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Msaddak A, Quiñones MA, Mars M, Pueyo JJ. The Beneficial Effects of Inoculation with Selected Nodule-Associated PGPR on White Lupin Are Comparable to Those of Inoculation with Symbiotic Rhizobia. PLANTS (BASEL, SWITZERLAND) 2023; 12:4109. [PMID: 38140436 PMCID: PMC10747367 DOI: 10.3390/plants12244109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
Nodule endophytes and associated bacteria are non-symbiotic bacteria that colonize legume nodules. They accompany nodulating rhizobia and can form beneficial associations, as some of them are plant growth-promoting rhizobacteria (PGPR) that are able to promote germination and plant growth and increase tolerance to biotic and abiotic stress. White lupin (Lupinus albus) is a legume crop that is gaining relevance as a suitable alternative to soybean as a plant protein source. Eleven nodule-associated bacteria were isolated from white lupin nodules grown in a Tunisian soil. They belonged to the genera Rhizobium, Ensifer, Pseudomonas and Bacillus. Their plant growth-promoting (PGP) and enzymatic activities were tested in vitro. Strains Pseudomonas sp., L1 and L12, displayed most PGP activities tested, and were selected for in planta assays. Inoculation with strains L1 or L12 increased seed germination and had the same positive effects on all plant growth parameters as did inoculation with symbiotic Bradyrhizobium canariense, with no significant differences among treatments. Inoculation with efficient nitrogen-fixing rhizobia must compete with rhizobia present in the soil that sometimes nodulate efficiently but fix nitrogen poorly, leading to a low response to inoculation. In such cases, inoculation with highly effective PGPR might represent a feasible alternative to boost crop productivity.
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Affiliation(s)
- Abdelhakim Msaddak
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain;
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia;
| | - Miguel A. Quiñones
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain;
| | - Mohamed Mars
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia;
| | - José J. Pueyo
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain;
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Flores-Félix JD, Sánchez-Juanes F, Araujo J, Díaz-Alcántara CA, Velázquez E, González-Andrés F. Two novel symbiovars of Bradyrhizobium yuanmingense, americaense and caribense, the symbiovar tropici of Bradyrhizobium pachyrhizi and the symbiovar cajani of Bradyrhizobium cajani are microsymbionts of the legume Cajanus cajan in Dominican Republic. Syst Appl Microbiol 2023; 46:126454. [PMID: 37703769 DOI: 10.1016/j.syapm.2023.126454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/09/2023] [Accepted: 09/03/2023] [Indexed: 09/15/2023]
Abstract
Cajanus cajan L. (guandul) is commonly cultivated in Dominican Republic where this legume is a subsistence crop. Here we identified through MALDI-TOF MS several rhizobial strains nodulating C. cajan in two Dominican locations as Bradyrhizobium yuanmingense. The phylogenetic analysis of recA and glnII housekeeping genes showed that these strains belong to a wide cluster together with the type strain of B. yuanmingense and other C. cajan nodulating strains previously isolated in Dominican Republic. The comparison of genomes from strains representative of different lineages within this cluster support the existence of several genospecies within B. yuanmingense, which is the major microsymbiont of C. cajan in Dominican Republic where it is also nodulated by Bradyrhizobium cajani and Bradyrhizobium pachyrhizi. The analysis of the symbiotic nodC gene showed that the C. cajan nodulating strains from the B. yuanmingense complex belong to two clusters with less than 90% similarity between them. The strains from these two clusters showed nodC gene similarity values lower than 90% with respect to the remaining Bradyrhizobium symbiovars and then they correspond to two new symbiovars for which we propose the names americaense and caribense. The results of the nodC gene analysis also showed that C. cajan is nodulated by the symbiovar tropici, which has been found by first time in this work within the species Bradyrhizobium pachyrhizi. These results confirmed the high promiscuity degree of C. cajan, which is also nodulated by the symbiovar cajani of Bradyrhizobium cajani in Dominican Republic.
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Affiliation(s)
| | - Fernando Sánchez-Juanes
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, Salamanca, Spain
| | - Juan Araujo
- Facultad de Ciencias Agronómicas y Veterinarias. Universidad Autónoma de Santo Domingo, Dominican Republic
| | | | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain; Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain; Grupo de Interacción Planta-Microorganismo, USAL, Unidad Asociada al CSIC por el IRNASA, Salamanca, Spain.
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Msaddak A, Mars M, Quiñones MA, Lucas MM, Pueyo JJ. Lupin, a Unique Legume That Is Nodulated by Multiple Microsymbionts: The Role of Horizontal Gene Transfer. Int J Mol Sci 2023; 24:ijms24076496. [PMID: 37047476 PMCID: PMC10094711 DOI: 10.3390/ijms24076496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Lupin is a high-protein legume crop that grows in a wide range of edaphoclimatic conditions where other crops are not viable. Its unique seed nutrient profile can promote health benefits, and it has been proposed as a phytoremediation plant. Most rhizobia nodulating Lupinus species belong to the genus Bradyrhizobium, comprising strains that are phylogenetically related to B. cytisi, B. hipponenese, B. rifense, B. iriomotense/B. stylosanthis, B. diazoefficiens, B. japonicum, B. canariense/B. lupini, and B. retamae/B. valentinum. Lupins are also nodulated by fast-growing bacteria within the genera Microvirga, Ochrobactrum, Devosia, Phyllobacterium, Agrobacterium, Rhizobium, and Neorhizobium. Phylogenetic analyses of the nod and nif genes, involved in microbial colonization and symbiotic nitrogen fixation, respectively, suggest that fast-growing lupin-nodulating bacteria have acquired their symbiotic genes from rhizobial genera other than Bradyrhizobium. Horizontal transfer represents a key mechanism allowing lupin to form symbioses with bacteria that were previously considered as non-symbiotic or unable to nodulate lupin, which might favor lupin’s adaptation to specific habitats. The characterization of yet-unstudied Lupinus species, including microsymbiont whole genome analyses, will most likely expand and modify the current lupin microsymbiont taxonomy, and provide additional knowledge that might help to further increase lupin’s adaptability to marginal soils and climates.
