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Karasev ES, Hosid SL, Aksenova TS, Onishchuk OP, Kurchak ON, Dzyubenko NI, Andronov EE, Provorov NA. Impacts of Natural Selection on Evolution of Core and Symbiotically Specialized ( sym) Genes in the Polytypic Species Neorhizobium galegae. Int J Mol Sci 2023; 24:16696. [PMID: 38069024 PMCID: PMC10706768 DOI: 10.3390/ijms242316696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Nodule bacteria (rhizobia) represent a suitable model to address a range of fundamental genetic problems, including the impacts of natural selection on the evolution of symbiotic microorganisms. Rhizobia possess multipartite genomes in which symbiotically specialized (sym) genes differ from core genes in their natural histories. Diversification of sym genes is responsible for rhizobia microevolution, which depends on host-induced natural selection. By contrast, diversification of core genes is responsible for rhizobia speciation, which occurs under the impacts of still unknown selective factors. In this paper, we demonstrate that in goat's rue rhizobia (Neorhizobium galegae) populations collected at North Caucasus, representing two host-specific biovars orientalis and officianalis (N2-fixing symbionts of Galega orientalis and G. officinalis), the evolutionary mechanisms are different for core and sym genes. In both N. galegae biovars, core genes are more polymorphic than sym genes. In bv. orientalis, the evolution of core genes occurs under the impacts of driving selection (dN/dS > 1), while the evolution of sym genes is close to neutral (dN/dS ≈ 1). In bv. officinalis, the evolution of core genes is neutral, while for sym genes, it is dependent on purifying selection (dN/dS < 1). A marked phylogenetic congruence of core and sym genes revealed using ANI analysis may be due to a low intensity of gene transfer within and between N. galegae biovars. Polymorphism in both gene groups and the impacts of driving selection on core gene evolution are more pronounced in bv. orientalis than in bv. officianalis, reflecting the diversities of their respective host plant species. In bv. orientalis, a highly significant (P0 < 0.001) positive correlation is revealed between the p-distance and dN/dS values for core genes, while in bv. officinalis, this correlation is of low significance (0.05 < P0 < 0.10). For sym genes, the correlation between p-distance and dN/dS values is negative in bv. officinalis but is not revealed in bv. orientalis. These data, along with the functional annotation of core genes implemented using Gene Ontology tools, suggest that the evolution of bv. officinalis is based mostly on adaptation for in planta niches while in bv. orientalis, evolution presumably depends on adaptation for soil niches. New insights into the tradeoff between natural selection and genetic diversity are presented, suggesting that gene nucleotide polymorphism may be extended by driving selection only in ecologically versatile organisms capable of supporting a broad spectrum of gene alleles in their gene pools.
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Affiliation(s)
- Evgeny S. Karasev
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Sergey L. Hosid
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Tatiana S. Aksenova
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Olga P. Onishchuk
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Oksana N. Kurchak
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
| | - Nikolay I. Dzyubenko
- All-Russia Research Institute of Plant Genetic Resources, 190031 St. Petersburg, Russia;
| | - Evgeny E. Andronov
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
- Dokuchaev Soil Science Institute, 119017 Moscow, Russia
| | - Nikolay A. Provorov
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (E.S.K.); (S.L.H.); (T.S.A.); (O.P.O.); (O.N.K.); (N.A.P.)
