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Rivera Ortuña FN, Guevara-Luna J, Yan J, Lopez Amezcua E, Arroyo-Herrera I, Li Y, Vásquez-Murrieta MS, Rojas Arellano D, Wang ET. Rhizobium hidalgonense and Rhizobium redzepovicii as faba bean (Vicia faba L.) microsymbionts in Mexican soils. Arch Microbiol 2024; 206:281. [PMID: 38805057 DOI: 10.1007/s00203-024-03989-3] [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: 10/19/2023] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
Abstract
As a legume crop widely cultured in the world, faba bean (Vicia faba L.) forms root nodules with diverse Rhizobium species in different regions. However, the symbionts associated with this plant in Mexico have not been studied. To investigate the diversity and species/symbiovar affiliations of rhizobia associated with faba bean in Mexico, rhizobia were isolated from this plant grown in two Mexican sites in the present study. Based upon the analysis of recA gene phylogeny, two genotypes were distinguished among a total of 35 isolates, and they were identified as Rhizobium hidalgonense and Rhizobium redzepovicii, respectively, by the whole genomic sequence analysis. Both the species harbored identical nod gene cluster and the same phylogenetic positions of nodC and nifH. So, all of them were identified into the symbiovar viciae. As a minor group, R. hidalgonense was only isolated from slightly acid soil and R. redzepovicii was the dominant group in both the acid and neutral soils. In addition, several genes related to resistance to metals (zinc, copper etc.) and metalloids (arsenic) were detected in genomes of the reference isolates, which might offer them some adaptation benefits. As conclusion, the community composition of faba bean rhizobia in Mexico was different from those reported in other regions. Furthermore, our study identified sv. viciae as the second symbiovar in the species R. redzepovicii. These results added novel evidence about the co-evolution, diversification and biogeographic patterns of rhizobia in association with their host legumes in distinct geographic regions.
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Affiliation(s)
- Flor N Rivera Ortuña
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Joseph Guevara-Luna
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Jun Yan
- National Observation Station of Hailun Agro-Ecology System, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Eloisa Lopez Amezcua
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Ivan Arroyo-Herrera
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Yan Li
- College of Life Science, Yantai University, Shandong Province, Yantai City, 264005, China
| | - Maria Soledad Vásquez-Murrieta
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Danae Rojas Arellano
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México.
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Janczarek M, Kozieł M, Adamczyk P, Buczek K, Kalita M, Gromada A, Mordzińska-Rak A, Polakowski C, Bieganowski A. Symbiotic efficiency of Rhizobium leguminosarum sv. trifolii strains originating from the subpolar and temperate climate regions. Sci Rep 2024; 14:6264. [PMID: 38491088 PMCID: PMC10943007 DOI: 10.1038/s41598-024-56988-1] [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: 08/07/2023] [Accepted: 03/13/2024] [Indexed: 03/18/2024] Open
Abstract
Red clover (Trifolium pratense L.) is a forage legume cultivated worldwide. This plant is capable of establishing a nitrogen-fixing symbiosis with Rhizobium leguminosarum symbiovar trifolii strains. To date, no comparative analysis of the symbiotic properties and heterogeneity of T. pratense microsymbionts derived from two distinct geographic regions has been performed. In this study, the symbiotic properties of strains originating from the subpolar and temperate climate zones in a wide range of temperatures (10-25 °C) have been characterized. Our results indicate that all the studied T. pratense microsymbionts from two geographic regions were highly efficient in host plant nodulation and nitrogen fixation in a wide range of temperatures. However, some differences between the populations and between the strains within the individual population examined were observed. Based on the nodC and nifH sequences, the symbiotic diversity of the strains was estimated. In general, 13 alleles for nodC and for nifH were identified. Moreover, 21 and 61 polymorphic sites in the nodC and nifH sequences were found, respectively, indicating that the latter gene shows higher heterogeneity than the former one. Among the nodC and nifH alleles, three genotypes (I-III) were the most frequent, whereas the other alleles (IV-XIII) proved to be unique for the individual strains. Based on the nodC and nifH allele types, 20 nodC-nifH genotypes were identified. Among them, the most frequent were three genotypes marked as A (6 strains), B (5 strains), and C (3 strains). Type A was exclusively found in the temperate strains, whereas types B and C were identified in the subpolar strains. The remaining 17 genotypes were found in single strains. In conclusion, our data indicate that R. leguminosarum sv. trifolii strains derived from two climatic zones show a high diversity with respect to the symbiotic efficiency and heterogeneity. However, some of the R. leguminosarum sv. trifolii strains exhibit very good symbiotic potential in the wide range of the temperatures tested; hence, they may be used in the future for improvement of legume crop production.
