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Cavassim MIA, Andersen SU, Bataillon T, Schierup MH. Recombination facilitates adaptive evolution in rhizobial soil bacteria. Mol Biol Evol 2021; 38:5480-5490. [PMID: 34410427 PMCID: PMC8662638 DOI: 10.1093/molbev/msab247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Homologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations and by readily creating new combinations of beneficial alleles. Here, we investigate how the proportion of amino acid substitutions fixed by adaptive evolution (α) depends on the recombination rate in bacteria. We analyze 3,086 core protein-coding sequences from 196 genomes belonging to five closely related species of the genus Rhizobium. These genes are found in all species and do not display any signs of introgression between species. We estimate α using the site frequency spectrum (SFS) and divergence data for all pairs of species. We evaluate the impact of recombination within each species by dividing genes into three equally sized recombination classes based on their average level of intragenic linkage disequilibrium. We find that α varies from 0.07 to 0.39 across species and is positively correlated with the level of recombination. This is both due to a higher estimated rate of adaptive evolution and a lower estimated rate of nonadaptive evolution, suggesting that recombination both increases the fixation probability of advantageous variants and decreases the probability of fixation of deleterious variants. Our results demonstrate that homologous recombination facilitates adaptive evolution measured by α in the core genome of prokaryote species in agreement with studies in eukaryotes.
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Affiliation(s)
- Maria Izabel A Cavassim
- Bioinformatics Research Centre, Aarhus University, Aarhus, 8000, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, 8000, Denmark
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2
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Van Cauwenberghe J, Santamaría RI, Bustos P, Juárez S, Ducci MA, Figueroa Fleming T, Etcheverry AV, González V. Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication. THE ISME JOURNAL 2021; 15:2092-2106. [PMID: 33558688 PMCID: PMC8245606 DOI: 10.1038/s41396-021-00907-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/14/2021] [Accepted: 01/21/2021] [Indexed: 01/30/2023]
Abstract
Bacteriophages play significant roles in the composition, diversity, and evolution of bacterial communities. Despite their importance, it remains unclear how phage diversity and phage-host interactions are spatially structured. Local adaptation may play a key role. Nitrogen-fixing symbiotic bacteria, known as rhizobia, have been shown to locally adapt to domesticated common bean at its Mesoamerican and Andean sites of origin. This may affect phage-rhizobium interactions. However, knowledge about the diversity and coevolution of phages with their respective Rhizobium populations is lacking. Here, through the study of four phage-Rhizobium communities in Mexico and Argentina, we show that both phage and host diversity is spatially structured. Cross-infection experiments demonstrated that phage infection rates were higher overall in sympatric rhizobia than in allopatric rhizobia except for one Argentinean community, indicating phage local adaptation and host maladaptation. Phage-host interactions were shaped by the genetic identity and geographic origin of both the phage and the host. The phages ranged from specialists to generalists, revealing a nested network of interactions. Our results suggest a key role of local adaptation to resident host bacterial communities in shaping the phage genetic and phenotypic composition, following a similar spatial pattern of diversity and coevolution to that in the host.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico.
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
| | - Rosa I Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico
| | - Soledad Juárez
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico
| | - Maria Antonella Ducci
- Instituto Nacional de Tecnología Agropecuaria, Universidad Nacional de Salta, Salta, Argentina
| | | | | | - Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico.
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3
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Gunnabo AH, van Heerwaarden J, Geurts R, Wolde-Meskel E, Degefu T, Giller KE. Phylogeography and Symbiotic Effectiveness of Rhizobia Nodulating Chickpea (Cicer arietinum L.) in Ethiopia. MICROBIAL ECOLOGY 2021; 81:703-716. [PMID: 33098438 PMCID: PMC7982387 DOI: 10.1007/s00248-020-01620-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Chickpea (Cicer arietinum L.) used to be considered a restrictive host that nodulated and fixed nitrogen only with Mesorhizobium ciceri and M. mediterraneum. Recent analysis revealed that chickpea can also establish effective symbioses with strains of several other Mesorhizobium species such as M. loti, M. haukuii, M. amorphae, M. muleiense, etc. These strains vary in their nitrogen fixation potential inviting further exploration. We characterized newly collected mesorhizobial strains isolated from various locations in Ethiopia to evaluate genetic diversity, biogeographic structure and symbiotic effectiveness. Symbiotic effectiveness was evaluated in Leonard Jars using a locally released chickpea cultivar "Nattoli". Most of the new isolates belonged to a clade related to M. plurifarium, with very few sequence differences, while the total collection of strains contained three additional mesorhizobial genospecies associated with M. ciceri, M. abyssinicae and an unidentified Mesorhizobium species isolated from a wild host in Eritrea. The four genospecies identified represented a subset of the eight major Mesorhizobium clades recently reported for Ethiopia based on metagenomic data. All Ethiopian strains had nearly identical symbiotic genes that grouped them in a single cluster with M. ciceri, M. mediterraneum and M. muleiense, but not with M. plurifarium. Some phylogeographic structure was observed, with elevation and geography explaining some of the genetic differences among strains, but the relation between genetic identity and symbiotic effectiveness was observed to be weak.
