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Comparative Genomics of Bradyrhizobium Japonicum CPAC
Siqueira et al. BMC Genomics 2014, 15:420 http://www.biomedcentral.com/1471-2164/15/420 RESEARCH ARTICLE Open Access Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean Arthur Fernandes Siqueira1,2†, Ernesto Ormeño-Orrillo3†,RangelCelsoSouza4,ElisetePainsRodrigues5, Luiz Gonzaga Paula Almeida4, Fernando Gomes Barcellos5, Jesiane Stefânia Silva Batista6, Andre Shigueyoshi Nakatani2, Esperanza Martínez-Romero3, Ana Tereza Ribeiro Vasconcelos4 and Mariangela Hungria1,2* Abstract Background: The soybean-Bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. Here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. B. japonicum CPAC 15 (=SEMIA 5079) is outstanding in its saprophytic capacity and competitiveness, whereas B. diazoefficiens CPAC 7 (=SEMIA 5080) is known for its high efficiency in fixing nitrogen. Both are well adapted to tropical soils. The genomes of CPAC 15 and CPAC 7 were compared to each other and also to those of B. japonicum USDA 6T and B. diazoefficiens USDA 110T. Results: Differences in genome size were found between species, with B. japonicum having larger genomes than B. diazoefficiens. Although most of the four genomes were syntenic, genome rearrangements within and between species were observed, including events in the symbiosis island. In addition to the symbiotic region, several genomic islands were identified. Altogether, these features must confer high genomic plasticity that might explain adaptation and differences in symbiotic performance. It was not possible to attribute known functions to half of the predicted genes. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Bacteria-Inducing Legume Nodules Involved in the Improvement of Plant Growth, Health and Nutrition
Bacteria-Inducing Legume Nodules Involved in the Improvement of Plant 4 Growth, Health and Nutrition Encarna Velázquez, Lorena Carro, José David Flores-Félix, Esther Menéndez, Martha-Helena Ramírez-Bahena, and Alvaro Peix Abstract Bacteria-inducing legume nodules are known as rhizobia and belong to the class Alphaproteobacteria and Betaproteobacteria. They promote the growth and nutrition of their respective legume hosts through atmospheric nitrogen fixation which takes place in the nodules induced in their roots or stems. In addition, rhizobia have other plant growth-promoting mechanisms, mainly solubilization of phosphate and production of indoleacetic acid, ACC deaminase and sidero- phores. Some of these mechanisms have been reported for strains of rhizobia which are also able to promote the growth of several nonlegumes, such as cere- als, oilseeds and vegetables. Less studied are the mechanisms that have the rhi- zobia to promote the plant health; however, these bacteria are able to exert biocontrol of some phytopathogens and to induce the plant resistance. In this chapter, we revised the available data about the ability of the legume nodule- inducing bacteria for improving the plant growth, health and nutrition of both legumes and nonlegumes. These data showed that rhizobia meet all the require- ments of sustainable agriculture to be used as bio-inoculants allowing the total or partial replacement of chemicals used for fertilization or protection of crops. E. Velázquez (*) Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain Unidad Asociada Universidad de Salamanca- CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain e-mail: [email protected] L. Carro · J. D. Flores-Félix · E. Menéndez · M.-H. -
Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California
Microb Ecol (2016) 71:700–710 DOI 10.1007/s00248-015-0685-5 PLANT MICROBE INTERACTIONS Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California A. C. Hollowell1 & J. U. Regus1 & K. A. Gano1 & R. Bantay1 & D. Centeno1 & J. Pham1 & J.Y. Lyu1 & D. Moore1 & A. Bernardo1 & G. Lopez1 & A. Patil1 & S. Patel1 & Y. Lii1 & J. L. Sachs1,2 Received: 8 April 2015 /Accepted: 28 September 2015 /Published online: 14 October 2015 # Springer Science+Business Media New York 2015 Abstract The patterns and drivers of bacterial strain domi- the acquisition of accessory loci as occurs in key human nance remain poorly understood in natural populations. Here, pathogens. we cultured 1292 Bradyrhizobium isolates from symbiotic root nodules and the soil root interface of the host plant Keywords Rhizobia . Symbiosis . Epidemic . Population Acmispon strigosus across a >840-km transect in California. genetics . Evolution To investigate