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Dolatabad HK, Mahjenabadi VAJ. Geographical and climatic distribution of lentil-nodulating rhizobia in Iran. FEMS Microbiol Ecol 2024; 100:fiae046. [PMID: 38587812 PMCID: PMC11044965 DOI: 10.1093/femsec/fiae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 04/09/2024] Open
Abstract
Lentil is one of the most important legumes cultivated in various provinces of Iran. However, there is limited information about the symbiotic rhizobia of lentils in this country. In this study, molecular identification of lentil-nodulating rhizobia was performed based on 16S-23S rRNA intergenic spacer (IGS) and recA, atpD, glnII, and nodC gene sequencing. Using PCR-RFLP analysis of 16S-23S rRNA IGS, a total of 116 rhizobia isolates were classified into 20 groups, leaving seven strains unclustered. Phylogenetic analysis of representative isolates revealed that the rhizobia strains belonged to Rhizobium leguminosarum and Rhizobium laguerreae, and the distribution of the species is partially related to geographical location. Rhizobium leguminosarum was the dominant species in North Khorasan and Zanjan, while R. laguerreae prevailed in Ardabil and East Azerbaijan. The distribution of the species was also influenced by agroecological climates; R. leguminosarum thrived in cold semiarid climates, whereas R. laguerreae adapted to humid continental climates. Both species exhibited equal dominance in the Mediterranean climate, characterized by warm, dry summers and mild, wet winters, in Lorestan and Kohgiluyeh-Boyer Ahmad provinces.
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Affiliation(s)
- Hossein Kari Dolatabad
- Soil Biology and Biotechnology Department, Soil and Water Research Institute, Agriculture Research, Education and Extension Organization, Meshkin Dasht Road, Karaj 31785-311, Iran
| | - Vahid Alah Jahandideh Mahjenabadi
- Soil Biology and Biotechnology Department, Soil and Water Research Institute, Agriculture Research, Education and Extension Organization, Meshkin Dasht Road, Karaj 31785-311, Iran
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2
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Liu S, Magne K, Zhou J, Laude J, Dalmais M, Le Signor C, Bendahmane A, Thompson R, Couzigou JM, Ratet P. The transcriptional co-regulators NBCL1 and NBCL2 redundantly coordinate aerial organ development and root nodule identity in legumes. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:194-213. [PMID: 36197099 DOI: 10.1093/jxb/erac389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Medicago truncatula NODULE ROOT1 (MtNOOT1) and Pisum sativum COCHLEATA1 (PsCOCH1) are orthologous genes belonging to the NOOT-BOP-COCH-LIKE (NBCL) gene family which encodes key transcriptional co-regulators of plant development. In Mtnoot1 and Pscoch1 mutants, the development of stipules, flowers, and symbiotic nodules is altered. MtNOOT2 and PsCOCH2 represent the single paralogues of MtNOOT1 and PsCOCH1, respectively. In M. truncatula, MtNOOT1 and MtNOOT2 are both required for the establishment and maintenance of symbiotic nodule identity. In legumes, the role of NBCL2 in above-ground development is not known. To better understand the roles of NBCL genes in legumes, we used M. truncatula and P. sativum nbcl mutants, isolated a knockout mutant for the PsCOCH2 locus and generated Pscoch1coch2 double mutants in P. sativum. Our work shows that single Mtnoot2 and Pscoch2 mutants develop wild-type stipules, flowers, and symbiotic nodules. However, the number of flowers was increased and the pods and seeds were smaller compared to the wild type. Furthermore, in comparison to the corresponding nbcl1 single mutants, both the M. truncatula and P. sativum nbcl double mutants show a drastic alteration in stipule, inflorescence, flower, and nodule development. Remarkably, in both M. truncatula and P. sativum nbcl double mutants, stipules are transformed into a range of aberrant leaf-like structures.
