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UNIVERSIDAD POLITÉCNICA DE CARTAGENA ESCUELA TÉCNICA SUPERIOR DE INGENIERÍA AGRONÓMICA DEPARTAMENTO DE PRODUCCIÓN VEGETAL INGENIERO AGRÓNOMO PROYECTO FIN DE CARRERA: “AISLAMIENTO E IDENTIFICACIÓN DE LOS RIZOBIOS ASOCIADOS A LOS NÓDULOS DE ASTRAGALUS NITIDIFLORUS”. Realizado por: Noelia Real Giménez Dirigido por: María José Vicente Colomer Francisco José Segura Carreras Cartagena, Julio de 2014. ÍNDICE GENERAL 1. Introducción…………………………………………………….…………………………………………………1 1.1. Astragalus nitidiflorus………………………………..…………………………………………………2 1.1.1. Encuadre taxonómico……………………………….…..………………………………………………2 1.1.2. El origen de Astragalus nitidiflorus………………………………………………………………..4 1.1.3. Descripción de la especie………..…………………………………………………………………….5 1.1.4. Biología…………………………………………………………………………………………………………7 1.1.4.1. Ciclo vegetativo………………….……………………………………………………………………7 1.1.4.2. Fenología de la floración……………………………………………………………………….9 1.1.4.3. Sistema de reproducción……………………………………………………………………….10 1.1.4.4. Dispersión de los frutos…………………………………….…………………………………..11 1.1.4.5. Nodulación con Rhizobium…………………………………………………………………….12 1.1.4.6. Diversidad genética……………………………………………………………………………....13 1.1.5. Ecología………………………………………………………………………………………………..…….14 1.1.6. Corología y tamaño poblacional……………………………………………………..…………..15 1.1.7. Protección…………………………………………………………………………………………………..18 1.1.8. Amenazas……………………………………………………………………………………………………19 1.1.8.1. Factores bióticos…………………………………………………………………………………..19 1.1.8.2. Factores abióticos………………………………………………………………………………….20 1.1.8.3. Factores antrópicos………………..…………………………………………………………….21 -
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. -
Genomic Encyclopedia of Sugar Utilization Pathways in The
Rodionov et al. BMC Genomics 2010, 11:494 http://www.biomedcentral.com/1471-2164/11/494 RESEARCH ARTICLE Open Access Genomic encyclopedia of sugar utilization pathways in the Shewanella genus Dmitry A Rodionov1,2, Chen Yang1,3, Xiaoqing Li1, Irina A Rodionova1, Yanbing Wang4, Anna Y Obraztsova4,7, Olga P Zagnitko5, Ross Overbeek5, Margaret F Romine6, Samantha Reed6, James K Fredrickson6, Kenneth H Nealson4,7, Andrei L Osterman1,5* Abstract Background: Carbohydrates are a primary source of carbon and energy for many bacteria. Accurate projection of known carbohydrate catabolic pathways across diverse bacteria with complete genomes constitutes a substantial challenge due to frequent variations in components of these pathways. To address a practically and fundamentally important challenge of reconstruction of carbohydrate utilization machinery in any microorganism directly from its genomic sequence, we combined a subsystems-based comparative genomic approach with experimental validation of selected bioinformatic predictions by a combination of biochemical, genetic and physiological experiments. Results: We applied this integrated approach to systematically map carbohydrate utilization pathways in 19 genomes from the Shewanella genus. The obtained genomic encyclopedia of sugar utilization includes ~170 protein families (mostly metabolic enzymes, transporters and transcriptional regulators) spanning 17 distinct pathways with a mosaic distribution across Shewanella species providing insights into their ecophysiology and adaptive evolution. Phenotypic -
Metagenomes of Native and Electrode-Enriched Microbial Communities from the Soudan Iron Mine Jonathan P
Metagenomes of native and electrode-enriched microbial communities from the Soudan Iron Mine Jonathan P. Badalamenti and Daniel R. Bond Department of Microbiology and BioTechnology Institute, University of Minnesota - Twin Cities, Saint Paul, Minnesota, USA Twitter: @JonBadalamenti @wanderingbond Summary Approach - compare metagenomes from native and electrode-enriched deep subsurface microbial communities 30 Despite apparent carbon limitation, anoxic deep subsurface brines at the Soudan ) enriched 2 Underground Iron Mine harbor active microbial communities . To characterize these 20 A/cm µ assemblages, we performed shotgun metagenomics of native and enriched samples. enrich ( harvest cells collect inoculate +0.24 V extract 10 Follwing enrichment on poised electrodes and long read sequencing, we recovered Soudan brine electrode 20° C from DNA biodreactors current electrodes from the metagenome the closed, circular genome of a novel Desulfuromonas sp. 0 0 10 20 30 40 filtrate PacBio RS II Illumina HiSeq with remarkable genomic features that were not fully resolved by short read assem- extract time (d) long reads short reads TFF DNA unenriched bly alone. This organism was essentially absent in unenriched Soudan communities, 0.1 µm retentate assembled metagenomes reconstruct long read return de novo complete genome(s) assembly indicating that electrodes are highly selective for putative metal reducers. Native HGAP assembly community metagenomes suggest that carbon cycling is driven by methyl-C me- IDBA_UD 1 hybrid tabolism, in particular methylotrophic methanogenesis. Our results highlight the 3 µm prefilter assembly N4 binning promising potential for long reads in metagenomic surveys of low-diversity environ- borehole N4 binning read trimming and filtering brine de novo ments. -