epidemiology and the potential role of accesso- ry loci as epidemic drivers, isolates were genotyped at two chromosomal loci and were assayed for presence or absence Introduction of accessory Bsymbiosis island^ loci that encode capacity to form nodules on hosts. We found that Bradyrhizobium popu- A critical goal in bacteriology is to understand patterns of lations were very diverse but dominated by few haplotypes— genotypic abundance and epidemic spread. Of particular in- with a single Bepidemic^ haplotype constituting nearly 30 % terest are host-associated bacteria, including pathogens and of collected isolates and spreading nearly statewide. In many symbionts. These diverse bacterial lineages colonize host sur- Bradyrhizobium lineages, we inferred presence and absence faces, inhabit specific tissues or cells, and can often persist of the symbiosis island suggesting recurrent evolutionary gain free in soils and or aquatic habitats between phases of host and or loss of symbiotic capacity. -
International Journal of Systematic Evolutionary Microbiology
International Journal of Systematic and Evolutionary Microbiology (2015), 65, 4441–4448 DOI 10.1099/ijsem.0.000591 Bradyrhizobium viridifuturi sp. nov., encompassing nitrogen-fixing symbionts of legumes used for green manure and environmental services Luisa Caroline Ferraz Helene,1,2 Jakeline Renata Marc¸on Delamuta,1,2 Renan Augusto Ribeiro,3 Ernesto Ormen˜o-Orrillo,4 Marco Antonio Rogel,5 Esperanza Martı´nez-Romero5 and Mariangela Hungria1,2,3 Correspondence 1Embrapa Soja, C.P. 231, 86001-970, Londrina, Parana´, Brazil Mariangela Hungria 2Universidade Estadual de Londrina, Dept. of Microbiology, C.P. 10.011, 86057-970, Londrina, [email protected]; Parana´, Brazil [email protected]; 3Conselho Nacional de Desenvolvimento Cientı´fico e Tecnolo´gico, SHIS QI 1 Conjunto B – Blocos [email protected] A, B, C e D, Lago Sul, 71605-001, Brası´lia, Distrito Federal, Brazil 4Universidad Nacional Agraria La Molina, Av. La Molina s/n La Molina, Lima, Peru 5Centro de Ciencias Geno´micas, Universidad Nacional Auto´noma de Me´xico, Cuernavaca, Morelos, Mexico Symbiotic nitrogen-fixing bacteria, commonly called rhizobia, are agronomically important because they can provide significant amounts of nitrogen to plants and help in recovery of impoverished soils and improvement of degraded environments. In recent years, with advances in molecular techniques, several studies have shown that these bacteria have high levels of genetic diversity, resulting in taxonomic reclassifications and descriptions of new species. However, despite the advances achieved, highly conserved 16S ribosomal genes (16S rRNA) do not elucidate differences between species of several genera, including the genus Bradyrhizobium. Other methodologies, such as multilocus sequence analysis (MLSA), have been used in such cases, with good results. -
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. -
International Committee on Systematics Of
ICSP - MINUTES de Lajudie and Martinez-Romero, Int J Syst Evol Microbiol 2017;67:516– 520 DOI 10.1099/ijsem.0.001597 International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Agrobacterium and Rhizobium Minutes of the meeting, 7 September 2014, Tenerife, Spain Philippe de Lajudie1,* and Esperanza Martinez-Romero2 MINUTE 1. CALL TO ORDER (Chinese Agricultural University, Beijing, China) was later elected (online, November 2015) as a member of the subcom- The closed meeting was called by the Chairperson, E. Marti- mittee. It was agreed to invite representative scientist(s) from nez-Romero, at 14:00 on 7 September 2014 during the 11th Africa who have published validated novel rhizobial/agrobac- European Nitrogen Fixation Conference in Costa Adeje, Ten- terial species descriptions to become members of the subcom- erife, Spain. mittee. Several tentative names came up. MINUTE 2. RECORD OF ATTENDANCE MINUTE 6. THE HOME PAGE The members present were J. P. W. Young, E. Martinez- The website of the subcommittee can be accessed at http:// Romero, P. Vinuesa, B. Eardly and P. de Lajudie. K. Lind- edzna.ccg.unam.mx/rhizobialtaxonomy. It would be very ström was represented by S. A. Mousavi. All subcommittee useful to list genome sequenced type strains on the website. members had the opportunity to participate in the online discussions. K. Lindström, secretary of the subcommittee since 1996, resigned from this responsibility, but expressed MINUTE 7. GUIDELINES FOR THE her willingness to continue to act as an active subcommittee DESCRIPTION OF NEW TAXA member. P. Vinuesa agreed to act as a temporary secretary Some years ago, E. -
