1
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Hernández I, Taulé C, Pérez-Pérez R, Battistoni F, Fabiano E, Rivero D, Nápoles MC. Endophytic rhizobia promote the growth of Cuban rice cultivar. Symbiosis 2021. [DOI: 10.1007/s13199-021-00803-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2
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Taha K, Berraho EB, El Attar I, Dekkiche S, Aurag J, Béna G. Rhizobium laguerreae is the main nitrogen-fixing symbiont of cultivated lentil ( Lens culinaris ) in Morocco. Syst Appl Microbiol 2018; 41:113-121. [DOI: 10.1016/j.syapm.2017.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/18/2017] [Accepted: 09/22/2017] [Indexed: 10/18/2022]
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3
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Tampakaki AP, Fotiadis CT, Ntatsi G, Savvas D. Phylogenetic multilocus sequence analysis of indigenous slow-growing rhizobia nodulating cowpea ( Vigna unguiculata L.) in Greece. Syst Appl Microbiol 2017; 40:179-189. [DOI: 10.1016/j.syapm.2017.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 12/01/2022]
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4
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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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5
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Pohajda I, Babić KH, Rajnović I, Kajić S, Sikora S. Genetic Diversity and Symbiotic Efficiency of Indigenous Common Bean Rhizobia in Croatia. Food Technol Biotechnol 2017; 54:468-474. [PMID: 28115905 DOI: 10.17113/ftb.54.04.16.4740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nodule bacteria (rhizobia) in symbiotic associations with legumes enable considerable entries of biologically fixed nitrogen into soil. Efforts are therefore made to intensify the natural process of symbiotic nitrogen fixation by legume inoculation. Studies of field populations of rhizobia open up the possibility to preserve and probably exploit some indigenous strains with hidden symbiotic or ecological potentials. The main aim of the present study is to determine genetic diversity of common bean rhizobia isolated from different field sites in central Croatia and to evaluate their symbiotic efficiency and compatibility with host plants. The isolation procedure revealed that most soil samples contained no indigenous common bean rhizobia. The results indicate that the cropping history had a significant impact on the presence of indigenous strains. Although all isolates were found to belong to species Rhizobium leguminosarum, significant genetic diversity at the strain level was determined. Application of both random amplification of polymorphic DNA (RAPD) and enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC- -PCR) methods resulted in similar grouping of strains. Symbiotic efficiency of indigenous rhizobia as well as their compatibility with two commonly grown bean varieties were tested in field experiments. Application of indigenous rhizobial strains as inoculants resulted in significantly different values of nodulation, seed yield as well as plant nitrogen and seed protein contents. The most abundant nodulation and the highest plant nitrogen and protein contents were determined in plants inoculated with R. leguminosarum strains S17/2 and S21/6. Although, in general, the inoculation had a positive impact on seed yield, differences depending on the applied strain were not determined. The overall results show the high degree of symbiotic efficiency of the specific indigenous strain S21/6. These results indicate different symbiotic potential of indigenous strains and confirmed the importance of rhizobial strain selection. These are the first studies of indigenous common bean rhizobia in Croatia that provide the basis for further characterization and selection of highly efficient indigenous strains and their potential use in agricultural practice and future research.