Electron Transfer Through the Outer Membrane of Geobacter Sulfurreducens a DISSERTATION SUBMITTED to the FACULTY of the UNIVE
Electron transfer through the outer membrane of Geobacter sulfurreducens A DISSERTATION SUBMITTED TO THE FACULTY OF THE UNIVERSITY OF MINNESOTA BY Fernanda Jiménez Otero IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR IN PHILOSOPHY Dr. Daniel R. Bond May, 2018 Fernanda Jiménez Otero, 2018, © Acknowledgements This dissertation and the degree I have gained with it, would not have been possible without the help and support from an invaluable group of people. The training I received from Chi Ho Chan and Caleb Levar continues to be essential in the way I approach scientific endeavors. The quality of genetic studies and rigor in microbiology techniques they taught me is a standard I hope to meet throughout my career. Daniel Bond has been much more than I ever expected from an advisor. I have not only gained scientific knowledge from him, but I will take with me the example of what a great mentor represents. His enthusiasm for science is only rivaled by his commitment to past and present members of his laboratory. I am extremely honored to be able to count myself in that group, and I will do my best to represent him proudly in future endeavors. Throughout these five years, Jeff Gralnick has given me numerous opportunities to explore all aspects of a scientific career. Not only is Chapter 2 a result of his vision, but I feel less intimidated by a career in science as a result of his mentoring and support. The faculty members in my committee- Carrie Wilmot, Brandy Toner, and Larry Wackett, have made sure I am well prepared for i every step through graduate school. -
Identification of Small Non-Coding Rnas from Rhizobium Etli By
Rajendran et al. ExRNA (2020) 2:14 https://doi.org/10.1186/s41544-020-00054-1 ExRNA RESEARCH Open Access Identification of small non-coding RNAs from Rhizobium etli by integrated genome- wide and transcriptome-based methods Kasthuri Rajendran1, Vikram Kumar2, Ilamathi Raja1, Manoharan Kumariah1 and Jebasingh Tennyson2* Abstract Background: Small non-coding RNAs (sRNAs) are regulatory molecules, present in all forms of life, known to regulate various biological processes in response to the different environmental signals. In recent years, deep sequencing and various other computational prediction methods have been employed to identify and analyze sRNAs. Results: In the present study, we have applied an improved sRNA scanner method to predict sRNAs from the genome of Rhizobium etli, based on PWM matrix of conditional sigma factor 32. sRNAs predicted from the genome are integrated with the available stress specific transcriptome data to predict putative conditional specific sRNAs. A total of 271 sRNAs from the genome and 173 sRNAs from the transcriptome are computationally predicted. Of these, 25 sRNAs are found in both genome and transcriptome data. Putative targets for these sRNAs are predicted using TargetRNA2 and these targets are involved in a wide array of cellular functions such as cell division, transport and metabolism of amino acids, carbohydrates, energy production and conversion, translation, cell wall/membrane biogenesis, post- translation modification, protein turnover and chaperones. Predicted targets are functionally classified based on COG analysis and GO annotations. Conclusion: sRNAs predicted from the genome, using PWM matrices for conditional sigma factor 32 could be a better method to identify the conditional specific sRNAs which expand the list of putative sRNAs from the intergenic regions (IgRs) of R. -
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. -
Influence of Rhizobia Inoculation on Biomass Gain and Tissue Nitrogen Content of Leucaena Leucocephala Seedlings Under Drought
Forests 2015, 6, 3686-3703; doi:10.3390/f6103686 OPEN ACCESS forests ISSN 1999-4907 www.mdpi.com/journal/forests Article Influence of Rhizobia Inoculation on Biomass Gain and Tissue Nitrogen Content of Leucaena leucocephala Seedlings under Drought Gabriela Pereyra 1,*, Henrik Hartmann 1, Beate Michalzik 2, Waldemar Ziegler 1 and Susan Trumbore 1 1 Max Planck Institute for Biogeochemistry, Hans-Knöll-str. 10, 07745 Jena, Germany; E-Mails: [email protected] (H.H.); [email protected] (W.Z.); [email protected] (S.T.) 2 Institute of Geography, Faculty of Chemical and Earth Sciences, Friedrich-Schiller-Universität Jena, Löbdergraben 32, 07743 Jena, Germany; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +49-3641-576176. Academic Editors: Reynaldo Campos Santana and Eric J. Jokela Received: 25 June 2015 / Accepted: 10 October 2015 / Published: 15 October 2015 Abstract: Anticipated increases in the frequency of heat waves and drought spells may have negative effects on the ability of leguminous trees to fix nitrogen (N). In seedlings of Leucaena leucocephala inoculated with Mesorhizobium loti or Rhizobium tropici, we investigated how the developmental stage and a short drought influenced overall biomass and the accumulation of carbon and N in plant tissues. In early developmental stages, the number of nodules and nodule biomass were correlated with total plant biomass and δ15N, and nodules and roots contributed 33%–35% of the seedling total N. Seedlings associated with R. tropici fixed more N and exhibited higher overall biomass compared with M. -