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Affiliation(s)
- Abdelhakim Msaddak
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia
| | - Mohamed Mars
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia
| | - Miguel A. Quiñones
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
| | - M. Mercedes Lucas
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
| | - José J. Pueyo
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
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Phylogenetic and symbiotic diversity of Lupinus albus and L. angustifolius microsymbionts in the maamora forest, morocco. Syst Appl Microbiol 2022; 45:126338. [DOI: 10.1016/j.syapm.2022.126338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/28/2022] [Accepted: 05/23/2022] [Indexed: 11/22/2022]
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Alami S, Lamin H, Bennis M, Bouhnik O, Lamrabet M, El Hachimi ML, Abdelmoumen H, Bedmar EJ, Missbah El Idrissi M. Characterization of Retama sphaerocarpa microsymbionts in Zaida lead mine tailings in the Moroccan middle Atlas. Syst Appl Microbiol 2021; 44:126207. [PMID: 34015589 DOI: 10.1016/j.syapm.2021.126207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 11/25/2022]
Abstract
In the Moroccan Middle Atlas, the tailings rich in lead and other metal residues, in the abandoned Zaida mining district, represent a real threat to environment and the neighboring villages' inhabitants' health. In this semi-arid to arid area, phytostabilisation would be the best choice to limit the transfer of heavy metals to populations and groundwater. The aim of this work was to characterize the bacteria that nodulate Retama sphaerocarpa, spontaneous nitrogen fixing shrubby legume, native to the Zaida mining area, with great potential to develop for phytostabilisation. Forty-three bacteria isolated from root nodules of the plant were characterized. Based on REP-PCR and ARDRA, four strains were selected for further molecular analyzes. The 16S rRNA gene sequences analysis revealed that the isolated strains are members of the genus Bradyrhizobium, and the phylogenetic analysis of the housekeeping genes glnII, atpD, gyrB, rpoB, recA and dnaK individual sequences and their concatenation showed that the strains are close to B. algeriense RST89T and B. valentinum LmjM3T with similarity percentages of 89.07% to 95.66% which suggest that the newly isolated strains from this mining site may belong to a potential novel species. The phylogeny of the nodA and nodC genes showed that the strains belong to the symbiovar retamae of the genus Bradyrhizobium. These strains nodulate also R. monosperma, R. dasycarpa and Lupinus luteus.
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Affiliation(s)
- Soufiane Alami
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Hanane Lamin
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Meryeme Bennis
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Omar Bouhnik
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Mouad Lamrabet
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | | | - Hanaa Abdelmoumen
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), E-419, 18080 Granada, Spain
| | - Mustapha Missbah El Idrissi
- Centre de Biotechnologies végétales et microbiennes, Biodiversité et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, Rabat, Morocco.
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Rejili M, Off K, Brachmann A, Marín M. Bradyrhizobium hipponense sp. nov., isolated from Lupinus angustifolius growing in the northern region of Tunisia. Int J Syst Evol Microbiol 2020; 70:5539-5550. [PMID: 32897848 DOI: 10.1099/ijsem.0.004445] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Strain aSej3T was isolated from a root nodule of a Lupinus angustifolius plant growing in Bizerte, Tunisia. 16S rRNA gene analysis placed this strain within the genus Bradyrhizobium. Multilocus sequence analysis (MLSA) including three housekeeping genes (glnII, gyrB and recA) grouped aSej3T together with Bradyrhizobium rifense CTAW71T, Bradyrhizobium cytisi CTAW11T, Bradyrhizobium ganzhouense RITF806T, Bradyrhizobium lupini USDA 3051T and Bradyrhizobium canariense BTA-1T. MLSA with five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed that this strain shares less than 93.5 % nucleotide identity with other type strains. Genome sequencing and inspection revealed a genome size of 8.83 Mbp with a G+C content of 62.8 mol%. Genome-wide average nucleotide identity and digital DNA-DNA hybridization values were below 87.5 and 36.2 %, respectively, when compared to described Bradyrhizobium species. Strain aSej3T nodulated L. angustifolius plants under axenic conditions and its nodC gene clustered within the genistearum symbiovar. Altogether, the phylogenetic data and the chemotaxonomic characteristics of this strain support that aSej3T represents a new species for which we propose the name Bradyrhizobium hipponense sp. nov. with the type strain aSej3T (=DSM 108913T=LMG 31020T).
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Affiliation(s)
- Mokhtar Rejili
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA), Faculty of Sciences, Gabes University, Tunisia
| | - Katja Off
- Chair of Genetics, Faculty of Biology, Ludwig Maximilians University Munich, Germany
| | - Andreas Brachmann
- Chair of Genetics, Faculty of Biology, Ludwig Maximilians University Munich, Germany
| | - Macarena Marín
- Chair of Genetics, Faculty of Biology, Ludwig Maximilians University Munich, Germany
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Novel putative Mesorhizobium and Ensifer genomospecies together with a novel symbiovar psoraleae nodulate legumes of agronomic interest grown in Tunisia. Syst Appl Microbiol 2020; 43:126067. [PMID: 32005490 DOI: 10.1016/j.syapm.2020.126067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 11/22/2022]
Abstract
Forty rhizobial strains were isolated from Lotus creticus, L. pusillus and Bituminaria bituminosa endemic to Tunisia, and they belonged to the Mesorhizobium and Ensifer genera based on 16S rDNA sequence phylogeny. According to the concatenated recA and glnII sequence-based phylogeny, four Bituminaria isolates Pb5, Pb12, Pb8 and Pb17 formed a monophyletic group with Mesorhizobium chacoense ICMP14587T, whereas four other strains Pb1, Pb6, Pb13 and Pb15 formed two separate lineages within the Ensifer genus. Among the L. pusillus strains, Lpus9 and Lpus10 showed a 96% identical nucleotide with Ensifer meliloti CCBAU83493T; whereas six other strains could belong to previously undescribed Mesorhizobium and Ensifer species. For L. creticus strains, Lcus37, Lcus39 and Lcus44 showed 98% sequence identity with Ensifer aridi JNVU TP6, and Lcus42 shared a 96% identical nucleotide with Ensifer meliloti CCBAU83493T; whereas another four strains were divergent from all the described Ensifer and Mesorhizobium species. The analysis of the nodC gene-based phylogeny identified four symbiovar groups; Mesorhizobium sp. sv. anthyllidis (Lpus3 and Lpus11 from L. pusillus, Lcus43 from L. creticus), Ensifer medicae sv. meliloti (four strains from L. creticus and two strains from L. pusillus), E. meliloti sv. meliloti (four from L. creticus, four from L. pusillus and four from B. bituminosa). In addition, four B. bituminosa strains (Pb5, Pb8, Pb12, and Pb17) displayed a distinctive nodC sequence distant from those of other symbiovars described to date. According to their symbiotic gene sequences and host range, the B. bituminosa symbionts (Pb5, Pb8, Pb12 and Pb17) would represent a new symbiovar of M. chacoense for which sv. psoraleae is proposed.
