DOCSLIB.ORG

Caracterización Molecular Y Funcional De Biofertilizantes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Caracterización Molecular Y Funcional De Biofertilizantes UNIVERSIDAD DE SALAMANCA DEPARTAMENTO DE MICROBIOLOGÍA Y GENÉTICA INSTITUTO HISPANOLUSO DE INVESTIGACIONES AGRARIAS TESIS DOCTORAL Caracterización molecular y funcional de biofertilizantes bacterianos, y análisis de su potencial para mejorar la producción de cultivos de maíz, guisante, lechuga, fresa y zanahoria Memoria presentada por José David Flores Félix para optar al Grado de Doctor por la Universidad de Salamanca Fdo. José David Flores Félix Salamanca, 2018 Dr. Eustoquio Martínez Molina, Catedrático del área de Microbiología, Dra. Mª de la Encarnación Velázquez Pérez, Catedrática del área de Microbiología, y Dr. Raúl Rivas Gónzalez, Profesor Titular del área de Microbiología. AUTORIZAN: La presentación y defensa de la Tesis Doctoral titulada “Caracterización molecular y funcional de biofertilizantes bacterianos, y análisis de su potencial para mejorar la producción de cultivos de maíz, guisante, lechuga, fresa y zanahoria”, elaborada por Don José David Flores Félix y realizada bajo nuestra dirección en el Departamento de Microbiología y Genética de la Universidad de Salamanca, para la obtención del grado de Doctor. Y para que así conste, extendemos la presente autorización en Salamanca, a 14 de Junio de 2018. Fdo. Dr. D. Eustoquio Martínez Molina Fdo. Dra. Dª. Mª de la Encarnación Velázquez Pérez Fdo. Dr. D. Raúl Rivas González “Todos somos ignorantes. Lo que ocurre es que no todos ignoramos las mismas cosas” Albert Einstein Agradecimientos En primer lugar, a mis tres directores, comenzando por la Catedrática Mª de la Encarnación Velázquez sin cuya inestimable ayuda esta tesis no hubiera sido posible, por ser una infinita fuente de conocimientos, por su esfuerzo y dedicación en una etapa que ha durado más de lo que debería, pero menos de lo que desearía. Tu capacidad de esfuerzo y tesón son y serán una inspiración. Al Dr. Raúl Rivas, por la magnífica oportunidad que me brindó allá por un ya lejano año 2009, permitiéndome conocer la microbiología y sumergirme en el fantástico mundo de la investigación donde cada día es un reto y una meta en sí mismo. Por enseñarme que no hay más límite que el que uno se marca, buscando incansablemente una manera de demostrar al mundo las virtudes de la microbiología Al Catedrático Eustoquio Martínez, por todos y cada uno de los consejos y enseñanzas que siempre han llegado en el momento más oportuno, por aportar cuando más se ha necesitado esa sabiduría salomónica que ha dado calma y tranquilidad en tanto momentos de desesperación que ha tenido esta etapa. No menos importante ha sido la ayuda y guía del Catedrático Pedro Mateos, por cada uno de tanto consejos y momentos, tanto académicos como gastronómicos que durante esta tesis he tenido el placer de disfrutar. Por presentarme al Dr. Andrea Squartini, “il caro professore”, al que no puedo menos de agradecerle eternamente la oportunidad que me dio para, bajo su tutela, descubrir el mundo del Quorum sensing. A mis compañeros del grupo de batalla, a los que están, a los que se fueron y a los que han vuelto, Alexandra, Alex, Lorenas (Carro y Celador), Marta, Xavier, Sergio, Pilar, Esther, Zaki, Pepín, Rebeca, Lina, Marta Robledo. Por todas y cada una de las vivencias que hemos compartido en este camino, congresos, ratos de invernadero, radio, talleres y sobre todo ensayos de campo. Especial agradecimiento al grupo del IRNASA de la Unidad Asociada, Álvaro, Mariano y Helena por todo el apoyo y disposición para solucionar cualquier adversidad haciendo de este camino mucho más agradable. Gracias por prestarnos las instalaciones siempre que las hemos necesitado aportando como el resto su granito de arena. Por supuesto, gracias a todos aquéllos que durante este largo camino han hecho de él, un viaje inolvidable en nuestro departamento, Inma, Luis, Nieves, Mamen, Pilar, Ricardo, Manolo y Fernando. A la gente de la Universidad de León, Fernando, Rebeca, Raquel, Daniel, Cesar y Juan. A mis compañeros de Agripolis, Jesus, Vincius, Armin, Junior, Sabrina, Laura, los Lorenzos, Madiha, Guilherme, mil gracias por aceptarme y hacerme sentir tan querido, por todos y cada uno de los baccaros, por el comedor y por todos los buenos ratos, que no fueron pocos. A mis amigos, a todos y cada uno, a los que acaban de llegar y a los que están por llegar, gracias por vuestro apoyo y comprensión, por estar ahí siempre, por esas cervezas que sirven para detener el mundo y resetear. Por esas noches de billar y diana, y porque el Carro (con mayúsculas, que se lo ha ganado) nos aguante muchos años, que menos que un beso a la derecha para celebrarlo. Una mención para Pablo por tantas tardes aguantando mis penas y pesares. No puedo menos que agradécerle infinitamente a mis padres por todo su apoyo y ayuda, por preocuparse y darme todo para llegar hasta donde he llegado, por preocuparse en tantos momentos de desesperación. Esta tesis también es mérito vuestro y lleva un pedacito de ambos. Por supuesto a Natalie, por haber sufrido todos y cada uno de los momentos que han llevado hasta este día, por la comprensión y por la ayuda que tanto me ha hecho falta, por darme alegría todos los días porque no han sido pocos los momentos en los que he necesitado un empujón, una sonrisa y un beso. Índice Índice Introducción 1. Agricultura en el siglo XXI ................................................................................. 