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Affiliation(s)
- A H Gunnabo
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands.
| | - J van Heerwaarden
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands.
| | - R Geurts
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - E Wolde-Meskel
- World Agroforestry Centre (ICRAF), Addis Ababa, Ethiopia
| | - T Degefu
- International Crops Research Institute for the Semi-Arid Tropics, Addis Ababa, Ethiopia
| | - K E Giller
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands
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4
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Hailu Gunnabo A, Geurts R, Wolde-meskel E, Degefu T, E. Giller K, van Heerwaarden J. Phylogeographic distribution of rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia. FEMS Microbiol Ecol 2021; 97:fiab046. [PMID: 33724341 PMCID: PMC8016211 DOI: 10.1093/femsec/fiab046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/13/2021] [Indexed: 11/19/2022] Open
Abstract
Rhizobia are soilborne bacteria that form symbiotic relations with legumes and fix atmospheric nitrogen. The nitrogen fixation potential depends on several factors such as the type of host and symbionts and on environmental factors that affect the distribution of rhizobia. We isolated bacteria nodulating common bean in Southern Ethiopia to evaluate their genetic diversity and phylogeography at nucleotide, locus (gene/haplotype) and species levels of genetic hierarchy. Phylogenetically, eight rhizobial genospecies (including previous collections) were determined that had less genetic diversity than found among reference strains. The limited genetic diversity of the Ethiopian collections was due to absence of many of the Rhizobium lineages known to nodulate beans. Rhizobium etli and Rhizobiumphaseoli were predominant strains of bean-nodulating rhizobia in Ethiopia. We found no evidence for a phylogeographic pattern in strain distribution. However, joint analysis of the current and previous collections revealed differences between the two collections at nucleotide level of genetic hierarchy. The differences were due to genospecies Rhizobium aethiopicum that was only isolated in the earlier collection.
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Affiliation(s)
- Ashenafi Hailu Gunnabo
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Endalkachew Wolde-meskel
- World Agroforestry Centre (ICRAF), c/o ILRI Campus, Gurd Shola PO Box 5689, Addis Ababa, 4 Ethiopia
| | - Tulu Degefu
- International Crops Research Institute for the Semi-Arid Tropics, c/o ILRI Campus, Gurd Shola PO Box 5689, Addis Ababa, Ethiopia
| | - Ken E. Giller
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Joost van Heerwaarden
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
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5
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Boivin S, Ait Lahmidi N, Sherlock D, Bonhomme M, Dijon D, Heulin‐Gotty K, Le‐Queré A, Pervent M, Tauzin M, Carlsson G, Jensen E, Journet E, Lopez‐Bellido R, Seidenglanz M, Marinkovic J, Colella S, Brunel B, Young P, Lepetit M. Host-specific competitiveness to form nodules in Rhizobium leguminosarum symbiovar viciae. THE NEW PHYTOLOGIST 2020; 226:555-568. [PMID: 31873949 PMCID: PMC7687279 DOI: 10.1111/nph.16392] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 12/09/2019] [Indexed: 05/07/2023]
Abstract
Fabeae legumes such as pea and faba bean form symbiotic nodules with a large diversity of soil Rhizobium leguminosarum symbiovar viciae (Rlv) bacteria. However, bacteria competitive to form root nodules (CFN) are generally not the most efficient to fix dinitrogen, resulting in a decrease in legume crop yields. Here, we investigate differential selection by host plants on the diversity of Rlv. A large collection of Rlv was collected by nodule trapping with pea and faba bean from soils at five European sites. Representative genomes were sequenced. In parallel, diversity and abundance of Rlv were estimated directly in these soils using metabarcoding. The CFN of isolates was measured with both legume hosts. Pea/faba bean CFN were associated to Rlv genomic regions. Variations of bacterial pea and/or faba bean CFN explained the differential abundance of Rlv genotypes in pea and faba bean nodules. No evidence was found for genetic association between CFN and variations in the core genome, but variations in specific regions of the nod locus, as well as in other plasmid loci, were associated with differences in CFN. These findings shed light on the genetic control of CFN in Rlv and emphasise the importance of host plants in controlling Rhizobium diversity.