Bacteria Related to Bradyrhizobium Yuanmingense from Ghana Are Effective Groundnut Micro-Symbionts
Applied Soil Ecology xxx (xxxx) xxx–xxx Contents lists available at ScienceDirect Applied Soil Ecology journal homepage: www.elsevier.com/locate/apsoil Bacteria related to Bradyrhizobium yuanmingense from Ghana are effective groundnut micro-symbionts Ophelia Oseia, Robert C. Abaidoob,c, Benjamin D.K. Ahiabord, Robert M. Boddeye, ⁎ Luc F.M. Rouwse, a Department of Crop and Soil Sciences, Faculty of Agriculture, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana b Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana c International Institute of Tropical Agriculture, PMB 5320, Ibadan, Nigeria d CSIR, Savannah Agricultural Research Institute, P.O. Box 52, Tamale, Ghana e Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil ARTICLE INFO ABSTRACT Keywords: The identification of locally-adapted rhizobia for effective inoculation of grain legumes in Africa’s semiarid Native isolates regions is strategic for developing and optimizing cheap nitrogen fixation technologies for smallholder farmers. Biological nitrogen fixation This study was aimed at selecting and characterising effective native rhizobia, from Ghanaian soils for groundnut Genetic diversity (Arachis hypogaea L.) inoculation. From surface-disinfected root nodules of cowpea and groundnut plants grown Arachis hypogaea L. on farmers’ fields, 150 bacterial isolates were obtained, 30 of which were eventually found to nodulate groundnut plants. After testing the symbiotic potential of these isolates on groundnut on sterilized substrate, seven of them, designated as KNUST 1001–1007, were evaluated in an open field pot experiment using 15N- labelled soil. Although 15N dilution analyses did not indicate differences among treatments in the proportion of nitrogen (N) derived from the atmosphere (%Ndfa), all seven strains increased total N derived from N2 fixation by inoculated groundnut plants as compared to the non-inoculated control. -
Bradyrhizobium Daqingense Sp. Nov., Isolated from Soybean Nodules
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 616–624 DOI 10.1099/ijs.0.034280-0 Bradyrhizobium daqingense sp. nov., isolated from soybean nodules Jing Yu Wang,13 Rui Wang,13 Yan Ming Zhang,1 Hong Can Liu,2 Wen Feng Chen,1 En Tao Wang,1,3 Xin Hua Sui1 and Wen Xin Chen1 Correspondence 1State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural Xinhua Sui University, Beijing 100193, PR China [email protected] 2Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China 3Departamento de Microbiologı´a, Escuela Nacional de Ciencias Biolo´gicas, Instituto Polite´cnico Nacional, 11340 Me´xico DF, Mexico Thirteen slow-growing rhizobial strains isolated from root nodules of soybean (Glycine max L.) grown in Daqing city in China were classified in the genus Bradyrhizobium based on 16S rRNA gene sequence analysis. Multilocus sequence analysis of IGS, atpD, glnII and recA genes revealed that the isolates represented a novel clade in this genus. DNA–DNA relatedness lower than 42.5 % between the representative strain CCBAU 15774T and the type strains of the closely related species Bradyrhizobium liaoningense USDA 3622T, Bradyrhizobium yuanmingense CCBAU 10071T and Bradyrhizobium betae LMG 21987T, further confirmed that this group represented a novel species. CCBAU 15774T shared seven cellular fatty acids with the three above-mentioned species, but the fatty acids 15 : 0 iso and summed feature 5 (18 : 2v6,9c and/or 18 : 0 anteiso) were unique for this strain. The respiratory quinone in CCBAU 15774T was ubiquinone-10 and the cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, cardiolipin and unknown aminolipid, polar lipid and phospholipid. -
Presence of Natural Variants of Bradyrhizobium Elkanii And
