy of bacteria has been revolutionized several times. At present, 30 phyla belong to the domain “Bacteria”, which includes over 9600 species. Unlike many eukaryotes, bacteria lack complex morphological characters and practically phylogenetically informative fossils. It is partly due to these reasons that bacterial taxonomy is complicated. -
1 Horizontal Gene Transfer of a Unique Nif Island Drives Convergent Evolution of Free-Living
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.03.429501; this version posted February 3, 2021. 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-ND 4.0 International license. 1 Horizontal gene transfer of a unique nif island drives convergent evolution of free-living 2 N2-fixing Bradyrhizobium 3 4 Jinjin Tao^, Sishuo Wang^, Tianhua Liao, Haiwei Luo* 5 6 Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of 7 Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 8 9 ^These authors contribute equally to this work. 10 11 *Corresponding author: 12 Haiwei Luo 13 School of Life Sciences, The Chinese University of Hong Kong 14 Shatin, Hong Kong SAR 15 Phone: (+852) 39436121 16 E-mail: [email protected] 17 18 Running Title: Free-living Bradyrhizobium evolution 19 Keywords: free-living Bradyrhizobium, nitrogen fixation, lifestyle, HGT 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.03.429501; this version posted February 3, 2021. 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-ND 4.0 International license. 20 Summary 21 The alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that 22 nodulate legumes, supported by the nif and nod gene clusters. -
Stem-Nodulating Nitrogen-Fixing Bacterium Isolated from Sesbania Rostrata
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1988, p. 89-98 Vol. 38, No. 1 0020-7713/88/010089-10$02 .OO/O Copyright 0 1988, International Union of Microbiological Societies Characterization of Azorhizobium caulinodans gen. nov. sp. nov., a Stem-Nodulating Nitrogen-Fixing Bacterium Isolated from Sesbania rostrata B. DREYFUS,1*2*J. L. GARCIA,3 AND M. GILLIS4 Laboratoire de Biologie des Sols, O.R.S.T.O.M.,B.P. 1386, Dakar, Senegal’; Laboratorium voor Genetica, Rijksuniversiteit, Ledeganckstraat 35, B-9000 Gent, Belgium2; Laboratoire de Microbiologie, O.R.S.T.O.M., Universite‘ de Provence, 13331 Marseille Cedex, France3; and Laboratorium voor Microbiologie en Microbiele Genetica, Ruksuniversiteit, B-9000 Gent, Belgium4 Twenty stem- and root-nodulating bacterial strains isolated from stem nodules of Sesbania rostrata were compared by numerical analysis of 221 phenotypic features with nine strains which effectively nodulate only the roots of this plant and with representative strains from the genera Rhizobium and Bradyrhizobium. Representative organisms from the different clusters were investigated further, together with possibly related organisms, by performing comparative gel electrophoresis of whole-cell proteins and by performing deoxyri- bonucleic acid (DNA)-DNA and DNA-ribosomal ribonucleic acid (rRNA) hybridizations. 3H-labeledrRNA was prepared from Sesbunia stem- and root-nodulating bacterial strain ORS 571T (T = type strain); [14C]rRNA from Bradyrhizobium japonicum NZP 5549T was also used. The following conclusions were drawn: (i) the Sesbania root-nodulating bacterial strains are genuine rhizobia; (ii) the Sesbania stem- and root-nodulating strains are quite different from Rhizobium and Bradyrhizobium, and thus they constitute a separate rRNA subbranch on the Rhodopseudomonas palusfris rRNA branch in rRNA superfamily IV; and (iii) the closest relative of these organisms is Xanthobacfer, but they are phenotypically and genotypically sufficiently different from the latter genus to deserve a separate generic rank. -
2010.-Hungria-MLI.Pdf