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Affiliation(s)
- Stéphane Boivin
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Nassima Ait Lahmidi
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | | | - Maxime Bonhomme
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPSUniversité de Toulouse31326Castanet‐TolosanFrance
| | - Doriane Dijon
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Karine Heulin‐Gotty
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Antoine Le‐Queré
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Marjorie Pervent
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Marc Tauzin
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Georg Carlsson
- Department of Biosystems and TechnologySwedish University of Agricultural SciencesSE‐230 53AlnarpSweden
| | - Erik Jensen
- Department of Biosystems and TechnologySwedish University of Agricultural SciencesSE‐230 53AlnarpSweden
| | - Etienne‐Pascal Journet
- AGroécologie, Innovation et teRritoires (AGIR) INRAEENSAT31326Castanet‐TolosanFrance
- Laboratoire des Interactions Plantes MicrorganismesUniversité de Toulouse, INRAE, CNRS31326Castanet‐TolosanFrance
| | - Raphael Lopez‐Bellido
- Departamento de Ciencias y Recursos Agrícolas y ForestalesUniversity of Córdoba14071CórdobaSpain
| | | | | | - Stefano Colella
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Brigitte Brunel
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Peter Young
- Department of BiologyUniversity of YorkYorkYO10 5DDUK
| | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
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6
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Liu Z, Chen W, Jiao S, Wang X, Fan M, Wang E, Wei G. New Insight into the Evolution of Symbiotic Genes in Black Locust-Associated Rhizobia. Genome Biol Evol 2019; 11:1736-1750. [PMID: 31192354 PMCID: PMC6698633 DOI: 10.1093/gbe/evz116] [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] [Accepted: 06/09/2019] [Indexed: 11/29/2022] Open
Abstract
Nitrogen fixation in legumes occurs via symbiosis with rhizobia. This process involves packages of symbiotic genes on mobile genetic elements that are readily transferred within or between rhizobial species, furnishing the recipient with the ability to interact with plant hosts. However, it remains elusive whether plant host migration has played a role in shaping the current distribution of genetic variation in symbiotic genes. Herein, we examined the genetic structure and phylogeographic pattern of symbiotic genes in 286 symbiotic strains of Mesorhizobium nodulating black locust (Robinia pseudoacacia), a cross-continental invasive legume species that is native to North America. We conducted detailed phylogeographic analysis and approximate Bayesian computation to unravel the complex demographic history of five key symbiotic genes. The sequencing results indicate an origin of symbiotic genes in Germany rather than North America. Our findings provide strong evidence of prehistoric lineage splitting and spatial expansion events resulting in multiple radiations of descendent clones from founding sequence types worldwide. Estimates of the timescale of divergence in North American and Chinese subclades suggest that black locust-specific symbiotic genes have been present in these continent many thousands of years before recent migration of plant host. Although numerous crop plants, including legumes, have found their centers of origin as centers of evolution and diversity, the number of legume-specific symbiotic genes with a known geographic origin is limited. This work sheds light on the coevolution of legumes and rhizobia.