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Artigas Ramírez MD, España M, Lewandowska S, Yuan K, Okazaki S, Ohkama-Ohtsu N, Yokoyama T. Phylogenetic Analysis of Symbiotic Bacteria Associated with Two Vigna Species under Different Agro-Ecological Conditions in Venezuela. Microbes Environ 2020; 35:ME19120. [PMID: 31932537 PMCID: PMC7104274 DOI: 10.1264/jsme2.me19120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 11/10/2019] [Indexed: 12/26/2022] Open
Abstract
Vigna is a genus of legumes cultivated in specific areas of tropical countries. Species in this genus are important crops worldwide. Vigna species are of great agronomic interest in Venezuela because Vigna beans are an excellent alternative to other legumes. However, this type of crop has some cultivation issues due to sensitivity to acidic soils, high temperatures, and salinity stress, which are common in Venezuela. Vigna species establish symbioses mainly with Bradyrhizobium and Ensifer, and Vigna-rhizobia interactions have been examined in Asia, Africa, and America. However, the identities of the rhizobia associated with V. radiata and V. unguiculata in Venezuela remain unknown. In the present study, we isolated Venezuelan symbiotic rhizobia associated with Vigna species from soils with contrasting agroecosystems or from fields in Venezuela. Several types of soils were used for bacterial isolation and nodules were sampled from environments characterized by abiotic stressors, such as high temperatures, high concentrations of NaCl, and acidic or alkaline pH. Venezuelan Vigna-rhizobia were mainly fast-growing. Sequencing of several housekeeping genes showed that in contrast to other continents, Venezuelan Vigna species were nodulated by rhizobia genus including Burkholderia, containing bacteria from several new phylogenetic lineages within the genus Bradyrhizobium. Some Rhizobium and Bradyrhizobium isolates were tolerant of high salinity and Al toxicity. The stress tolerance of strains was dependent on the type of rhizobia, soil origin, and cultivation history. An isolate classified as R. phaseoli showed the highest plant biomass, nitrogen fixation, and excellent abiotic stress response, suggesting a novel promising inoculant for Vigna cultivation in Venezuela.
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Affiliation(s)
- María Daniela Artigas Ramírez
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
| | | | - Sylwia Lewandowska
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, 50–363 Wrocław, 24A, Grunwaldzki—Poland
| | - Kun Yuan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
| | - Shin Okazaki
- United Graduated School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
| | - Naoko Ohkama-Ohtsu
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo—Japan
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Missbah El Idrissi M, Lamin H, ElFaik S, Tortosa G, Peix A, Bedmar E, Abdelmoumen H. Microvirga
sp. symbiovar mediterranense nodulates
Lupinus cosentinii
grown wild in Morocco. J Appl Microbiol 2019; 128:1109-1118. [DOI: 10.1111/jam.14526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 01/14/2023]
Affiliation(s)
- M. Missbah El Idrissi
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
| | - H. Lamin
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
| | - S. ElFaik
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
| | - G. Tortosa
- Department of Soil Microbiology and Symbiotic Systems Estación Experimental del Zaidín Consejo Superior de Investigaciones Científicas Granada Spain
| | - A. Peix
- Instituto de Recursos Naturales y Agrobiología IRNASA‐CSIC Salamanca Spain
| | - E.J. Bedmar
- Department of Soil Microbiology and Symbiotic Systems Estación Experimental del Zaidín Consejo Superior de Investigaciones Científicas Granada Spain
| | - H. Abdelmoumen
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
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Ramírez-Bahena MH, Flores-Félix JD, Velázquez E, Peix Á. The Mimosoid tree Leucaena leucocephala can be nodulated by the symbiovar genistearum of Bradyrhizobium canariense. Syst Appl Microbiol 2019; 43:126041. [PMID: 31767155 DOI: 10.1016/j.syapm.2019.126041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 11/16/2022]
Abstract
Leucaena leucocephala is a Mimosoid legume tree indigenous to America that has spread to other continents, although it is not still present in some European countries such as Portugal. Nevertheless, we found that this legume can be nodulated in this country by slow-growing rhizobial strains which were identified as Bradyrhizobium canariense trough the analysis of the core genes recA and glnII. The analysis of the symbiotic gene nodC showed that these strains belong to the symbiovar genistearum, which commonly nodulates Genistoid legumes. Although two strains nodulating L. leucocephala in China and Brazil were classified within the genus Bradyrhizobium, they belong to undescribed species and to the symbiovars glycinearum and tropici, respectively. Therefore, we report here for the first time the ability of L. leucocephala to establish symbiosis with strains of B. canariense sv genistearum confirming the high promiscuity of L. leucocephala, that allows it to establish symbiosis with rhizobia native to different continents increasing its invasiveness potential.
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Affiliation(s)
| | - José David Flores-Félix
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias(CIALE), Universidad de Salamanca, Edificio Departamental de Biología, Lab 209. Av. Doctores de la Reina S/N, 37007 Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias(CIALE), Universidad de Salamanca, Edificio Departamental de Biología, Lab 209. Av. Doctores de la Reina S/N, 37007 Salamanca, Spain; Unidad Asociada Grupo de Interacción planta-microorganismo (Universidad de Salamanca-IRNASA-CSIC), Salamanca, Spain
| | - Álvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain; Unidad Asociada Grupo de Interacción planta-microorganismo (Universidad de Salamanca-IRNASA-CSIC), Salamanca, Spain.
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11
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Rejili M, Msaddak A, Filali I, Benabderrahim MA, Mars M, Marín M. New chromosomal lineages within Microvirga and Bradyrhizobium genera nodulate Lupinus angustifolius growing on different Tunisian soils. FEMS Microbiol Ecol 2019; 95:5537381. [DOI: 10.1093/femsec/fiz118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
ABSTRACTThirty-one rhizobial isolates nodulating native Lupinus angustifolius (blue lupine) plants growing in Northern Tunisian soils were isolated and analysed using different chromosomal and symbiotic gene markers. Phylogenetic analyses based on recA partial sequences grouped them into at least five groups: four of them within the genus Bradyrhizobium (26 isolates) and one into the genus Microvirga (5 isolates). Representative strains were analysed by multilocus sequence analysis of three housekeeping genes rrs-recA-glnII and rrs-gyrB-dnaK for Bradyrhizobium and Microvirga isolates, respectively. Based on this analysis, eight isolates clustered with the previously described strains Bradyrhizobium lupini USDA3051 and Bradyrhizobium canariense BTA-1. However, five of the isolates clustered separately and may constitute a new species within the Bradyrhizobium genus. The remaining five isolates were closely related to the strain Microvirga sp. LmiM8 and may constitute a new Microvirga species. The analysis of the nodC gene showed that all Bradyrhizobium strains nodulating blue lupine belong to the symbiovar genistearum, whereas the Microvirga isolates are associated with the symbiovar mediterranense. The results of this study support that the L. angustifolius root nodule symbionts isolated in Northern Tunisia belong mostly to the B. canariense/B. lupini lineages. However, new clades of Bradyrhizobium and Microvirga have been identified as L. angustifolius endosymbionts.
