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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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Martins da Costa E, de Lima W, de Almeida Ribeiro PR, de Souza Moreira FM. Acid and high-temperature tolerant Bradyrhizobium spp. strains from Brazilian soils are able to promote Acacia mangium and Stizolobium aterrimum growth. Symbiosis 2020. [DOI: 10.1007/s13199-020-00732-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Bouznif B, Guefrachi I, Rodríguez de la Vega RC, Hungria M, Mars M, Alunni B, Shykoff JA. Phylogeography of the Bradyrhizobium spp. Associated With Peanut, Arachis hypogaea: Fellow Travelers or New Associations? Front Microbiol 2019; 10:2041. [PMID: 31551977 PMCID: PMC6737463 DOI: 10.3389/fmicb.2019.02041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 08/19/2019] [Indexed: 11/24/2022] Open
Abstract
Legume plants have colonized almost all terrestrial biotopes. Their ecological success is partly due to the selective advantage provided by their symbiotic association with nitrogen-fixing bacteria called rhizobia, which allow legumes to thrive on marginal lands and nitrogen depleted soils where non-symbiotic plants cannot grow. Additionally, their symbiotic capacities result in a high protein content in their aerial parts and seeds. This interesting nutritional value has led to the domestication and agricultural exploitation of several legumes grown for seeds and/or fodder for human and domestic animal consumption. Several cultivated legume species are thus grown far beyond their natural geographic range. Other legume species have become invasives, spreading into new habitats. The cultivation and establishment of legume species outside of their original range requires either that they are introduced or cultivated along with their original symbiotic partner or that they find an efficient symbiotic partner in their introduced habitat. The peanut, Arachis hypogaea, a native of South America, is now cultivated throughout the world. This species forms root nodules with Bradyrhizobium, but it is unclear whether these came with the seeds from their native range or were acquired locally. Here we propose to investigate the phylogeography of Bradyrhizobium spp. associated with a number of different wild and cultivated legume species from a range of geographical areas, including numerous strains isolated from peanut roots across the areas of peanut cultivation. This will allow us to address the question of whether introduced/cultivated peanuts associate with bacteria from their original geographic range, i.e., were introduced together with their original bacterial symbionts, or whether they acquired their current associations de novo from the bacterial community within the area of introduction. We will base the phylogenetic analysis on sequence data from both housekeeping and core genes and a symbiotic gene (nif). Differences between the phylogenetic signal of symbiotic and non-symbiotic genes could result from horizontal transfer of symbiosis capacity. Thus this study will also allow us to elucidate the processes by which this symbiotic association has evolved within this group of Bradyrhizobium spp.
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Affiliation(s)
- Besma Bouznif
- Écologie, Systématique et Évolution, CNRS, University Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- Research Unit Biodiversity and Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Ibtissem Guefrachi
- Écologie, Systématique et Évolution, CNRS, University Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | | | | | - Mohamed Mars
- Research Unit Biodiversity and Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Benoit Alunni
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Jacqui Anne Shykoff
- Écologie, Systématique et Évolution, CNRS, University Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
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Burghardt LT, Epstein B, Tiffin P. Legacy of prior host and soil selection on rhizobial fitness in planta. Evolution 2019; 73:2013-2023. [PMID: 31334838 DOI: 10.1111/evo.13807] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 01/03/2023]
Abstract
Measuring selection acting on microbial populations in natural or even seminatural environments is challenging because many microbial populations experience variable selection. The majority of rhizobial bacteria are found in the soil. However, they also live symbiotically inside nodules of legume hosts and each nodule can release thousands of daughter cells back into the soil. We tested how past selection (i.e., legacies) by two plant genotypes and by the soil alone affected selection and genetic diversity within a population of 101 strains of Ensifer meliloti. We also identified allelic variants most strongly associated with soil- and host-dependent fitness. In addition to imposing direct selection on rhizobia populations, soil and host environments had lasting effects across host generations. Host presence and genotype during the legacy period explained 22% and 12% of the variance in the strain composition of nodule communities in the second cohort, respectively. Although strains with high host fitness in the legacy cohort tended to be enriched in the second cohort, the diversity of the strain community was greater when the second cohort was preceded by host rather than soil legacies. Our results indicate the potential importance of soil selection driving the evolution of these plant-associated microbes.