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Affiliation(s)
- Zhenshan Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinye Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Miaochun Fan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México, D.F., Mexico
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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Molecular diversity and phylogeny of indigenous Rhizobium leguminosarum strains associated with Trifolium repens plants in Romania. Antonie van Leeuwenhoek 2017; 111:135-153. [DOI: 10.1007/s10482-017-0934-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/20/2017] [Indexed: 11/30/2022]
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8
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Kutkowska J, Marek-Kozaczuk M, Wielbo J, Wójcik M, Urbanik-Sypniewska T. Electrophoretic profiles of lipopolysaccharides from Rhizobium strains nodulating Pisum sativum do not reflect phylogenetic relationships between these strains. Arch Microbiol 2017; 199:1011-1021. [PMID: 28386666 PMCID: PMC5548859 DOI: 10.1007/s00203-017-1374-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 03/24/2017] [Accepted: 03/30/2017] [Indexed: 11/03/2022]
Abstract
Rhizobia that nodulate peas comprise a heterogeneous group of bacteria. The aim of this study was to investigate the relationship between phylogeny and electrophoretic and hydroxy fatty acid lipopolysaccharide (LPS) profiles of pea microsymbionts. Based on amplified fragment length polymorphism (AFLP) fingerprinting data, the pea microsymbionts were grouped into two clusters distinguished at 58% similarity level. Based on the concatenated 16S rRNA, recA, and atpD housekeeping gene data, the microsymbionts appeared to be most closely related to Rhizobium leguminosarum biovars viciae and trifolii. Applying cluster analysis to their LPS electrophoretic profiles, the strains were assigned to two major groups with different banding patterns. All hydroxy fatty acids common to R. leguminosarum and R. etli were detected in each examined strain. Differences in the proportions of 3- to ω-1 hydroxy fatty acids allowed us to distinguish two groups of strains. This classification did not overlap with one based on LPS electrophoretic profiles. No clear correlation was apparent between the genetic traits and LPS profiles of the pea nodule isolates.
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Affiliation(s)
- Jolanta Kutkowska
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland.
| | - Monika Marek-Kozaczuk
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Jerzy Wielbo
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Wójcik
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland
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9
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Beligala DH, Michaels HJ, Devries M, Phuntumart V. Multilocus Sequence Analysis of Root Nodule Bacteria Associated with <i>Lupinus</i> spp. and <i>Glycine max</i>. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/aim.2017.711063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Zou L, Chen YX, Penttinen P, Lan Q, Wang K, Liu M, Peng D, Zhang X, Chen Q, Zhao K, Zeng X, Xu KW. Genetic Diversity and Symbiotic Efficiency of Nodulating Rhizobia Isolated from Root Nodules of Faba Bean in One Field. PLoS One 2016; 11:e0167804. [PMID: 27936180 PMCID: PMC5147995 DOI: 10.1371/journal.pone.0167804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/21/2016] [Indexed: 11/19/2022] Open
Abstract
Thirty-one nodulating rhizobium strains were collected from root nodules of spring and winter type faba bean cultivars grown in micro ecoarea, i.e. the same field in Chengdu plain, China. The symbiotic efficiency and phylogeny of these strains were studied. Effectively nitrogen fixing strains were isolated from both winter type and spring type cultivars. Based on phylogenetic analysis of 16S rRNA gene and concatenated sequence of atpD, glnII and recA genes, the isolates were assigned as Rhizobium anhuiense and a potential new Rhizobium species. The isolates were diverse on symbiosis related gene level, carrying five, four and three variants of nifH, nodC and nodD, respectively. Strains carrying similar gene combinations were trapped by both winter and spring cultivars, disagreeing with the specificity of symbiotic genotypes to reported earlier faba bean ecotypes.
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Affiliation(s)
- Lan Zou
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yuan Xue Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- * E-mail: (KWX); (YXC)
| | - Petri Penttinen
- Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Qin Lan
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Wang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ming Liu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Dan Peng
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiangzhong Zeng
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Kai Wei Xu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- * E-mail: (KWX); (YXC)
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11
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The Plasmid Mobilome of the Model Plant-Symbiont Sinorhizobium meliloti: Coming up with New Questions and Answers. Microbiol Spectr 2016; 2. [PMID: 26104371 DOI: 10.1128/microbiolspec.plas-0005-2013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobia are Gram-negative Alpha- and Betaproteobacteria living in the underground which have the ability to associate with legumes for the establishment of nitrogen-fixing symbioses. Sinorhizobium meliloti in particular-the symbiont of Medicago, Melilotus, and Trigonella spp.-has for the past decades served as a model organism for investigating, at the molecular level, the biology, biochemistry, and genetics of a free-living and symbiotic soil bacterium of agricultural relevance. To date, the genomes of seven different S. meliloti strains have been fully sequenced and annotated, and several other draft genomic sequences are also available. The vast amount of plasmid DNA that S. meliloti frequently bears (up to 45% of its total genome), the conjugative ability of some of those plasmids, and the extent of the plasmid diversity has provided researchers with an extraordinary system to investigate functional and structural plasmid molecular biology within the evolutionary context surrounding a plant-associated model bacterium. Current evidence indicates that the plasmid mobilome in S. meliloti is composed of replicons varying greatly in size and having diverse conjugative systems and properties along with different evolutionary stabilities and biological roles. While plasmids carrying symbiotic functions (pSyms) are known to have high structural stability (approaching that of chromosomes), the remaining plasmid mobilome (referred to as the non-pSym, functionally cryptic, or accessory compartment) has been shown to possess remarkable diversity and to be highly active in conjugation. In light of the modern genomic and current biochemical data on the plasmids of S. meliloti, the current article revises their main structural components, their transfer and regulatory mechanisms, and their potential as vehicles in shaping the evolution of the rhizobial genome.