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Affiliation(s)
- M Rejili
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) – Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - A Msaddak
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) – Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - I Filali
- College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, Riyadh PO Box 84428, Saudi Arabia
| | - M A Benabderrahim
- Arid and Oases Cropping Laboratory, Arid Area Institute, Gabes 6051, Tunisia
| | - M Mars
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) – Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - M Marín
- Institute of Genetics, Ludwig Maximilians University of Munich (LMU), Grosshaderner Str. 2–4, D-82152 Martinsried, Germany
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12
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Isolation, identification and plant growth promotion ability of endophytic bacteria associated with lupine root nodule grown in Tunisian soil. Arch Microbiol 2019; 201:1333-1349. [PMID: 31309236 DOI: 10.1007/s00203-019-01702-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 10/26/2022]
Abstract
The present study aims to characterize nodule endophytic bacteria of spontaneous lupine plants regarding their diversity and their plant growth promoting (PGP) traits. The potential of PGPR inoculation was investigated to improve white lupine growth across controlled, semi-natural and field conditions. Lupinus luteus and Lupinus angustifolius nodules were shown inhabited by a large diversity of endophytes. Several endophytes harbor numerous plant growth promotion traits such as phosphates solubilization, siderophores production and 1-aminocyclopropane-1-carboxylate deaminase activity. In vivo analysis confirmed the plant growth promotion ability of two strains (Paenibacillus glycanilyticus LJ121 and Pseudomonas brenneri LJ215) in both sterilized and semi-natural conditions. Under field conditions, the co-inoculation of lupine by these strains increased shoot N content and grain yield by 25% and 36%, respectively. These two strains Paenibacillus glycanilyticus LJ121 and Pseudomonas brenneri LJ215 are effective plant growth-promoting bacteria and they may be used to develop an eco-friendly biofertilizer to boost white lupine productivity.
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13
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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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14
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Phylogenetic diversity of Bradyrhizobium strains nodulating Calicotome spinosa in the Northeast of Algeria. Syst Appl Microbiol 2018; 41:452-459. [DOI: 10.1016/j.syapm.2018.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/24/2018] [Accepted: 05/24/2018] [Indexed: 11/20/2022]
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15
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Andrews M, De Meyer S, James EK, Stępkowski T, Hodge S, Simon MF, Young JPW. Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance. Genes (Basel) 2018; 9:E321. [PMID: 29954096 PMCID: PMC6071183 DOI: 10.3390/genes9070321] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 01/17/2023] Open
Abstract
Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume⁻rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.
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Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch 6150, Australia.
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium.
| | - Euan K James
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland.
| | - Simon Hodge
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Marcelo F Simon
- Embrapa Genetic Resources and Biotechnology, Brasilia DF 70770-917, Brazil.
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK.
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16
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Msaddak A, Rejili M, Durán D, Rey L, Palacios JM, Imperial J, Ruiz-Argüeso T, Mars M. Definition of two new symbiovars, sv. lupini and sv. mediterranense, within the genera Bradyrhizobium and Phyllobacterium efficiently nodulating Lupinus micranthus in Tunisia. Syst Appl Microbiol 2018; 41:487-493. [PMID: 29803609 DOI: 10.1016/j.syapm.2018.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/21/2018] [Accepted: 04/14/2018] [Indexed: 10/17/2022]
Abstract
In this study, a polyphasic approach was used to analyze three representative strains (LmiH4, LmiM2 and LmiT21) from a collection of six previously described strains isolated in Tunisia from root nodules of Lupinus micranthus. The phylogenetic analysis of the concatenated rrs, recA and glnII genes showed that strain LmiH4 had 100% concatenated gene sequence identity with the type strain Bradyrhizobium retamae Ro19T. Similarly, strain LmiM2 shared 100% concatenated gene sequence identity with the species Bradyrhizobium valentinum LmjM3T. However, strain LmiT21 showed an identical concatenated gene sequence with reference strain Phyllobacterium sophorae CCBAU03422T. The recA-glnII concatenated protein-coding genes used produced incongruent phylogenies compared with 16S rDNA phylogeny. The nodC gene analysis showed that the strains were phylogenetically divergent to the Bradyrhizobium symbiovars defined to date, and represented two new symbiovars. Plant infection analysis revealed that the three strains showed moderate host range and symbiotic specificities. Based on their symbiotic characteristics, we propose that the three strains isolated from Lupinus micranthus nodules belong to two new symbiovars, with the first denominated lupini within the two species Bradyrhizobium valentinum (type strain LmiM2) and B. retamae (type strain LmiH4), and the second denominated mediterranense within the species P. sophorae (type strain LmiT21).
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Affiliation(s)
- Abdelhakim Msaddak
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) - Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
| | - Mokhtar Rejili
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) - Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia.
| | - David Durán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - José Manuel Palacios
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain; Instituto de Ciencias Agrarias, CSIC, 28006, Madrid, Spain
| | | | - Mohamed Mars
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) - Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
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17
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Stępkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP. Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae. Genes (Basel) 2018. [PMID: 29538303 PMCID: PMC5867884 DOI: 10.3390/genes9030163] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes. This indicates that the capacity for nodulation of Genisteae spp. has evolved independently in various symbiotic gene clades, and that it has not been a long-multi-step process. The exception is Bradyrhizobium Clade II, which unlike other clades comprises strains that are specialized in nodulation of Genisteae, but also Loteae spp. Presumably, Clade II represents an example of long-lasting co-evolution of bradyrhizobial symbionts with their legume hosts.
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Affiliation(s)
- Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Joanna Banasiewicz
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Camille E Granada
- Universidade do Vale do Taquari-UNIVATES, Rua Avelino Tallini, 171, 95900-000 Lajeado, RS, Brazil.
| | - Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil.
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18
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Molecular phylogeny of Bradyrhizobium bacteria isolated from root nodules of tribe Genisteae plants growing in southeast Poland. Syst Appl Microbiol 2017; 40:482-491. [DOI: 10.1016/j.syapm.2017.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/24/2017] [Accepted: 09/20/2017] [Indexed: 01/27/2023]
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19
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Msaddak A, Rejili M, Durán D, Rey L, Imperial J, Palacios JM, Ruiz-Argüeso T, Mars M. Members of Microvirga and Bradyrhizobium genera are native endosymbiotic bacteria nodulating Lupinus luteus in Northern Tunisian soils. FEMS Microbiol Ecol 2017; 93:3828104. [PMID: 28505340 DOI: 10.1093/femsec/fix068] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/12/2017] [Indexed: 11/14/2022] Open
Abstract
The genetic diversity of bacterial populations nodulating Lupinus luteus (yellow lupine) in Northern Tunisia was examined. Phylogenetic analyses of 43 isolates based on recA and gyrB partial sequences grouped them in three clusters, two of which belong to genus Bradyrhizobium (41 isolates) and one, remarkably, to Microvirga (2 isolates), a genus never previously described as microsymbiont of this lupine species. Representatives of the three clusters were analysed in-depth by multilocus sequence analysis of five housekeeping genes (rrs, recA, glnII, gyrB and dnaK). Surprisingly, the Bradyrhizobium cluster with the two isolates LluI4 and LluTb2 may constitute a new species defined by a separate position between Bradyrhizobium manausense and B. denitrificans. A nodC-based phylogeny identified only two groups: one formed by Bradyrhizobium strains included in the symbiovar genistearum and the other by the Microvirga strains. Symbiotic behaviour of representative isolates was tested, and among the seven legumes inoculated only a difference was observed i.e. the Bradyrhizobium strains nodulated Ornithopus compressus unlike the two strains of Microvirga. On the basis of these data, we conclude that L. luteus root nodule symbionts in Northern Tunisia are mostly strains within the B. canariense/B. lupini lineages, and the remaining strains belong to two groups not previously identified as L. luteus endosymbionts: one corresponding to a new clade of Bradyrhizobium and the other to the genus Microvirga.
