Diversity of<i>Sinorhizobium</i>strains nodulating<i>Medicago sativa</i>from different Iranian regions

Talebi, Majid; Bahar, Masoud; Saeidi, Ghodratollah; Mengoni, Alessio; Bazzicalupo, Marco

doi:10.1111/j.1574-6968.2008.01329.x

Cited by 27 publications

(13 citation statements)

References 28 publications

(35 reference statements)

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“…The megaplasmid shows a similar signature, even at the accessory genome level. The Kazakhstan strains clustered together in all the fraction of pSymA megaplasmid and in total and pSymB chromid coding fraction in agreement with previous observations about the role of geographical isolation in S. meliloti differentiation (Talebi Bedaf et al 2008). The chromosome showed a higher compactness, as expected for this more evolutionary conserved replicon, with two clusters for the coding and the accessory component and three clusters for the noncoding component.…”

Section: Resultssupporting

confidence: 91%

“…All AK-coded strains were initially isolated from root nodules of Medicago plants in the North Aral Sea region in Kazakhstan and are deposited, as original specimens after initial isolation, in the culture collection of All-Russia Institute of Agricultural Microbiology (St. Petersburg, Russia) and as duplicated at BIO. Strain 1A42 was isolated from root nodules of alfalfa in Iran (Talebi Bedaf et al 2008) and deposited at BIO by M. Talebi Bedaf. Rm1021 is the model strain for S. meliloti .…”

Section: Methodsmentioning

confidence: 99%

“…Previous population genetics investigations have shown that strains of S. meliloti are highly variable, and various studies explored the relationship between the pattern of genetic variation and environmental variables (Paffetti et al 1996, 1998; Carelli et al 2000; Jebara et al 2001; Bailly et al 2006; Talebi Bedaf et al 2008; Trabelsi et al 2010), highlighting the influence of both host plant genotype and geographical separation on S. meliloti populations. More recently, both S. meliloti and its cogeneric species S. medicae have been used in parallel for population genomics investigations (Guo et al 2009; Bailly et al 2011; Epstein et al 2012).…”

Section: Introductionmentioning

confidence: 99%

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Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

Galardini

Pini

Bazzicalupo

et al. 2013

Genome Biology and Evolution

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106

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Many bacterial species, such as the alphaproteobacterium Sinorhizobium meliloti, are characterized by open pangenomes and contain multipartite genomes consisting of a chromosome and other large-sized replicons, such as chromids, megaplasmids, and plasmids. The evolutionary forces in both functional and structural aspects that shape the pangenome of species with multipartite genomes are still poorly understood. Therefore, we sequenced the genomes of 10 new S. meliloti strains, analyzed with four publicly available additional genomic sequences. Results indicated that the three main replicons present in these strains (a chromosome, a chromid, and a megaplasmid) partly show replicon-specific behaviors related to strain differentiation. In particular, the pSymB chromid was shown to be a hot spot for positively selected genes, and, unexpectedly, genes resident in the pSymB chromid were also found to be more widespread in distant taxa than those located in the other replicons. Moreover, through the exploitation of a DNA proximity network, a series of conserved “DNA backbones” were found to shape the evolution of the genome structure, with the rest of the genome experiencing rearrangements. The presented data allow depicting a scenario where the pSymB chromid has a distinctive role in intraspecies differentiation and in evolution through positive selection, whereas the pSymA megaplasmid mostly contributes to structural fluidity and to the emergence of new functions, indicating a specific evolutionary role for each replicon in the pangenome evolution.

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Section: Resultssupporting

confidence: 91%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

Galardini

Pini

Bazzicalupo

et al. 2013

Genome Biology and Evolution

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106

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“…The influence of soil properties, plant host, and other biotic 260 factors including microbial communities, bacteriophages, plasmids, and other invasive DNA 261 elements all surely play a role in the generation of rhizobial diversity (Bromfield et al 1987, 262 Harrison et al 1989, Carelli et al 2000, Silva et al 2007, Talebi et al 2008, Toro et al 2018. to the symbiotic process, revealing that key symbiotic genes can be located on megaplasmids, that 277 optimal symbiotic performance often requires more than one megaplasmid, and that megaplasmids 278 can carry loci required for effective competition for nodule occupancy (Barbour and Elkan 1989, 279 Hynes and McGregor 1990, Baldani et al 1992, Brom et al 1992, Hu et al 2007, Barreto et al 280 2012, Stasiak et al 2014. In contrast, some rhizobial plasmids impair symbiotic development.…”