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Affiliation(s)
- Ines Pohajda
- Advisory Service, Savska cesta 41, HR-10000 Zagreb, Croatia
| | | | - Ivana Rajnović
- University of Zagreb, Faculty of Agriculture, Department of Microbiology, Svetošimunska 25,
HR-10000 Zagreb, Croatia
| | - Sanja Kajić
- University of Zagreb, Faculty of Agriculture, Department of Microbiology, Svetošimunska 25,
HR-10000 Zagreb, Croatia
| | - Sanja Sikora
- University of Zagreb, Faculty of Agriculture, Department of Microbiology, Svetošimunska 25,
HR-10000 Zagreb, Croatia
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6
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Gehlot HS, Ardley J, Tak N, Tian R, Poonar N, Meghwal RR, Rathi S, Tiwari R, Adnawani W, Seshadri R, Reddy TBK, Pati A, Woyke T, Pillay M, Markowitz V, Baeshen MN, Al-Hejin AM, Ivanova N, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India. Stand Genomic Sci 2016; 11:43. [PMID: 27340511 PMCID: PMC4918122 DOI: 10.1186/s40793-016-0157-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 05/18/2016] [Indexed: 11/17/2022] Open
Abstract
Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.) Druce (Khejri), which is a keystone species that grows in arid and semi-arid regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as species of mimosoid trees and shrubs. Here we describe the features of Ensifer sp. PC2, together with genome sequence information and its annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.
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Affiliation(s)
- Hukam Singh Gehlot
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Julie Ardley
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Nisha Tak
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Rui Tian
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Neetu Poonar
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Raju R Meghwal
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Sonam Rathi
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Ravi Tiwari
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Wan Adnawani
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Rekha Seshadri
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California USA
| | - Mohammed N Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M Al-Hejin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California USA ; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
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7
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The diversity of rhizobia nodulating the Medicago, Melilotus and Trigonella inoculation group in Egypt is marked by the dominance of two genetic types. Symbiosis 2015. [DOI: 10.1007/s13199-015-0365-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Cicer canariense, an endemic legume to the Canary Islands, is nodulated in mainland Spain by fast-growing strains from symbiovar trifolii phylogenetically related to Rhizobium leguminosarum. Syst Appl Microbiol 2015; 38:346-50. [DOI: 10.1016/j.syapm.2015.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/16/2015] [Accepted: 03/19/2015] [Indexed: 11/21/2022]
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9
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Ramírez-Bahena MH, Vargas M, Martín M, Tejedor C, Velázquez E, Peix Á. Alfalfa microsymbionts from different ITS and nodC lineages of Ensifer meliloti and Ensifer medicae symbiovar meliloti establish efficient symbiosis with alfalfa in Spanish acid soils. Appl Microbiol Biotechnol 2015; 99:4855-65. [DOI: 10.1007/s00253-014-6347-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/12/2014] [Accepted: 12/14/2014] [Indexed: 10/24/2022]
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10
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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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11
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Díaz-Alcántara CA, Ramírez-Bahena MH, Mulas D, García-Fraile P, Gómez-Moriano A, Peix A, Velázquez E, González-Andrés F. Analysis of rhizobial strains nodulating Phaseolus vulgaris from Hispaniola Island, a geographic bridge between Meso and South America and the first historical link with Europe. Syst Appl Microbiol 2014; 37:149-56. [DOI: 10.1016/j.syapm.2013.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/15/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
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12
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Harun-or Rashid M, Gonzalez J, Young JPW, Wink M. Rhizobium leguminosarum is the symbiont of lentils in the Middle East and Europe but not in Bangladesh. FEMS Microbiol Ecol 2013; 87:64-77. [PMID: 24033582 DOI: 10.1111/1574-6941.12190] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 01/07/2023] Open
Abstract
Lentil is the oldest of the crops that have been domesticated in the Fertile Crescent and spread to other regions during the Bronze Age, making it an ideal model to study the evolution of rhizobia associated with crop legumes. Housekeeping and nodulation genes of lentil-nodulating rhizobia from the region where lentil originated (Turkey and Syria) and regions to which lentil was introduced later (Germany and Bangladesh) were analyzed to determine their genetic diversity, population structure, and taxonomic position. There are four different lineages of rhizobia associated with lentil nodulation, of which three are new and endemic to Bangladesh, while Mediterranean and Central European lentil symbionts belong to the Rhizobium leguminosarum lineage. The endemic lentil grex pilosae may have played a significant role in the origin of these new lineages in Bangladesh. The presence of R. leguminosarum with lentil at the center of origin and in countries where lentil was introduced later suggests that R. leguminosarum is the original symbiont of lentil. Lentil seeds may have played a significant role in the initial dispersal of this Rhizobium species within the Middle East and on to other countries. Nodulation gene sequences revealed a high similarity to those of symbiovar viciae.