3 1.1. Técnicas agrícolas sostenibles ............................................................................ 4 2. La agricultura en España. .................................................................................... 7 2.1. Alubia. ................................................................................................................. 9 2.2. Guisante. .......................................................................................................... 10 2.3. Maíz. ................................................................................................................ 11 2.4. Fresa. ................................................................................................................. 12 2.5. Zanahoria. ......................................................................................................... 13 2.6. Lechuga. ............................................................................................................ 14 3. Microorganismos en agricultura. ...................................................................... 15 3.1. Rizosfera y endosfera. ....................................................................................... 15 3.2. Interacciones planta-microorganismo. .............................................................. 16 3.3. Bacterias promotoras del crecimiento vegetal. ................................................. 17 3.3.1. Diversidad microbiana. ..................................................................................... 17 3.3.1.1. Bacterias endófitas. ............................................................................. 18 3.3.1.1.1. Bacterias endófitas de nódulos de leguminosas. ................................ 19 3.3.1.2. Aplicaciones de las bacterias endófitas. .............................................. 22 3.3.2. Mecanismos de promoción del crecimiento vegetal. ........................................ 23 3.3.2.1. Mecanismos directos ........................................................................... 24 3.3.2.1.1. Fijación de nitrógeno .......................................................................... 24 3.3.2.1.1.1. Los rhizobia. ....................................................................................... 28 3.3.2.1.1.2. Proceso de infección. ......................................................................... 30 3.3.2.1.1.3. Simbiovariedades ................................................................................ 34 3.3.2.1.2. Solubilización de fosfato. .................................................................... 36 3.3.2.1.3. Producción de sideróforos................................................................... 38 3.3.2.1.4. Síntesis de fitohormonas. .................................................................... 40 3.3.2.2. Mecanismos indirectos........................................................................ 42 4. Taxonomía y filogenia bacteriana ..................................................................... 43 4.1. Criterios fenotípicos y quimiotaxonómicos. ..................................................... 44 4.2. Criterios genotípicos. ........................................................................................ 45 Objetivos Materiales y métodos 1. Aislamiento de bacterias a partir de nódulos de leguminosas .......................... 53 2. Mantenimiento y conservación de las cepas. .................................................... 54 3. Caracterización genotípica. ............................................................................... 54 3.1. Extracción y purificación de ADN. ................................................................... 54 3.2. Amplificación de ADN mediante PCR. ............................................................ 54 3.3. Electroforesis. ................................................................................................... 55 3.4. Obtención de perfiles de RAPD. ....................................................................... 55 3.5. Análisis matemático de los perfiles de RAPD .................................................. 56 3.6. Amplificación y secuenciación del gen ribosómico
Load more

Recommended publications
  • Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations
    fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells.