Section: Competitiveness (Queiroux Et Al 2012) These Results Illustmentioning

confidence: 99%

Multi-disciplinary approaches for studying rhizobium – legume symbioses

diCenzo

Zamani

Checcucci

et al. 2018

Preprint

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24The rhizobium-legume symbiosis is a major source of fixed nitrogen (ammonia) in the 25 biosphere. The potential for this process to increase agricultural yield while reducing the reliance 26 on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. 27For decades, rhizobium research has benefited from the use of leading techniques from a very 28 broad set of fields, including population genetics, molecular genetics, genomics, and systems 29 biology. In this review, we summarize many of the research strategies that have been employed in 30 the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on 31 genome and systems-level approaches. We then describe ongoing synthetic biology approaches 32 aimed at improving existing symbioses or engineering completely new symbiotic interactions. The 33 review concludes with our perspective of the future directions and challenges of the field, with an 34 emphasis on how the application of a multi-disciplinary approach and the development of new 35 methods will be necessary to ensure successful biotechnological manipulation of the symbiosis. SYMBIOTIC NITROGEN FIXATION: CHALLENGES AND PROSPECTS 60Biological nitrogen fixation (BNF) is an agriculturally and ecologically crucial process that 61 is performed by prokaryotes in two ecological groups: i) BNF performed by free-living cells often 62 in close association with plants, or ii) by rhizobia that fix nitrogen during an endosymbiotic 63 relationship with legumes. The fixation of N2-gas into ammonia by root-nodule bacteria (rhizobia) 64 is referred to as symbiotic nitrogen fixation (SNF), and it is a more efficient process in terms of 65 supplying nitrogen to the plant. Phylogenetically, most rhizobia are α-proteobacteria, but some 66 rhizobia are β-proteobacteria ( Figure 1). The various genetic, biochemical, and evolutionary 67 aspects of the symbiotic interaction have been reviewed over the years (Long 1996, Gage 2004, 68 MacLean et al. 2007, Jones et al. 2007, Gibson et al. 2008, Oldroyd and Downie 2008, Masson-69 Boivin et al. 2009, Downie 2010, Oldroyd et al. 2011, Udvardi and Poole 2013, Haag et al. 2013, 70 Remigi et al. 2016, Mus et al. 2016, Poole et al. 2018. In brief, the symbiosis is initiated following 71an exchange of signals between the roots of the plant and free-living rhizobia in root-proximal soil 72 (the rhizosphere). As root nodule tissue develops (Figure 2), the rhizobia enter this specialized 73 tissue through an extracellular infection thread; as these inwardly growing threads reach 74 differentiated nodule cells, the bacteria become surrounded by a plant-derived membrane and 75 taken up into the plant cytosol, where they are known as bacteroids. The nascent bacteroids then 76 undergo major morphological and transcriptional changes, leading to active nitrogen fixation, 77 which is the conversion of atmospheric N2 into NH3 for the plant. 78It has been estimated that BNF contributes several teragrams of nitr...

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“…We also identified four potential PGPB (Pt17,18,19,and 20) that are associated with the α-Proteobacteria class. These four isolates were associated with the bacteria Rhizobium lusitanum, Agrobacterium rhizogenes, and Sinorhizobium sp, which are known to contribute to plant growth and development by fixing atmospheric N 2 (Kanvinde and Sastry, 1990;Valverde et al, 2006;Talebi et al, 2008). Endophytic bacteria related to the β-proteobacteria class included the Pt21, 22, and 23 isolates.…”

Section: Endophytic Bacteria Of P Tuberculatum Are Associated With Pmentioning

confidence: 99%

Endophytic bacteria from Piper tuberculatum Jacq.: isolation, molecular characterization, and in vitro screening for the control of Fusarium solani f. sp piperis, the causal agent of root rot disease in black pepper (Piper nigrum L.)

et al. 2015

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Diversity ofSinorhizobiumstrains nodulatingMedicago sativafrom different Iranian regions

Cited by 27 publications

References 28 publications

Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

Multi-disciplinary approaches for studying rhizobium – legume symbioses

Endophytic bacteria from Piper tuberculatum Jacq.: isolation, molecular characterization, and in vitro screening for the control of Fusarium solani f. sp piperis, the causal agent of root rot disease in black pepper (Piper nigrum L.)

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