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Baymiev AK, Akimova ES, Koryakov IS, Vladimirova AA, Baymiev AK. The Composition of Lotus corniculatus Root Nodule Bacteria Depending on the Host Plant Vegetation Stage. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722601154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Adjei JA, Aserse AA, Yli-Halla M, Ahiabor BDK, Abaidoo RC, Lindstrom K. Phylogenetically diverse Bradyrhizobium genospecies nodulate Bambara groundnut (Vigna subterranea L. Verdc) and soybean (Glycine max L. Merril) in the northern savanna zones of Ghana. FEMS Microbiol Ecol 2022; 98:fiac043. [PMID: 35404419 PMCID: PMC9329091 DOI: 10.1093/femsec/fiac043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
Abstract
A total of 102 bacterial strains isolated from nodules of three Bambara groundnut and one soybean cultivars grown in nineteen soil samples collected from northern Ghana were characterized using multilocus gene sequence analysis. Based on a concatenated sequence analysis (glnII-rpoB-recA-gyrB-atpD-dnaK), 54 representative strains were distributed in 12 distinct lineages, many of which were placed mainly in the Bradyrhizobium japonicum and Bradyrhizobium elkanii supergroups. Twenty-four of the 54 representative strains belonged to seven putative novel species, while 30 were conspecific with four recognized Bradyrhizobium species. The nodA phylogeny placed all the representative strains in the cosmopolitan nodA clade III. The strains were further separated in seven nodA subclusters with reference strains mainly of African origin. The nifH phylogeny was somewhat congruent with the nodA phylogeny, but both symbiotic genes were mostly incongruent with the core housekeeping gene phylogeny indicating that the strains acquired their symbiotic genes horizontally from distantly related Bradyrhizobium species. Using redundancy analysis, the distribution of genospecies was found to be influenced by the edaphic factors of the respective sampling sites. In general, these results mainly underscore the high genetic diversity of Bambara groundnut-nodulating bradyrhizobia in Ghanaian soils and suggest a possible vast resource of adapted inoculant strains.
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Affiliation(s)
- Josephine A Adjei
- Department of Crop and Soil Sciences, Faculty of Agriculture, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana
- Faculty of Biological and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, PO Box 52, Tamale, Ghana
| | - Aregu A Aserse
- Faculty of Biological and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Markku Yli-Halla
- Department of Agricultural Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Benjamin D K Ahiabor
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, PO Box 52, Tamale, Ghana
| | - Robert C Abaidoo
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana
- International Institute of Tropical Agriculture, PMB 5320, Ibadan, Nigeria
| | - Kristina Lindstrom
- Faculty of Biological and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
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Igolkina AA, Bazykin GA, Chizhevskaya EP, Provorov NA, Andronov EE. Matching population diversity of rhizobial nodA and legume NFR5 genes in plant-microbe symbiosis. Ecol Evol 2019; 9:10377-10386. [PMID: 31624556 PMCID: PMC6787799 DOI: 10.1002/ece3.5556] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 07/07/2019] [Accepted: 07/15/2019] [Indexed: 12/31/2022] Open
Abstract
We hypothesized that population diversities of partners in nitrogen-fixing rhizobium-legume symbiosis can be matched for "interplaying" genes. We tested this hypothesis using data on nucleotide polymorphism of symbiotic genes encoding two components of the plant-bacteria signaling system: (a) the rhizobial nodA acyltransferase involved in the fatty acid tail decoration of the Nod factor (signaling molecule); (b) the plant NFR5 receptor required for Nod factor binding. We collected three wild-growing legume species together with soil samples adjacent to the roots from one large 25-year fallow: Vicia sativa, Lathyrus pratensis, and Trifolium hybridum nodulated by one of the two Rhizobium leguminosarum biovars (viciae and trifolii). For each plant species, we prepared three pools for DNA extraction and further sequencing: the plant pool (30 plant indiv.), the nodule pool (90 nodules), and the soil pool (30 samples). We observed the following statistically significant conclusions: (a) a monotonic relationship between the diversity in the plant NFR5 gene pools and the nodule rhizobial nodA gene pools; (b) higher topological similarity of the NFR5 gene tree with the nodA gene tree of the nodule pool, than with the nodA gene tree of the soil pool. Both nonsynonymous diversity and Tajima's D were increased in the nodule pools compared with the soil pools, consistent with relaxation of negative selection and/or admixture of balancing selection. We propose that the observed genetic concordance between NFR5 gene pools and nodule nodA gene pools arises from the selection of particular genotypes of the nodA gene by the host plant.