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Affiliation(s)
- Shengbin Liu
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Kévin Magne
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Jing Zhou
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320, Auzeville Tolosane, France
| | - Juliette Laude
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Marion Dalmais
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Christine Le Signor
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRAE), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Richard Thompson
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRAE), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Jean-Malo Couzigou
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320, Auzeville Tolosane, France
| | - Pascal Ratet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
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Mendoza-Suárez M, Andersen SU, Poole PS, Sánchez-Cañizares C. Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses. FRONTIERS IN PLANT SCIENCE 2021; 12:690567. [PMID: 34489993 PMCID: PMC8416774 DOI: 10.3389/fpls.2021.690567] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Biological nitrogen fixation by Rhizobium-legume symbioses represents an environmentally friendly and inexpensive alternative to the use of chemical nitrogen fertilizers in legume crops. Rhizobial inoculants, applied frequently as biofertilizers, play an important role in sustainable agriculture. However, inoculants often fail to compete for nodule occupancy against native rhizobia with inferior nitrogen-fixing abilities, resulting in low yields. Strains with excellent performance under controlled conditions are typically selected as inoculants, but the rates of nodule occupancy compared to native strains are rarely investigated. Lack of persistence in the field after agricultural cycles, usually due to the transfer of symbiotic genes from the inoculant strain to naturalized populations, also limits the suitability of commercial inoculants. When rhizobial inoculants are based on native strains with a high nitrogen fixation ability, they often have superior performance in the field due to their genetic adaptations to the local environment. Therefore, knowledge from laboratory studies assessing competition and understanding how diverse strains of rhizobia behave, together with assays done under field conditions, may allow us to exploit the effectiveness of native populations selected as elite strains and to breed specific host cultivar-rhizobial strain combinations. Here, we review current knowledge at the molecular level on competition for nodulation and the advances in molecular tools for assessing competitiveness. We then describe ongoing approaches for inoculant development based on native strains and emphasize future perspectives and applications using a multidisciplinary approach to ensure optimal performance of both symbiotic partners.
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Affiliation(s)
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Hailu Gunnabo A, Geurts R, Wolde-meskel E, Degefu T, E. Giller K, van Heerwaarden J. Phylogeographic distribution of rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia. FEMS Microbiol Ecol 2021; 97:fiab046. [PMID: 33724341 PMCID: PMC8016211 DOI: 10.1093/femsec/fiab046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/13/2021] [Indexed: 11/19/2022] Open
Abstract
Rhizobia are soilborne bacteria that form symbiotic relations with legumes and fix atmospheric nitrogen. The nitrogen fixation potential depends on several factors such as the type of host and symbionts and on environmental factors that affect the distribution of rhizobia. We isolated bacteria nodulating common bean in Southern Ethiopia to evaluate their genetic diversity and phylogeography at nucleotide, locus (gene/haplotype) and species levels of genetic hierarchy. Phylogenetically, eight rhizobial genospecies (including previous collections) were determined that had less genetic diversity than found among reference strains. The limited genetic diversity of the Ethiopian collections was due to absence of many of the Rhizobium lineages known to nodulate beans. Rhizobium etli and Rhizobiumphaseoli were predominant strains of bean-nodulating rhizobia in Ethiopia. We found no evidence for a phylogeographic pattern in strain distribution. However, joint analysis of the current and previous collections revealed differences between the two collections at nucleotide level of genetic hierarchy. The differences were due to genospecies Rhizobium aethiopicum that was only isolated in the earlier collection.
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Affiliation(s)
- Ashenafi Hailu Gunnabo
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Endalkachew Wolde-meskel
- World Agroforestry Centre (ICRAF), c/o ILRI Campus, Gurd Shola PO Box 5689, Addis Ababa, 4 Ethiopia
| | - Tulu Degefu
- International Crops Research Institute for the Semi-Arid Tropics, c/o ILRI Campus, Gurd Shola PO Box 5689, Addis Ababa, Ethiopia
| | - Ken E. Giller
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Joost van Heerwaarden
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
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Efstathiadou E, Savvas D, Tampakaki AP. Genetic diversity and phylogeny of indigenous rhizobia nodulating faba bean (Vicia faba L.) in Greece. Syst Appl Microbiol 2020; 43:126149. [PMID: 33161357 DOI: 10.1016/j.syapm.2020.126149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/19/2020] [Accepted: 09/19/2020] [Indexed: 12/16/2022]
Abstract
The genetic diversity and phylogeny of fast-growing rhizobia isolated from root nodules of Vicia faba grown in different geographical regions of Greece were assessed. Although Rhizobium leguminosarum sv. viciae is the most common symbiont of Vicia spp. in European soils, there is no available information on native rhizobia nodulating faba bean in Greece. Seventy bacterial strains were isolated and grouped into sixteen distinct profiles based on BOX-PCR fingerprinting. The phylogenetic affiliation was further defined by sequence analysis of the rrs and multilocus sequence analysis (MLSA) of three housekeeping genes (recA, atpD and gyrB). Fifty-eight isolates were affiliated with recently described genospecies gsF-2, represented by R. laguerreae FB206T, whereas six isolates were closely related to gsB and two isolates might belong to gsA. Two isolates assigned to R. hidalgonense and another two non-nodulating strains could not be assigned to any validly defined species and possibly belong to a new rhizobial lineage. Interestingly, R. laguerreae strains were commonly found at all sampling sites, suggesting that they could be the main symbionts of faba beans in Greek soils. According to the phylogenies of two symbiosis-related genes (nodC and nifH), all nodulating isolates belonged to symbiovar (sv.) viciae harboring four distinct nodC gene haplotypes and they were grouped into two clades together with strains assigned to R. laguerreae and genospecies of R. leguminosarum isolated from other countries and continents. This is the first report that R. hidalgonense strains belong to sv. viciae. No correlation was observed between the nodC haplotypes, geographic origin and chromosomal background of the isolates in the study.