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Affiliation(s)
- M Harun-or Rashid
- Department of Biology, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany; Soil Microbiology Laboratory, Soil Science Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh, Bangladesh
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13
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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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14
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Phylogenetic multilocus sequence analysis identifies seven novel
Ensifer
genospecies isolated from a less-well-explored biogeographical region in East Africa. Int J Syst Evol Microbiol 2012; 62:2286-2295. [DOI: 10.1099/ijs.0.039230-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The diversity of 71 rhizobial strains belonging to the genus
Ensifer
, isolated from root nodules of woody legumes growing in southern Ethiopia, was studied using multilocus sequence analysis (MLSA) and phenotypic approaches. Phylogenetic analyses based on core genes revealed that 43 strains were clustered in seven distinct and consistent positions (genospecies I–VII), while another 25 strains were also distinct but were discrepant in their placement on the different gene trees. The remaining three strains occupied the same phylogenetic branches as defined
Ensifer
species and thus were not distinct. Irrespective of their chromosomal background, the majority of the test strains were highly related with respect to their nifH and nodC gene sequences, suggesting that these symbionts might have acquired these genes recently from a common origin. On the nifH phylogenetic tree, the branch containing the test strains and reference species isolated from woody legumes in Africa was clearly separate from those isolated outside the continent, suggesting that these symbionts have a long history of separate evolution within
Ensifer
for this gene. A cross-inoculation study showed that our strains were capable of eliciting effective nodulation on the homologous host and on other host species. This suggests a potential to improve nitrogen fixation by selecting for broad-host-range inoculants. Our study confirms the presence of a wide diversity of
Ensifer
in East Africa and, while contributing to the general knowledge of the biodiversity within the genus, also highlights the need to focus on previously less-well-explored biogeographical regions to unravel as-yet-unidentified rhizobial resources.
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Faghire M, Mandri B, Oufdou K, Bargaz A, Ghoulam C, Ramírez-Bahena M, Velázquez E, Peix A. Identification at the species and symbiovar levels of strains nodulating Phaseolus vulgaris in saline soils of the Marrakech region (Morocco) and analysis of the otsA gene putatively involved in osmotolerance. Syst Appl Microbiol 2012; 35:156-64. [DOI: 10.1016/j.syapm.2012.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 02/03/2012] [Accepted: 02/04/2012] [Indexed: 11/29/2022]
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16
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Genetic diversity of rhizobia nodulating lentil (Lens culinaris) in Bangladesh. Syst Appl Microbiol 2012; 35:98-109. [DOI: 10.1016/j.syapm.2011.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/17/2011] [Accepted: 11/20/2011] [Indexed: 11/23/2022]
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17
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Robledo M, Velázquez E, Ramírez-Bahena MH, García-Fraile P, Pérez-Alonso A, Rivas R, Martínez-Molina E, Mateos PF. The celC gene, a new phylogenetic marker useful for taxonomic studies in Rhizobium. Syst Appl Microbiol 2011; 34:393-9. [DOI: 10.1016/j.syapm.2011.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/15/2011] [Accepted: 01/17/2011] [Indexed: 11/17/2022]
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18
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Evidence of an American origin for symbiosis-related genes in Rhizobium lusitanum. Appl Environ Microbiol 2011; 77:5665-70. [PMID: 21705533 DOI: 10.1128/aem.02017-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Randomly amplified polymorphic DNA (RAPD) analysis was used to investigate the diversity of 179 bean isolates recovered from six field sites in the Arcos de Valdevez region of northwestern Portugal. The isolates were divided into 6 groups based on the fingerprint patterns that were obtained. Representatives for each group were selected for sequence analysis of 4 chromosomal DNA regions. Five of the groups were placed within Rhizobium lusitanum, and the other group was placed within R. tropici type IIA. Therefore, the collection of Portuguese bean isolates was shown to include the two species R. lusitanum and R. tropici. In plant tests, the strains P1-7, P1-1, P1-2, and P1-16 of R. lusitanum nodulated and formed nitrogen-fixing symbioses both with Phaseolus vulgaris and Leucaena leucocephala. A methyltransferase-encoding nodS gene identical with the R. tropici locus that confers wide host range was detected in the strain P1-7 as well as 24 others identified as R. lusitanum. A methyltransferase-encoding nodS gene also was detected in the remaining isolates of R. lusitanum, but in this case the locus was that identified with the narrow-host-range R. etli. Representatives of isolates with the nodS of R. etli formed effective nitrogen-fixing symbioses with P. vulgaris and did not nodulate L. leucocephala. From sequence data of nodS, the R. lusitanum genes for symbiosis were placed within those of either R. tropici or R. etli. These results would support the suggestion that R. lusitanum was the recipient of the genes for symbiosis with beans from both R. tropici and R. etli.