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Affiliation(s)
- Anna A. Igolkina
- ARRIAM, All‐Russia Research Institute for Agricultural MicrobiologyPushkinRussia
- Peter the Great St. Petersburg Polytechnic UniversitySaint‐PetersburgRussia
| | - Georgii A. Bazykin
- Center for Life SciencesSkolkovo Institute of Science and TechnologyMoscowRussia
- Laboratory for Molecular EvolutionKharkevich Institute of Information Transmission Problems of the Russian Academy of SciencesMoscowRussia
| | | | - Nikolai A. Provorov
- ARRIAM, All‐Russia Research Institute for Agricultural MicrobiologyPushkinRussia
| | - Evgeny E. Andronov
- ARRIAM, All‐Russia Research Institute for Agricultural MicrobiologyPushkinRussia
- Saint‐Petersburg State UniversitySaint‐PetersburgRussia
- Dokuchaev Soil Science InstituteMoscowRussia
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Bromfield ESP, Cloutier S, Robidas C, Tran Thi TV, Darbyshire SJ. Invasive Galega officinalis (Goat's rue) plants in Canada form a symbiotic association with strains of Neorhizobium galegae sv. officinalis originating from the Old World. Ecol Evol 2019; 9:6999-7004. [PMID: 31380028 PMCID: PMC6662265 DOI: 10.1002/ece3.5266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/23/2019] [Accepted: 04/29/2019] [Indexed: 11/09/2022] Open
Abstract
The toxic legume plant, Galega officinalis, is native to the Eastern Mediterranean and Black Sea regions. This legume is considered to be a noxious weed, and its establishment in Canada may have resulted from ornamental planting and/or field trials. In its native range, a highly specific nitrogen-fixing symbiosis with the bacterium, Neorhizobium galegae symbiovar (sv.) officinalis, is required for normal growth. In North America, nothing is known about the bacterial symbionts of G. officinalis. Our purpose was to determine the species and symbiovar identity of symbiotic bacteria associated with invasive plants of G. officinalis at five sites in the province of Ontario, Canada. Sequence analysis of four housekeeping (16S rRNA, atpD, glnII, and recA) and two symbiosis (nodC and nifH) genes showed that all 50 bacterial isolates from root nodules of G. officinalis at the five Canadian sites were identical to strains of N. galegae sv. officinalis originating either from Europe or the Caucasus. Plant tests indicated that soils collected from four Canadian sites without a history of agriculture or presence of G. officinalis were deficient in symbiotic bacteria capable of eliciting nodules on this plant. Collectively our data support the hypothesis of anthropogenic co-introduction of G. officinalis and its specific symbiotic bacterium into Canada from the Old World. Factors that may limit the spread of G. officinalis in new environments are discussed.
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Affiliation(s)
- Eden S. P. Bromfield
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaOntarioCanada
| | - Sylvie Cloutier
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaOntarioCanada
| | - Catherine Robidas
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaOntarioCanada
| | - Thu Van Tran Thi
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaOntarioCanada
| | - Stephen J. Darbyshire
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaOntarioCanada
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Karasev ES, Andronov EE, Aksenova TS, Chizhevskaya EP, Tupikin AE, Provorov NA. Evolution of Goat’s Rue Rhizobia (Neorhizobium galegae): Analysis of Polymorphism of the Nitrogen Fixation and Nodule Formation Genes. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419020078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Degefu T, Wolde-meskel E, Woliy K, Frostegård Å. Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of tree and annual legume species growing in Ethiopia. Syst Appl Microbiol 2017; 40:205-214. [DOI: 10.1016/j.syapm.2017.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/27/2022]
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Local genetic structure and worldwide phylogenetic position of symbiotic Rhizobium leguminosarum strains associated with a traditional cultivated crop, Vicia ervilia, from Northern Morocco. Syst Appl Microbiol 2016; 39:409-17. [DOI: 10.1016/j.syapm.2016.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/03/2016] [Accepted: 06/08/2016] [Indexed: 11/15/2022]
