Molecular Identification of Azospirillum Spp
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Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
Chapter 1-General Introduction
Tuscia University Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE) XXVI Cycle of Doctorate in Plant Protection In collaboration with INRA Institute of Avignon, France, Department of Plant Pathology Thesis: Importance of environmental habitats as a reservoir of phytopathogenic bacteria and their role in the evolution of pathogenicity traits AGR/12 By: Dott. Claudia Bartoli Coordinator and Supervisor: Assistant supervisor Prof. Leonardo Varvaro Dott. Cindy E. Morris Signature Signature Dott. Giorgio M. Balestra Signature Defended on: Monday 30 June 2014 Thesis Committee Prof. Laura Mugnai Dr. Elena Di Mattia Prof. Kubilay Kurtulus Bastas Referee Prof. Matthieu Arlat Prof. Gonçalo Almeida Importance of environmental habitats as a reservoir of phytopathogenic bacteria and their role in the evolution of pathogenicity traits Claudia Bartoli Thesis Submitted in partial fulfilment of requirements for the degree of Doctor of Philosophy in Plant Protection at Tuscia University by the authority of the Rector Magnificus Prof. Alessandro Ruggieri In the presence of the Thesis committed appointed by the Doctorate Board To be defended in public On Monday 30 June 2014 Ai miei ragazzacci Himal and Jay Ram Fidelity is the faithful driver Microbes depend on good housekeeping They thrive, survive and flourish Yet new forms appear Confounding the scientist Woe to the status quo . David Sands Contents Chapter 1- General Introduction...................................................................................1 Chapter 2 - Methyl-directed mismatch repair: a mechanism underlying emergence of pathogenic bacteria...................................................................................7 Chapter 3 - A user’s guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex.........................25 Chapter 4 - The Pseudomonas viridiflava phylogroups in the P. -
Characterization of Chemosensing in the Alphaproteobacterium <I> Azospirillum Brasilense </I>
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 8-2012 Characterization of Chemosensing in the Alphaproteobacterium Azospirillum brasilense Matthew Hamilton Russell University of Tennessee - Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Organismal Biological Physiology Commons Recommended Citation Russell, Matthew Hamilton, "Characterization of Chemosensing in the Alphaproteobacterium Azospirillum brasilense . " PhD diss., University of Tennessee, 2012. https://trace.tennessee.edu/utk_graddiss/1469 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Matthew Hamilton Russell entitled "Characterization of Chemosensing in the Alphaproteobacterium Azospirillum brasilense ." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Biochemistry and Cellular and Molecular Biology. Gladys M. Alexandre, Major Professor We have read this dissertation and recommend its acceptance: Dan Roberts, Andreas Nebenfuehr, Erik Zinser Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Characterization of the chemosensory abilities of the alphaproteobacterium Azospirillum brasilense A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Matthew Hamilton Russell August 2012 ii Copyright © 2012 by Matthew Russell All rights reserved. -
Complete Genome Sequence of the Nitrogen-Fixing Bacterium Azospirillum Humicireducens Type Strain Sgz-5T
Yu et al. Standards in Genomic Sciences (2018) 13:28 https://doi.org/10.1186/s40793-018-0322-2 SHORT GENOME REPORT Open Access Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5T Zhen Yu1, Guiqin Yang1, Xiaoming Liu1, Yueqiang Wang1, Li Zhuang2* and Shungui Zhou3 Abstract The Azospirillum humicireducens strain SgZ-5T, belonging to the Order Rhodospirillales and the Family Rhodospirillaceae, was isolated from a microbial fuel cell inoculated with paddy soil. A previous work has shown that strain SgZ-5T was able to fix atmospheric nitrogen involved in plant growth promotion. Here we present the complete genome of A. humicireducens SgZ-5T, which consists of a circular chromosome and six plasmids with the total genome size of 6,834,379 bp and the average GC content of 67.55%. Genome annotations predicted 5969 protein coding and 85 RNA genes including 14 rRNA and 67 tRNA genes. By genomic analysis, we identified a complete set of genes that is potentially involved in