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Affiliation(s)
- Monika Janczarek
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland.
| | - Marta Kozieł
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Paulina Adamczyk
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Katarzyna Buczek
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Anna Gromada
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Aleksandra Mordzińska-Rak
- Department of Biochemistry and Molecular Biology, Faculty of Medical Studies, Medical University in Lublin, 1 Chodźki, 20-093, Lublin, Poland
| | - Cezary Polakowski
- Department of Natural Environment Biogeochemistry, Institute of Agrophysics, Polish Academy of Sciences, 4 Doświadczalna, 20-290, Lublin, Poland
| | - Andrzej Bieganowski
- Department of Natural Environment Biogeochemistry, Institute of Agrophysics, Polish Academy of Sciences, 4 Doświadczalna, 20-290, Lublin, Poland
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Definition of the symbiovar viciae in the species Rhizobium azibense and biogeographic implications. Arch Microbiol 2023; 205:18. [PMID: 36480106 PMCID: PMC9732059 DOI: 10.1007/s00203-022-03330-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/06/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Vicia faba L. (faba bean) is a legume cultivated worldwide which commonly establishes effective symbiosis with the symbiovar viciae of species from the Rhizobium leguminosarum phylogenetic group. However, on the basis of the rrs, recA, and atpD gene phylogenies, in this work we identified a strain named EFBRI 42 nodulating V. faba as Rhizobium azibense. This is the first report on the nodulation of Vicia by R. azibense which commonly nodulates P. vulgaris and to date encompasses strains harboring the nodC genes typical of the symbiovars gallicum and phaseoli. However, the strain EFBRI 42 carries a nodC gene typical of the symbiovar viciae for which we report here by the first time this symbiovar in R. azibense. This finding showed the existence of symbiotic genes horizontal transfer events during the coevolution of R. azibense with P. vulgaris and V. faba in their respective distribution centers of Mesoamerica and the Middle East.
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Kozieł M, Kalita M, Janczarek M. Genetic diversity of microsymbionts nodulating Trifolium pratense in subpolar and temperate climate regions. Sci Rep 2022; 12:12144. [PMID: 35840628 PMCID: PMC9287440 DOI: 10.1038/s41598-022-16410-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Rhizobia are soil-borne bacteria forming symbiotic associations with legumes and fixing atmospheric dinitrogen. The nitrogen-fixation potential depends on the type of host plants and microsymbionts as well as environmental factors that affect the distribution of rhizobia. In this study, we compared genetic diversity of bacteria isolated from root nodules of Trifolium pratense grown in two geographical regions (Tromsø, Norway and Lublin, Poland) located in distinct climatic (subpolar and temperate) zones. To characterize these isolates genetically, three PCR-based techniques (ERIC, BOX, and RFLP of the 16S-23S rRNA intergenic spacer), 16S rRNA sequencing, and multi-locus sequence analysis of chromosomal house-keeping genes (atpD, recA, rpoB, gyrB, and glnII) were done. Our results indicate that a great majority of the isolates are T. pratense microsymbionts belonging to Rhizobium leguminosarum sv. trifolii. A high diversity among these strains was detected. However, a lower diversity within the population derived from the subpolar region in comparison to that of the temperate region was found. Multi-locus sequence analysis showed that a majority of the strains formed distinct clusters characteristic for the individual climatic regions. The subpolar strains belonged to two (A and B) and the temperate strains to three R. leguminosarum genospecies (B, E, and K), respectively.
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Affiliation(s)
- Marta Kozieł
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Monika Janczarek
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland.