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Affiliation(s)
- Evdoxia Efstathiadou
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855 Athens, Greece
| | - Dimitrios Savvas
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855 Athens, Greece
| | - Anastasia P Tampakaki
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855 Athens, Greece.
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Taha K, Berraho EB, El Attar I, Dekkiche S, Aurag J, Béna G. Rhizobium laguerreae is the main nitrogen-fixing symbiont of cultivated lentil ( Lens culinaris ) in Morocco. Syst Appl Microbiol 2018; 41:113-121. [DOI: 10.1016/j.syapm.2017.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/18/2017] [Accepted: 09/22/2017] [Indexed: 10/18/2022]
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7
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Rapeseed-legume intercrops: plant growth and nitrogen balance in early stages of growth and development. Heliyon 2017; 3:e00261. [PMID: 28337486 PMCID: PMC5352734 DOI: 10.1016/j.heliyon.2017.e00261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/27/2017] [Accepted: 03/08/2017] [Indexed: 11/21/2022] Open
Abstract
In this study we tested whether legumes can improve the growth and N and S nutrition of rapeseed in an intercropping system and compared the effect of mixtures on legume N-fixation and soil N-resources. Rapeseed was cultivated in low N conditions in monocrops using one (R) or two plants (RR) per pot and in mixtures with lupine, clover or vetch. The R monocrop was the most relevant control, intraspecific competition inducing a significant growth delay resulting in a significantly lower leaf number, in RR monocrop compared to R and the three mixtures considered. Plant biomass, and the N and S contents of rapeseed grown in mixtures were the same than those measured in R monocrop. Compared to the monocrop, the proportion of N derived from the atmosphere was increased by 34, 140 and 290% in lupine, clover and vetch, respectively when intercropped with rapeseed. In mixture with clover and lupine, the soil N pool at harvest was higher than in other treatments, while N export by crop was constant. Legumes suffered from competition for soil S resulting in a decrease of 40% in their S content compared to the monocrop. Compared to rapeseeds grown in R monocrop and in mixture with lupine and vetch, rapeseed mixed with clover showed significantly higher SPAD values in old leaves. In our conditions, mixing legumes with rapeseed is relevant to reduce N fertilization and improve nutrition and growth of rapeseed.
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Génard T, Etienne P, Laîné P, Yvin JC, Diquélou S. Nitrogen transfer from Lupinus albus L., Trifolium incarnatum L. and Vicia sativa L. contribute differently to rapeseed (Brassica napus L.) nitrogen nutrition. Heliyon 2016; 2:e00150. [PMID: 27656683 PMCID: PMC5021797 DOI: 10.1016/j.heliyon.2016.e00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/22/2016] [Accepted: 08/26/2016] [Indexed: 11/22/2022] Open
Abstract
Nitrogen (N) transfer is well documented in legume-cereal intercropping but this is less often reported for legume-Brassica intercrops even though Brassica crops require higher levels of N fertilizers. The present study was carried out to quantify N transfer from legumes (Lupinus albus L., Trifolium incarnatum L. or Vicia sativa L.) to rapeseed (Brassica napus L.) using the split-root (15)N-labelling method. After three months we observed that legumes did not alter the growth of rapeseed. Vetch showed the lowest growth and demonstrated low (15)N shoot to root translocation and no significant N transfer to rapeseed. In contrast, significant (15)N enrichment was found in lupine and clover and (15)N was transferred to the associated rapeseed plants (around 6 and 4 mg N plant(-1), respectively), which contributed 2 to 3% of the rapeseed total N. Additionally, the data revealed that N2 fixation dominated the N nutrition in lupine despite the high N level provided in the donor compartment, suggesting a greater niche segregation between companion plants. Based on the results of this study we suggest that intercropping can be a relevant contributor to rapeseed N nutrition. Among the three legumes tested, clover and lupine seemed to be the best intercropping candidates.