    [Show full text]
  • Genome Sequence of the Lotus Spp. Microsymbiont Mesorhizobium Loti
    Kelly et al. Standards in Genomic Sciences 2014, 9:7 http://www.standardsingenomics.com/content/9/1/7 SHORT GENOME REPORT Open Access Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037 Simon Kelly1, John Sullivan1, Clive Ronson1, Rui Tian2, Lambert Bräu3, Karen Davenport4, Hajnalka Daligault4, Tracy Erkkila4, Lynne Goodwin4, Wei Gu4, Christine Munk4, Hazuki Teshima4, Yan Xu4, Patrick Chain4, Tanja Woyke5, Konstantinos Liolios5, Amrita Pati5, Konstantinos Mavromatis6, Victor Markowitz6, Natalia Ivanova5, Nikos Kyrpides5,7 and Wayne Reeve2* Abstract Mesorhizobium loti strain NZP2037 was isolated in 1961 in Palmerston North, New Zealand from a Lotus divaricatus root nodule. Compared to most other M. loti strains, it has a broad host range and is one of very few M. loti strains able to form effective nodules on the agriculturally important legume Lotus pedunculatus. NZP2037 is an aerobic, Gram negative, non-spore-forming rod. This report reveals that the genome of M. loti strain NZP2037 does not harbor any plasmids and contains a single scaffold of size 7,462,792 bp which encodes 7,318 protein-coding genes and 70 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. Keywords: Root-nodule bacteria, Nitrogen fixation, Symbiosis, Alphaproteobacteria Introduction whether the polysaccharide is necessary for nodulation Mesorhizobium loti strain NZP2037 (ICMP1326) was of L. pedunculatus has not been established. isolated in 1961 from a root nodule off a Lotus divarica- Nodulation and nitrogen fixation genes in Mesorhizo- tus plant growing near Palmerston North airport, New bium loti strains are encoded on the chromosome on Zealand [1].
    [Show full text]
  • Reclassification of Agrobacterium Ferrugineum LMG 128 As Hoeflea
    International Journal of Systematic and Evolutionary Microbiology (2005), 55, 1163–1166 DOI 10.1099/ijs.0.63291-0 Reclassification of Agrobacterium ferrugineum LMG 128 as Hoeflea marina gen. nov., sp. nov. Alvaro Peix,1 Rau´l Rivas,2 Martha E. Trujillo,2 Marc Vancanneyt,3 Encarna Vela´zquez2 and Anne Willems3 Correspondence 1Departamento de Produccio´n Vegetal, Instituto de Recursos Naturales y Agrobiologı´a, Encarna Vela´zquez IRNA-CSIC, Spain [email protected] 2Departamento de Microbiologı´a y Gene´tica, Lab. 209, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain 3Laboratory of Microbiology, Dept Biochemistry, Physiology and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium Members of the species Agrobacterium ferrugineum were isolated from marine environments. The type strain of this species (=LMG 22047T=ATCC 25652T) was recently reclassified in the new genus Pseudorhodobacter, in the order ‘Rhodobacterales’ of the class ‘Alphaproteobacteria’. Strain LMG 128 (=ATCC 25654) was also initially classified as belonging to the species Agrobacterium ferrugineum; however, the nearly complete 16S rRNA gene sequence of this strain indicated that it does not belong within the genus Agrobacterium or within the genus Pseudorhodobacter. The closest related organism, with 95?5 % 16S rRNA gene similarity, was Aquamicrobium defluvii from the family ‘Phyllobacteriaceae’ in the order ‘Rhizobiales’. The remaining genera from this order had 16S rRNA gene sequence similarities that were lower than 95?1 % with respect to strain LMG 128. These phylogenetic distances suggested that strain LMG 128 belonged to a different genus. The major fatty acid present in strain LMG 128 was mono-unsaturated straight chain 18 : 1v7c.