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Youseif SH, Abd El-Megeed FH, Abdelaal AS, Ageez A, Martínez-Romero E. Plant-microbe-microbe interactions influence the faba bean nodule colonization by diverse endophytic bacteria. FEMS Microbiol Ecol 2021; 97:6381688. [PMID: 34610117 DOI: 10.1093/femsec/fiab138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/30/2021] [Indexed: 11/14/2022] Open
Abstract
Legume root nodules harbor rhizobia and other non-nodulating endophytes known as nodule-associated bacteria (NAB) whose role in the legume symbiosis is still unknown. We analysed the genetic diversity of 34 NAB isolates obtained from the root nodules of faba bean grown under various soil conditions in Egypt using 16S rRNA and concatenated sequences of three housekeeping genes. All isolates were identified as members of the family Enterobacteriaceae belonging to the genera Klebsiella, Enterobacter and Raoultella. We identified nine enterobacterial genospecies, most of which have not been previously reported as NAB. All isolated strains harbored nifH gene sequences and most of them possessed plant growth-promoting (PGP) traits. Upon co-inoculation with an N2 fixing rhizobium (Rlv NGB-FR128), two strains (Enterobacter sichanensis NGB-FR97 and Klebsiella variicola NGB-FR116) significantly increased nodulation, growth and N-uptake of faba bean plants over the single treatments or the uninoculated control. The presence of these enterobacteria in nodules was significantly affected by the host plant genotype, symbiotic rhizobium genotype and endophyte genotype, indicating that the nodule colonization process is regulated by plant-microbe-microbe interactions. This study emphasizes the importance of nodule-associated enterobacteria and suggests their potential role in improving the effectiveness of rhizobial inoculants.
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Affiliation(s)
- Sameh H Youseif
- Department of Microbial Genetic Resources, National Gene Bank, Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Fayrouz H Abd El-Megeed
- Department of Microbial Genetic Resources, National Gene Bank, Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Ali S Abdelaal
- Department of Genetics, Faculty of Agriculture, Damietta University, Damietta 34517, Egypt
| | - Amr Ageez
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center (ARC), Giza 12619, Egypt.,Faculty of Biotechnology, MSA University, 6th of October City 12451, Egypt
| | - Esperanza Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
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Ilahi H, Hsouna J, Ellouze W, Gritli T, Chihaoui SA, Barhoumi F, Najib Elfeddy M, Bachkouel S, Ouahmane L, Tambong JT, Mnasri B. Phylogenetic study of rhizobia nodulating pea (Pisum sativum) isolated from different geographic locations in Tunisia. Syst Appl Microbiol 2021; 44:126221. [PMID: 34119907 DOI: 10.1016/j.syapm.2021.126221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 11/28/2022]
Abstract
Nodulated Pisum sativum plants showed the presence of native rhizobia in 16 out of 23 soil samples collected especially in northern and central Tunisia. A total of 130 bacterial strains were selected and three different ribotypes were revealed after PCR-RFLP analysis. Sequence analyses of rrs and four housekeeping genes (recA, atpD, dnaK and glnII) assigned 35 isolates to Rhizobium laguerreae, R. ruizarguesonis, Agrobacterium radiobacter, Ensifer meliloti and two putative genospecies. R. laguerreae was the most dominant species nodulating P. sativum with 63%. The isolates 21PS7 and 21PS15 were assigned to R. ruizarguesonis, and this is the first report of this species in Tunisia. Two putative new lineages were identified, since strains 25PS6, 10PS4 and 12PS15 clustered distinctly from known rhizobia species but within the R. leguminosarum complex (Rlc) with the most closely related species being R. indicum with 96.4% sequence identity. Similarly, strains 16PS2, 3PS9 and 3PS18 showed 97.4% and 97.6% similarity with R. sophorae and R. laguerreae, respectively. Based on 16S-23S intergenic spacer (IGS) fingerprinting, there was no clear association between the strains and their geographic locations. According to nodC and nodA phylogenies, strains of Rlc species and, interestingly, strain 8PS18 identified as E. meliloti, harbored the symbiotic genes of symbiovar viciae and clustered in two different clades showing heterogeneity within the symbiovar. All these strains nodulated and fixed nitrogen with pea plants. However, the strains belonging to A. radiobacter and the two remaining strains of E. meliloti were unable to nodulate P. sativum, suggesting that they were non-symbiotic strains. The results of this study further suggest that the Tunisian Rhizobium community is more diverse than previously reported.
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Affiliation(s)
- Houda Ilahi
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Jihed Hsouna
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Walid Ellouze
- Agriculture and Agri-Food Canada, Vineland Station, Ontario L0R 2E0, Canada
| | - Takwa Gritli
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Saif-Allah Chihaoui
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Fathi Barhoumi
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Mohamed Najib Elfeddy
- Phytobacteriology Laboratory, Plant Protection Research Unit, CRRA Marrakesh, National Institute for Agronomical Research, Marrakesh 40000, Morocco
| | - Sarra Bachkouel
- Research Support and Technology Transfer Unity, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Lahcen Ouahmane
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - James T Tambong
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Bacem Mnasri
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia.