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Affiliation(s)
- Thaïs Génard
- Normandie Université, Caen, France
- UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, UNICAEN, Caen, France
- UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, INRA, Caen, France
| | - Philippe Etienne
- Normandie Université, Caen, France
- UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, UNICAEN, Caen, France
- UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, INRA, Caen, France
| | - Philippe Laîné
- Normandie Université, Caen, France
- UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, UNICAEN, Caen, France
- UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, INRA, Caen, France
| | - Jean-Claude Yvin
- Centre Mondial d’Innovation, Groupe Roullier, Saint Malo, France
| | - Sylvain Diquélou
- Normandie Université, Caen, France
- UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, UNICAEN, Caen, France
- UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, INRA, Caen, France
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9
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Sami D, Mokhtar R, Peter M, Mohamed M. Rhizobium leguminosarum symbiovar trifolii, Ensifer numidicus and Mesorhizobium amorphae symbiovar ciceri (or Mesorhizobium loti) are new endosymbiotic bacteria of Lens culinaris Medik. FEMS Microbiol Ecol 2016; 92:fiw118. [PMID: 27267929 DOI: 10.1093/femsec/fiw118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2016] [Indexed: 11/13/2022] Open
Abstract
A total of 142 rhizobial bacteria were isolated from root nodules of Lens culinaris Medik endemic to Tunisia and they belonged to the species Rhizobium leguminosarum, and for the first time to Ensifer and Mesorhizobium, genera never previously described as microsymbionts of lentil. Phenotypically, our results indicate that L. culinaris Medik strains showed heterogenic responses to the different phenotypic features and they effectively nodulated their original host. Based on the concatenation of the 16S rRNA with relevant housekeeping genes (glnA, recA, dnaK), rhizobia that nodulate lentil belonged almost exclusively to the known R. leguminosarum sv. viciae. Interestingly, R. leguminosarum sv. trifolii, Ensifer numidicus (10 isolates) and Mesorhizobium amorphae (or M. loti) (9 isolates) isolates species, not considered, up to now, as a natural symbiont of lentil are reported. The E. numidicus and M. amorphae (or M. loti) strains induced fixing nodules on Medicago sativa and Cicer arietinum host plants, respectively. Symbiotic gene phylogenies showed that the E. numidicus, new symbiont of lentil, markedly diverged from strains of R. leguminosarum, the usual symbionts of lentil, and converged to the symbiovar meliloti so far described within E. meliloti Indeed, the nodC and nodA genes from the M. amorphae showed more than 99% similarity with respect to those from M. mediterraneum, the common chickpea nodulating species, and would be included in the new infrasubspecific division named M. amorphae symbiovar ciceri, or to M. loti, related to the strains able to effectively nodulate C. arietinum host plant. On the basis of these data, R. leguminosarum sv. trifolii (type strain LBg3 (T)), M. loti or M. amorphae sv. ciceri (type strain LB4 (T)) and E. numidicus (type strain LBi2 (T)) are proposed as new symbionts of L. culinaris Medik.
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Affiliation(s)
- Dhaoui Sami
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
| | - Rejili Mokhtar
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
| | - Mergaert Peter
- Institute for IntegrativeBiology of the Cell, Centre National de la Recherche Scientifique, Avenue de la Terrasse Bât. 34, 91198 Gif-sur-Yvette, France
| | - Mars Mohamed
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
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10
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Riah N, Béna G, Djekoun A, Heulin K, de Lajudie P, Laguerre G. Genotypic and symbiotic diversity of Rhizobium populations associated with cultivated lentil and pea in sub-humid and semi-arid regions of Eastern Algeria. Syst Appl Microbiol 2014; 37:368-75. [PMID: 24582507 DOI: 10.1016/j.syapm.2013.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/27/2013] [Accepted: 12/04/2013] [Indexed: 11/19/2022]
Abstract
The genetic structure of rhizobia nodulating pea and lentil in Algeria, Northern Africa was determined. A total of 237 isolates were obtained from root nodules collected on lentil (Lens culinaris), proteaginous and forage pea (Pisum sativum) growing in two eco-climatic zones, sub-humid and semi-arid, in Eastern Algeria. They were characterised by PCR-restriction fragment length polymorphism (RFLP) of the 16S-23S rRNA intergenic region (IGS), and the nodD-F symbiotic region. The combination of these haplotypes allowed the isolates to be clustered into 26 distinct genotypes, and all isolates were classified as Rhizobium leguminosarum. Symbiotic marker variation (nodD-F) was low but with the predominance of one nod haplotype (g), which had been recovered previously at a high frequency in Europe. Sequence analysis of the IGS further confirmed its high variability in the studied strains. An AMOVA analysis showed highly significant differentiation in the IGS haplotype distribution between populations from both eco-climatic zones. This differentiation was reflected by differences in dominant genotype frequencies. Conversely, no host plant effect was detected. The nodD gene sequence-based phylogeny suggested that symbiotic gene diversity in pea and lentil nodulating rhizobial populations in Algeria was low compared to that reported elsewhere in the world.