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Österman J, Mousavi SA, Koskinen P, Paulin L, Lindström K. Genomic features separating ten strains of Neorhizobium galegae with different symbiotic phenotypes. BMC Genomics 2015; 16:348. [PMID: 25933608 PMCID: PMC4417242 DOI: 10.1186/s12864-015-1576-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/24/2015] [Indexed: 11/10/2022] Open
Abstract
Background The symbiotic phenotype of Neorhizobium galegae, with strains specifically fixing nitrogen with either Galega orientalis or G. officinalis, has made it a target in research on determinants of host specificity in nitrogen fixation. The genomic differences between representative strains of the two symbiovars are, however, relatively small. This introduced a need for a dataset representing a larger bacterial population in order to make better conclusions on characteristics typical for a subset of the species. In this study, we produced draft genomes of eight strains of N. galegae having different symbiotic phenotypes, both with regard to host specificity and nitrogen fixation efficiency. These genomes were analysed together with the previously published complete genomes of N. galegae strains HAMBI 540T and HAMBI 1141. Results The results showed that the presence of an additional rpoN sigma factor gene in the symbiosis gene region is a characteristic specific to symbiovar orientalis, required for nitrogen fixation. Also the nifQ gene was shown to be crucial for functional symbiosis in both symbiovars. Genome-wide analyses identified additional genes characteristic of strains of the same symbiovar and of strains having similar plant growth promoting properties on Galega orientalis. Many of these genes are involved in transcriptional regulation or in metabolic functions. Conclusions The results of this study confirm that the only symbiosis-related gene that is present in one symbiovar of N. galegae but not in the other is an rpoN gene. The specific function of this gene remains to be determined, however. New genes that were identified as specific for strains of one symbiovar may be involved in determining host specificity, while others are defined as potential determinant genes for differences in efficiency of nitrogen fixation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1576-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janina Österman
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00790, Helsinki, Finland. .,Department of Environmental Sciences, University of Helsinki, Viikinkaari 2a, 00790, Helsinki, Finland.
| | - Seyed Abdollah Mousavi
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00790, Helsinki, Finland. .,Department of Environmental Sciences, University of Helsinki, Viikinkaari 2a, 00790, Helsinki, Finland.
| | - Patrik Koskinen
- Institute of Biotechnology, University of Helsinki, Viikinkaari 9, 00790, Helsinki, Finland.
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Viikinkaari 9, 00790, Helsinki, Finland.
| | - Kristina Lindström
- Department of Environmental Sciences, University of Helsinki, Viikinkaari 2a, 00790, Helsinki, Finland.
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Andronov EE, Onishchuk OP, Kurchak ON, Provorov NA. Population structure of the clover rhizobia Rhizobium leguminosarum bv. trifolii upon transition from soil into the nodular niche. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714030035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Roumiantseva ML, Muntyan VS, Mengoni A, Simarov BV. ITS-polymorphism of salt-tolerant and salt-sensitive native isolates of Sinorhizoblum meliloti-symbionts of alfalfa, clover and fenugreek plants. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414040103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ardley JK, Reeve WG, O'Hara GW, Yates RJ, Dilworth MJ, Howieson JG. Nodule morphology, symbiotic specificity and association with unusual rhizobia are distinguishing features of the genus Listia within the Southern African crotalarioid clade Lotononis s.l. ANNALS OF BOTANY 2013; 112:1-15. [PMID: 23712451 PMCID: PMC3690986 DOI: 10.1093/aob/mct095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 03/25/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS The legume clade Lotononis sensu lato (s.l.; tribe Crotalarieae) comprises three