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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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Provorov NA, Andronov EE, Kimeklis AK, Onishchuk OP, Igolkina AA, Karasev ES. Microevolution, speciation and macroevolution in rhizobia: Genomic mechanisms and selective patterns. FRONTIERS IN PLANT SCIENCE 2022; 13:1026943. [PMID: 36388581 PMCID: PMC9640933 DOI: 10.3389/fpls.2022.1026943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Nodule bacteria (rhizobia), N2-fixing symbionts of leguminous plants, represent an excellent model to study the fundamental issues of evolutionary biology, including the tradeoff between microevolution, speciation, and macroevolution, which remains poorly understood for free-living organisms. Taxonomically, rhizobia are extremely diverse: they are represented by nearly a dozen families of α-proteobacteria (Rhizobiales) and by some β-proteobacteria. Their genomes are composed of core parts, including house-keeping genes (hkg), and of accessory parts, including symbiotically specialized (sym) genes. In multipartite genomes of evolutionary advanced fast-growing species (Rhizobiaceae), sym genes are clustered on extra-chromosomal replicons (megaplasmids, chromids), facilitating gene transfer in plant-associated microbial communities. In this review, we demonstrate that in rhizobia, microevolution and speciation involve different genomic and ecological mechanisms: the first one is based on the diversification of sym genes occurring under the impacts of host-induced natural selection (including its disruptive, frequency-dependent and group forms); the second one-on the diversification of hkgs under the impacts of unknown factors. By contrast, macroevolution represents the polyphyletic origin of super-species taxa, which are dependent on the transfer of sym genes from rhizobia to various soil-borne bacteria. Since the expression of newly acquired sym genes on foreign genomic backgrounds is usually restricted, conversion of resulted recombinants into the novel rhizobia species involves post-transfer genetic changes. They are presumably supported by host-induced selective processes resulting in the sequential derepression of nod genes responsible for nodulation and of nif/fix genes responsible for symbiotic N2 fixation.
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Affiliation(s)
- Nikolay A. Provorov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
| | - Evgeny E. Andronov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
- Laboratory of Soil Biology and Biochemistry, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
| | - Anastasiia K. Kimeklis
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia
| | - Olga P. Onishchuk
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
| | - Anna A. Igolkina
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Evgeny S. Karasev
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
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Van Dingenen J, Garcia Mendez S, Beirinckx S, Vlaminck L, De Keyser A, Stuer N, Verschaete S, Clarysse A, Pannecoucque J, Rombauts S, Roldan-Ruiz I, Willems A, Goormachtig S. Flemish soils contain rhizobia partners for Northwestern Europe-adapted soybean cultivars. Environ Microbiol 2022; 24:3334-3354. [PMID: 35212122 DOI: 10.1111/1462-2920.15941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 11/28/2022]
Abstract
In Europe, soybean (Glycine max) used for food and feed has to be imported, causing negative socioeconomic and environmental impacts. To increase the local production, breeding generated varieties that grow in colder climates, but the yield using the commercial inoculants is not satisfactory in Belgium because of variable nodulation efficiencies. To look for indigenous nodulating strains possibly adapted to the local environment, we initiated a nodulation trap by growing early-maturing cultivars under natural and greenhouse conditions in 107 garden soils in Flanders. Nodules occurred in 18 and 21 soils in the garden and greenhouse experiments respectively. By combining 16S rRNA PCR on single isolates with HiSeq 16S metabarcoding on nodules, we found a large bacterial richness and diversity from different soils. Furthermore, using Oxford Nanopore Technologies sequencing of DNA from one nodule, we retrieved the entire genome of a Bradyrhizobium species, not previously isolated, but profusely present in that nodule. These data highlight the need of combining diverse identification techniques to capture the true nodule rhizobial community. Eight selected rhizobial isolates were subdivided by whole-genome analysis in three genera containing six genetically distinct species that, except for two, aligned with known type strains and were all able to nodulate soybean in the laboratory.
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Affiliation(s)
- Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Sonia Garcia Mendez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, 9000, Belgium
| | - Stien Beirinckx
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Lena Vlaminck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Naomi Stuer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Severine Verschaete
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Alexander Clarysse
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Joke Pannecoucque
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke, 9820, Belgium
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Isabel Roldan-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke, 9820, Belgium
| | - Anne Willems
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, 9000, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
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Rhizobia Isolated from the Relict Legume Vavilovia formosa Represent a Genetically Specific Group within Rhizobium leguminosarum biovar viciae. Genes (Basel) 2019; 10:genes10120991. [PMID: 31805683 PMCID: PMC6947851 DOI: 10.3390/genes10120991] [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: 10/23/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 01/09/2023] Open
Abstract
Twenty-two rhizobia strains isolated from three distinct populations (North Ossetia, Dagestan, and Armenia) of a relict legume Vavilovia formosa were analysed to determine their position within Rhizobium leguminosarum biovar viciae (Rlv). These bacteria are described as symbionts of four plant genera Pisum, Vicia, Lathyrus, and Lens from the Fabeae tribe, of which Vavilovia is considered to be closest to its last common ancestor (LCA). In contrast to biovar viciae, bacteria from Rhizobium leguminosarum biovar trifolii (Rlt) inoculate plants from the Trifolieae tribe. Comparison of house-keeping (hkg: 16S rRNA, glnII, gltA, and dnaK) and symbiotic (sym: nodA, nodC, nodD, and nifH) genes of the symbionts of V. formosa with those of other Rlv and Rlt strains reveals a significant group separation, which was most pronounced for sym genes. A remarkable feature of the strains isolated from V. formosa was the presence of the nodX gene, which was commonly found in Rlv strains isolated from Afghanistan pea genotypes. Tube testing of different strains on nine plant species, including all genera from the Fabeae tribe, demonstrated that the strains from V. formosa nodulated the same cross inoculation group as the other Rlv strains. Comparison of nucleotide similarity in sym genes suggested that their diversification within sym-biotypes of Rlv was elicited by host plants. Contrariwise, that of hkg genes could be caused by either local adaptation to soil niches or by genetic drift. Long-term ecological isolation, genetic separation, and the ancestral position of V. formosa suggested that symbionts of V. formosa could be responsible for preserving ancestral genotypes of the Rlv biovar.
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