Nodule-Forming Sinorhizobium and Arbuscular
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BMC Genomics (2016) 17:711 DOI 10.1186/S12864-016-3053-Z
Peralta et al. BMC Genomics (2016) 17:711 DOI 10.1186/s12864-016-3053-z RESEARCH ARTICLE Open Access Genomic studies of nitrogen-fixing rhizobial strains from Phaseolus vulgaris seeds and nodules Humberto Peralta, Alejandro Aguilar, Rafael Díaz, Yolanda Mora, Gabriel Martínez-Batallar, Emmanuel Salazar, Carmen Vargas-Lagunas, Esperanza Martínez, Sergio Encarnación, Lourdes Girard and Jaime Mora* Abstract Background: Rhizobia are soil bacteria that establish symbiotic relationships with legumes and fix nitrogen in root nodules. We recently reported that several nitrogen-fixing rhizobial strains, belonging to Rhizobium phaseoli, R. trifolii, R. grahamii and Sinorhizobium americanum, were able to colonize Phaseolus vulgaris (common bean) seeds. To gain further insight into the traits that support this ability, we analyzed the genomic sequences and proteomes of R. phaseoli (CCGM1) and S. americanum (CCGM7) strains from seeds and compared them with those of the closely related strains CIAT652 and CFNEI73, respectively, isolated only from nodules. Results: In a fine structural study of the S. americanum genomes, the chromosomes, megaplasmids and symbiotic plasmids were highly conserved and syntenic, with the exception of the smaller plasmid, which appeared unrelated. The symbiotic tract of CCGM7 appeared more disperse, possibly due to the action of transposases. The chromosomes of seed strains had less transposases and strain-specific genes. The seed strains CCGM1 and CCGM7 shared about half of their genomes with their closest strains (3353 and 3472 orthologs respectively), but a large fraction of the rest also had homology with other rhizobia. They contained 315 and 204 strain-specific genes, respectively, particularly abundant in the functions of transcription, motility, energy generation and cofactor biosynthesis. -
Sinorhizobium Indiaense Sp. Nov. and Sinorhizobium Abri Sp. Nov. Isolated from Tropical Legumes, Sesbania Rostrata and Abrus Precatorius, Respectively
Symbiosis, 34 (2003) 53-68 53 Balaban, Philadelphia/Rehovot Sinorhizobium indiaense sp. nov. and Sinorhizobium abri sp. nov. Isolated from Tropical Legumes, Sesbania rostrata and Abrus precatorius, Respectively M. OGASAWARAl, T. SUZUKil, I. MUTOHl, K. ANNAPURNA2, N.K. ARORA3, Y. NISHIMURAl, and D.K. MAHESHWAR13* l Department of Applied Biological Science, Science University of Tokyo, 2641, Yamazaki, Noda, Chiba 278-8510, Japan, Tel. +81-471-241501, Fax. +81-471-239767; 2 Division of Microbiology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India; 3Department of Botany and Microbiology, Gurukul Kangri University, Hardwar 249404, India, Tel. +91-133-416767, Fax. +91-133-416366, Email. [email protected] Received July 28, 2002; Accepted November 24, 2002 Abstract Strains of root nodulating bacteria isolated from the leguminous plants Sesbania rostrata and Abrus precatorius growing in the sub Himalayan tract in the western Uttar Pradesh, a tropical region of India, were compared with the reference strains of Sinorhizobium, Rhizobium, Azorhizobium and Agrobacterium. The phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates from S. rostrata and strains from A. precatorius, were the members of the genus Sinorhizobium. The 16S rRNA gene sequence similarity values of representative strain Ra-3 (from S. rostrata) and HA-1 (from A. precatorius) showed low values in species level, namely those of 97.1 % to Sinorhizobium arboris and 96.1 % to S. fredii and S. xinjiangense, respectively. Similarity values of both strains and other Sinorhizobium spp. were mostly lower than those of the above species. On the basis of the results, with the data of phenotypic characteristics, cellular fatty acid compositions (major, 18:1 "The author to whom correspondence should be sent. -
Genomic Identification of Rhizobia-Related Strains And