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12
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Lemaire B, Van Cauwenberghe J, Chimphango S, Stirton C, Honnay O, Smets E, Muasya AM. Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome. FEMS Microbiol Ecol 2015; 91:fiv118. [PMID: 26433010 DOI: 10.1093/femsec/fiv118] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2015] [Indexed: 11/14/2022] Open
Abstract
The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types.
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Affiliation(s)
- Benny Lemaire
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium
| | - Jannick Van Cauwenberghe
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Samson Chimphango
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Charles Stirton
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Olivier Honnay
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium
| | - Erik Smets
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium Naturalis Biodiversity Center, Leiden University, 2300 RA Leiden, the Netherlands
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
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13
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Wielbo J, Podleśna A, Kidaj D, Podleśny J, Skorupska A. The Diversity of Pea Microsymbionts in Various Types of Soils and Their Effects on Plant Host Productivity. Microbes Environ 2015; 30:254-61. [PMID: 26370165 PMCID: PMC4567564 DOI: 10.1264/jsme2.me14141] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 07/06/2015] [Indexed: 11/17/2022] Open
Abstract
The growth and yield of peas cultivated on eight different soils, as well as the diversity of pea microsymbionts derived from these soils were investigated in the present study. The experimental plot was composed of soils that were transferred from different parts of Poland more than a century ago. The soils were located in direct vicinity of each other in the experimental plot. All soils examined contained pea microsymbionts, which were suggested to belong to Rhizobium leguminosarum sv. viciae based on the nucleotide sequence of the partial 16S rRNA gene. PCR-RFLP analyses of the 16S-23S rRNA gene ITS region and nodD alleles revealed the presence of numerous and diversified groups of pea microsymbionts and some similarities between the tested populations, which may have been the result of the spread or displacement of strains. However, most populations retained their own genetic distinction, which may have been related to the type of soil. Most of the tested populations comprised low-effective strains for the promotion of pea growth. No relationships were found between the characteristics of soil and symbiotic effectiveness of rhizobial populations; however, better seed yield was obtained for soil with medium biological productivity inhabited by high-effective rhizobial populations than for soil with high agricultural quality containing medium-quality pea microsymbionts, and these results showed the importance of symbiosis for plant hosts.
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Affiliation(s)
- Jerzy Wielbo
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University,
Akademicka 19 str., 20–033 Lublin,
Poland
| | - Anna Podleśna
- Institute of Soil Science and Plant Cultivation—State Research Institute,
Czartoryskich 8 str., 24–100 Puławy,
Poland
| | - Dominika Kidaj
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University,
Akademicka 19 str., 20–033 Lublin,
Poland
| | - Janusz Podleśny
- Institute of Soil Science and Plant Cultivation—State Research Institute,
Czartoryskich 8 str., 24–100 Puławy,
Poland
| | - Anna Skorupska
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University,
Akademicka 19 str., 20–033 Lublin,
Poland
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14
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Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JPW, Bailly X. Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biol 2015; 5:140133. [PMID: 25589577 PMCID: PMC4313370 DOI: 10.1098/rsob.140133] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny.