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Affiliation(s)
- Liana T Burghardt
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
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5
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Helene LCF, Delamuta JRM, Ribeiro RA, Hungria M. Bradyrhizobium mercantei sp. nov., a nitrogen-fixing symbiont isolated from nodules of Deguelia costata (syn. Lonchocarpus costatus). Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001870] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Luisa Caroline Ferraz Helene
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Jakeline Renata Marçon Delamuta
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
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Whole-Genome Sequence of Bradyrhizobium elkanii Strain UASWS1016, a Potential Symbiotic Biofertilizer for Agriculture. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01095-16. [PMID: 27795259 PMCID: PMC5054329 DOI: 10.1128/genomea.01095-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Bradyrhizobium elkanii UASWS1016 has been isolated from a wet oxidation sewage plant in Italy. Fully equipped for ammonia assimilation, heavy metal resistances, and aromatic compounds degradation, it carries a large type IV secretion system, specific of plant-associated microbes. Deprived of toxins, it could be considered for agricultural and environmental uses.
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7
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Le Roux C, Tournier E, Lies A, Sanguin H, Chevalier G, Duponnois R, Mousain D, Prin Y. Bacteria of the genus Rhodopseudomonas (Bradyrhizobiaceae): obligate symbionts in mycelial cultures of the black truffles Tuber melanosporum and Tuber brumale. SPRINGERPLUS 2016; 5:1085. [PMID: 27468385 PMCID: PMC4947074 DOI: 10.1186/s40064-016-2756-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/05/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND This work aimed at characterizing 12 isolates of the genus Tuber including Tuber melanosporum (11 isolates) and Tuber brumale (one isolate). This was done using internal transcribed spacer (ITS) sequences, confirming their origin. RESULTS Analysis of their mating type revealed that both MAT1-1 and MAT1-2 exist within these isolates (with 3 and 8 of each, respectively). We observed that each of these cultures was consistently associated with one bacterium that was intimately linked to fungal growth. These bacterial associates failed to grow in the absence of fungus. We extracted DNA from bacterial colonies in the margin of mycelium and sequenced a nearly complete 16S rDNA gene and a partial ITS fragment. We found they all belonged to the genus Rhodopseudomonas, fitting within different phylogenetic clusters. No relationships were evidenced between bacterial and fungal strains or mating types. Rhodopseudomonas being a sister genus to Bradyrhizobium, we tested the nodulation ability of these bacteria on a promiscuously nodulating legume (Acacia mangium), without success. We failed to identify any nifH genes among these isolates, using two different sets of primers. CONCLUSIONS While the mechanisms of interaction between Tuber and Rhodopseudomonas remain to be elucidated, their interdependency for in vitro growth seems a novel feature of this fungus.
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Affiliation(s)
| | | | - Adrien Lies
- />CIRAD, UMR LSTM, 34398 Montpellier Cedex 5, France
| | - Hervé Sanguin
- />CIRAD, UMR LSTM, 34398 Montpellier Cedex 5, France
| | - Gérard Chevalier
- />INRA Centre de Recherche de Clermont-Theix, 63039 Clermont-Ferrand Cedex, France
| | | | - Daniel Mousain
- />Société d’Horticulture et d’Histoire Naturelle de l’Hérault, Parc à Ballon 1, bâtiment B, 125 rue du Moulin de Sémalen, 34000 Montpellier, France
| | - Yves Prin
- />CIRAD, UMR LSTM, 34398 Montpellier Cedex 5, France
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Hollowell AC, Regus JU, Turissini D, Gano-Cohen KA, Bantay R, Bernardo A, Moore D, Pham J, Sachs JL. Metapopulation dominance and genomic-island acquisition of Bradyrhizobium with superior catabolic capabilities. Proc Biol Sci 2016; 283:20160496. [PMID: 27122562 PMCID: PMC4855393 DOI: 10.1098/rspb.2016.0496] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/04/2016] [Indexed: 01/05/2023] Open
Abstract
Root nodule-forming rhizobia exhibit a bipartite lifestyle, replicating in soil and also within plant cells where they fix nitrogen for legume hosts. Host control models posit that legume hosts act as a predominant selective force on rhizobia, but few studies have examined rhizobial fitness in natural populations. Here, we genotyped and phenotyped Bradyrhizobium isolates across more than 800 km of the native Acmispon strigosus host range. We sequenced chromosomal genes expressed under free-living conditions and accessory symbiosis loci expressed in planta and encoded on an integrated 'symbiosis island' (SI). We uncovered a massive clonal expansion restricted to the Bradyrhizobium chromosome, with a single chromosomal haplotype dominating populations, ranging more than 700 km, and acquiring 42 divergent SI haplotypes, none of which were spatially widespread. For focal genotypes, we quantified utilization of 190 sole-carbon sources relevant to soil fitness. Chromosomal haplotypes that were both widespread and dominant exhibited superior growth on diverse carbon sources, whereas these patterns were not mirrored among SI haplotypes. Abundance, spatial range and catabolic superiority of chromosomal, but not symbiosis genotypes suggests that fitness in the soil environment, rather than symbiosis with hosts, might be the key driver of Bradyrhizobium dominance.