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19
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Ferreira L, Sánchez-Juanes F, García-Fraile P, Rivas R, Mateos PF, Martínez-Molina E, González-Buitrago JM, Velázquez E. MALDI-TOF mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family Rhizobiaceae. PLoS One 2011; 6:e20223. [PMID: 21655291 PMCID: PMC3105015 DOI: 10.1371/journal.pone.0020223] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/21/2011] [Indexed: 11/19/2022] Open
Abstract
Family Rhizobiaceae includes fast growing bacteria currently arranged into three genera, Rhizobium, Ensifer and Shinella, that contain pathogenic, symbiotic and saprophytic species. The identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae. In this work we evaluated the suitability of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for this purpose. Firstly, we evaluated the capability of this methodology to differentiate among species of family Rhizobiaceae including those closely related and then we extended the database of MALDI Biotyper 2.0 including the type strains of 56 species from genera Rhizobium, Ensifer and Shinella. Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences. The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.
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Affiliation(s)
- Laura Ferreira
- Unidad de Investigación, Hospital Universitario de Salamanca, Salamanca, Spain
| | | | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Pedro F. Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | | | - José Manuel González-Buitrago
- Unidad de Investigación, Hospital Universitario de Salamanca, Salamanca, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- * E-mail:
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Fterich A, Mahdhi M, Caviedes MA, Pajuelo E, Rivas R, Rodriguez-Llorente ID, Mars M. Characterization of root-nodulating bacteria associated to Prosopis farcta growing in the arid regions of Tunisia. Arch Microbiol 2011; 193:385-97. [PMID: 21359955 DOI: 10.1007/s00203-011-0683-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/02/2011] [Accepted: 02/04/2011] [Indexed: 10/18/2022]
Abstract
Diversity of 50 bacterial isolates recovered from root nodules of Prosopis farcta grown in different arid soils in Tunisia, was investigated. Characterization of isolates was assessed using a polyphasic approach including phenotypic characteristics, 16S rRNA gene PCR--RFLP and sequencing, nodA gene sequencing and MLSA. It was found that most of isolates are tolerant to high temperature (40°C) and salinity (3%). Genetic characterization emphasizes that isolates were assigned to the genus Ensifer (80%), Mesorhizobium (4%) and non-nodulating endophytic bacteria (16%). Forty isolates belonging to the genus Ensifer were affiliated to Ensifer meliloti, Ensifer xinjiangense/Ensifer fredii and Ensifer numidicus species. Two isolates belonged to the genus Mesorhizobium. Eight isolates failing to renodulate their host plant were endophytic bacteria and belonged to Bacillus, Paenibacillus and Acinetobacter genera. Symbiotic properties of nodulating isolates showed a diversity in their capacity to infect their host plant and fix atmospheric nitrogen. Isolate PG29 identified as Ensifer meliloti was the most effective one. Ability of Prosopis farcta to establish symbiosis with rhizobial species confers an important advantage for this species to be used in reforestation programs. This study offered the first systematic information about the diversity of microsymbionts nodulating Prosopis farcta in the arid regions of Tunisia.