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Affiliation(s)
- Nitin Kumar
- Department of Biology, University of York, York YO10 5DD, UK
| | - Ganesh Lad
- Department of Biology, University of York, York YO10 5DD, UK
| | - Elisa Giuntini
- Department of Biology, University of York, York YO10 5DD, UK
| | - Maria E Kaye
- Department of Biology, University of York, York YO10 5DD, UK
| | | | | | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Xavier Bailly
- Department of Biology, University of York, York YO10 5DD, UK
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15
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Zhang XX, Guo HJ, Wang R, Sui XH, Zhang YM, Wang ET, Tian CF, Chen WX. Genetic divergence of bradyrhizobium strains nodulating soybeans as revealed by multilocus sequence analysis of genes inside and outside the symbiosis island. Appl Environ Microbiol 2014; 80:3181-90. [PMID: 24632260 PMCID: PMC4018923 DOI: 10.1128/aem.00044-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/07/2014] [Indexed: 01/26/2023] Open
Abstract
The genus Bradyrhizobium has been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among Bradyrhizobium strains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (SMc00019, thrA, and truA). This was also supported by analyses of eight genes outside the symbiosis island ("off-island" genes; SMc00019, thrA, truA, fabB, glyA, phyR, exoN, and hsfA). However, seven genes inside the symbiosis island ("island" genes; nifA, nifH, nodC, nodV, fixA, trpD, and rhcC2) showed contrasting lower levels of nucleotide diversity and recombination rates than did off-island genes. Island genes had significantly incongruent gene phylogenies compared to the species tree. Four phylogenetic clusters were observed in island genes, and the epidemic cluster IV (harbored by Bradyrhizobium japonicum, Bradyrhizobium diazoefficiens, Bradyrhizobium huanghuaihaiense, Bradyrhizobium liaoningense, Bradyrhizobium daqingense, Bradyrhizobium sp. I, Bradyrhizobium sp. III, and Bradyrhizobium sp. IV) was not found in Bradyrhizobium yuanmingense, Bradyrhizobium sp. II, or Bradyrhizobium elkanii. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes.
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Affiliation(s)
- Xing Xing Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Hui Juan Guo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Rui Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Yan Ming Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
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16
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Guo HJ, Wang ET, Zhang XX, Li QQ, Zhang YM, Tian CF, Chen WX. Replicon-dependent differentiation of symbiosis-related genes in Sinorhizobium strains nodulating Glycine max. Appl Environ Microbiol 2014; 80:1245-55. [PMID: 24317084 PMCID: PMC3911071 DOI: 10.1128/aem.03037-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/30/2013] [Indexed: 01/09/2023] Open
Abstract
In order to investigate the genetic differentiation of Sinorhizobium strains nodulating Glycine max and related microevolutionary mechanisms, three housekeeping genes (SMc00019, truA, and thrA) and 16 symbiosis-related genes on the chromosome (7 genes), pSymA (6 genes), and pSymB (3 genes) were analyzed. Five distinct species were identified among the test strains by calculating the average nucleotide identity (ANI) of SMc00019-truA-thrA: Sinorhizobium fredii, Sinorhizobium sojae, Sinorhizobium sp. I, Sinorhizobium sp. II, and Sinorhizobium sp. III. These species assignments were also supported by population genetics and phylogenetic analyses of housekeeping genes and symbiosis-related genes on the chromosome and pSymB. Different levels of genetic differentiation were observed among these species or different replicons. S. sojae was the most divergent from the other test species and was characterized by its low intraspecies diversity and limited geographic distribution. Intergenic recombination dominated the evolution of 19 genes from different replicons. Intraspecies recombination happened frequently in housekeeping genes and symbiosis-related genes on the chromosome and pSymB, whereas pSymA genes showed a clear pattern of lateral-transfer events between different species. Moreover, pSymA genes were characterized by a lower level of polymorphism and recombination than those on the chromosome and pSymB. Taken together, genes from different replicons of rhizobia might be involved in the establishment of symbiosis with legumes, but these symbiosis-related genes might have evolved differently according to their corresponding replicons.