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Affiliation(s)
- Amanda C Hollowell
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - John U Regus
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - David Turissini
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Roxanne Bantay
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Andrew Bernardo
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Devora Moore
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Jonathan Pham
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Joel L Sachs
- Department of Biology, University of California, Riverside, CA 92521, USA Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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Borges WL, Prin Y, Ducousso M, Le Roux C, de Faria SM. Rhizobial characterization in revegetated areas after bauxite mining. Braz J Microbiol 2016; 47:314-21. [PMID: 26991294 PMCID: PMC4874681 DOI: 10.1016/j.bjm.2016.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/23/2015] [Indexed: 11/18/2022] Open
Abstract
Little is known regarding how the increased diversity of nitrogen-fixing bacteria contributes to the productivity and diversity of plants in complex communities. However, some authors have shown that the presence of a diverse group of nodulating bacteria is required for different plant species to coexist. A better understanding of the plant symbiotic organism diversity role in natural ecosystems can be extremely useful to define recovery strategies of environments that were degraded by human activities. This study used ARDRA, BOX-PCR fingerprinting and sequencing of the 16S rDNA gene to assess the diversity of root nodule nitrogen-fixing bacteria in former bauxite mining areas that were replanted in 1981, 1985, 1993, 1998, 2004 and 2006 and in a native forest. Among the 12 isolates for which the 16S rDNA gene was partially sequenced, eight, three and one isolate(s) presented similarity with sequences of the genera Bradyrhizobium, Rhizobium and Mesorhizobium, respectively. The richness, Shannon and evenness indices were the highest in the area that was replanted the earliest (1981) and the lowest in the area that was replanted most recently (2006).
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Affiliation(s)
| | - Yves Prin
- CIRAD, UMR 82, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus International de Baillarguet, Montpellier, France
| | - Marc Ducousso
- CIRAD, UMR 82, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus International de Baillarguet, Montpellier, France
| | - Christine Le Roux
- CIRAD, UMR 82, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus International de Baillarguet, Montpellier, France
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10
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Differing courses of genetic evolution of Bradyrhizobium inoculants as revealed by long-term molecular tracing in Acacia mangium plantations. Appl Environ Microbiol 2014; 80:5709-16. [PMID: 25002434 DOI: 10.1128/aem.02007-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Introducing nitrogen-fixing bacteria as an inoculum in association with legume crops is a common practice in agriculture. However, the question of the evolution of these introduced microorganisms remains crucial, both in terms of microbial ecology and agronomy. We explored this question by analyzing the genetic and symbiotic evolution of two Bradyrhizobium strains inoculated on Acacia mangium in Malaysia and Senegal 15 and 5 years, respectively, after their introduction. Based on typing of several loci, we showed that these two strains, although closely related and originally sampled in Australia, evolved differently. One strain was recovered in soil with the same five loci as the original isolate, whereas the symbiotic cluster of the other strain was detected with no trace of the three housekeeping genes of the original inoculum. Moreover, the nitrogen fixation efficiency was variable among these isolates (either recombinant or not), with significantly high, low, or similar efficiencies compared to the two original strains and no significant difference between recombinant and nonrecombinant isolates. These data suggested that 15 years after their introduction, nitrogen-fixing bacteria remain in the soil but that closely related inoculant strains may not evolve in the same way, either genetically or symbiotically. In a context of increasing agronomical use of microbial inoculants (for biological control, nitrogen fixation, or plant growth promotion), this result feeds the debate on the consequences associated with such practices.