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Youseif SH, Abd El-Megeed FH, Abu Zeid AZA, Abd-Elrahman RA, Mohamed AH, Khalifa MA, Saleh SA. Alleviating the deleterious effects of soil salinity and alkalinity on faba bean ( Vicia faba L.) production using Rhizobium/Agrobacterium inoculants. ARCHIVES OF AGRONOMY AND SOIL SCIENCE 2021; 67:577-593. [DOI: 10.1080/03650340.2020.1849626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/07/2020] [Indexed: 09/02/2023]
Affiliation(s)
- Sameh H. Youseif
- Department of Microbial Genetic Resources; National Gene Bank, Agricultural Research Center (ARC), Giza, Egypt
| | - Fayrouz H. Abd El-Megeed
- Department of Microbial Genetic Resources; National Gene Bank, Agricultural Research Center (ARC), Giza, Egypt
| | - Abu Zeid A. Abu Zeid
- Food Legumes Research Department; Field Crops Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Rehab A.M. Abd-Elrahman
- Food Legumes Research Department; Field Crops Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Akram H. Mohamed
- Department of Microbial Genetic Resources; National Gene Bank, Agricultural Research Center (ARC), Giza, Egypt
| | - Mohamed A. Khalifa
- Maize Research Department; Field Crops Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Saleh A. Saleh
- Agricultural Microbiology Research Department, Soils, Water and Environment Research Institute, Agricultural Research Center (ARC), Giza, Egypt
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Youseif SH, Abd El-Megeed FH, Mohamed AH, Ageez A, Veliz E, Martínez-Romero E. Diverse Rhizobium strains isolated from root nodules of Trifolium alexandrinum in Egypt and symbiovars. Syst Appl Microbiol 2020; 44:126156. [PMID: 33232849 DOI: 10.1016/j.syapm.2020.126156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/01/2020] [Accepted: 11/02/2020] [Indexed: 12/18/2022]
Abstract
Berseem clover (T. alexandrinum) is the main forage legume crop used as animal feed in Egypt. Here, eighty rhizobial isolates were isolated from root nodules of berseem clover grown in different regions in Egypt and were grouped by RFLP-16S rRNA ribotyping. Representative isolates were characterized using phylogenetic analyses of the 16S rRNA, rpoB, glnA, pgi, and nodC genes. We also investigated the performance of these isolates using phenotypic tests and nitrogen fixation efficiency assays. The majority of strains (<90%) were closely related to Rhizobium aegyptiacum and Rhizobium aethiopicum and of the remaining strains, six belonged to the Rhizobium leguminosarum genospecies complex and only one strain was assigned to Agrobacterium fabacearum. Despite their heterogeneous chromosomal background, most of the strains shared nodC gene alleles corresponding to symbiovar trifolii. Some of the strains closely affiliated to R. aegyptiacum and R. aethiopicum had superior nodulation and nitrogen fixation capabilities in berseem clover, compared to the commercial inoculant (Okadein®) and N-added treatments. R. leguminosarum strain NGB-CR 17 that harbored a nodC allele typical of symbiovar viciae, was also able to form an effective symbiosis with clover. Two strains with nodC alleles of symbiovar trifolii, R. aegyptiacum strains NGB-CR 129 and 136, were capable of forming effective nodules in Phaseolus vulgaris in axenic greenhouse conditions. This adds the symbiovar trifolii which is well-established in the Egyptian soils to the list of symbiovars that form nodules in P. vulgaris.
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Affiliation(s)
- Sameh H Youseif
- Department of Microbial Genetic Resources, National Gene Bank, Agricultural Research Center (ARC), Giza 12619, Egypt.