Mohammad Saghir Khan l Almas Zaidi Javed Musarrat Editors Microbes for Legume Improvement SpringerWienNewYork Editors Dr. Mohammad Saghir Khan Dr. Almas Zaidi Aligarh Muslim University Aligarh Muslim University Fac. Agricultural Sciences Fac. Agricultural Sciences Dept. Agricultural Microbiology Dept. Agricultural Microbiology 202002 Aligarh 202002 Aligarh India India [email protected] [email protected] Prof. Dr. Javed Musarrat Aligarh Muslim University Fac. Agricultural Sciences Dept. Agricultural Microbiology 202002 Aligarh India [email protected] This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically those of translation, reprinting, re-use of illustrations, broadcasting, reproduction by photocopying machines or similar means, and storage in data banks. Product Liability: The publisher can give no guarantee for all the information contained in this book. 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. # 2010 Springer-Verlag/Wien Printed in Germany SpringerWienNewYork is a part of Springer Science+Business Media springer.at Typesetting: SPI, Pondicherry, India Printed on acid-free and chlorine-free bleached paper SPIN: 12711161 With 23 (partly coloured) Figures Library of Congress Control Number: 2010931546 ISBN 978-3-211-99752-9 e-ISBN 978-3-211-99753-6 DOI 10.1007/978-3-211-99753-6 SpringerWienNewYork Preface The farmer folks around the world are facing acute problems in providing plants with required nutrients due to inadequate supply of raw materials, poor storage quality, indiscriminate uses and unaffordable hike in the costs of synthetic chemical fertilizers. -
Identification of Culturable Endophytes in 'Champaka' Pineapple Grown In
Vol. 8(26), pp. 3422-3430, 11 July, 2013 DOI: 10.5897/AJAR2012.2308 African Journal of Agricultural ISSN 1991-637X ©2013 Academic Journals Research http://www.academicjournals.org/AJAR Full Length Research Paper Identification of culturable endophytes in ‘Champaka’ pineapple grown in an organic system Olmar Baller Weber1*, Sandy Sampaio Videira2 and Jean Luiz Simões de Araújo2 1Embrapa Tropical Agroindustry, Dra. Sara Mesquita, 2270, Pici, 60511-110, Fortaleza, Ceará, Brazil. 2Embrapa Agrobiology, BR 465, km07, 23890-000, Seropédica, Rio de Janeiro, Brazil. Accepted 26 March, 2013 The objective of the study was to characterize culturable diazotrophic endophytic bacteria from ‘Champaka’ pineapple plants during the fruiting period in an organic system. Micropropagated plants were inoculated with the diazotrophic endophytic bacterium, strain AB 219a, during acclimatization phase. In the field, the plants were fertilized with different dosages and sources of organic compost. After 17 months of field cultivation, roots and stems were collected for the isolation of endophytes, DNA extraction, 16S rDNA amplification and molecular analysis. A total of nine bacterial groups were identified, and species Burkholderia silvatlantica, Azorhizobium caulinodans, Pantoea eucrina, Erwinia sp. and unculturable bacterium occurred in inoculated plants. In contrast, non-inoculated plants were associated endophytes related to Burkholderia cenocepacia, Azospirillum brasilense, Enterobacter oryzae, Erwinia sp. and Sphingobium yanoikuyae. Segments of 360 base pair from nifH gene were amplified from representative endophytes within identified species, except from the Pantoea eucrina strain AB 295. 16S rDNA phylogenetic analysis of endophytes isolated from inoculated plants revealed distinct families: Xanthobacteraceae, Burkholderiaceae and Enterobacteriaceae; and from non- inoculated plants, Rodospirillaceae and Sphingomonadaceae families were also identified. -
Enzyme Polymorphism of Azorhizobium Strains and Other Stem- and Root-Nodulating Bacteria Isolated from Sesbanìa Rostrata
O INSTITUTPASTEUR/ELSEVIER Res. Microbiol. Paris 1993 1993, 144, 55-67 kc,f Enzyme polymorphism of Azorhizobium strains and other stem- and root-nodulating bacteria isolated from Sesbanìa rostrata G. Rinaudo (l), M.P. Fernandez (2), A. Effosse (2), B. Picard (3) and R. Bardin (2) (I) Institut Français de Recherche Scientifique pour le Développement en Coopération (ORSTOM), (2) Unite‘ de Recherche Associée au Centre National de Recherche Scientifique 1450, (’I 2, Laboratoire d’Ecologie microbienne du Sol, université Claude-Bernard-Lyon I, 69622 Villeurbanne Cedex (France), and (3) Laboratoire de Microbiologie, Hôpital Beaujon, 92110 Clichy (France) SUMMARY Relationships between bacterial groups nodulating Sesbania rostrata were evaluat- ed through examination of electrophoretic polymorphism