    [Show full text]
  • 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.
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
    FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities.
    [Show full text]
  • Research Collection
    Research Collection Doctoral Thesis Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil Author(s): Ragot, Sabine A. Publication Date: 2016 Permanent Link: https://doi.org/10.3929/ethz-a-010630685 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO.23284 DEVELOPMENT AND APPLICATION OF MOLECULAR TOOLS TO INVESTIGATE MICROBIAL ALKALINE PHOSPHATASE GENES IN SOIL A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) presented by SABINE ANNE RAGOT Master of Science UZH in Biology born on 25.02.1987 citizen of Fribourg, FR accepted on the recommendation of Prof. Dr. Emmanuel Frossard, examiner PD Dr. Else Katrin Bünemann-König, co-examiner Prof. Dr. Michael Kertesz, co-examiner Dr. Claude Plassard, co-examiner 2016 Sabine Anne Ragot: Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil, c 2016 ⃝ ABSTRACT Phosphatase enzymes play an important role in soil phosphorus cycling by hydrolyzing organic phosphorus to orthophosphate, which can be taken up by plants and microorgan- isms. PhoD and PhoX alkaline phosphatases and AcpA acid phosphatase are produced by microorganisms in response to phosphorus limitation in the environment. In this thesis, the current knowledge of the prevalence of phoD and phoX in the environment and of their taxonomic distribution was assessed, and new molecular tools were developed to target the phoD and phoX alkaline phosphatase genes in soil microorganisms.
    [Show full text]
  • Genome Sequence of the Lotus Spp
    This is the published version Kelly,S, Sullivan,J, Ronson,C, Tian,R, Brau,L, Munk,C, Goodwin,L, Han,C, Woyke,T, Reddy,T, Huntemann,M, Pati,A, Mavromatis,K, Markowitz,V, Ivanova,N, Kyrpides,N and Reeve,W 2014, Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A, Standards in genomic sciences, vol. 9, pp. 1-7. Available from Deakin Research Online http://hdl.handle.net/10536/DRO/DU:30072117 Reproduced with the kind permission of the copyright owner Copyright: 2014, Genomic Standards Consortium, Michigan State University Kelly et al. Standards in Genomic Sciences 2014, 9:6 http://www.standardsingenomics.com/content/9/1/6 SHORT GENOME REPORT Open Access Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A Simon Kelly1, John Sullivan1, Clive Ronson1, Rui Tian2, Lambert Bräu3, Christine Munk4, Lynne Goodwin4, Cliff Han4, Tanja Woyke5, Tatiparthi Reddy5, Marcel Huntemann5, Amrita Pati5, Konstantinos Mavromatis6, Victor Markowitz6, Natalia Ivanova5, Nikos Kyrpides5,7 and Wayne Reeve2* Abstract Mesorhizobium loti strain R7A was isolated in 1993 in Lammermoor, Otago, New Zealand from a Lotus corniculatus root nodule and is a reisolate of the inoculant strain ICMP3153 (NZP2238) used at the site. R7A is an aerobic, Gram-negative, non-spore-forming rod. The symbiotic genes in the strain are carried on a 502-kb integrative and conjugative element known as the symbiosis island or ICEMlSymR7A. M. loti is the microsymbiont of the model legume Lotus japonicus and strain R7A has been used extensively in studies of the plant-microbe interaction. This report reveals thatthegenomeofM. loti strain R7A does not harbor any plasmids and contains a single scaffold of size 6,529,530 bp which encodes 6,323 protein-coding genes and 75 RNA-only encoding genes.