International Journal of Environmental & Agriculture Research (IJOEAR) ISSN:[2454-1850] [Vol-2, Issue-6, June- 2016] Genomic identification of rhizobia-related strains and threshold of ANI and core-genome for family, genus and species Qian Wang1, Wentao Zhu2, Entao Wang3, Linshuang Zhang4, Xiangyang Li5, Gejiao Wang6* 1,2,4,5,6State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China *Email: [email protected] 3Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, Mexico Email: [email protected] Abstract—Aiming at accurately and rapidly identifying our heavy metal resistant rhizobial strains, genomic average nucleotide identity (ANI) and core genome analyses were performed to investigate the phylogenetic relationships among 45 strains in the families of Rhizobiaceae and Bradyrhizobiaceae. The results showed that both of the ANI and core-genome phylogenetic trees revealed similar relationship. In ANI analysis, the 90%, 75% and 70% ANI values could be the thresholds for species, genus and family, respectively. Analyzing the genomes using multi-dimensional scaling and scatter plot showed highly consistent with the ANI and core-genome phylogenetic results. With these thresholds, the 45 strains were divided into 24 genomic species within the genera Agrobacterium, Allorhizobium, Bradyrhizobium, Sinorhizobium and a putative novel genus represented by Ag. albertimagni AOL15. The ten arsenite-oxidizing and antimonite tolerant strains were identified as Ag. radiobacter, and two Sinorhizobium genomic species differing from S. fredii. In addition, the description of Pararhizobium is questioned because ANI values greater than 75% were detected between P. giardinii H152T and Sinorhizobium strains. -
Sinorhizobium Meliloti RNA-Hfq Protein Associations in Vivo Mengsheng Gao1*, Anne Benge1, Julia M
Gao et al. Biological Procedures Online (2018) 20:8 https://doi.org/10.1186/s12575-018-0075-8 METHODOLOGY Open Access Use of RNA Immunoprecipitation Method for Determining Sinorhizobium meliloti RNA-Hfq Protein Associations In Vivo Mengsheng Gao1*, Anne Benge1, Julia M. Mesa1, Regina Javier1 and Feng-Xia Liu2 Abstract Background: Soil bacterium Sinorhizobium meliloti (S. meliloti) forms an endosymbiotic partnership with Medicago truncatula (M. truncatula) roots which results in root nodules. The bacteria live within root nodules where they function to fix atmospheric N2 and supply the host plant with reduced nitrogen. The bacterial RNA-binding protein Hfq (Hfq) is an important regulator for the effectiveness of the nitrogen fixation. RNA immunoprecipitation (RIP) method is a powerful method for detecting the association of Hfq protein with specific RNA in cultured bacteria, yet a RIP method for bacteria living in root nodules remains to be described. Results: A modified S. meliloti gene encoding a His-tagged Hfq protein (HfqHis) was placed under the regulation of His thenativeHfqgenepromoter(Phfqsm). The trans produced Hfq protein was accumulated at its nature levels during all stages of the symbiosis, allowing RNAs that associated with the given protein to be immunoprecipitated with the anti-His antibody against the protein from root nodule lysates. RNAs that associated with the protein were selectively enriched in the immunoprecipitated sample. The RNAs were recovered by a simple method using heat and subsequently analyzed by RT-PCR. The nature of PCR products was determined by DNA sequencing. Hfq association with specific RNAs can be analyzed at different conditions (e. g. -
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. -
Population Genomics of Sinorhizobium Medicae Based On
Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates Xavier Bailly, Elisa Giuntini, Connor M Sexton, Ryan Pj Lower, Peter W Harrison, Nitin Kumar, J Peter W Young To cite this version: Xavier Bailly, Elisa Giuntini, Connor M Sexton, Ryan Pj Lower, Peter W Harrison, et al.. Popu- lation genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates. ISME Journal, Nature Publishing Group, 2011, 5 (11), pp.1722-1734. 10.1038/ismej.2011.55. hal- 02652397 HAL Id: hal-02652397 https://hal.inrae.fr/hal-02652397 Submitted on 29 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. The ISME Journal (2011) 5, 1722–1734 & 2011 International Society for Microbial Ecology All rights reserved 1751-7362/11 www.nature.com/ismej ORIGINAL ARTICLE Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates Xavier Bailly1, Elisa Giuntini, M Connor Sexton, Ryan PJ Lower, Peter W Harrison, Nitin Kumar and J Peter W Young Department of Biology, University of York, York, UK We investigated the genomic diversity of a local population of the symbiotic bacterium Sinorhizobium medicae, isolated from the roots of wild Medicago lupulina plants, in order to assess genomic diversity, to identify genomic regions influenced by duplication, deletion or strong selection, and to explore the composition of the pan-genome. -
Unesco – Eolss Sample Chapters