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Affiliation(s)
- Abdelhakim Msaddak
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA)-Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
| | - Mokhtar Rejili
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA)-Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
| | - David Durán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain.,CSIC and Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Jose Manuel Palacios
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Tomas Ruiz-Argüeso
- CSIC and Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Mohamed Mars
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA)-Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
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20
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Araújo J, Flores-Félix JD, Igual JM, Peix A, González-Andrés F, Díaz-Alcántara CA, Velázquez E. Bradyrhizobium cajani sp. nov. isolated from nodules of Cajanus cajan. Int J Syst Evol Microbiol 2017; 67:2236-2241. [PMID: 28671523 DOI: 10.1099/ijsem.0.001932] [Citation(s) in RCA: 17] [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
Two slow-growing strains, AMBPC1010T and AMBPC1011, were isolated from nodules of Cajanus cajan in the Dominican Republic. 16S rRNA gene analysis placed these strains within the genus Bradyrhizobium, being phylogenetically equidistant to several species of this genus. Analysis of the recA and atpD genes showed that the strains isolated belong to a cluster containing the strains Bradyrhizobium ottawaense OO99T, 'Bradyrhizobium americanum' CMVU44 and Bradyrhizobium daqingense CCBAU 15774T, and presented similarity values lower than 96 % for both genes with respect to the strains nodulating C. cajan. DNA-DNA hybridization analysis showed averages of 36, 40 and 39 % relatedness with respect to the representative strains of Bradyrhizobium ottawaense, 'Bradyrhizobium americanum' and Bradyrhizobium daqingense, respectively. Phenotypic characteristics also differed from those of the most closely related species of the genus Bradyrhizobium. Therefore, based on the data obtained in this study, we propose to classify the strains AMBPC1010T (=LMG 29967T=CECT 9227T) and AMBPC1011 into a novel species named Bradyrhizobium cajani sp. nov.
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Affiliation(s)
- Juan Araújo
- Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - José David Flores-Félix
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas. (IRNASA-CSIC), Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas. (IRNASA-CSIC), Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Fernando González-Andrés
- Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de León, León, Spain
| | - César Antonio Díaz-Alcántara
- Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - Encarna Velázquez
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
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21
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Valverde A, González-Tirante M, Medina-Sierra M, Rivas R, Santa-Regina I, Igual JM. Culturable bacterial diversity from the chestnut ( Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases. AIMS Microbiol 2017; 3:293-314. [PMID: 31294162 PMCID: PMC6605015 DOI: 10.3934/microbiol.2017.2.293] [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: 03/01/2017] [Accepted: 04/21/2017] [Indexed: 11/18/2022] Open
Abstract
The phyllosphere supports a large and complex bacterial community that varies both across plant species and geographical locations. Phyllosphere bacteria can have important effects on plant health. The sweet chestnut (Castanea sativa Mill.) is an economically important tree species affected worldwide by the fungal pathogens Cryphonectria parasitica and Phytophthora cinnamomi. We examined the culturable phyllosphere bacterial community of the sweet chestnut at two nearby locations in Central Spain in order to know its geographical variability and to explore its potential as source of biological control agents against these two pathogenic fungi. The bacterial diversity at strain level was high but it varied significantly between locations; however, phylotype richness and diversity were more comparable. The isolates were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Most of them were members of recognized bacterial species, with a notable proportion of representative of the genera Dietzia and Lonsdalea, but a small fraction of the strains revealed the existence of several potential novel species or even genera. Antagonism tests showed the occurrence in the chestnut phyllosphere of bacterial strains potentially useful as biological control agents against the two pathogenic fungi, some of which belong to species never before described as fungal antagonists. Chestnut phyllosphere, therefore, contains a great diversity of culturable bacteria and may represent an untapped source of potential biocontrol agents against the fungi causing blight and ink diseases of this tree species.
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Affiliation(s)
- Angel Valverde
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA), Consejo Superior de Investigaciones Científicas (CSIC), 37008 Salamanca, Spain.,Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria 0028, South Africa
| | - María González-Tirante
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA), Consejo Superior de Investigaciones Científicas (CSIC), 37008 Salamanca, Spain.,Estación Biológica de Doñana, 41001 Sevilla, Spain
| | - Marisol Medina-Sierra
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA), Consejo Superior de Investigaciones Científicas (CSIC), 37008 Salamanca, Spain.,Escuela de Producción Agropecuaria, Group GRICA (Grupo de Investigación en Ciencias Agrarias), Facultad de Ciencias Agrarias, Universidad de Antioquia, Medellín, Colombia
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, 37007 Salamanca, Spain.,Unidad Asociada Universidad de Salamanca-CSIC (IRNASA), Salamanca, Spain
| | - Ignacio Santa-Regina
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA), Consejo Superior de Investigaciones Científicas (CSIC), 37008 Salamanca, Spain.,Unidad Asociada Universidad de Salamanca-CSIC (IRNASA), Salamanca, Spain
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA), Consejo Superior de Investigaciones Científicas (CSIC), 37008 Salamanca, Spain.,Unidad Asociada Universidad de Salamanca-CSIC (IRNASA), Salamanca, Spain
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22
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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: 134] [Impact Index Per Article: 19.1] [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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23
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Diverse Bacteria Affiliated with the Genera Microvirga, Phyllobacterium, and Bradyrhizobium Nodulate Lupinus micranthus Growing in Soils of Northern Tunisia. Appl Environ Microbiol 2017; 83:AEM.02820-16. [PMID: 28062461 DOI: 10.1128/aem.02820-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/03/2017] [Indexed: 11/20/2022] Open
Abstract
The genetic diversity of bacterial populations nodulating Lupinus micranthus in five geographical sites from northern Tunisia was examined. Phylogenetic analyses of 50 isolates based on partial sequences of recA and gyrB grouped strains into seven clusters, five of which belong to the genus Bradyrhizobium (28 isolates), one to Phyllobacterium (2 isolates), and one, remarkably, to Microvirga (20 isolates). The largest Bradyrhizobium cluster (17 isolates) grouped with the B. lupini species, and the other five clusters were close to different recently defined Bradyrhizobium species. Isolates close to Microvirga were obtained from nodules of plants from four of the five sites sampled. We carried out an in-depth phylogenetic study with representatives of the seven clusters using sequences from housekeeping genes (rrs, recA, glnII, gyrB, and dnaK) and obtained consistent results. A phylogeny based on the sequence of the symbiotic gene nodC identified four groups, three formed by Bradyrhizobium isolates and one by the Microvirga and Phyllobacterium isolates. Symbiotic behaviors of the representative strains were tested, and some congruence between symbiovars and symbiotic performance was observed. These data indicate a remarkable diversity of L. micranthus root nodule symbionts in northern Tunisia, including strains from the Bradyrhizobiaceae, Methylobacteriaceae, and Phyllobacteriaceae families, in contrast with those of the rhizobial populations nodulating lupines in the Old World, including L. micranthus from other Mediterranean areas, which are nodulated mostly by Bradyrhizobium strains.IMPORTANCELupinus micranthus is a legume broadly distributed in the Mediterranean region and plays an important role in soil fertility and vegetation coverage by fixing nitrogen and solubilizing phosphate in semiarid areas. Direct sowing to extend the distribution of this indigenous legume can contribute to the prevention of soil erosion in pre-Saharan lands of Tunisia. However, rhizobial populations associated with L. micranthus are poorly understood. In this context, the diversity of endosymbionts of this legume was investigated. Most Lupinus species are nodulated by Bradyrhizobium strains. This work showed that about half of the isolates from northern Tunisian soils were in fact Bradyrhizobium symbionts, but the other half were found unexpectedly to be bacteria within the genera Microvirga and Phyllobacterium These unusual endosymbionts may have a great ecological relevance. Inoculation with the appropriate selected symbiotic bacterial partners will increase L. micranthus survival with consequent advantages for the environment in semiarid areas of Tunisia.