genera: Listia, Leobordea and Lotononis sensu stricto (s.s.). Listia species are symbiotically specific and form lupinoid nodules with rhizobial species of Methylobacterium and Microvirga. This work investigated whether these symbiotic traits were confined to Listia by determining the ability of rhizobial strains isolated from species of Lotononis s.l. to nodulate Listia, Leobordea and Lotononis s.s. hosts and by examining the morphology and structure of the resulting nodules. METHODS Rhizobia were characterized by sequencing their 16S rRNA and nodA genes. Nodulation and N2 fixation on eight taxonomically diverse Lotononis s.l. species were determined in glasshouse trials. Nodules of all hosts, and the process of infection and nodule initiation in Listia angolensis and Listia bainesii, were examined by light microscopy. KEY RESULTS Rhizobia associated with Lotononis s.l. were phylogenetically diverse. Leobordea and Lotononis s.s. isolates were most closely related to Bradyrhizobium spp., Ensifer meliloti, Mesorhizobium tianshanense and Methylobacterium nodulans. Listia angolensis formed effective nodules only with species of Microvirga. Listia bainesii nodulated only with pigmented Methylobacterium. Five lineages of nodA were found. Listia angolensis and L. bainesii formed lupinoid nodules, whereas nodules of Leobordea and Lotononis s.s. species were indeterminate. All effective nodules contained uniformly infected central tissue. Listia angolensis and L. bainesii nodule initials occurred on the border of the hypocotyl and along the tap root, and nodule primordia developed in the outer cortical layer. Neither root hair curling nor infection threads were seen. CONCLUSIONS Two specificity groups occur within Lotononis s.l.: Listia species are symbiotically specific, while species of Leobordea and Lotononis s.s. are generally promiscuous and interact with rhizobia of diverse chromosomal and symbiotic lineages. The seasonally waterlogged habitat of Listia species may favour the development of symbiotic specificity.
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Affiliation(s)
- Julie K Ardley
- Centre for Rhizobium Studies, Murdoch University, Murdoch WA 6150, Australia.
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Osterman J, Chizhevskaja EP, Andronov EE, Fewer DP, Terefework Z, Roumiantseva ML, Onichtchouk OP, Dresler-Nurmi A, Simarov BV, Dzyubenko NI, Lindström K. Galega orientalis is more diverse than Galega officinalis in Caucasus--whole-genome AFLP analysis and phylogenetics of symbiosis-related genes. Mol Ecol 2011; 20:4808-21. [PMID: 21980996 DOI: 10.1111/j.1365-294x.2011.05291.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Legume plants can obtain combined nitrogen for their growth in an efficient way through symbiosis with specific bacteria. The symbiosis between Rhizobium galegae and its host plant Galega is an interesting case where the plant species G. orientalis and G. officinalis form effective, nitrogen-fixing, symbioses only with the appropriate rhizobial counterpart, R. galegae bv. orientalis and R. galegae bv. officinalis, respectively. The symbiotic properties of nitrogen-fixing rhizobia are well studied, but more information is needed on the properties of the host plants. The Caucasus region in Eurasia has been identified as the gene centre (centre of origin) of G. orientalis, although both G. orientalis and G. officinalis can be found in this region. In this study, the diversity of these two Galega species in Caucasus was investigated to test the hypothesis that in this region G. orientalis is more diverse than G. officinalis. The amplified fragment length polymorphism fingerprinting performed here showed that the populations of G. orientalis and R. galegae bv. orientalis are more diverse than those of G. officinalis and R. galegae bv. officinalis, respectively. These results support the centre of origin status of Caucasus for G. orientalis at a genetic level. Analysis of the symbiosis-related plant genes NORK and Nfr5 reveals remarkable diversity within the Nfr5 sequence, although no evidence of adaptive evolution could be found.
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Affiliation(s)
- J Osterman
- Department of Food and Environmental Sciences, Viikinkaari 9, Biocenter 1, PO Box 56, FI-00014 University of Helsinki, Helsinki, Finland.