BIOTECHNOLOGY – Vol VIII - Essentials of Nitrogen Fixation Biotechnology - James H. P. Kahindi, Nancy K. Karanja ESSENTIALS OF NITROGEN FIXATION BIOTECHNOLOGY James H. P. Kahindi United States International University, Nairobi, KENYA Nancy K. Karanja Nairobi Microbiological Resources Centre, University of Nairobi, KENYA Keywords: Rhizobium, Bradyrhizobium, Sinorhizobium, Azorhizobium, Legumes, Nitrogen Fixation Contents 1. Introduction 2. Crop Requirements for Nitrogen 3. Potential for Biological Nitrogen Fixation [BNF] Systems 4. Diversity of Rhizobia 4.l. Factors Influencing Biological Nitrogen Fixation [BNF] 5. The Biochemistry of Biological Nitrogen Fixation: The Nitrogenase System 5.1. The Molybdenum Nitrogenase System 5.1.1. The Iron Protein (Fe protein) 5.1.2. The MoFe Protein 5.2. The Vanadium Nitrogenase 5.3. Nitrogenase-3 6. The Genetics of Nitrogen Fixation 6.1. The Mo-nitrogenase Structural Genes (nif H,D,K) 6.2. Genes for nitrogenase-2 (vnf H,D,G,K,vnfA,vnfE,N,X) 6.3. Regulation of Nif Gene Expression 7. The Potential for Biological Nitrogen Fixation with Non-legumes 7.1. Frankia 7.2. Associative Nitrogen Fixation 8. Application of Biological Nitrogen Fixation Technology 8.1. Experiences of the Biological Nitrogen Fixation -MIRCENs 8.2 Priorities for Action Glossary UNESCO – EOLSS Bibliography Biographical Sketches Summary SAMPLE CHAPTERS Nitrogen constitutes 78% of the Earth’s atmosphere, yet it is frequently the limiting nutrient to agricultural productivity. This necessitates the addition of nitrogen to the soil either through industrial nitrogen fertilizers, which is accomplished at a substantial energy cost, or by transformation of atmospheric nitrogen into forms which plants can take up for protein synthesis. This latter form is known as biological nitrogen fixation and is accomplished by free-living and symbiotic microorganisms endowed with the enzyme nitrogenase. -
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. -
(Ensifer) Meliloti Psyma Required for Efficient Symbiosis with Medicago
Minimal gene set from Sinorhizobium (Ensifer) meliloti pSymA required for efficient symbiosis with Medicago Barney A. Geddesa,1, Jason V. S. Kearsleya, Jiarui Huanga, Maryam Zamania, Zahed Muhammeda, Leah Sathera, Aakanx K. Panchala, George C. diCenzoa,2, and Turlough M. Finana,3 aDepartment of Biology, McMaster University, Hamilton, ON, Canada L8S 4K1 Edited by Éva Kondorosi, Hungarian Academy of Sciences, Biological Research Centre, Szeged, Hungary, and approved December 2, 2020 (received for review August 25, 2020) Reduction of N2 gas to ammonia in legume root nodules is a key to the oxygen-limited environment of the nodule that includes component of sustainable agricultural systems. Root nodules are producing a high O2-affinity cytochrome oxidase (encoded by fix the result of a symbiosis between leguminous plants and bacteria genes) (7). Symbiosis genes are encoded on extrachromosomal called rhizobia. Both symbiotic partners play active roles in estab- replicons or integrative conjugative elements that allow the ex- lishing successful symbiosis and nitrogen fixation: while root nod- change of symbiotic genes by horizontal gene transfer (8). ule development is mostly controlled by the plant, the rhizobia However, horizontal transfer of essential symbiotic genes (nod, induce nodule formation, invade, and perform N2 fixation once nif, fix) alone is often not sufficient to convert a naive bacterium inside the plant cells. Many bacterial genes involved in the into a compatible symbiont for a legume (9). Therefore, eluci- rhizobia–legume symbiosis are known, and there is much interest dating the complete complement of genes required for the es- in engineering the symbiosis to include major nonlegume crops tablishment of a productive symbiosis between rhizobia and such as corn, wheat, and rice. -
Phylogeny of Fast-Growing Soybean-Nodulating Rhizobia Supports Synonymy of Sinovhizobium and Rhizobium and Assignment to Rhizobium Fredii
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1992, p. 93-96 Vol. 42, No. 1 0020-7713/92/010093-O4$02.OO/O Phylogeny of Fast-Growing Soybean-Nodulating Rhizobia Supports Synonymy of Sinovhizobium and Rhizobium and Assignment to Rhizobium fredii B. D. W. JARVIS,l* H. L. DOWNER,* AND J. P. W.YOUNG2 Department of Microbiology and Genetics, Massey University, Palmerston North, New Zealand,l and John Innes Institute, Norwich NR4 7UH, England2 We determined the sequences for a 260-base segment amplified by the polymerase chain reaction (corresponding to positions 44 to 337 in the Escherichia coli 16s rRNA sequence) from seven strains of fast-growing soybean-nodulating rhizobia (including the type strains of Rhizobium fredii chemovar fredii, Rhizobium fredii chemovar siensis, Sinorhizobium fredii, and Sinorhizobium xinjiangensis) and broad-host- range Rhizobium