of esterases and metabolic en- zymes. The following conclusions were drawn: (i)the differentiation of two genomic species within Azorhizobium strains and a group of non-identified strains (probably ßhizo- bium) was strongly supported by enzyme electrophoresis ;(i¡) esterases were more elec- trophoretically polymorphic than metabolic enzymes, since 35 and 11 electrophoretic types, respectively, were detected within the 57 strains studied ; (iii)strains isolated from stem or root nodules were genetically very similar and could not be differentiated; (iv) six Azorhizobium strains isolated from plants growing in saline soils could not be grouped separately from the other strains, which might be attributed to the adaptation of azorhizobia to epiphytic conditions; and (VIa comparative study of esterase patterns of azorhizobia showed that strains isolated in the Philippines probably originated in north- ern Senegal, but did not reveal a clear separation between strains originating from north- ern and central Senegal. -
Characterization of the Endosymbiotic Forms of Sinorhizobium Sp. Strain
UNIVERSITÉ DE GENÈVE FACULTÉ DES SCIENCES Département de Botanique et Biologie Végétale Dr. Xavier Perret, MER ___________________________________________________________________ Characterization of the Endosymbiotic Forms of Sinorhizobium sp. Strain NGR234 THÈSE présentée à la Faculté des sciences de l’Université de Genève pour obtenir le grade de Docteur ès sciences, mention biologie par Nadia BAKKOU de Salé (Maroc) Thèse N° 4286 Genève Atelier d’impression ReproMail 2011 Remerciements Cette thèse a été réalisée au sein de l’Unité de Microbiologie dans le département de Botanique et Biologie végétale à l’université de Genève. Je tiens à remercier en premier lieu le Dr. Xavier Perret qui a dirigé cette thèse, pour sa disponibilité et pour sa confiance, qui m’ont permis de mener à bien ce projet. Je tiens également à remercier le Prof. Jurek Paszkowski, pour m’avoir permis de réaliser ma thèse dans ce département. Je remercie les membres du jury: le Dr. Cornelia Reimmann et le Prof. Hans-Martin Fischer, pour m’avoir fait l’honneur d’accepter de juger mon travail, pour leur remarques et conseils pertinents. Je tiens à associer à ces remerciements toutes les personnes qui ont participé à ce projet et sans qui ce travail n’aurait pas été possible. Je remercie donc le Dr. Michèle Crèvecœur, le Dr. Peter Mergaert et le Prof. Eva Kondorosi pour leur collaboration et leur aide scientifique et technique lors de la caractérisation morphologique et physiologique des bactéroides de Sinorhizobium sp. NGR234. Je remercie sincèrement Madame Yin Aung, le Dr. William Deakin et le Prof. Bill Broughton pour leur disponibilité, leurs conseils avisés et leur soutien tout au long de ce travail. -
Evolution of Methanotrophy in the Beijerinckiaceae&Mdash
The ISME Journal (2014) 8, 369–382 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis Ivica Tamas1, Angela V Smirnova1, Zhiguo He1,2 and Peter F Dunfield1 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada and 2Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. -
Experimental Evolution of Legume Symbionts: What Have We Learnt? Ginaini Grazielli Doin De Moura, Philippe Remigi, Catherine Masson-Boivin, Delphine Capela
Experimental Evolution of Legume Symbionts: What Have We Learnt? Ginaini Grazielli Doin de Moura, Philippe Remigi, Catherine Masson-Boivin, Delphine Capela To cite this version: Ginaini Grazielli Doin de Moura, Philippe Remigi, Catherine Masson-Boivin, Delphine Capela. Ex- perimental Evolution of Legume Symbionts: What Have We Learnt?. Genes, MDPI, 2020, 11 (3), pp.339. 10.3390/genes11030339. hal-02566829 HAL Id: hal-02566829 https://hal.archives-ouvertes.fr/hal-02566829 Submitted on 7 May 2020 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. Distributed under a Creative Commons Attribution| 4.0 International License G C A T T A C G G C A T genes Review Experimental Evolution of Legume Symbionts: What Have We Learnt? Ginaini Grazielli Doin de Moura, Philippe Remigi, Catherine Masson-Boivin and Delphine Capela * LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31320, France; [email protected] (G.G.D.d.M.); [email protected] (P.R.); [email protected] (C.M.-B.) * Correspondence: [email protected]; Tel.: +33-561-285-454 Received: 3 March 2020; Accepted: 20 March 2020; Published: 23 March 2020 Abstract: Rhizobia, the nitrogen-fixing symbionts of legumes, are polyphyletic bacteria distributed in many alpha- and beta-proteobacterial genera. -