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Diversity of Bradyrhizobium strains nodulating Lupinus micranthus on both sides of the Western Mediterranean: Algeria and Spain. Syst Appl Microbiol 2016; 39:266-274. [DOI: 10.1016/j.syapm.2016.04.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/15/2016] [Accepted: 04/18/2016] [Indexed: 11/17/2022]
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Peix A, Ramírez-Bahena MH, Flores-Félix JD, Alonso de la Vega P, Rivas R, Mateos PF, Igual JM, Martínez-Molina E, Trujillo ME, Velázquez E. Revision of the taxonomic status of the species Rhizobium lupini and reclassification as Bradyrhizobium lupini comb. nov. Int J Syst Evol Microbiol 2015; 65:1213-1219. [DOI: 10.1099/ijs.0.000082] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The species
Rhizobium lupini
was isolated from Lupinus nodules and included in the Approved Lists of Bacterial Names in 1980. Nevertheless, on the basis of the analysis of the type strain of this species available in DSMZ, DSM 30140T, whose 16S rRNA gene was identical to that of the type strain of
Bradyrhizobium japonicum
,
R. lupini
was considered a later synonym of this species. In this study we confirmed that the strain DSM 30140T belongs to the species
B. japonicum
, but also that it cannot be the original strain of
R. lupini
because this species effectively nodulated Lupinus whereas strain DSM 30140T was able to nodulate soybean but not Lupinus. Since the original type strain of
R. lupini
was deposited into the USDA collection by L. W. Erdman under the accession number USDA 3051T we analysed the taxonomic status of this strain showing that although it belongs to the genus
Bradyrhizobium
instead of genus
Rhizobium
, it is phylogenetically distant from
B. japonicum
and closely related to
Bradyrhizobium canariense
. The type strains
R. lupini
USDA 3051T and
B. canariense
BTA-1T share 16S rRNA, recA and glnII gene sequences with similarities of 99.8 %, 96.5 % and 97.1 %, respectively. They presented a DNA–DNA hybridization value of 36 % and also differed in phenotypic characteristics and slightly in the proportions of some fatty acids. Therefore we propose the reclassification of the species
Rhizobium lupini
as Bradyrhizobium lupini comb. nov. The type strain is USDA 3051T ( = CECT 8630T = LMG 28514T).
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Affiliation(s)
- Alvaro Peix
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Martha Helena Ramírez-Bahena
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - José David Flores-Félix
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
| | | | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
| | - Pedro F. Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
| | - José M. Igual
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC ‘Interacción Planta-Microorganismo’, Salamanca, Spain
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Vigna unguiculata is nodulated in Spain by endosymbionts of Genisteae legumes and by a new symbiovar (vignae) of the genus Bradyrhizobium. Syst Appl Microbiol 2014; 37:533-40. [DOI: 10.1016/j.syapm.2014.04.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/15/2014] [Accepted: 04/16/2014] [Indexed: 11/22/2022]
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Durán D, Rey L, Navarro A, Busquets A, Imperial J, Ruiz-Argüeso T. Bradyrhizobium valentinum sp. nov., isolated from effective nodules of Lupinus mariae-josephae, a lupine endemic of basic-lime soils in Eastern Spain. Syst Appl Microbiol 2014; 37:336-41. [DOI: 10.1016/j.syapm.2014.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 05/01/2014] [Accepted: 05/02/2014] [Indexed: 11/28/2022]
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Carro L, Flores-Félix JD, Ramírez-Bahena MH, García-Fraile P, Martínez-Hidalgo P, Igual JM, Tejedor C, Peix A, Velázquez E. Paenibacillus lupini sp. nov., isolated from nodules of Lupinus albus. Int J Syst Evol Microbiol 2014; 64:3028-3033. [PMID: 24928428 DOI: 10.1099/ijs.0.060830-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A bacterial strain designated RLAHU15(T) was isolated from root nodules of Lupinus albus in Spain. Phylogenetic analyses based on 16S rRNA gene sequences placed the isolate in the genus Paenibacillus, with its closest relatives being Paenibacillus catalpae D75(T), Paenibacillus glycanilyticus DS-1(T), Paenibacillus endophyticus PECAE04(T) and Paenibacillus xinjiangensis B538(T) with 98.8 %, 98.9 %, 97.4 % and 97.4 % similarity, respectively. DNA-DNA hybridization studies showed values lower than 45 % between the strain RLAHU15(T) and any of these species. The isolate was a Gram-stain positive, motile and sporulating rod. Catalase activity was weak and oxidase activity was positive. Casein and starch were hydrolysed but gelatin was not. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the only menaquinone detected and anteiso-C15 : 0 and iso-C16 : 0 were the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and an unidentified lipid. meso-Diaminopimelic acid was detected in the peptidoglycan. The DNA G+C content was 54.4 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain RLAHU15(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus lupini sp. nov. is proposed. The type strain is RLAHU15(T) ( = LMG 27296(T) = CECT 8235(T)).