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Degefu T, Wolde-meskel E, Frostegård Å. Multilocus sequence analyses reveal several unnamed Mesorhizobium genospecies nodulating Acacia species and Sesbania sesban trees in Southern regions of Ethiopia. Syst Appl Microbiol 2011; 34:216-26. [DOI: 10.1016/j.syapm.2010.09.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 08/14/2010] [Accepted: 09/28/2010] [Indexed: 11/17/2022]
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Rogel MA, Ormeño-Orrillo E, Martinez Romero E. Symbiovars in rhizobia reflect bacterial adaptation to legumes. Syst Appl Microbiol 2011; 34:96-104. [DOI: 10.1016/j.syapm.2010.11.015] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/24/2010] [Accepted: 11/27/2010] [Indexed: 11/27/2022]
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Lindström K, Murwira M, Willems A, Altier N. The biodiversity of beneficial microbe-host mutualism: the case of rhizobia. Res Microbiol 2010; 161:453-63. [PMID: 20685242 DOI: 10.1016/j.resmic.2010.05.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2009] [Revised: 04/27/2010] [Accepted: 05/04/2010] [Indexed: 11/18/2022]
Abstract
Symbiotic nitrogen fixation is the main route for sustainable input of nitrogen into ecosystems. Nitrogen fixation in agriculture can be improved by inoculation of legume crops with suitable rhizobia. Knowledge of the biodiversity of rhizobia and of local populations is important for the design of successful inoculation strategies. Soybeans are major nitrogen-fixing crops in many parts of the world. Bradyrhizobial inoculants for soybean are very diverse, yet classification and characterization of strains have long been difficult. Recent genetic characterization methods permit more reliable identification and will improve our knowledge of local populations. Forage legumes form another group of agronomically important legumes. Research and extension policies valorizing rhizobial germplasm diversity and preservation, farmer training for proper inoculant use and legal enforcement of commercial inoculant quality have proved a successful approach to promoting the use of forage legumes while enhancing biological N(2) fixation. It is worth noting that taxonomically important strains may not necessarily be important reference strains for other uses such as legume inoculation and genomics due to specialization of the different fields. This article points out both current knowledge and gaps remaining to be filled for further interaction and improvement of a rhizobial commons.
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Affiliation(s)
- Kristina Lindström
- Department of Food and Environmental Sciences, Division of Microbiology and HAMBI Culture Collection, Biocenter 1, P.O. Box 56, University of Helsinki, FI-00014 Helsinki, Finland.
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Li Q, Zhang X, Zou L, Chen Q, Fewer DP, Lindström K. Horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plantsAstragalus luteolusandAstragalus ernestiiin Sichuan, China. FEMS Microbiol Ecol 2009; 70:71-9. [DOI: 10.1111/j.1574-6941.2009.00776.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Nandwani R, Dudeja SS. Molecular diversity of a native mesorhizobial population of nodulating chickpea (Cicer arietinumL.) in Indian soils. J Basic Microbiol 2009; 49:463-70. [DOI: 10.1002/jobm.200800355] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Legume nodules, specialized structures for nitrogen fixation, are probably the result of coevolution of plants and ancestral rhizobia. Among the evolutionary processes leading to legume radiation and divergence, coevolution with rhizobia might have occurred. Alternatively, bacteria could have been constantly selected by plants, with bacteria slightly influencing plant evolution (required to fulfill the criteria for a coevolutionary hypothesis). Evidence of bacterial effects on plant evolution is scarce but being searched for. Bacterial genetic plasticity may be indicative of the large capacity of Rhizobium to adapt to legumes. Events such as symbiotic replacement, easy recruitment of symbiotic bacteria by legume plants, and lateral transfer of symbiotic genes seem to erase the coevolutionary or selected relationships in rhizobial-legume symbiosis. In particular, the hypotheses proposed are (1) Rhizobium replaced Bradyrhizobium in a few hosts of the Phaseoleae tribe, Phaseolus vulgaris and P. coccineus; (2) Rhizobium etli as a species did not coevolve with bean; and (3) beta-Proteobacteria replaced alpha-Proteobacteria in South American mimosas. Novel results on symbiosis suggest a more complex evolutionary process for nodulation that may include multiple organisms, such as mycorrhiza, nematodes, and other bacteria in addition to rhizobia.