| | - Fayrouz H Abd El-Megeed
- Department of Microbial Genetic Resources, National Gene Bank, Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Akram H Mohamed
- Department of Microbial Genetic Resources, National Gene Bank, Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Amr Ageez
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center (ARC), Giza 12619, Egypt; Faculty of Biotechnology, MSA University, 6 October City, Egypt
| | - Esteban Veliz
- Department of Plant Biology, University of California, Davis, Life Sciences Addition, 1 Shields Ave., Davis, CA, 95616, USA
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, UNAM Cuernavaca, Morelos, Mexico
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Gritli T, Ellouze W, Chihaoui SA, Barhoumi F, Mhamdi R, Mnasri B. Genotypic and symbiotic diversity of native rhizobia nodulating red pea (Lathyrus cicera L.) in Tunisia. Syst Appl Microbiol 2019; 43:126049. [PMID: 31870686 DOI: 10.1016/j.syapm.2019.126049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 11/24/2019] [Accepted: 12/02/2019] [Indexed: 11/15/2022]
Abstract
Nodulation and genetic diversity of native rhizobia nodulating Lathyrus cicera plants grown in 24 cultivated and marginal soils collected from northern and central Tunisia were studied. L. cicera plants were nodulated and showed the presence of native rhizobia in 21 soils. A total of 196 bacterial strains were selected and three different ribotypes were revealed after PCR-RFLP analysis. The sequence analysis of the rrs and two housekeeping genes (recA and thrC) from 36 representative isolates identified Rhizobium laguerreae as the dominant (53%) rhizobia nodulating L. cicera. To the best of our knowledge, this is the first time that this species has been reported among wild populations of the rhizobia-nodulating Lathyrus genus. Twenty-five percent of the isolates were identified as R. leguminosarum and isolates LS11.5, LS11.7 and LS8.8 clustered with Ensifer meliloti. Interestingly, five isolates (LS20.3, LS18.3, LS19.10, LS1.2 and LS21.20) were segregated from R. laguerreae and clustered as a separate clade. These isolates possibly belong to new species. According to nodC and nodA phylogeny, strains of R. laguerreae and R. leguminosarum harbored the symbiotic genes of symbiovar viciae and clustered in three different clades showing heterogeneity within the symbiovar. Strains of E. meliloti harbored symbiotic genes of Clade V and induced inefficient nodules.
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Affiliation(s)
- Takwa Gritli
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Walid Ellouze
- Agriculture and Agri-Food Canada, Vineland Station, Ontario L0R 2E0, Canada
| | - Saif-Allah Chihaoui
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Fathi Barhoumi
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Ridha Mhamdi
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Bacem Mnasri
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia.
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Genetic diversity of rhizobia associated with root nodules of white lupin (Lupinus albus L.) in Tunisian calcareous soils. Syst Appl Microbiol 2019; 42:448-456. [DOI: 10.1016/j.syapm.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/26/2019] [Accepted: 04/04/2019] [Indexed: 11/30/2022]
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11
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Chen YX, Zou L, Penttinen P, Chen Q, Li QQ, Wang CQ, Xu KW. Faba Bean ( Vicia faba L.) Nodulating Rhizobia in Panxi, China, Are Diverse at Species, Plant Growth Promoting Ability, and Symbiosis Related Gene Levels. Front Microbiol 2018; 9:1338. [PMID: 29973926 PMCID: PMC6019463 DOI: 10.3389/fmicb.2018.01338] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/31/2018] [Indexed: 01/05/2023] Open
Abstract
We isolated 65 rhizobial strains from faba bean (Vicia faba L.) from Panxi, China, studied their plant growth promoting ability with nitrogen free hydroponics, genetic diversity with clustered analysis of combined ARDRA and IGS-RFLP, and phylogeny by sequence analyses of 16S rRNA gene, three housekeeping genes and symbiosis related genes. Eleven strains improved the plant shoot dry mass significantly comparing to that of not inoculated plants. According to the clustered analysis of combined ARDRA and IGS-RFLP the isolates were genetically diverse. Forty-one of 65 isolates represented Rhizobium anhuiense, and the others belonged to R. fabae, Rhizobium vallis, Rhizobium sophorae, Agrobacterium radiobacter, and four species related to Rhizobium and Agrobacterium. The isolates carried four and five genotypes of nifH and nodC, respectively, in six different nifH-nodC combinations. When looking at the species-nifH-nodC combinations it is noteworthy that all but two of the six R. anhuiense isolates were different. Our results suggested that faba bean rhizobia in Panxi are diverse at species, plant growth promoting ability and symbiosis related gene levels.