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Affiliation(s)
- A Fterich
- Laboratoire de Biotechnologies Végétales Appliquées à l'Amélioration des Cultures, Faculté des Sciences de Gabès, Université de Gabes, Cité Erriadh Zrig, 6072, Gabès, Tunisia
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Ren DW, Wang ET, Chen WF, Sui XH, Zhang XX, Liu HC, Chen WX. Rhizobium herbae sp. nov. and Rhizobium giardinii-related bacteria, minor microsymbionts of various wild legumes in China. Int J Syst Evol Microbiol 2010; 61:1912-1920. [PMID: 20833881 DOI: 10.1099/ijs.0.024943-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven Rhizobium strains associated with various legume species grown in different geographical regions of China were defined into four genomic groups related to Rhizobium giardinii, based upon ribosomal intergenic spacer RFLP, phylogenies of 16S rRNA and housekeeping (atpD, recA and glnII) genes, and DNA relatedness. Three strains in group I were classified as R. giardinii, as they showed high gene sequence similarities (>97 %) and DNA relatedness (64.3-67.5 %) to R. giardinii H152(T). Groups II, III and IV differed from all defined Rhizobium species based upon the consensus of all analyses. As group II contained two strains that originated from two distinct populations, we propose this group as a novel species, Rhizobium herbae sp. nov., with strain CCBAU 83011(T) ( = LMG 25718(T) = HAMBI 3117(T)) as the type strain.
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Affiliation(s)
- Da Wei Ren
- State Key Laboratories for Agrobiotechnology/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D. F., Mexico.,State Key Laboratories for Agrobiotechnology/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Feng Chen
- State Key Laboratories for Agrobiotechnology/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Laboratories for Agrobiotechnology/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xiao Xia Zhang
- Agricultural Culture Collection of China, Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 10081, PR China
| | - Hong Can Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen Xin Chen
- State Key Laboratories for Agrobiotechnology/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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García-Fraile P, Mulas-García D, Peix A, Rivas R, González-Andrés F, Velázquez E. Phaseolus vulgaris is nodulated in northern Spain by Rhizobium leguminosarum strains harboring two nodC alleles present in American Rhizobium etli strains: biogeographical and evolutionary implications. Can J Microbiol 2010; 56:657-66. [DOI: 10.1139/w10-048] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study a collection of rhizobial strains were isolated from effective nodules of Phaseolus vulgaris in a wide region of northern Spain, which is the major producer region of this legume in Spain. The analysis of their core genes, rrs, atpD, and recA, and the 16S–23S intergenic spacer showed that all isolates belong to the phylogenetic group of Rhizobium leguminosarum and some of them were identical to those of strains nodulating Vicia or Trifolium . None of the isolates was identified as Rhizobium etli ; however, all of them carry the nodC alleles α and γ harboured by American strains of this species. These alleles were also found in strains nodulating P. vulgaris in southern Spain identified as R. etli. These results suggest that R. etli was carried from America to Spain with common bean seeds, but that they could have found difficulties persisting in the soils of northern Spain, probably because of the climatic conditions. The symbiotic genes of this species could have been transferred, after the arrival of P. vulgaris, to strains of R. leguminosarum already present in northern Spanish soils.