    [Show full text]
  • Diverse Bacteria Affiliated with the Genera Microvirga, Phyllobacterium
    PLANT MICROBIOLOGY crossm Diverse Bacteria Affiliated with the Genera Microvirga, Phyllobacterium, and Bradyrhizobium Nodulate Lupinus micranthus Growing in Soils of Northern Tunisia Downloaded from Abdelhakim Msaddak,a David Durán,b Mokhtar Rejili,a Mohamed Mars,a Tomás Ruiz-Argüeso,c Juan Imperial,b,c José Palacios,b Luis Reyb Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA), Faculty of Sciences of Gabès Erriadh, Zrig,Tunisiaa; Centro de Biotecnología y Genómica de Plantas (UPM-INIA), ETSI Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spainb; CSIC, Madrid, Spainc http://aem.asm.org/ ABSTRACT The genetic diversity of bacterial populations nodulating Lupinus micran- Received 10 October 2016 Accepted 3 thus in five geographical sites from northern Tunisia was examined. Phylogenetic January 2017 analyses of 50 isolates based on partial sequences of recA and gyrB grouped strains Accepted manuscript posted online 6 into seven clusters, five of which belong to the genus Bradyrhizobium (28 isolates), January 2017 one to Phyllobacterium (2 isolates), and one, remarkably, to Microvirga (20 isolates). Citation Msaddak A, Durán D, Rejili M, Mars M, Ruiz-Argüeso T, Imperial J, Palacios J, Rey L. The largest Bradyrhizobium cluster (17 isolates) grouped with the B. lupini species, 2017. Diverse bacteria affiliated with the and the other five clusters were close to different recently defined Bradyrhizobium genera Microvirga, Phyllobacterium, and Bradyrhizobium nodulate Lupinus micranthus on March 2, 2017 by guest species. Isolates close to Microvirga were obtained from nodules of plants from growing in soils of northern Tunisia. Appl four of the five sites sampled.
    [Show full text]
  • Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
    Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju.
    [Show full text]
  • Horizontal Transfer of Symbiosis Genes Within and Between Rhizobial Genera: Occurrence and Importance
    G C A T T A C G G C A T genes Review Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance Mitchell Andrews 1,*, Sofie De Meyer 2,3 ID , Euan K. James 4 ID , Tomasz St˛epkowski 5, Simon Hodge 1 ID , Marcelo F. Simon 6 ID and J. Peter W. Young 7 ID 1 Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand; [email protected] 2 Centre for Rhizobium Studies, Murdoch University, Murdoch 6150, Australia; [email protected] 3 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium 4 James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; [email protected] 5 Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland; [email protected] 6 Embrapa Genetic Resources and Biotechnology, Brasilia DF 70770-917, Brazil; [email protected] 7 Department of Biology, University of York, York YO10 5DD, UK; [email protected] * Correspondence: [email protected]; Tel.: +64-3-423-0692 Received: 6 May 2018; Accepted: 21 June 2018; Published: 27 June 2018 Abstract: Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume–rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated.
    [Show full text]
  • Isolation and Diversity of Sediment Bacteria in The
    bioRxiv preprint doi: https://doi.org/10.1101/638304; this version posted May 14, 2019. 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 4.0 International license. 1 Isolation and Diversity of Sediment Bacteria in the 2 Hypersaline Aiding Lake, China 3 4 Tong-Wei Guan, Yi-Jin Lin, Meng-Ying Ou, Ke-Bao Chen 5 6 7 Institute of Microbiology, Xihua University, Chengdu 610039, P. R. China. 8 9 Author for correspondence: 10 Tong-Wei Guan 11 Tel/Fax: +86 028 87720552 12 E-mail: [email protected] 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 bioRxiv preprint doi: https://doi.org/10.1101/638304; this version posted May 14, 2019. 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 4.0 International license. 29 Abstract A total of 343 bacteria from sediment samples of Aiding Lake, China, were isolated using 30 nine different media with 5% or 15% (w/v) NaCl. The number of species and genera of bacteria recovered 31 from the different media significantly varied, indicating the need to optimize the isolation conditions. 32 The results showed an unexpected level of bacterial diversity, with four phyla (Firmicutes, 33 Actinobacteria, Proteobacteria, and Rhodothermaeota), fourteen orders (Actinopolysporales, 34 Alteromonadales, Bacillales, Balneolales, Chromatiales, Glycomycetales, Jiangellales, Micrococcales, 35 Micromonosporales, Oceanospirillales, Pseudonocardiales, Rhizobiales, Streptomycetales, and 36 Streptosporangiales), including 17 families, 41 genera, and 71 species.
    [Show full text]