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Tian CF, Wang ET, Han TX, Sui XH, Chen WX. Genetic diversity of rhizobia associated with Vicia faba in three ecological regions of China. Arch Microbiol 2007; 188:273-82. [PMID: 17479251 DOI: 10.1007/s00203-007-0245-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 03/03/2007] [Accepted: 04/02/2007] [Indexed: 10/23/2022]
Abstract
Great genetic diversity was revealed among 75 rhizobal isolates associated with Vicia faba grown in Chinese fields with AFLP, ARDRA, 16S rDNA sequencing, DNA-DNA hybridization, BOX-PCR and RFLP of PCR-amplified nodD and nodC. Most of the isolates were Rhizobium leguminosarum, and six isolates belonged to an unnamed Rhizobium species. In the homogeneity analysis, the isolates were grouped into three clusters corresponding to (1) autumn sowing (subtropical) region where the winter ecotype of V. faba was cultivated, (2) spring sowing (temperate) region where the spring ecotype was grown, and (3) Yunnan province where the intermediate ecotype was sown either in spring or in autumn. Nonrandom associations were found among the nod genotypes, genomic types and ecological regions, indicating an epidemic symbiotic gene transfer pattern among different genomic backgrounds within an ecological region and a relatively limited transfer pattern between different regions. Conclusively, the present results suggested an endemic population structure of V. faba rhizobia in Chinese fields and demonstrated a novel rhizobium associated with faba bean.
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Affiliation(s)
- Chang Fu Tian
- Key Laboratory of Agro-Microbial Resource and Application, Ministry of Agriculture/College of Biological Sciences, China Agricultural University, 100094 Beijing, China
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Sarma AD, Emerich DW. A comparative proteomic evaluation of culture grownvs nodule isolatedBradyrhizobium japonicum. Proteomics 2006; 6:3008-28. [PMID: 16688787 DOI: 10.1002/pmic.200500783] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Total protein extract of Bradyrhizobium japonicum cultivated in HM media were resolved by 2-D PAGE using narrow range IPG strips. More than 1200 proteins were detected, of which nearly 500 proteins were analysed by MALDI-TOF and 310 spots were tentatively identified. The present study describes at the proteome level a significant number of metabolic pathways related to important cellular events in free-living B. japonicum. A comparative analysis of proteomes of free-living and nodule residing bacteria revealed major differences and similarities between the two states. Proteins related to fatty acid, nucleic acid and cell surface synthesis were significantly higher in cultured cells. Nitrogen metabolism was more pronounced in bacteroids whereas carbon metabolism was similar in both states. Relative percentage of proteins related to global functions like protein synthesis, maturation & degradation and membrane transporters were similar in both forms, however, different proteins provided these functions in the two states.
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Affiliation(s)
- Annamraju D Sarma
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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Sarma AD, Emerich DW. Global protein expression pattern of Bradyrhizobium japonicum bacteroids: a prelude to functional proteomics. Proteomics 2005; 5:4170-84. [PMID: 16254929 DOI: 10.1002/pmic.200401296] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As a prelude to using functional proteomics towards understanding the process of symbiotic nitrogen fixation between the legume soybean and the soil bacteria Bradyrhizobium japonicum, we examined the total protein expression pattern of the nodule bacteria, often referred to as bacteroids. A partial proteome map was constructed by separating the total bacteroid proteins using high-resolution 2-DE. Of the several hundred protein spots analyzed using PMF, 180 spots were tentatively identified by searching the available database for B. japonicum, (http://www.kazusa.or.jp/index.html). The data showed that the bacteroid expressed a dominant and elaborate protein network for nitrogen and carbon metabolism, which is closely dependent on the plant supplied metabolites, and seems aptly supported by a selective group of bacteroid transporter proteins. However, they seem to lack a defined fatty acid and nucleic acid metabolism. Interestingly, the proteins related to protein synthesis, scaffolding and degradation were among the most predominant spots of the bacteroid proteome. In addition, several proteins, which showed fairly good expression, were identified to be involved with cellular detoxification, stress regulation and signaling communication components. This preliminary proteomic data matches very well with several biochemical and genetic reports, and clearly shows the inter-connection between several metabolic pathways that meet the needs of the bacteroid. It is expected that in the future this will allow us to develop testable hypotheses about the roles of several of these proteins in context to the metabolic pathway connections and metabolite fluxes.