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Affiliation(s)
- Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Laboratorio 209, Edificio Departamental de Biología, Campus Miguel de Unamuno, Salamanca 37007, Spain
- Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, León 24071, Spain
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca 37008, Spain
| | - Daniel Mulas-García
- Departamento de Microbiología y Genética, Universidad de Salamanca, Laboratorio 209, Edificio Departamental de Biología, Campus Miguel de Unamuno, Salamanca 37007, Spain
- Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, León 24071, Spain
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca 37008, Spain
| | - Alvaro Peix
- Departamento de Microbiología y Genética, Universidad de Salamanca, Laboratorio 209, Edificio Departamental de Biología, Campus Miguel de Unamuno, Salamanca 37007, Spain
- Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, León 24071, Spain
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca 37008, Spain
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Laboratorio 209, Edificio Departamental de Biología, Campus Miguel de Unamuno, Salamanca 37007, Spain
- Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, León 24071, Spain
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca 37008, Spain
| | - Fernando González-Andrés
- Departamento de Microbiología y Genética, Universidad de Salamanca, Laboratorio 209, Edificio Departamental de Biología, Campus Miguel de Unamuno, Salamanca 37007, Spain
- Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, León 24071, Spain
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca 37008, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Laboratorio 209, Edificio Departamental de Biología, Campus Miguel de Unamuno, Salamanca 37007, Spain
- Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, León 24071, Spain
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca 37008, Spain
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Velázquez E, Valverde A, Rivas R, Gomis V, Peix Á, Gantois I, Igual JM, León-Barrios M, Willems A, Mateos PF, Martínez-Molina E. Strains nodulating Lupinus albus on different continents belong to several new chromosomal and symbiotic lineages within Bradyrhizobium. Antonie van Leeuwenhoek 2010; 97:363-76. [DOI: 10.1007/s10482-010-9415-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2009] [Accepted: 01/12/2010] [Indexed: 11/25/2022]
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Ramírez-Bahena MH, Velázquez E, Fernández-Santos F, Peix A, Martínez-Molina E, Mateos PF. Phenotypic, genotypic, and symbiotic diversities in strains nodulating clover in different soils in Spain. Can J Microbiol 2009; 55:1207-16. [PMID: 19935893 DOI: 10.1139/w09-074] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Trifolium species are the most common legumes present in wild Spanish soils; however, there are no studies to date on the diversity of rhizobia nodulating clover in Spain. Twenty strains from different Spanish soils with acidic, neutral, and basic pH were selected to study their genotypic, phenotypic, and symbiotic features. The results showed that the isolates were genotypically diverse, displaying 12 different DNA fingerprint patterns and also 14 different plasmid profiles. Although they have 16S rRNA gene sequences that are nearly identical to that of the type strain of Rhizobium leguminosarum, their recA and atpD gene sequences were phylogenetically divergent from those of R. leguminosarum reference strains, and phenotypic divergence as well as different host ranges were also found. Although most of them nodulated both Trifolium and Phaseolus, only 5 strains were also able to nodulate Pisum. The results of the effectiveness analysis showed a high variability in the symbiotic characteristics of our strains and suggested that Pisum is the more restrictive host of this group. Interestingly, some of the Trifolium isolates showed an ability to promote growth of Pisum in the absence of nodulation.
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Rivas R, García-Fraile P, Velázquez E. Taxonomy of Bacteria Nodulating Legumes. Microbiol Insights 2009. [DOI: 10.4137/mbi.s3137] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Over the years, the term “rhizobia” has come to be used for all the bacteria that are capable of nodulation and nitrogen fixation in association with legumes but the taxonomy of rhizobia has changed considerably over the last 30 year. Recently, several non-rhizobial species belonging to alpha and beta subgroup of Proteobacteria have been identified as nitrogen-fixing legume symbionts. Here we provide an overview of the history of the rhizobia and the widespread phylogenetic diversity of nitrogen-fixing legume symbionts.