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Affiliation(s)
- Hui Juan Guo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico D.F., Mexico
| | - Xing Xing Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Qin Qin Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Yan Ming Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
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17
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Tang J, Bromfield ESP, Rodrigue N, Cloutier S, Tambong JT. Microevolution of symbiotic Bradyrhizobium populations associated with soybeans in east North America. Ecol Evol 2012; 2:2943-61. [PMID: 23301163 PMCID: PMC3538991 DOI: 10.1002/ece3.404] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 09/17/2012] [Indexed: 11/22/2022] Open
Abstract
Microevolution and origins of Bradyrhizobium populations associated with soybeans at two field sites (A and B, 280 km apart in Canada) with contrasting histories of inoculation was investigated using probabilistic analyses of six core (housekeeping) gene sequences. These analyses supported division of 220 isolates in five lineages corresponding either to B. japonicum groups 1 and 1a or to one of three novel lineages within the genus Bradyrhizobium. None of the isolates from site A and about 20% from site B (the only site with a recent inoculation history) were attributed to inoculation sources. The data suggest that most isolates were of indigenous origin based on sequence analysis of 148 isolates of soybean-nodulating bacteria from native legumes (Amphicarpaea bracteata and Desmodium canadense). Isolates from D. canadense clustered with B. japonicum group 1, whereas those from A. bracteata were placed in two novel lineages encountered at soybean field sites. One of these novel lineages predominated at soybean sites and exhibited a significant clonal expansion likely reflecting selection by the plant host. Homologous recombination events detected in the 35 sequence types from soybean sites had an effect on genetic diversification that was approximately equal to mutation. Interlineage transfer of core genes was infrequent and mostly attributable to gyrB that had a history of frequent recombination. Symbiotic gene sequences (nodC and nifH) of isolates from soybean sites and native legumes clustered in two lineages corresponding to B. japonicum and B. elkani with the inheritance of these genes appearing predominantly by vertical transmission. The data suggest that soybean-nodulating bacteria associated with native legumes represent a novel source of ecologically adapted bacteria for soybean inoculation.
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Affiliation(s)
- Jie Tang
- Agriculture and Agri-Food Canada 960 Carling Ave, Ottawa, Ontario, Canada, K1A 0C6
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18
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Gurkanli CT, Ozkoc I, Gunduz I. Genetic diversity of rhizobia nodulating common bean (Phaseolus vulgaris L.) in the Central Black Sea Region of Turkey. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0551-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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19
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Zhang YM, Tian CF, Sui XH, Chen WF, Chen WX. Robust markers reflecting phylogeny and taxonomy of rhizobia. PLoS One 2012; 7:e44936. [PMID: 23028691 PMCID: PMC3444505 DOI: 10.1371/journal.pone.0044936] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 08/10/2012] [Indexed: 12/17/2022] Open
Abstract
Genomic ANI (Average Nucleotide Identity) has been found to be able to replace DNA-DNA hybridization in prokaryote taxonomy. The ANI of each of the core genes that has a phylogeny congruent with the reference species tree of rhizobia was compared to the genomic ANI. This allowed us to identify three housekeeping genes (SMc00019-truA-thrA) whose ANI reflected the intraspecies and interspecies genomic ANI among rhizobial strains, revealing an ANI gap (≥2%) between the inter- and intra-species comparisons. The intraspecies (96%) and interspecies (94%) ANI boundaries calculated from three genes (SMc00019-truA-thrA) provided a criterion for bacterial species definition and confirmed 621/629 of known interspecies relationships within Bradyrhizobium, Mesorhizobium, Sinorhizobium and Rhizobium. Some widely studied strains should be renamed. The SMc00019-truA-thrA ANI also correlates well with the genomic ANI of strains in Agrobacterium, Methylobacterium, Ralstonia, Rhodopseudomonas, Cupriavidus and Burkholderia, suggesting their wide applicability in other bacteria.