sp. strain NGR 234. These sequences were compared with the corresponding previously published sequences of Rhizobium leguminosarum, Rhizobium meliloti, Agrobacterium tumefaciens, Azorhizo- bium caulinodans, and Bradyrhizobium japonicum. All of the sequences of the fast-growing soybean rhizobia, including strain NGR 234, were identical to the sequence of R. rneliloti and similar to the sequence of R. leguminosarum. These results are discussed in relation to previous findings; we concluded that the fast-growing soybean-nodulating rhizobia belong in the genus Rhizobium and should be called Rhizobium fredii. In 1982 Keyser et al. described fast-growing rhizobia MATERIALS AND METHODS which produced nodules and fixed atmospheric nitrogen on the roots of soybeans and were isolated in the People’s Bacterial strains and growth conditions. The strains which Republic of China (15). -
Nucleotide Sequence and Predicted Functions of the Entire Sinorhizobium Meliloti Psyma Megaplasmid
Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid Melanie J. Barnetta, Robert F. Fishera, Ted Jonesb, Caridad Kompb, A. Pia Abolab, Fre´ de´ rique Barloy-Hublerc, Leah Bowserb, Delphine Capelac,d,e, Francis Galibertc,Je´ roˆ me Gouzyd, Mani Gurjalb, Andrea Honga, Lucas Huizarb, Richard W. Hymanb, Daniel Kahnd, Michael L. Kahnf, Sue Kalmanb,g, David H. Keatinga,h, Curtis Palmb, Melicent C. Pecka, Raymond Surzyckib,i, Derek H. Wellsa, Kuo-Chen Yeha,h,j, Ronald W. Davisb, Nancy A. Federspielb,k, and Sharon R. Longa,h,l aDepartment of Biological Sciences, and hHoward Hughes Medical Institute, Stanford University, Stanford, CA 94305; bStanford Center for DNA Sequencing and Technology, 855 California Avenue, Palo Alto, CA 94304; cLaboratoire de Ge´ne´ tique et De´veloppement, Faculte´deMe´ decine, 2 Avenue du Pr. Le´on Bernard, F-35043 Rennes Cedex, France; dLaboratoire de Biologie Mole´culaire de Relations Plantes–Microorganisms, Unite´Mixte de Recherche, 215 Institut National de la Recherche Agronomique–Centre National de la Recherche Scientifique, F-31326 Castanet Tolosan, France; and fInstitute of Biological Chemistry, Washington State University, Pullman, WA 99164 Contributed by Sharon R. Long, June 12, 2001 The symbiotic nitrogen-fixing soil bacterium Sinorhizobium me- pSymA provide versatility to S. meliloti and may be adaptive in liloti contains three replicons: pSymA, pSymB, and the chromo- both the free-living and symbiotic states. some. We report here the complete 1,354,226-nt sequence of pSymA. In addition to a large fraction of the genes known to be Materials and Methods specifically involved in symbiosis, pSymA contains genes likely to Library Construction and Sequencing. -
Agrobacterium Is a Definable Genus of the Family Rhizobiaceae
International Journal of Systematic and Evolutionary Microbiology (2003), 53, 1681–1687 DOI 10.1099/ijs.0.02445-0 Taxonomic Agrobacterium is a definable genus of the family Note Rhizobiaceae Stephen K. Farrand,1 Peter B. van Berkum2 and Philippe Oger3 Correspondence 1Departments of Crop Sciences and Microbiology, University of Illinois at Urbana-Champaign, Stephen K. Farrand 240 ERML, 1201 West Gregory Drive, Urbana, IL 61801, USA [email protected] 2Soybean Genomics and Improvement Laboratory, Plant Sciences Institute, USDA-ARS, Beltsville, MD, 20705, USA 3Laboratoire de Sciences de la Terre, Ecole Normale Superieure de Lyon, 69364 Lyon Cedex 07, France Members of the genus Agrobacterium constitute a diverse group of organisms, all of which, when harbouring the appropriate plasmids, are capable of causing neoplastic growths on susceptible host plants. The agrobacteria, which are members of the family Rhizobiaceae, can be differentiated into at least three biovars, corresponding to species divisions based on differential biochemical and physiological tests. Recently, Young et al. [Int J Syst Evol Microbiol 51 (2003), 89–103] proposed to incorporate all members of the genus Agrobacterium into the genus Rhizobium.We present evidence from classical and molecular comparisons that supports the conclusion that the biovar 1 and biovar 3 agrobacteria are sufficiently different from members of the genus Rhizobium to warrant retention of the genus Agrobacterium. The biovar 2 agrobacteria cluster more closely to the genus Rhizobium, but some studies suggest that these isolates differ from species of Rhizobium with respect to their capacity to interact with plants. We conclude that there is little scientific support for the proposal to group the agrobacteria into the genus Rhizobium and consequently recommend retention of the genus Agrobacterium.