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Affiliation(s)
- Lorena Carro
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | | | - Martha-Helena Ramírez-Bahena
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | | | - José M Igual
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Carmen Tejedor
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Alvaro Peix
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Encarna Velázquez
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
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Cobo-Díaz JF, Martínez-Hidalgo P, Fernández-González AJ, Martínez-Molina E, Toro N, Velázquez E, Fernández-López M. The endemic Genista versicolor from Sierra Nevada National Park in Spain is nodulated by putative new Bradyrhizobium species and a novel symbiovar (sierranevadense). Syst Appl Microbiol 2014; 37:177-85. [DOI: 10.1016/j.syapm.2013.09.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 11/30/2022]
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Cytisus villosus from Northeastern Algeria is nodulated by genetically diverse Bradyrhizobium strains. Antonie van Leeuwenhoek 2014; 105:1121-9. [DOI: 10.1007/s10482-014-0173-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/08/2014] [Indexed: 11/30/2022]
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31
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Armas-Capote N, Pérez-Yépez J, Martínez-Hidalgo P, Garzón-Machado V, del Arco-Aguilar M, Velázquez E, León-Barrios M. Core and symbiotic genes reveal nine Mesorhizobium genospecies and three symbiotic lineages among the rhizobia nodulating Cicer canariense in its natural habitat (La Palma, Canary Islands). Syst Appl Microbiol 2014; 37:140-8. [DOI: 10.1016/j.syapm.2013.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 07/30/2013] [Accepted: 08/03/2013] [Indexed: 11/16/2022]
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Flores-Félix JD, Carro L, Ramírez-Bahena MH, Tejedor C, Igual JM, Peix A, Velázquez E. Cohnella lupini sp. nov., an endophytic bacterium isolated from root nodules of Lupinus albus. Int J Syst Evol Microbiol 2014; 64:83-87. [DOI: 10.1099/ijs.0.050849-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated RLAHU4BT was isolated from root nodules of Lupinus albus in León (Spain). The 16S rRNA gene sequence of this strain showed similarities lower than 97 % with respect to species of the genus
Cohnella
. The strain was a Gram-variable, sporulating rod, motile by means of peritrichous flagella, and facultatively anaerobic. It was positive for oxidase, catalase and β-galactosidase production but negative for urease, amylase and gelatinase. Strain RLAHU4BT grew in the presence of 5 % NaCl. MK-7 was the predominant menaquinone and meso-diaminopimelic acid was present in the peptidoglycan. anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0 and C16 : 0 were the major fatty acids. Major polar lipids of strain RLAHU4BT were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, two unknown aminophospholipids and one unknown lipid. The DNA G+C content was 57.8 mol%. Strain RLAHU4BT presented phenotypic differences from all recognized species of the genus
Cohnella
. The phylogenetic, chemotaxonomic and phenotypic data indicated that strain RLAHU4BT belongs to a novel species of the genus
Cohnella
, for which the name Cohnella lupini sp. nov. is proposed, with strain RLAHU4BT ( = LMG 27416T = CECT 8236T) as the type strain.
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Affiliation(s)
| | - Lorena Carro
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Martha-Helena Ramírez-Bahena
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Carmen Tejedor
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - José M. Igual
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Alvaro Peix
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Encarna Velázquez
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
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MALDI-TOF mass spectrometry as a tool for differentiation of Bradyrhizobium species: application to the identification of Lupinus nodulating strains. Syst Appl Microbiol 2013; 36:565-71. [PMID: 24168963 DOI: 10.1016/j.syapm.2013.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 09/14/2013] [Accepted: 09/23/2013] [Indexed: 11/22/2022]
Abstract
Genus Bradyrhizobium includes slow growing bacteria able to nodulate different legumes as well as species isolated from plant tumours. The slow growth presented by the members of this genus and the phylogenetic closeness of most of its species difficults their identification. In the present work we applied for the first time Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to the analysis of Bradyrhizobium species after the extension of MALDI Biotyper 2.0 database with the currently valid species of this genus. With this methodology it was possible to identify strains belonging to phylogenetically closely related species of genus Bradyrhizobium allowing the discrimination among species with rrs gene identities higher than 99%. The application of MALDI-TOF MS to strains isolated from nodules of different Lupinus species in diverse geographical locations allowed their correct identification when comparing with the results of rrs gene and ITS analyses. The nodulation of Lupinus gredensis, an endemic species of the west of Spain, by B. canariense supports the European origin of this species.
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Guerrouj K, Ruíz-Díez B, Chahboune R, Ramírez-Bahena MH, Abdelmoumen H, Quiñones MA, El Idrissi MM, Velázquez E, Fernández-Pascual M, Bedmar EJ, Peix A. Definition of a novel symbiovar (sv. retamae) within Bradyrhizobium retamae sp. nov., nodulating Retama sphaerocarpa and Retama monosperma. Syst Appl Microbiol 2013; 36:218-23. [DOI: 10.1016/j.syapm.2013.03.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 03/07/2013] [Accepted: 03/10/2013] [Indexed: 10/26/2022]
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Ramírez-Bahena MH, Chahboune R, Velázquez E, Gómez-Moriano A, Mora E, Peix A, Toro M. Centrosema is a promiscuous legume nodulated by several new putative species and symbiovars of Bradyrhizobium in various American countries. Syst Appl Microbiol 2013; 36:392-400. [PMID: 23688383 DOI: 10.1016/j.syapm.2013.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/05/2013] [Accepted: 03/15/2013] [Indexed: 11/29/2022]
Abstract
Centrosema is an American indigenous legume that can be used in agroecosystems for recovery of acidic and degraded soils. In this study, a Centrosema-nodulating rhizobial collection of strains isolated in a poor acid savanna soil from Venezuela was characterized, and the members of the collection were compared to other Centrosema strains from America. The analysis of the rrs gene showed that the strains nodulating Centrosema in American countries were closely related to different species of the genus Bradyrhizobium. However, the analysis of the atpD and recA genes, as well as the 16S-23S ITS region, showed that they formed several new phylogenetic lineages within this genus. The Venezuela strains formed three lineages that were divergent among themselves and with respect to those formed by Centrosema strains isolated in other countries, as well as to the currently described species and genospecies of Bradyrhizobium. In addition, the symbiotic genes nodC and nifH carried by Centrosema-nodulating strains were analyzed for the first time, and it was shown that they belonged to three new phylogenetic lineages within Bradyrhizobium. The nodC genes of the Centrosema strains were divergent among themselves and with respect to the genistearum and glycinearum symbiovars, indicating that Centrosema is a promiscuous legume. According to these results, the currently known Centrosema-nodulating strains represent several new putative species and symbiovars of the genus Bradyrhizobium.