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Affiliation(s)
- Yan Ming Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
- * E-mail:
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Wen Feng Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
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20
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Tian CF, Zhou YJ, Zhang YM, Li QQ, Zhang YZ, Li DF, Wang S, Wang J, Gilbert LB, Li YR, Chen WX. Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. Proc Natl Acad Sci U S A 2012; 109:8629-34. [PMID: 22586130 PMCID: PMC3365164 DOI: 10.1073/pnas.1120436109] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The rhizobium-legume symbiosis has been widely studied as the model of mutualistic evolution and the essential component of sustainable agriculture. Extensive genetic and recent genomic studies have led to the hypothesis that many distinct strategies, regardless of rhizobial phylogeny, contributed to the varied rhizobium-legume symbiosis. We sequenced 26 genomes of Sinorhizobium and Bradyrhizobium nodulating soybean to test this hypothesis. The Bradyrhizobium core genome is disproportionally enriched in lipid and secondary metabolism, whereas several gene clusters known to be involved in osmoprotection and adaptation to alkaline pH are specific to the Sinorhizobium core genome. These features are consistent with biogeographic patterns of these bacteria. Surprisingly, no genes are specifically shared by these soybean microsymbionts compared with other legume microsymbionts. On the other hand, phyletic patterns of 561 known symbiosis genes of rhizobia reflected the species phylogeny of these soybean microsymbionts and other rhizobia. Similar analyses with 887 known functional genes or the whole pan genome of rhizobia revealed that only the phyletic distribution of functional genes was consistent with the species tree of rhizobia. Further evolutionary genetics revealed that recombination dominated the evolution of core genome. Taken together, our results suggested that faithfully vertical genes were rare compared with those with history of recombination including lateral gene transfer, although rhizobial adaptations to symbiotic interactions and other environmental conditions extensively recruited lineage-specific shell genes under direct or indirect control through the speciation process.
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Affiliation(s)
- Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Yuan Jie Zhou
- Beijing Genomics Institute (BGI)–Shenzhen, 518000, Shenzhen, China; and
| | - Yan Ming Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Qin Qin Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Yun Zeng Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Dong Fang Li
- Beijing Genomics Institute (BGI)–Shenzhen, 518000, Shenzhen, China; and
| | - Shuang Wang
- Beijing Genomics Institute (BGI)–Shenzhen, 518000, Shenzhen, China; and
| | - Jun Wang
- Beijing Genomics Institute (BGI)–Shenzhen, 518000, Shenzhen, China; and
| | - Luz B. Gilbert
- Laboratoire de Recherche en Sciences Végétales, Centre National de la Recherche Scientifique–Université Paul Sabatier, Unité Mixte de Recherche 5546, 31326 Castanet Tolosan, France
| | - Ying Rui Li
- Beijing Genomics Institute (BGI)–Shenzhen, 518000, Shenzhen, China; and
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
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21
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Bosi E, Fani R, Fondi M. The mosaicism of plasmids revealed by atypical genes detection and analysis. BMC Genomics 2011; 12:403. [PMID: 21824433 PMCID: PMC3166947 DOI: 10.1186/1471-2164-12-403] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 08/08/2011] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND From an evolutionary viewpoint, prokaryotic genomes are extremely plastic and dynamic, since large amounts of genetic material are continuously added and/or lost through promiscuous gene exchange. In this picture, plasmids play a key role, since they can be transferred between different cells and, through genetic rearrangement(s), undergo gene(s) load, leading, in turn, to the appearance of important metabolic innovations that might be relevant for cell life. Despite their central position in bacterial evolution, a massive analysis of newly acquired functional blocks [likely the result of horizontal gene transfer (HGT) events] residing on plasmids is still missing. RESULTS We have developed a computational, composition-based, pipeline to scan almost 2000 plasmids for genes that differ significantly from their hosting molecule. Plasmids atypical genes (PAGs) were about 6% of the total plasmids ORFs and, on average, each plasmid possessed 4.4 atypical genes. Nevertheless, conjugative plasmids were shown to possess an amount of atypical genes than that found in not mobilizable plasmids, providing strong support for the central role suggested for conjugative plasmids in the context of HGT. Part of the retrieved PAGs are organized into (mainly short) clusters and are involved in important biological processes (detoxification, antibiotic resistance, virulence), revealing the importance of HGT in the spreading of metabolic pathways within the whole microbial community. Lastly, our analysis revealed that PAGs mainly derive from other plasmid (rather than coming from phages and/or chromosomes), suggesting that plasmid-plasmid DNA exchange might be the primary source of metabolic innovations in this class of mobile genetic elements. CONCLUSIONS In this work we have performed the first large scale analysis of atypical genes that reside on plasmid molecules to date. Our findings on PAGs function, organization, distribution and spreading reveal the importance of plasmids-mediated HGT within the complex bacterial evolutionary network and in the dissemination of important biological traits.
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Affiliation(s)
- Emanuele Bosi
- Lab, of Microbial and Molecular Evolution, Dept, of Evolutionary Biology, University of Florence, Italy
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