nitrogen fixation and its regulation. This genome also harbors numerous genes that are likely responsible for phytohormones production. We anticipate that the A. humicireducens SgZ-5T genome will contribute insights into plant growth promoting properties of Azospirillum strains. Keywords: Azospirillum humicireducens, Complete genome, Nitrogen fixation, PGPP Introduction report [11], the nitrogen-fixing capability of strain Bacteria that live in the plant rhizosphere and possess a SgZ-5T was confirmed by acetylene-reduction assay and large array of potential mechanisms to enhance plant identification of a nifH gene. Furthermore, this strain growth are considered as PGPR [1–3]. -
Azospirillum Canadense Sp. Nov., a Nitrogen-Fixing Bacterium Isolated
International Journal of Systematic and Evolutionary Microbiology (2007), 57, 620–624 DOI 10.1099/ijs.0.64804-0 Azospirillum canadense sp. nov., a nitrogen-fixing bacterium isolated from corn rhizosphere Samina Mehnaz, Brian Weselowski and George Lazarovits Correspondence Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, George Lazarovits 1391 Sandford Street, London, Ontario N5V4T3, Canada [email protected] A free-living diazotrophic strain, DS2T, was isolated from corn rhizosphere. Polyphasic taxonomy was performed including morphological characterization, Biolog analysis, and 16S rRNA, cpn60 and nifH gene sequence analyses. 16S rRNA gene sequence analysis indicated that strain DS2T was closely related to the genus Azospirillum (96 % similarity). Chemotaxonomic characteristics (DNA G+C content 67.9 mol%; Q-10 quinone system; major fatty acid 18 : 1v7c) were also similar to those of the genus Azospirillum. In all the analyses, including phenotypic characterization using Biolog analysis and comparison of cellular fatty acids, this isolate was found to be different from the closely related species Azospirillum lipoferum, Azospirillum oryzae and Azospirillum brasilense. On the basis of these results, a novel species is proposed for this nitrogen-fixing strain. The name Azospirillum canadense sp. nov. is suggested with the type strain DS2T (=NCCB 100108T=LMG 23617T). The genus Azospirillum was first described by Tarrand et al. for 48–72 h. The bacterium formed wet, white colonies (1978) with two species, Azospirillum lipoferum and which later turned light-pink. Cell morphology was observed Azospirillum brasilense. At present the genus comprises using a scanning electron microscope. Cells of the bacterium nine species, including, in addition to A. -
The Rhizobiome of Vachellia (Acacia) Woodlands Surrounding Witwatersrand Gold and Uranium Mine Tailings
The rhizobiome of Vachellia (Acacia) woodlands surrounding Witwatersrand gold and uranium mine tailings Michelle Toni Buck A Thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfillment for the degree of Doctor of Philosophy Declaration I, Michelle Toni Buck (Person number: 322062), am a student registered for the degree of Doctor of Philosophy (PhD) in the academic year 2018. I hereby declare the following: I am aware that plagiarism (the use of someone else‟s work without their permission and/or without acknowledging the original source) is wrong. I confirm that the work submitted for assessment for the above degree is my own unaided work except where I have explicitly indicated otherwise and acknowledged. In this context, I understand that the use of editing services is considered airded work and must be declared. I have not submitted this work before for any other degree or examination at this or any other University. The informationing used in the Thesis HAS NOT been obtained by me while employed by, or working under the aegis of, any person or organization other than the University. I have followed the required conventions in referencing the thoughts and ideas of others. I understand that the University of the Witwatersrand may take disciplinary action against me if there is a belief that this is not my own unaided work or that I have failed to acknowledge the source of the ideas or words in my writing Signature: Date: 8th August 2018 i Abstract Phytoremediation of mine tailings and surrounding areas provide the most cost-effective means of alleviating their pollutant effects. -
Impact of Plant Genotype and Nitrogen Level on Rice Growth Response to Inoculation with Azospirillum Sp