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MESH Headings
- Algeria
- Bacterial Proteins/genetics
- Cluster Analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Intergenic/chemistry
- DNA, Intergenic/genetics
- Genetic Variation
- Haplotypes
- Lens Plant/microbiology
- Molecular Sequence Data
- Pisum sativum/microbiology
- Phylogeny
- Plant Roots/microbiology
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Rhizobium leguminosarum/classification
- Rhizobium leguminosarum/genetics
- Rhizobium leguminosarum/physiology
- Sequence Analysis, DNA
- Symbiosis
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Affiliation(s)
- Nassira Riah
- Laboratoire de Génétique, Biochimie et Biotechnologies Végétalesm, Faculté des Sciences de la Nature, Université Constantine 1, Route Ain El Bey 25000, Algeria; IRD - INRA LSTM, Tropical and Mediterranean Symbiosis Laboratory, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Gilles Béna
- IRD - INRA LSTM, Tropical and Mediterranean Symbiosis Laboratory, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France.
| | - Abdelhamid Djekoun
- Laboratoire de Génétique, Biochimie et Biotechnologies Végétalesm, Faculté des Sciences de la Nature, Université Constantine 1, Route Ain El Bey 25000, Algeria
| | - Karine Heulin
- IRD - INRA LSTM, Tropical and Mediterranean Symbiosis Laboratory, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Philippe de Lajudie
- IRD - INRA LSTM, Tropical and Mediterranean Symbiosis Laboratory, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Gisèle Laguerre
- IRD - INRA LSTM, Tropical and Mediterranean Symbiosis Laboratory, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
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11
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García-de Los Santos A, Brom S, Romero D. Rhizobium plasmids in bacteria-legume interactions. World J Microbiol Biotechnol 2014; 12:119-25. [PMID: 24415159 DOI: 10.1007/bf00364676] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The functional analysis of plasmids in Rhizobium strains has concentrated mainly on the symbiotic plasmid (pSym). However, genetic information relevant to both symbiotic and saprophytic Rhizobium life cycles, localized on other 'cryptic' replicons, has also been reported. Information is reviewed which concerns functional features encoded in plasmids other than the pSym: biosynthesis of cell surface polysaccharides, metabolic processes, the utilization of plant exudates, aromatic compounds and diverse sugars, and features involved symbiotic performance. In addition, factors which affect plasmid evolution through their influence on structural features of the plasmids, such as conjugative transfer and genomic rearrangements, is discussed. Based on the overall data, we propose that together the plasmids and the chromosome constitute a fully integrated genomic complex, entailing structural features as well as saprophytic and cellular functions.
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Harun-or Rashid M, Gonzalez J, Young JPW, Wink M. Rhizobium leguminosarum is the symbiont of lentils in the Middle East and Europe but not in Bangladesh. FEMS Microbiol Ecol 2013; 87:64-77. [PMID: 24033582 DOI: 10.1111/1574-6941.12190] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 01/07/2023] Open
Abstract
Lentil is the oldest of the crops that have been domesticated in the Fertile Crescent and spread to other regions during the Bronze Age, making it an ideal model to study the evolution of rhizobia associated with crop legumes. Housekeeping and nodulation genes of lentil-nodulating rhizobia from the region where lentil originated (Turkey and Syria) and regions to which lentil was introduced later (Germany and Bangladesh) were analyzed to determine their genetic diversity, population structure, and taxonomic position. There are four different lineages of rhizobia associated with lentil nodulation, of which three are new and endemic to Bangladesh, while Mediterranean and Central European lentil symbionts belong to the Rhizobium leguminosarum lineage. The endemic lentil grex pilosae may have played a significant role in the origin of these new lineages in Bangladesh. The presence of R. leguminosarum with lentil at the center of origin and in countries where lentil was introduced later suggests that R. leguminosarum is the original symbiont of lentil. Lentil seeds may have played a significant role in the initial dispersal of this Rhizobium species within the Middle East and on to other countries. Nodulation gene sequences revealed a high similarity to those of symbiovar viciae.