R ESEARCH ARTICLE ScienceAsia 38 (2012): 24–29 doi: 10.2306/scienceasia1513-1874.2012.38.024 Presence of natural variants of Bradyrhizobium elkanii and Bradyrhizobium japonicum and detection of Bradyrhizobium yuanmingense in Phitsanulok province, Thailand Sujidkanlaya Maruekarajtinplenga, Wipa Homhaulb, Kanjana Chansa-ngaveja;∗ a Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Bangkok 10330 Thailand b Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok 65000 Thailand ∗Corresponding author, e-mail: [email protected] Received 20 Sep 2011 Accepted 25 Jan 2012 ABSTRACT: Soybean rhizobia are Gram negative bacteria that fix nitrogen in root nodules of soybeans. Selection of soybean rhizobia from present and previous soybean cultivation areas is one way to obtain efficient strains for inoculant production. At present, information on the diversity of soybean rhizobia in Thailand is scarce. The experiments aimed to isolate and characterize soybean rhizobium strains in soils from 16 subdistricts in Phitsanulok province, Thailand. Host trapping method was used to isolate bacteria from root nodules of 5 soybean cultivars grown in soils from the 16 subdistricts. Identical RAPD-PCR fingerprints revealed the 202 slow-growing isolates consisted of 121 strains. Authentication tests using 5 soybean cultivars showed all the 121 slow-growing strains had nodulated soybean roots. Four types of colony morphology on yeast extract mannitol containing congo red agar plates were obtained for all the isolated strains. Bromothymol blue (BTB) reactions on BTB agar plates revealed two types of slow-growing soybean rhizobia. Type 1 secreted alkali products after 5-day incubation, and acidic products upon prolonged incubation for another 5 days. -
Identification of Bradyrhizobium Elkanii USDA61 Type III Effectors
G C A T T A C G G C A T genes Article Identification of Bradyrhizobium elkanii USDA61 Type III Effectors Determining Symbiosis with Vigna mungo 1, 2 3 4 Hien P. Nguyen y , Safirah T. N. Ratu , Michiko Yasuda , Neung Teaumroong and Shin Okazaki 2,3,* 1 Institute of Global Innovation Research (IGIR), Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo 183-8538, Japan; [email protected] 2 United Graduate School of Agricultural Science, TUAT, Fuchu, Tokyo 183-8509, Japan; safi[email protected] 3 Graduate School of Agriculture, TUAT, Fuchu, Tokyo 183-8509, Japan; [email protected] 4 School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology (SUT), Ratchasima 30000, Thailand; [email protected] * Correspondence: [email protected]; Tel./Fax: +81-42-367-5847 Present address: Beltsville Agricultural Research Center (BARC), Agricultural Research Service (ARS), y the U.S. Department of Agriculture (USDA), Beltsville, MD 20705, USA. Received: 11 March 2020; Accepted: 24 April 2020; Published: 27 April 2020 Abstract: Bradyrhizobium elkanii USDA61 possesses a functional type III secretion system (T3SS) that controls host-specific symbioses with legumes. Here, we demonstrated that B. elkanii T3SS is essential for the nodulation of several southern Asiatic Vigna mungo cultivars. Strikingly, inactivation of either Nod factor synthesis or T3SS in B. elkanii abolished nodulation of the V. mungo plants. Among the effectors, NopL was identified as a key determinant for T3SS-dependent symbiosis. Mutations of other effector genes, such as innB, nopP2, and bel2-5, also impacted symbiotic effectiveness, depending on host genotypes. -
S41467-018-05663-X.Pdf
ARTICLE DOI: 10.1038/s41467-018-05663-x OPEN Variation in bradyrhizobial NopP effector determines symbiotic incompatibility with Rj2-soybeans via effector-triggered immunity Masayuki Sugawara1, Satoko Takahashi1, Yosuke Umehara2, Hiroya Iwano1, Hirohito Tsurumaru3, Haruka Odake1, Yuta Suzuki1, Hitoshi Kondo1, Yuki Konno1, Takeo Yamakawa4, Shusei Sato1, Hisayuki Mitsui1 & Kiwamu Minamisawa1 1234567890():,; Genotype-specific incompatibility in legume–rhizobium symbiosis has been suggested to be controlled by effector-triggered immunity underlying pathogenic host-bacteria interactions. However, the rhizobial determinant interacting with the host resistance protein (e.g., Rj2) and the molecular mechanism of symbiotic incompatibility remain unclear. Using natural mutants of Bradyrhizobium diazoefficiens USDA 122, we identified a type III-secretory protein NopP as the determinant of symbiotic incompatibility with Rj2-soybean. The analysis of nopP muta- tions and variants in a culture collection reveal that three amino acid residues (R60, R67, and H173) in NopP are required for Rj2-mediated incompatibility. Complementation of rj2-soy- bean by the Rj2 allele confers the incompatibility induced by USDA 122-type NopP. In response to incompatible strains, Rj2-soybean plants activate defense marker gene PR-2 and suppress infection thread number at 2 days after inoculation. These results suggest that Rj2- soybeans monitor the specific variants of NopP and reject bradyrhizobial infection via effector-triggered immunity mediated by Rj2 protein. 1 Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. 2 Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan. 3 Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan.