DOCSLIB.ORG

Population Genomics of Sinorhizobium Medicae Based On

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
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. Partial genome sequences of 12 isolates were obtained by Roche 454 shotgun sequencing (average 5.3 Mb per isolate) and compared with the published sequence of S. medicae WSM 419. Homologous recombination appears to have less impact on the polymorphism patterns of the chromosome than on the chromid pSMED01 and megaplasmid pSMED02. Moreover, pSMED02 is a hot spot of insertions and deletions. The whole chromosome is characterized by low sequence polymorphism, consistent with the high density of housekeeping genes. Similarly, the level of polymorphism of symbiosis genes (low) and of genes involved in polysaccharide synthesis (high) may reflect different selection. Finally, some isolates carry genes that may confer adaptations that S. medicae WSM 419 lacks, including homologues of genes encoding rhizobitoxine synthesis, iron uptake, response to autoinducer-2, and synthesis of distinct polysaccharides. The presence or absence of these genes was confirmed by PCR in each of these 12 isolates and a further 27 isolates from the same population. All isolates had rhizobitoxine genes, while the other genes were co-distributed, suggesting that they may be on the same mobile element. These results are discussed in relation to the ecology of Medicago symbionts and in the perspective of population genomics studies. The ISME Journal (2011) 5, 1722–1734; doi:10.1038/ismej.2011.55; published online 12 May 2011 Subject Category: evolutionary genetics Keywords: population genomics; genome evolution; horizontal gene pool; population structure; Sinorhizobium medicae Introduction sample of a defined local population. Comparison of such genomes has revealed extensive polymorphism There have been many studies of genetic diversity affecting both genome content and gene sequences within a bacterial species, and the majority have (Tettelin et al., 2005; Lefebure and Stanhope, 2007). adopted one of three approaches. Innumerable ‘clas- Based on such observations, the pan-genome of a sical’ studies have characterized isolates by their species has been defined as the total gene repertoire genotypes at a small number of marker loci. Recent of the species, including both core genes, which are advances in sequencing technology have facilitated present in the genome of (almost) all individuals two additional approaches: sequencing the entire within the species, and accessory genes, which have genomes of multiple isolates or sequencing ran- a sparser distribution. Theoretical studies suggest domly from an entire bacterial community (meta- that the frequency of a gene in a bacterial population genomics). While there are now many species for would depend on parameters related to its inheri- which several isolates have been sequenced, these tance mechanism and its fitness effect on the reci- isolates have generally been chosen from the global pient genome (Berg and Kurland, 2002; Novozhilov diversity of the species, and do not represent a et al., 2005), as would allele frequency at a given locus (Mes, 2008). Population genomics approaches Correspondence: JPW Young, Department of Biology, University using full genomes are giving insights into the para- of York, YO10 5DD, York, UK. meters that shape the diversity of bacterial species E-mail: [email protected] (Didelot et al., 2007), but estimates of diversity and 1Current address: INRA (Institut National de la Recherche recombination are not easily interpreted when the Agronomique), UR346 Epide´miologie Animale, 63122 Saint Gene`s Champanelle, France isolates are sparsely sampled from a global distribu- Received 25 January 2011; revised 28 March 2011; accepted 28 tion. By contrast, metagenomic studies do provide March 2011; published online 12 May 2011 samples of a local population, and gene-based Population genomics of Sinorhizobium medicae X Bailly et al 1723 estimates of diversity, but the partitioning of these plasmid called pSMED03. Although S. meliloti sequences into discrete genomes is not known. This 1021 does not have any comparable plasmid, hampers studies on recombination and selection, additional plasmids have also been observed in although some interesting analysis is still possible some other strains of this species (Mercado-Blanco (Allen et al., 2007; Eppley et al., 2007). These consi- and Olivares, 1993, 1994; Stiens et al., 2006, 2007; derations raise questions about the sampling strate- Kuhn et al., 2008). Based on sequencing of several loci, gies employed to study the genomic diversity of S. medicae is less diverse than S. meliloti, especially at bacteria (Rocha, 2008). Furthermore, it has been chromosomal loci (Bailly et al., 2006; van Berkum proposed that gene and allele frequencies obtained et al., 2006). Indications of directional and balancing from genomic data might be used in top-down selection have been identified for the nod gene region approaches (similar to association mapping) to on pSMED02/pSymA and the region involved identify, without a priori knowledge, genes that in polysaccharide synthesis on pSMED01/pSymB, could be involved in bacterial adaptations (Falush respectively, in sympatric populations of S. meliloti and Bowden, 2006). and S. medicae (Bailly et al., 2006). Such diversity In this context, we have acquired genomic data for patterns suggest that recombination has an important rhizobia, which are ecologically important bacteria role in shaping the diversity of both species. Within that have been extensively studied by both func- each species, linkage disequilibrium analyses suggest tional and evolutionary approaches, to assess the that homologous recombination occurs preferentially results that can be obtained from a population geno- at loci located on the chromid and megaplasmid, mic survey. Rhizobia constitute a functional group rather than the chromosome (Bailly et al., 2006). that includes both Alphaproteobacteria and Beta- The diversity of the accessory genome of S. meliloti proteobacteria able to form a nitrogen-fixing endo- has been studied using various approaches. Novel symbiosis with a legume host plant. To establish genomic sequences have been described both from this interaction, bacteria trigger the organogenesis of the cryptic plasmids of the strain SM11 (Stiens nodules, which are usually located on the roots of et al., 2006, 2007) and also from a representational the host. The association between plants belonging difference analysis based on the strain ATCC 9930 to the genus Medicago, such as alfalfa (Medicago (Guo et al., 2005). These new sequences occur with a sativa) or barrel medic (Medicago truncatula), and wide range of frequencies in natural populations of their specific symbionts, Sinorhizobium meliloti S. meliloti (Guo et al., 2005; Kuhn et al., 2008). Some and Sinorhizobium medicae, is one of the best- of this genetic material might have an important role studied systems. Bacterial genetic and post-genomic in the adaptation of Medicago symbionts. Finally, approaches have demonstrated the critical role the analysis of the genome content of four natural played by genes involved in the synthesis of isolates of S. meliloti using comparative genomic nodulation factors (that is, nod genes) and surface hybridization revealed that at least 12% of the polysaccharides (for example, exo or rkp genes) in genes of the model strain S. meliloti 1021 have been providing signals for the recognition of S. meliloti recently duplicated, gained or lost during the and S. medicae by their host (Jones et al., 2007). diversification of the species (Giuntini et al., While most functional studies have used S. meliloti 2005). Altogether, these data suggest that high rates as a model
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Sinorhizobium Meliloti
    Queiroux et al. BMC Microbiology 2012, 12:74 http://www.biomedcentral.com/1471-2180/12/74 RESEARCH ARTICLE Open Access A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules Clothilde Queiroux1, Brian K Washburn1, Olivia M Davis1,2†, Jamie Stewart1†, Tess E Brewer1, Michael R Lyons1,3 and Kathryn M Jones1* Abstract Background: We have used the genomic data in the Integrated Microbial Genomes system of the Department of Energy’s Joint Genome Institute to make predictions about rhizobial open reading frames that play a role in nodulation of host plants. The genomic data was screened by searching for ORFs conserved in α-proteobacterial rhizobia, but not conserved in closely-related non-nitrogen-fixing α-proteobacteria. Results: Using this approach, we identified many genes known to be involved in nodulation or nitrogen fixation, as well as several new candidate genes. We knocked out selected new genes and assayed for the presence of nodulation phenotypes and/or nodule-specific expression. One of these genes, SMc00911, is strongly expressed by bacterial cells within host plant nodules, but is expressed minimally by free-living bacterial cells. A strain carrying an insertion mutation in SMc00911 is not defective in the symbiosis with host plants, but in contrast to expectations, this mutant strain is able to out-compete the S. meliloti 1021 wild type strain for nodule occupancy in co- inoculation experiments. The SMc00911 ORF is predicted to encode a “SodM-like” (superoxide dismutase-like) protein containing a rhodanese sulfurtransferase domain at the N-terminus and a chromate-resistance superfamily domain at the C-terminus.
    [Show full text]
  • 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.
    [Show full text]
  • Ensifer (Sinorhizobium) Medicae Strain WSM419
    Standards in Genomic Sciences (2010) 2:77-86 DOI:10.4506/sigs.43526 Complete genome sequence of the Medicago microsym- biont Ensifer (Sinorhizobium) medicae strain WSM419 Wayne Reeve1*, Patrick Chain2,3, Graham O’Hara1, Julie Ardley1, Kemanthi Nandesena1, Lambert Bräu1, Ravi Tiwari1, Stephanie Malfatti2,3, Hajnalka Kiss2,3, Alla Lapidus2, Alex Co- peland2, Matt Nolan2, Miriam Land2,4, Loren Hauser2,4, Yun-Juan Chang2,4, Natalia Ivanova2, Konstantinos Mavromatis2, Victor Markowitz5, Nikos Kyrpides2, Margaret Gollagher6, Ron Yates1,7, Michael Dilworth1 & John Howieson1,7. 1 Centre for Rhizobium Studies, Murdoch University, Perth, Australia 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Lawrence Livermore National Laboratory, Livermore, California, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 Biological Data Management and Technology Center, Lawrence Berkeley National Labora- tory, Berkeley, California, USA 6 Institute for Sustainability and Technology Policy, Murdoch University, Perth, Australia 7 Department of Agriculture and Food, South Perth, Australia *Corresponding author: Wayne Reeve Keywords: microsymbiont, non-pathogenic, aerobic, Gram-negative rod, root-nodule bacte- ria, nitrogen fixation, Alphaproteobacteria Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range of annual Medicago (medic) species. Strain WSM419 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially in Australia as an inoculant for annual medics during 1985 to 1993 due to its nitrogen fixation, saprophytic competence and acid tolerance properties. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first report of a complete genome se- quence for a microsymbiont of the group of annual medic species adapted to acid soils.
    [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]
  • 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.
    [Show full text]
  • NAD1 Controls Defense-Like Responses in Medicago Truncatula Symbiotic Nitrogen Fixing Nodules Following Rhizobial Colonization in a Baca-Independent Manner
    G C A T T A C G G C A T genes Article NAD1 Controls Defense-Like Responses in Medicago truncatula Symbiotic Nitrogen Fixing Nodules Following Rhizobial Colonization in a BacA-Independent Manner Ágota Domonkos 1, Szilárd Kovács 2,3, Anikó Gombár 1, Ern˝oKiss 3, Beatrix Horváth 1, Gyöngyi Z. Kováts 1, Attila Farkas 2,Mónika T. Tóth 1, Ferhan Ayaydin 4,Károly Bóka 5, Lili Fodor 1, Pascal Ratet 6,7 ID , Attila Kereszt 2 ID , Gabriella Endre 2,3 and Péter Kaló 1,* 1 National Agricultural and Innovation Center, Agricultural Biotechnology Institute, 2100 Gödöll˝o,Hungary; [email protected] (A.D.); [email protected] (A.G.); [email protected] (B.H.); [email protected] (G.Z.K.); [email protected] (M.T.T.); [email protected] (L.F.); [email protected] (P.K.) 2 Institute of Plant Biology, Biological Research Center, 6726 Szeged, Hungary; [email protected] (S.K.); [email protected] (A.F.); [email protected] (A.K.); [email protected] (G.E.) 3 Institute of Genetics, Biological Research Center, 6726 Szeged, Hungary; [email protected] 4 Cellular Imaging Laboratory, Biological Research Center, 6726 Szeged, Hungary; [email protected] 5 Department of Plant Anatomy, Eötvös Loránd University, 1117 Budapest, Hungary; [email protected] 6 Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France; [email protected] 7 Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité,Bâtiment 630, 91405 Orsay, France * Correspondence: [email protected]; Tel.: +36-28-526-104 Received: 31 October 2017; Accepted: 11 December 2017; Published: 14 December 2017 Abstract: Legumes form endosymbiotic interaction with host compatible rhizobia, resulting in the development of nitrogen-fixing root nodules.
    [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]
  • (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.
    [Show full text]
  • 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).
    [Show full text]