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Affiliation(s)
- M Harun-or Rashid
- Department of Biology, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany; Soil Microbiology Laboratory, Soil Science Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh, Bangladesh
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Genetic diversity of rhizobia nodulating lentil (Lens culinaris) in Bangladesh. Syst Appl Microbiol 2012; 35:98-109. [DOI: 10.1016/j.syapm.2011.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/17/2011] [Accepted: 11/20/2011] [Indexed: 11/23/2022]
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14
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Li Q, Zhang X, Zou L, Chen Q, Fewer DP, Lindström K. Horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plantsAstragalus luteolusandAstragalus ernestiiin Sichuan, China. FEMS Microbiol Ecol 2009; 70:71-9. [DOI: 10.1111/j.1574-6941.2009.00776.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Laranjo M, Alexandre A, Rivas R, Velázquez E, Young JPW, Oliveira S. Chickpea rhizobia symbiosis genes are highly conserved across multiple Mesorhizobium species. FEMS Microbiol Ecol 2008; 66:391-400. [DOI: 10.1111/j.1574-6941.2008.00584.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Diversity of rhizobia nodulating wild shrubs of Sicily and some neighbouring islands. Arch Microbiol 2008; 190:461-70. [DOI: 10.1007/s00203-008-0394-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 05/19/2008] [Accepted: 05/26/2008] [Indexed: 10/21/2022]
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Mutch LA, Young JPW. Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes. Mol Ecol 2004; 13:2435-44. [PMID: 15245415 DOI: 10.1111/j.1365-294x.2004.02259.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The symbiotic partnerships between legumes and their root-nodule bacteria (rhizobia) vary widely in their degree of specificity, but the underlying reasons are not understood. To assess the potential for host-range evolution, we have investigated microheterogeneity among the shared symbionts of a group of related legume species. Host specificity and genetic diversity were characterized for a soil population of Rhizobium leguminosarum biovar viciae (Rlv) sampled using six wild Vicia and Lathyrus species and the crop plants pea (Pisum sativum) and broad bean (Vicia faba). Genetic variation among 625 isolates was assessed by restriction fragment length polymorphism (RFLP) of loci on the chromosome (ribosomal gene spacer) and symbiosis plasmid (nodD region). Broad bean strongly favoured a particular symbiotic genotype that formed a distinct phylogenetic subgroup of Rlv nodulation genotypes but was associated with a range of chromosomal backgrounds. Host range tests of 80 isolates demonstrated that only 34% of isolates were able to nodulate V. faba. By contrast, 89% were able to nodulate all the local wild hosts tested, so high genetic diversity of the rhizobial population cannot be ascribed directly to the diversity of host species at the site. Overall the picture is of a population of symbionts that is diversified by plasmid transfer and shared fairly indiscriminately by local wild legume hosts. The crop species are less promiscuous in their interaction with symbionts than the wild legumes.
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Affiliation(s)
- Lesley A Mutch
- Department of Biology (Area 3), University of York, PO Box 373, York YO10 5YW, UK
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Willems A, Fernández-López M, Muñoz-Adelantado E, Goris J, De Vos P, Martínez-Romero E, Toro N, Gillis M. Description of new Ensifer strains from nodules and proposal to transfer Ensifer adhaerens Casida 1982 to Sinorhizobium as Sinorhizobium adhaerens comb. nov. Request for an opinion. Int J Syst Evol Microbiol 2003; 53:1207-1217. [PMID: 12892151 DOI: 10.1099/ijs.0.02264-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A group of four diverse rhizobial isolates and two soil isolates that are highly related to Ensifer adhaerens were characterized by a polyphasic approach. On the basis of DNA-DNA hybridizations and phenotypic features, these strains cannot be distinguished clearly form Ensifer adhaerens, a soil bacterium that was described in 1982, mainly on the basis of phenotypic characteristics. Phylogenetically, Ensifer and Sinorhizobium form a single group in the 16S rDNA dendrogram of the alpha-Proteobacteria, as well as in an analysis of partial recA gene sequences. They may therefore be regarded as a single genus. Because Sinorhizobium was proposed in 1988, according to the Bacteriological Code (1990 Revision) the older name, Ensifer, has priority. However, there are several reasons why a change from Sinorhizobium to Ensifer may not be the best solution and making an exception to Rule 38 may be more appropriate. We therefore propose the species Sinorhizobium adhaerens comb. nov. and put forward a Request for an Opinion to the Judicial Commission regarding the conservation of Sinorhizobium adhaerens over Ensifer adhaerens.
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Affiliation(s)
- Anne Willems
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie, Microbiologie, Faculteit Wetenschappen, Universiteit Gent, Ledeganckstraat 35, B-9000 Belgium
| | - Manuel Fernández-López
- Grupo de Ecología Genética, Estación Experimental del Zaidin, CSIC, E-18008, Granada, Spain
| | | | - Johan Goris
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie, Microbiologie, Faculteit Wetenschappen, Universiteit Gent, Ledeganckstraat 35, B-9000 Belgium
| | - Paul De Vos
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie, Microbiologie, Faculteit Wetenschappen, Universiteit Gent, Ledeganckstraat 35, B-9000 Belgium
| | - Esperanza Martínez-Romero
- Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Ap. P. 565-A, Cuernavaca, Mexico
| | - Nicolas Toro
- Grupo de Ecología Genética, Estación Experimental del Zaidin, CSIC, E-18008, Granada, Spain
| | - Monique Gillis
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie, Microbiologie, Faculteit Wetenschappen, Universiteit Gent, Ledeganckstraat 35, B-9000 Belgium
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Mohmmed A, Sharma RS, Ali S, Babu CR. Molecular diversity of the plasmid genotypes among Rhizobium gene pools of sesbanias from different habitats of a semi-arid region (Delhi). FEMS Microbiol Lett 2001; 205:171-8. [PMID: 11750798 DOI: 10.1111/j.1574-6968.2001.tb10943.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Plasmid genotypes of root nodulating rhizobial isolates of Sesbania, sampled from six ecologically distinct habitats, were characterized. Plasmid profile analysis revealed nine different plasmid types having molecular masses ranging from 30 to 300 MDa, distributed among six profile types that grouped the isolates into six plasmid classes. The six plasmid profiles were diverged from each other and lack many common plasmid types among them. Variation in number and types of symbiotic (Sym) plasmid was assessed by hybridization of plasmid profiles with sym gene probes. Relatedness among different plasmid types was assessed by hybridization of total DNAs as well as plasmid profiles of different isolates with labelled intact plasmid. Plasticity of plasmid genotype and possible recombination between different plasmid types is suggested from the results obtained. Structural diversity among sym plasmids was assessed by PCR amplified product profiles using primer corresponding to the reiterated nif promoter consensus element (NPC-PCR). A total of 26 NPC-PCR profile types were recognized. Genetic diversity among sym plasmids of isolates belonging to the same plasmid class and having similar sym plasmid suggested recombinations and rearrangements of sequences within the sym plasmids. Cluster analysis based upon similarity among profile types sorted the isolates across the ecological gradient. We suggest that habitat heterogeneity and plasticity of plasmid genotype together contribute for the generation of genetic diversity leading to strainal differentiation in rhizobia.
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Affiliation(s)
- A Mohmmed
- Department of Botany, University of Delhi, India.
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Villadas PJ, Burgos P, RodrıÌguez-Navarro DN, Temprano F, Toro N. Characterization of rhizobia homologues of Sinorhizobium meliloti insertion sequences ISRm3 and ISRm4. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00485.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Rigottier-Gois L, Turner SL, Young JPW, Amarger N. Distribution of repC plasmid-replication sequences among plasmids and isolates of Rhizobium leguminosarum bv. viciae from field populations. Microbiology (Reading) 1998; 144:771-780. [DOI: 10.1099/00221287-144-3-771] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The distribution of four classes of related plasmid replication genes (repC) within three field populations of Rhizobium leguminosarum in France, Germany and the UK was investigated using RFLP, PCR-RFLP and plasmid profile analysis. The results suggest that the four repC classes are compatible: when two or more different repC sequences are present in a strain they are usually associated with different plasmids. Furthermore, classical incompatibility studies in which a Tn5-labelled plasmid with a group IV repC sequence was transferred into field isolates by conjugation demonstrated that group IV sequences are incompatible with each other, but compatible with the other repC groups. This supports the idea that the different repC groups represent different incompatibility groups. The same field isolates were also screened for chromosomal (plac12) and symbiotic gene (nodD-F region) variation. Comparison of these and the plasmid data suggest that plasmid transfer does occur within field populations of R. leguminosarum but that certain plasmid-chromosome combinations are favoured.
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Affiliation(s)
- Lionel Rigottier-Gois
- Laboratoire de Microbiologie des Sols, Institut National de la Recherche Agronomique,17 rue Sully, BV 1540, 21034 Dijon cedex,France
| | - Sarah L. Turner
- Department of Biology, University of York,PO Box 373, York YO1 5YW,UK
| | - J. Peter W. Young
- Department of Biology, University of York,PO Box 373, York YO1 5YW,UK
| | - Noëlle Amarger
- Laboratoire de Microbiologie des Sols, Institut National de la Recherche Agronomique,17 rue Sully, BV 1540, 21034 Dijon cedex,France
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Zahran HH. Chemotaxonomic characterization of some fast-growing rhizobia nodulating leguminous trees. Folia Microbiol (Praha) 1997. [DOI: 10.1007/bf02816952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Mazurier SI, Laguerre G. Unusual localization of nod and nif genes in Rhizobium leguminosarum bv. viciae. Can J Microbiol 1997. [DOI: 10.1139/m97-056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genomic DNA from seven strains of Rhizobium leguminosarum bv. viciae isolated from nodules of field-grown lentils showed homology to nod and nif gene probes, whereas plasmid DNA did not hybridize with these probes. The results suggest that symbiotic genes could be located on the chromosome or perhaps on a very large plasmid that could not be resolved in Eckhardt gels. Each strain contained one plasmid that hybridized with a pSym isolated from a R. leguminosarum strain of the same field population. This finding led us to hypothesize that the nod and nif genes of the seven strains might have originated from a Sym plasmid and have been integrated into another replicon. The ability to nodulate vetch was confirmed for all of the seven strains. Thus, wild strains of R. leguminosarum bv. viciae that nodulate vetch carry nod and nif genes either on the chromosome or on an extrachromosomal replicon of size much larger than the pSyms hitherto described.Key words: Rhizobium leguminosarum, nod genes, nif genes, chromosome, symbiotic plasmid, megaplasmid.
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Louvrier P, Laguerre G, Amarger N. Distribution of Symbiotic Genotypes in Rhizobium leguminosarum biovar viciae Populations Isolated Directly from Soils. Appl Environ Microbiol 1996; 62:4202-5. [PMID: 16535447 PMCID: PMC1388985 DOI: 10.1128/aem.62.11.4202-4205.1996] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The distribution of symbiotic (Sym) plasmid types across background genotypes was investigated in two field populations of Rhizobium leguminosarum biovar viciae isolated directly from soils. PCR-based methods were used to characterize the background genotypes and the Sym gene types. Identical Sym gene types were associated with a variable range of background genotypes, while the same background genotype could harbor distinct Sym gene types. Random distributions of Sym gene types in the background genotypes were observed in the two soil populations. These results suggest that Sym plasmid transfer is less restricted than previously thought on the basis of the analysis of strains isolated from legume nodules.
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Urtz BE, Elkan GH. Genetic diversity among bradyrhizobium isolates that effectively nodulate peanut (Arachis hypogaea). Can J Microbiol 1996; 42:1121-30. [PMID: 8941988 DOI: 10.1139/m96-144] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Symbiotic gene diversity and other measures of genetic diversity were examined in Bradyrhizobium isolates that form an effective symbiosis with peanut (Arachis hypogaea). Initially, restriction fragment length polymorphism (RFLP) analysis using a nitrogenase (nif) gene probe was performed on 33 isolates along with one Bradyrhizobium elkanii and two Bradyrhizobium japonicum strains. Considerable diversity was observed among the RFLP patterns of many of the isolates, especially those from South America. Some isolates, however, were found to have similar nif and subsequent nod (nodulation) gene RFLP patterns, indicating symbiotic gene relatedness. With some noted exceptions, symbiotic gene relatedness correlated with relatedness based on total DNA homology and ribotyping analyses. Symbiotic gene relatedness also correlated with symbiotic effectiveness. The RFLP and DNA homology analyses indicate that bradyrhizobia effective with peanut are genetically diverse and consist of at least three different species. This diversity, however, was not particularly evident with partial 16S rRNA gene sequencing. Sequences obtained from the isolates were very similar to each other as well as to sequences previously reported for other Bradyrhizobium strains.
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Affiliation(s)
- B E Urtz
- Microbiology Department, North Carolina State University, Raleigh 27695, USA
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Villadas PJ, Velazquez E, Martinez-Molina E, Toro N. Identification of nodule-dominant Rhizobium meliloti strains carrying pRmeGR4b-type plasmid within indigenous soil populations by PCR using primers derived from specific DNA sequences. FEMS Microbiol Ecol 1995. [DOI: 10.1111/j.1574-6941.1995.tb00139.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Parekh NR, Hartmann A, Charnay MP, Fournier JC. Diversity of carbofuran-degrading soil bacteria and detection of plasmid-encoded sequences homologous to the mcd gene. FEMS Microbiol Ecol 1995. [DOI: 10.1111/j.1574-6941.1995.tb00138.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Geniaux E, Amarger N. Diversity and stability of plasmid transfer in isolates from a single field population ofRhizobium leguminosarumbv.viciae. FEMS Microbiol Lett 1993. [DOI: 10.1111/j.1574-6968.1993.tb05816.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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