Soil Science and Plant Nutrition (2010) 56, 636–644 doi: 10.1111/j.1747-0765.2010.00499.x ORIGINAL ARTICLE⁄SHORT PAPER Impact of plant genotype and nitrogen level on rice growth response to inoculation with Azospirillum sp. strain B510 under paddy field conditions Kazuhiro SASAKI1,SeishiIKEDA1,2,ShimaEDA1, Hisayuki MITSUI1, Eiko HANZAWA1, Chiharu KISARA1,YuriKAZAMA1,AtsuhikoKUSHIDA2, Takuro SHINANO3,KiwamuMINAMISAWA1 and Tadashi SATO1 1Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan, 2Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Hokkaido 082-0081 and 3National Agricultural Research Center for Hokkaido Region, Hokkaido 062-8555, Japan Abstract Twenty rice cultivars, including three genetically-distinct groups (japonica, indica-1,andindica-2), were evaluated for their response to inoculation with Azospirillum sp.strainB510inpaddyfieldswithstandard nitrogen (SN) and low nitrogen (LN) fertilization. In the SN field, the tiller numbers in most indica-2 cultivars, 37 days after transplanting (DAT), were significantly increased by the B510 inoculation, whereas those in 4 japonica cultivars were significantly decreased. A similar growth response was observed in the LN field, although the impacts of theB510inoculationweremorevariedthanintheSNfield.At58DAT,thetiller numbers in most cultivars were lower or unaffected by the B510 inoculation under both SN and LN condi- tions, except that the tiller number of the Nipponbare cultivar, which is classified as japonica, was signifi- cantly higher in the LN field only. These results suggest that the effects of inoculation with Azospirillum sp. strain B510 on the growth of rice plants, especially on tiller numbers at the early growth stage, vary depend- ing on the rice genotype, as well as nitrogen level. -
Microbial Degradation of Organic Micropollutants in Hyporheic Zone Sediments
Microbial degradation of organic micropollutants in hyporheic zone sediments Dissertation To obtain the Academic Degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth by Cyrus Rutere Bayreuth, May 2020 This doctoral thesis was prepared at the Department of Ecological Microbiology – University of Bayreuth and AG Horn – Institute of Microbiology, Leibniz University Hannover, from August 2015 until April 2020, and was supervised by Prof. Dr. Marcus. A. Horn. This is a full reprint of the dissertation submitted to obtain the academic degree of Doctor of Natural Sciences (Dr. rer. nat.) and approved by the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth. Date of submission: 11. May 2020 Date of defense: 23. July 2020 Acting dean: Prof. Dr. Matthias Breuning Doctoral committee: Prof. Dr. Marcus. A. Horn (reviewer) Prof. Harold L. Drake, PhD (reviewer) Prof. Dr. Gerhard Rambold (chairman) Prof. Dr. Stefan Peiffer In the battle between the stream and the rock, the stream always wins, not through strength but by perseverance. Harriett Jackson Brown Jr. CONTENTS CONTENTS CONTENTS ............................................................................................................................ i FIGURES.............................................................................................................................. vi TABLES .............................................................................................................................. -
Procesos Microbianos
1 Lillian Frioni (*) PROCESOS MICROBIANOS EDITORIAL DE LA FUNDACION UNIVERSIDAD NACIONAL DE RIO CUARTO ARGENTINA 1999 Esta Editorial es miembro de la Red de Editoriales Universitarias Nacionales General Paz 1141 - Telefax (058) 4642727 (5800) Río Cuarto Armado e Impresión: Departamento de Imprenta y Publicaciones U.N.R.C. 1999 ISBN: 950-665-109-4 ISBN: 950-665-110 (Obra completa) Queda hecho el depósito que marca la ley 11.723 Impreso en Argentina - Printed in Argentina Queda prohibida la reproducción total o parcial del texto de la presente obra en cualquiera de sus formas, electrónica o mecánica, sin el consentimiento previo y escrito del autor y del Editor. 2 (*) Lillian Frioni es Profesora Titular de Microbiología en la Facultad de Agronomía (Universidad de la República del Uruguay). Trabajó por más de 10 años en la Facultad de Agronomía y Veterinaria de la Universidad Nacional de Río Cuarto y en la de Rosario, Santa Fe. Colaboró también con la Facultad de Ciencias Agronómicas de la Universidad Nacional de Córdoba, en la Argentina. Realizó estudios en la Universidad de la República de Uruguay, en la Universidad de Orsay (París), en el Centro de Pedología Biológica de Nancy (Francia), en el Instituto Pasteur de París y en el Laboratorio de Sistemas Simbióticos Fijadores de Nitrógeno Tropicales de Nogent sur Marne, Francia. Procesos Microbianos es su segundo libro. El primero: Ecología Microbiana del Suelos fue editado en diciembre de 1990 por la Universidad de la República del Uruguay, luego de obtener un premio de la Colección Reencuentro (Universidad-Banco de la República Oriental del Uruguay). -
Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach
fmicb-10-00242 February 15, 2019 Time: 15:34 # 1 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Ghent University Academic Bibliography REVIEW published: 15 February 2019 doi: 10.3389/fmicb.2019.00242 Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach Sam Lambrechts*, Anne Willems and Guillaume Tahon* Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on Edited by: Samuel Cirés, large parts of the microbial tree of life, arising from the fact that most microbial Autonomous University of Madrid, diversity on Earth has never been characterized in laboratory cultures. These unknown Spain prokaryotes, also known as microbial dark matter, have been dominantly detected Reviewed by: David Anthony Pearce, in all major environments on our planet. Laboratory cultures provide access to the Northumbria University, complete genome and the means to experimentally verify genomic predictions and United Kingdom metabolic functions and to provide evidence of horizontal gene transfer. -
Genetic Basis of Flocculation in Azospirillum Brasilense
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Masters Theses Graduate School 5-2012 Genetic Basis of Flocculation in Azospirillum brasilense. Priyanka Satish Mishra [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_gradthes Part of the Microbiology Commons, and the Molecular Biology Commons Recommended Citation Mishra, Priyanka Satish, "Genetic Basis of Flocculation in Azospirillum brasilense.. " Master's Thesis, University of Tennessee, 2012. https://trace.tennessee.edu/utk_gradthes/1186 This Thesis is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Masters Theses by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a thesis written by Priyanka Satish Mishra entitled "Genetic Basis of Flocculation in Azospirillum brasilense.." I have examined the final electronic copy of this thesis for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Master of Science, with a major in Life Sciences. Dr. Gladys Alexandre, Major Professor We have read this thesis and recommend its acceptance: Dr. Albrecht von Arnim, Dr. Engin Serpersu Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) GENETIC BASIS OF FLOCCULATION IN AZOSPIRILLUM BRASILENSE A Thesis Presented for the Master of Science Degree The University of Tennessee, Knoxville Priyanka Mishra May 2012 ii Copyright © 2012 by Priyanka Mishra All rights reserved. -
Physiological and Molecular Basis of Azospirillum-Arabidopsis Interaction
Physiological and molecular basis of Azospirillum-Arabidopsis Interaction Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades angefertigt am Institut für Molekulare Pflanzenphysiologie und Biophysik an der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Nazeer Ahmed aus Quetta (Pakistan) Würzburg 2010 Eingereicht am: Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Thomas Dandekar 1. Gutachter: PD Dr. Dirk Becker 2. Gutachter: PD Dr. Susanne Berger Tag des Promotionskolloquiums: …………………………… Doktorurkunde ausgehändigt am ……………………… Dedicated to My father Table of contents Table of contents 1 Introduction ........................................................................................... 14 1.1 Plants and the rhizospheric microbes ..................................................... 14 1.2 Mycorrhizal interactions .......................................................................... 15 1.3 Diazotrophs ............................................................................................. 18 1.3.1 Rhizobia-legume mutualism .................................................................... 19 1.3.2 Plant growth promoting Rhizobacteria / associative symbionts ............... 21 1.3.3 Azospirillum ............................................................................................. 22 1.3.3.1 Interaction with plants .......................................................................... 25 1.3.3.2 Azospirillum and plant growth promotion ............................................