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Durán D, Rey L, Sánchez-Cañizares C, Navarro A, Imperial J, Ruiz-Argueso T. Genetic diversity of indigenous rhizobial symbionts of the Lupinus mariae-josephae endemism from alkaline-limed soils within its area of distribution in Eastern Spain. Syst Appl Microbiol 2013; 36:128-36. [DOI: 10.1016/j.syapm.2012.10.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/23/2012] [Accepted: 10/24/2012] [Indexed: 11/27/2022]
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Chahboune R, Carro L, Peix A, Barrijal S, Velázquez E, Bedmar EJ. Bradyrhizobium cytisi sp. nov., isolated from effective nodules of Cytisus villosus. Int J Syst Evol Microbiol 2011; 61:2922-2927. [DOI: 10.1099/ijs.0.027649-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several strains isolated from Cytisus villosus nodules have been characterized based on their diverse genetic, phenotypic and symbiotic characteristics. According to 16S rRNA gene sequence analysis, the isolates formed a group that was closely related to Bradyrhizobium canariense BTA-1T with 99.4 % similarity. Analysis of three housekeeping genes, recA, atpD and glnII, suggested that the C. villosus strains represent a novel Bradyrhizobium species most closely related to B. canariense BTA-1T with similarities of 94.2, 96.7 and 94.5 %, respectively. All these differences were congruent with DNA–DNA hybridization analysis, which revealed 31 % relatedness between a representative strain (CTAW11T) isolated from C. villosus nodules and B. canariense BTA-1T. Phenotypic differences among the strains isolated from C. villosus and B. canariense were based on assimilation of carbon and nitrogen sources. The nodC and nifH genes of strain CTAW11T were phylogenetically related to those of strains belonging to bv. genistearum and divergent from those of bv. glycinearum and, accordingly, they do not nodulate soybean. Based on the genotypic and phenotypic data obtained in this study, our strains should be classified as representatives of a novel species for which the name Bradyrhizobium cytisi sp. nov. is proposed; the type strain is CTAW11T ( = LMG 25866T = CECT 7749T).
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Affiliation(s)
- Rajaa Chahboune
- Department of Biology, Faculty of Sciences and Techniques, University Abdelmalek Essaadi, Tangier, Morocco
| | - Lorena Carro
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Said Barrijal
- Department of Biology, Faculty of Sciences and Techniques, University Abdelmalek Essaadi, Tangier, Morocco
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Eulogio J. Bedmar
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Granada, Spain
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Valverde A, González-Tirante M, Medina-Sierra M, Santa-Regina I, García-Sánchez A, Igual JM. Diversity and community structure of culturable arsenic-resistant bacteria across a soil arsenic gradient at an abandoned tungsten-tin mining area. CHEMOSPHERE 2011; 85:129-134. [PMID: 21724233 DOI: 10.1016/j.chemosphere.2011.06.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 05/31/2011] [Accepted: 06/05/2011] [Indexed: 05/31/2023]
Abstract
We studied the bacterial diversity at a single location (the Terrubias mine; Salamanca province, Spain) with a gradient of soil As contamination to test if increasing levels of As would (1) change the preponderant groups of arsenic-resistant bacteria and (2) increase the tolerance thresholds to arsenite [As(III)] and arsenate [As(V)] of such bacteria. We studied the genetic and taxonomic diversity of culturable arsenic-resistant bacteria by PCR fingerprinting techniques and 16S rRNA gene sequencing. Then, the tolerance thresholds to As(III) and As(V) were determined for representative strains and mathematically analyzed to determine relationships between tolerances to As(III) and As(V), as well as these tolerances with the soil contamination level. The diversity of the bacterial community was, as expected, inversely related to the soil As content. The overall preponderant arsenic-resistant bacteria were Firmicutes (mainly Bacillus spp.) followed by γ-Proteobacteria (mainly Pseudomonas spp.), with increasing relative frequencies of the former as the soil arsenic concentration increased. Moreover, a strain of the species Rahnella aquatilis (γ-Proteobacteria class) exhibited strong endurance to arsenic, being described for the first time in literature such a phenotype within this bacterial species. Tolerances of the isolates to As(III) and As(V) were correlated but not with their origin (soil contamination level). Most of the strains (64%) showed relatively low tolerances to As(III) and As(V), but the second most numerous group of isolates (19%) showed increased tolerance to As(III) rather than to As(V), even though the As(V) anion is the prevalent arsenic species in soil solution at this location. To our knowledge, this is the first study to report a shift towards preponderance of Gram-positive bacteria (Firmicutes) related to high concentrations of soil arsenic. It was also shown that, under aerobic conditions, strains with relatively enhanced tolerance to As(III) predominated over the most As(V)-tolerant ones.
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Affiliation(s)
- Angel Valverde
- Instituto de Recursos Naturales y Agrobiología de Salamanca (CSIC), Apartado 257, 37071 Salamanca, Spain
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Sánchez-Cañizares C, Rey L, Durán D, Temprano F, Sánchez-Jiménez P, Navarro A, Polajnar M, Imperial J, Ruiz-Argüeso T. Endosymbiotic bacteria nodulating a new endemic lupine Lupinus mariae-josephi from alkaline soils in Eastern Spain represent a new lineage within the Bradyrhizobium genus. Syst Appl Microbiol 2011; 34:207-15. [DOI: 10.1016/j.syapm.2010.11.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 11/23/2010] [Accepted: 11/23/2010] [Indexed: 12/14/2022]
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Stępkowski T, Zak M, Moulin L, Króliczak J, Golińska B, Narożna D, Safronova VI, Mądrzak CJ. Bradyrhizobium canariense and Bradyrhizobium japonicum are the two dominant rhizobium species in root nodules of lupin and serradella plants growing in Europe. Syst Appl Microbiol 2011; 34:368-75. [PMID: 21514760 DOI: 10.1016/j.syapm.2011.03.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 02/26/2011] [Accepted: 03/01/2011] [Indexed: 10/18/2022]
Abstract
Forty three Bradyrhizobium strains isolated in Poland from root nodules of lupin species (Lupinus albus, L. angustifolius and L. luteus), and pink serradella (Ornithopus sativus) were examined based on phylogenetic analyses of three housekeeping (atpD, glnII and recA) and nodulation (nodA) gene sequences. Additionally, seven strains originating from root-nodules of yellow serradella (O. compressus) from Asinara Island (Italy) were included in this study. Phylogenetic trees revealed that 15 serradella strains, including all yellow serradella isolates, and six lupin strains grouped in Bradyrhizobium canariense (BC) clade, whereas eight strains from pink serradella and 15 lupin strains were assigned to Bradyrhizobium japonicum (BJ1). Apparently, these species are the two dominant groups in soils of central Europe, in the nodules of lupin and serradella plants. Only three strains belonged to other chromosomal lineages: one formed a cluster that was sister to B. canariense, one strain grouped outside the branch formed by B. japonicum super-group, and one strain occupied a distant position in the genus Bradyrhizobium, clustering with strains of the Rhodopseudomonas genus. All strains in nodulation nodA gene tree grouped in a cluster referred to as Clade II, which is in line with earlier data on this clade dominance among Bradyrhizobium strains in Europe. The nodA tree revealed four well-supported subgroups within Clade II (II.1-II.4). Interestingly, all B. canariense strains clustered in subgroup II.1 whereas B. japonicum strains dominated subgroups II.2-II.4.
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Affiliation(s)
- Tomasz Stępkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Noskowskiego 12/14, Poland
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