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Ng KW, Pointing SB, Dvornyk V. Patterns of nucleotide diversity of the ldpA circadian gene in closely related species of cyanobacteria from extreme cold deserts. Appl Environ Microbiol 2013; 79:1516-22. [PMID: 23263969 PMCID: PMC3591978 DOI: 10.1128/aem.03439-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 12/14/2012] [Indexed: 11/20/2022] Open
Abstract
In the circadian system of cyanobacteria, the ldpA gene is a component of the input to the clock. We comparatively analyzed nucleotide polymorphism of this gene in populations of two closely related species of cyanobacteria (denoted as Synechococcus species S1 and S2, respectively) from extreme cold deserts in Antarctica, the Canadian Arctic, and Tibet. Although both species manifested similarly high haplotype diversities (0.990 and 0.809, respectively), the nucleotide diversity differed significantly (0.0091 in S1 and 0.0037 in S2). The populations of species S2 were more differentiated (F(ST) = 0.2242) compared to those of species S1 (F(ST) between 0.0296 and 0.1188). An analysis of positive selection with several tests yielded highly significant values (P < 0.01) for both species. On the other hand, these results may be somewhat compromised by fluctuating population sizes of the species. The apparent selection pressure coupled with the pronounced demographic factors, such as population expansion, small effective population size, and genetic drift, may thus result in the observed significant interpopulation differentiation and subsequent speciation of cyanobacteria.
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Affiliation(s)
- Ka Wai Ng
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
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12
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Laranjo M, Young JPW, Oliveira S. Multilocus sequence analysis reveals multiple symbiovars within Mesorhizobium species. Syst Appl Microbiol 2012; 35:359-67. [DOI: 10.1016/j.syapm.2012.06.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/07/2012] [Accepted: 06/09/2012] [Indexed: 10/28/2022]
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Dvornyk V, Jahan AS. Extreme conservation and non-neutral evolution of the cpmA Circadian locus in a globally distributed Chroococcidiopsis sp. from naturally stressful habitats. Mol Biol Evol 2012; 29:3899-907. [PMID: 22844070 DOI: 10.1093/molbev/mss191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Cyanobacteria are among the most ancient organisms known to have circadian rhythms. The cpmA gene is involved in controlling the circadian output signal. We studied polymorphism and divergence of this gene in six populations of a stress-tolerant cyanobacterium, Chroococcidiopsis sp., sampled in extreme habitats across the globe. Despite high haplotype diversity (0.774), nucleotide diversity of cpmA is very low (π = 0.0034): the gene appears to be even more conserved than housekeeping genes. Even though the populations were sampled thousands kilometers apart, they manifested virtually no genetic differentiation at this locus (F(ST) = 0.0228). Using various tests for neutrality, we determined that evolution of cpmA significantly departures from the neutral model and is governed by episodic positive selection.
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Affiliation(s)
- Volodymyr Dvornyk
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
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14
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Boukhatem ZF, Domergue O, Bekki A, Merabet C, Sekkour S, Bouazza F, Duponnois R, Lajudie P, Galiana A. Symbiotic characterization and diversity of rhizobia associated with native and introduced acacias in arid and semi-arid regions in Algeria. FEMS Microbiol Ecol 2012; 80:534-47. [DOI: 10.1111/j.1574-6941.2012.01315.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 01/02/2012] [Accepted: 01/23/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Zineb Faiza Boukhatem
- Laboratoire de Biotechnologie des Rhizobiums et Amélioration des Plantes; Département de Biotechnologie; Université d'Oran; Es Senia; Algeria
| | - Odile Domergue
- INRA; Laboratoire des Symbioses Tropicales et Méditerranéennes; UMR LSTM; Montpellier; France
| | - Abdelkader Bekki
- Laboratoire de Biotechnologie des Rhizobiums et Amélioration des Plantes; Département de Biotechnologie; Université d'Oran; Es Senia; Algeria
| | - Chahinez Merabet
- Laboratoire de Biotechnologie des Rhizobiums et Amélioration des Plantes; Département de Biotechnologie; Université d'Oran; Es Senia; Algeria
| | - Sonia Sekkour
- Laboratoire de Biotechnologie des Rhizobiums et Amélioration des Plantes; Département de Biotechnologie; Université d'Oran; Es Senia; Algeria
| | - Fatima Bouazza
- Laboratoire de Biotechnologie des Rhizobiums et Amélioration des Plantes; Département de Biotechnologie; Université d'Oran; Es Senia; Algeria
| | - Robin Duponnois
- IRD; Laboratoire des Symbioses Tropicales et Méditerranéennes; UMR LSTM; Montpellier; France
| | - Philippe Lajudie
- IRD; Laboratoire des Symbioses Tropicales et Méditerranéennes; UMR LSTM; Montpellier; France
| | - Antoine Galiana
- CIRAD; Laboratoire des Symbioses Tropicales et Méditerranéennes; UMR LSTM; Montpellier; France
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