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Affiliation(s)
- Yuan X Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Lan Zou
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- Zhejiang Provincial Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration, School of Environmental & Resource Sciences, Zhejiang Agriculture & Forestry University, Lin'an, China.,Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Qiang Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qi Q Li
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Chang Q Wang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Kai W Xu
- College of Resources, Sichuan Agricultural University, Chengdu, China
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Vicia faba L. in the Bejaia region of Algeria is nodulated by Rhizobium leguminosarum sv. viciae , Rhizobium laguerreae and two new genospecies. Syst Appl Microbiol 2018; 41:122-130. [DOI: 10.1016/j.syapm.2017.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/15/2017] [Accepted: 10/17/2017] [Indexed: 11/21/2022]
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13
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Stefan A, Van Cauwenberghe J, Rosu CM, Stedel C, Labrou NE, Flemetakis E, Efrose RC. Genetic diversity and structure of Rhizobium leguminosarum populations associated with clover plants are influenced by local environmental variables. Syst Appl Microbiol 2018; 41:251-259. [PMID: 29452714 DOI: 10.1016/j.syapm.2018.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 11/15/2022]
Abstract
The identification and conservation of indigenous rhizobia associated with legume plants and their application as biofertilizers is becoming an agricultural worldwide priority. However, little is known about the genetic diversity and phylogeny of rhizobia in Romania. In the present study, the genetic diversity and population composition of Rhizobium leguminosarum symbiovar trifolii isolates from 12 clover plants populations located across two regions in Romania were analyzed. Red clover isolates were phenotypically evaluated and genotyped by sequencing 16S rRNA gene, 16S-23S intergenic spacer, three chromosomal genes (atpD, glnII and recA) and two plasmid genes (nifH and nodA). Multilocus sequence typing (MLST) analysis revealed that red clover plants are nodulated by a wide genetic diversity of R. leguminosarum symbiovar trifolii sequence types (STs), highly similar to the ones previously found in white clover. Rhizobial genetic variation was found mainly within the two clover populations for both chromosomal and plasmid types. Many STs appear to be unique for this region and the genetic composition of rhizobia differs significantly among the clover populations. Furthermore, our results showed that both soil pH and altitude contributed to plasmid sequence type composition while differences in chromosomal composition were affected by the altitude and were strongly correlated with distance.
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Affiliation(s)
- Andrei Stefan
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania
| | - Jannick Van Cauwenberghe
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n Col. Chamilpa, Cuernavaca, Morelos CP 62210, Mexico; Plant Conservation and Population Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Craita M Rosu
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania
| | - Catalina Stedel
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Rodica C Efrose
- Department of Experimental and Applied Biology, NIRDBS-Institute of Biological Research Iasi, Lascar Catargi 47, 700107 Iasi, Romania.
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Benidire L, Lahrouni M, Daoui K, Fatemi ZEA, Gomez Carmona R, Göttfert M, Oufdou K. Phenotypic and genetic diversity of Moroccan rhizobia isolated from Vicia faba and study of genes that are likely to be involved in their osmotolerance. Syst Appl Microbiol 2018; 41:51-61. [DOI: 10.1016/j.syapm.2017.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 01/28/2023]
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15
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Tampakaki AP, Fotiadis CT, Ntatsi G, Savvas D. A novel symbiovar (aegeanense) of the genus Ensifer nodulates Vigna unguiculata. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:4314-4325. [PMID: 28220509 DOI: 10.1002/jsfa.8281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/10/2017] [Accepted: 02/16/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Cowpea (Vigna unguiculata) forms nitrogen-fixing root nodules with diverse symbiotic bacteria, mainly slow-growing rhizobial species belonging to the genus Bradyrhizobium, although a few studies have reported the isolation of fast-growing rhizobia under laboratory and field conditions. Although much research has been done on cowpea-nodulating bacteria in various countries around the world, very limited information is available on cowpea rhizobia in European soils. The aim of this study was to study the genetic and phenotypic diversity of indigenous cowpea-nodulating rhizobia in Greece. RESULTS The genetic diversity of indigenous rhizobia associated with cowpea was investigated through a polyphasic approach. ERIC-PCR based fingerprinting analysis grouped the isolates into three groups. Based on the analysis of the 16S rRNA genes, IGS and on the concatenation of six housekeeping genes (recA, glnII, gyrB, truA, thrA and SMc00019), rhizobial isolates were classified within the species Ensifer fredii. However, symbiotic gene phylogenies, based on nodC, nifH and rhcRST genes, showed that the Ensifer isolates are markedly diverged from type and reference strains of E. fredii and formed one clearly separate cluster. The E. fredii strains were able to nodulate and fix nitrogen in cowpea but not in soybean and common bean. CONCLUSION The present study showed that cowpea is nodulated under field conditions by fast-growing rhizobia belonging to the species E. fredii. Based on the phylogenies, similarity levels of symbiotic genes and the host range, the Ensifer isolates may constitute a new symbiovar for which the name 'aegeanense' is proposed. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Anastasia P Tampakaki
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Christos T Fotiadis
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Georgia Ntatsi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Savvas
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Athens, Greece
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Molecular diversity and phylogeny of indigenous Rhizobium leguminosarum strains associated with Trifolium repens plants in Romania. Antonie van Leeuwenhoek 2017; 111:135-153. [DOI: 10.1007/s10482-017-0934-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/20/2017] [Indexed: 11/30/2022]
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17
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Andrews M, Andrews ME. Specificity in Legume-Rhizobia Symbioses. Int J Mol Sci 2017; 18:E705. [PMID: 28346361 PMCID: PMC5412291 DOI: 10.3390/ijms18040705] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.