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Affiliation(s)
- Annamraju D Sarma
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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Wolde-Meskel E, Terefework Z, Frostegård Å, Lindström K. Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia. Int J Syst Evol Microbiol 2005; 55:1439-1452. [PMID: 16014464 DOI: 10.1099/ijs.0.63534-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR-RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500-1300 bp), and 58 strains contained double copies. UPGMA dendrograms generated from cluster analyses of the 16S and 23S rRNA gene PCR-RFLP data were in good agreement, and the combined distance matrices delineated 87 genotypes, indicating considerable genetic diversity among the isolates. Furthermore, partial sequence analysis of 67 representative strains revealed 46 16S rRNA gene sequence types, among which 12 were 100% similar to those of previously described species and 34 were novel sequences with 94-99% similarity to those of recognized species. The phylogenetic analyses suggested that strains indigenous to Ethiopia belonged to the genera Agrobacterium, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium and Sinorhizobium. Many of the rhizobia isolated from previously uninvestigated indigenous woody legumes had novel 16S rRNA gene sequences and were phylogenetically diverse. This study clearly shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity.
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Affiliation(s)
- Endalkachew Wolde-Meskel
- Norwegian University of Life Sciences, Department of Chemistry, Biotechnology and Food Science, PO Box 5040, N-1432 Ås, Norway
| | - Zewdu Terefework
- Department of Applied Chemistry and Microbiology, Biocenter 1, FIN-0014 University of Helsinki, Finland
| | - Åsa Frostegård
- Norwegian University of Life Sciences, Department of Chemistry, Biotechnology and Food Science, PO Box 5040, N-1432 Ås, Norway
| | - Kristina Lindström
- Department of Applied Chemistry and Microbiology, Biocenter 1, FIN-0014 University of Helsinki, Finland
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Baimiev AK, Gubaidullin II, Chemeris AV, Vakhitov VA. Structures of sugar-binding peptides of Galega orientalis and G. officinalis lectins determine the choice of partner in rhizobium?Legume symbiosis. Mol Biol 2005. [DOI: 10.1007/s11008-005-0013-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wolde-meskel E, Terefework Z, Lindström K, Frostegård A. Metabolic and genomic diversity of rhizobia isolated from field standing native and exotic woody legumes in southern Ethiopia. Syst Appl Microbiol 2004; 27:603-11. [PMID: 15490562 DOI: 10.1078/0723202041748145] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Eighty-seven rhizobial strains isolated from root nodules of field standing native and exotic woody legumes in southern Ethiopia were characterized using the Biolog method and AFLP fingerprinting technique. Cluster analysis of the metabolic and genomic fingerprints revealed 18 and 25 groups, respectively, demonstrating considerable diversity in rhizobial population indigenous to Ethiopian soils. While 25 strains (29%) were linked to members of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium or Sinorhizobium, the bulk of the strains formed several distinct groups in both methods and did not relate to reference species included in the study. In contrast to exotic species which formed symbiosis with strains of only one specific genomic group, indigenous host species nodulated by metabolically and genomically diverse groups. The results in this study support the view, that long-term association between the symbionts allows gradual differentiation and diversity in compatible rhizobial population resident in native soils. Lack of significant metabolic and genomic relatedness to the reference strains in our results suggested that test strains in our collection probably included 'unique' types, which belong to several yet undefined rhizobial species.
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Affiliation(s)
- Endalkachew Wolde-meskel
- Agricultural University of Norway, Department of Chemistry, Biotechnology and Food Science, As, Norway.
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