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Affiliation(s)
- Raúl Rivas
- Departamento de Microbiología y Genética, Laboratorio 209, Edificio Departamental de Biología, Doctores de la Reina s/n, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Laboratorio 209, Edificio Departamental de Biología, Doctores de la Reina s/n, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Laboratorio 209, Edificio Departamental de Biología, Doctores de la Reina s/n, Universidad de Salamanca, 37007 Salamanca, Spain
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Álvarez-Martínez ER, Valverde Á, Ramírez-Bahena MH, García-Fraile P, Tejedor C, Mateos PF, Santillana N, Zúñiga D, Peix A, Velázquez E. The analysis of core and symbiotic genes of rhizobia nodulating Vicia from different continents reveals their common phylogenetic origin and suggests the distribution of Rhizobium leguminosarum strains together with Vicia seeds. Arch Microbiol 2009; 191:659-68. [DOI: 10.1007/s00203-009-0495-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 05/31/2009] [Accepted: 07/02/2009] [Indexed: 11/30/2022]
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Rhizobia from Lanzarote, the Canary Islands, that nodulate Phaseolus vulgaris have characteristics in common with Sinorhizobium meliloti isolates from mainland Spain. Appl Environ Microbiol 2009; 75:2354-9. [PMID: 19218416 DOI: 10.1128/aem.02811-08] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stable, low-molecular-weight (LMW) RNA fractions of several rhizobial isolates of Phaseolus vulgaris grown in the soil of Lanzarote, an island of the Canary Islands, were identical to a less-common pattern found within Sinorhizobium meliloti (assigned to group II) obtained from nodules of alfalfa and alfalfa-related legumes grown in northern Spain. The P. vulgaris isolates and the group II LMW RNA S. meliloti isolates also were distinguishable in that both had two conserved inserts of 20 and 46 bp in the 16S-23S internal transcribed spacer region that were not present in other strains of S. meliloti. The isolates from P. vulgaris nodulated bean but not Medicago sativa, while those recovered from Medicago, Melilotus, and Trigonella spp. nodulated both host legumes. The bean isolates also were distinguished from those of Medicago, Melilotus, and Trigonella spp. by nodC sequence analysis. The nodC sequences of the bean isolates were most similar to those reported for S. meliloti bv. mediterranense and Sinorhizobium fredii bv. mediterranense (GenBank accession numbers DQ333891 and AF217267, respectively). None of the evidence placed the bean isolates from Lanzarote in the genus Rhizobium, which perhaps is inconsistent with seed-borne transmission of Rhizobium etli from the Americas to the Canaries as an explanation for the presence of bean-nodulating rhizobia in soils of Lanzarote.
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Del Villar M, Rivas R, Peix A, Mateos PF, Martínez-Molina E, van Berkum P, Willems A, Velázquez E. Stable low molecular weight RNA profiling showed variations within Sinorhizobium meliloti and Sinorhizobium medicae nodulating different legumes from the alfalfa cross-inoculation group. FEMS Microbiol Lett 2008; 282:273-81. [PMID: 18399993 DOI: 10.1111/j.1574-6968.2008.01139.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Four different low molecular weight (LMW) RNA profiles, designated I-IV, among 179 isolates from Medicago, Melilotus and Trigonella species growing in a field site in Northern Spain were identified. From sequence analysis of the 16S rRNA, atpD and recA genes as well as DNA-DNA hybridization analysis with representatives of each LMW RNA profile it was evident that isolates with LMW RNA profiles I and II belonged to Sinorhizobium meliloti and those displaying profiles III and IV to Sinorhizobium medicae. Therefore, two distinct LMW RNA electrophoretic mobility profiles were found within each of these two species. Collectively, LMW RNA profiles I and II (identified as S. meliloti) were predominant in Melilotus alba, Melilotus officinalis and Medicago sativa. Profiles III and IV (identified as S. medicae) were predominant in Melilotus parviflora, Medicago sphaerocarpa, Medicago lupulina and Trigonella foenum-graecum. All the four LMW RNA profiles were identified among isolates from Trigonella monspelliaca nodules. These results revealed a different specificity by the hosts of the alfalfa cross-inoculation group towards the two bacterial species found in this study.
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Affiliation(s)
- María Del Villar
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
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