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Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
| | - Morag E Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
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Analysis of rhizobial endosymbionts of Vicia, Lathyrus and Trifolium species used to maintain mountain firewalls in Sierra Nevada National Park (South Spain). Syst Appl Microbiol 2017; 40:92-101. [DOI: 10.1016/j.syapm.2016.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 10/20/2022]
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Improvement of Faba Bean Yield Using Rhizobium/Agrobacterium Inoculant in Low-Fertility Sandy Soil. AGRONOMY-BASEL 2017. [DOI: 10.3390/agronomy7010002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Zou L, Chen YX, Penttinen P, Lan Q, Wang K, Liu M, Peng D, Zhang X, Chen Q, Zhao K, Zeng X, Xu KW. Genetic Diversity and Symbiotic Efficiency of Nodulating Rhizobia Isolated from Root Nodules of Faba Bean in One Field. PLoS One 2016; 11:e0167804. [PMID: 27936180 PMCID: PMC5147995 DOI: 10.1371/journal.pone.0167804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/21/2016] [Indexed: 11/19/2022] Open
Abstract
Thirty-one nodulating rhizobium strains were collected from root nodules of spring and winter type faba bean cultivars grown in micro ecoarea, i.e. the same field in Chengdu plain, China. The symbiotic efficiency and phylogeny of these strains were studied. Effectively nitrogen fixing strains were isolated from both winter type and spring type cultivars. Based on phylogenetic analysis of 16S rRNA gene and concatenated sequence of atpD, glnII and recA genes, the isolates were assigned as Rhizobium anhuiense and a potential new Rhizobium species. The isolates were diverse on symbiosis related gene level, carrying five, four and three variants of nifH, nodC and nodD, respectively. Strains carrying similar gene combinations were trapped by both winter and spring cultivars, disagreeing with the specificity of symbiotic genotypes to reported earlier faba bean ecotypes.
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Affiliation(s)
- Lan Zou
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yuan Xue Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- * E-mail: (KWX); (YXC)
| | - Petri Penttinen
- Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Qin Lan
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Wang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ming Liu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Dan Peng
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiangzhong Zeng
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Kai Wei Xu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- * E-mail: (KWX); (YXC)
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Gnat S, Małek W, Oleńska E, Wdowiak-Wróbel S, Kalita M, Rogalski J, Wójcik M. Multilocus sequence analysis supports the taxonomic position of Astragalus glycyphyllos symbionts based on DNA–DNA hybridization. Int J Syst Evol Microbiol 2016; 66:1906-1912. [DOI: 10.1099/ijsem.0.000862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Sebastian Gnat
- Department of Veterinary Microbiology, University of Life Sciences, 13 Akademicka st., 20-950 Lublin, Poland
| | - Wanda Małek
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Ewa Oleńska
- Department of Genetics and Evolution, University of Bialystok, 1J Ciolkowskiego st., 15-245 Bialystok, Poland
| | - Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Jerzy Rogalski
- Department of Biochemistry, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Magdalena Wójcik
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
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Xu KW, Zou L, Penttinen P, Wang K, Heng NN, Zhang XP, Chen Q, Zhao K, Chen YX. Symbiotic effectiveness and phylogeny of rhizobia isolated from faba bean (Vicia faba L.) in Sichuan hilly areas, China. Syst Appl Microbiol 2015; 38:515-23. [DOI: 10.1016/j.syapm.2015.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 11/26/2022]
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