Plant Nodulation Inducers Enhance Horizontal Gene Transfer of Azorhizobium Caulinodans Symbiosis Island
Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island Jun Linga,1, Hui Wanga,1, Ping Wua, Tao Lia, Yu Tanga, Nawar Naseerb, Huiming Zhenga, Catherine Masson-Boivinc, Zengtao Zhonga,c,2, and Jun Zhua,b,2 aDepartment of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; bDepartment of Microbiology, University of Pennsylvania, Philadelphia, PA 19104; and cInstitut National de la Recherche Agronomique, UMR 441, Laboratoire des Interactions Plantes-Microorganismes, Castanet-Tolosan 31326, France Edited by Bonnie L. Bassler, Princeton University and Howard Hughes Medical Institute, Princeton, NJ, and approved October 19, 2016 (received for review September 9, 2016) Horizontal gene transfer (HGT) of genomic islands is a driving force of program leading to nodule organogenesis (7). Nod factors are bacterial evolution. Many pathogens and symbionts use this mech- lipochito-oligosaccharides of diverse structures and the major anism to spread mobile genetic elements that carry genes important determinants of host specificity. Rhizobia have evolved via hor- for interaction with their eukaryotic hosts. However, the role of the izontal transfer of essential nodulation and nitrogen fixation host in this process remains unclear. Here, we show that plant genes that are carried by either large plasmids or genomic is- compounds inducing the nodulation process in the rhizobium-legume lands. Exchange of symbiotic material between rhizobial species mutualistic symbiosis also enhance the transfer of symbiosis islands. and genera has been frequent during evolution (8). The symbiosis We demonstrate that the symbiosis island of the Sesbania rostrata islands of the Mesorhizobium, Azorhizobium,andBradyhizobium symbiont, Azorhizobium caulinodans, is an 87.6-kb integrative and species are mainly located on the chromosome (9–11). -
Starkeya Novella Type Strain (ATCC 8093T) Ulrike Kappler1, Karen Davenport2, Scott Beatson1, Susan Lucas3, Alla Lapidus3, Alex Copeland3, Kerrie W
Standards in Genomic Sciences (2012) 7:44-58 DOI:10.4056/sigs.3006378 Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093T) Ulrike Kappler1, Karen Davenport2, Scott Beatson1, Susan Lucas3, Alla Lapidus3, Alex Copeland3, Kerrie W. Berry3, Tijana Glavina Del Rio3, Nancy Hammon3, Eileen Dalin3, Hope Tice3, Sam Pitluck3, Paul Richardson3, David Bruce2,3, Lynne A. Goodwin2,3, Cliff Han2,3, Roxanne Tapia2,3, John C. Detter2,3, Yun-juan Chang3,4, Cynthia D. Jeffries3,4, Miriam Land3,4, Loren Hauser3,4, Nikos C. Kyrpides3, Markus Göker5, Natalia Ivanova3, Hans-Peter Klenk5, and Tanja Woyke3 1 The University of Queensland, Brisbane, Australia 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 DOE Joint Genome Institute, Walnut Creek, California, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany *Corresponding author(s): Hans-Peter Klenk ([email protected]) and Ulrike Kappler ([email protected]) Keywords: strictly aerobic, facultatively chemoautotrophic, methylotrophic and heterotrophic, Gram-negative, rod-shaped, non-motile, soil bacterium, Xanthobacteraceae, CSP 2008 Starkeya novella (Starkey 1934) Kelly et al. 2000 is a member of the family Xanthobacteraceae in the order ‘Rhizobiales’, which is thus far poorly characterized at the genome level. Cultures from this spe- cies are most interesting due to their facultatively chemolithoautotrophic lifestyle, which allows them to both consume carbon dioxide and to produce it. This feature makes S. novella an interesting model or- ganism for studying the genomic basis of regulatory networks required for the switch between con- sumption and production of carbon dioxide, a key component of the global carbon cycle.