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. -
Caractérisation De L'influence De Facteurs Environnementaux Sur L'écologie Microbienne Du Jambon Cuit Tranché
Caractérisation de l’influence de facteurs environnementaux sur l’écologie microbienne du jambon cuit tranché. Marine Zagdoun To cite this version: Marine Zagdoun. Caractérisation de l’influence de facteurs environnementaux sur l’écologie microbi- enne du jambon cuit tranché.. Biologie moléculaire. Université Paris-Saclay, 2020. Français. NNT : 2020UPASA003. tel-03270836 HAL Id: tel-03270836 https://pastel.archives-ouvertes.fr/tel-03270836 Submitted on 25 Jun 2021 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. Caractérisation de l’influence de facteurs environnementaux sur l’écologie microbienne du jambon cuit tranché Thèse de doctorat de l’Université Paris-Saclay École doctorale n°581, Agriculture Alimentation Biologie Environnement Santé (ABIES) Spécialité de doctorat : Biologie moléculaire et cellulaire Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France AgroParisTech Thèse présentée et soutenue à Jouy-en-Josas, le 27 février 2020, par Marine ZAGDOUN Composition du Jury Henry-Eric SPINNLER Président -
(Pelobacter) and Methanococcoides Are Responsible for Choline-Dependent Methanogenesis in a Coastal Saltmarsh Sediment
The ISME Journal https://doi.org/10.1038/s41396-018-0269-8 ARTICLE Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment 1 1 1 2 3 1 Eleanor Jameson ● Jason Stephenson ● Helen Jones ● Andrew Millard ● Anne-Kristin Kaster ● Kevin J. Purdy ● 4 5 1 Ruth Airs ● J. Colin Murrell ● Yin Chen Received: 22 January 2018 / Revised: 11 June 2018 / Accepted: 26 July 2018 © The Author(s) 2018. This article is published with open access Abstract Coastal saltmarsh sediments represent an important source of natural methane emissions, much of which originates from quaternary and methylated amines, such as choline and trimethylamine. In this study, we combine DNA stable isotope 13 probing with high throughput sequencing of 16S rRNA genes and C2-choline enriched metagenomes, followed by metagenome data assembly, to identify the key microbes responsible for methanogenesis from choline. Microcosm 13 incubation with C2-choline leads to the formation of trimethylamine and subsequent methane production, suggesting that 1234567890();,: 1234567890();,: choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate. Amplicon sequencing analysis identifies Deltaproteobacteria of the genera Pelobacter as the major choline utilizers. Methanogenic Archaea of the genera Methanococcoides become enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of metagenomic DNA results in the identification of bins classified as Pelobacter and Methanococcoides. Analyses of these bins reveal that Pelobacter have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway. -
Analysis of Rhizobial Strains Nodulating Phaseolus Vulgaris From
Systematic and Applied Microbiology 37 (2014) 149–156 Contents lists available at ScienceDirect Systematic and Applied Microbiology j ournal homepage: www.elsevier.de/syapm Analysis of rhizobial strains nodulating Phaseolus vulgaris from Hispaniola Island, a geographic bridge between Meso and South America and the first historical link with Europe a b,c d César-Antonio Díaz-Alcántara , Martha-Helena Ramírez-Bahena , Daniel Mulas , e b b,c e,∗ Paula García-Fraile , Alicia Gómez-Moriano , Alvaro Peix , Encarna Velázquez , d Fernando González-Andrés a Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo, Dominican Republic b Instituto de Recursos Naturales y Agrobiología, IRNASA (CSIC), Salamanca, Spain c Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA (CSIC), Spain d Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de León, Spain e Departamento de Microbiología y Genética, Universidad de Salamanca, Spain a r t i c l e i n f o a b s t r a c t Article history: Hispaniola Island was the first stopover in the travels of Columbus between America and Spain, and Received 13 July 2013 played a crucial role in the exchange of Phaseolus vulgaris seeds and their endosymbionts. The analysis of Received in revised form recA and atpD genes from strains nodulating this legume in coastal and inner regions of Hispaniola Island 15 September 2013 showed that they were almost identical to those of the American strains CIAT 652, Ch24-10 and CNPAF512, Accepted 18 September 2013 which were initially named as Rhizobium etli and have been recently reclassified into Rhizobium phaseoli after the analysis of their genomes.