Rhizobial communities in symbiosis with legumes: genetic diversity, competition and interactions with host plants

Wielbo, Jerzy

doi:10.2478/s11535-012-0032-5

Cited by 10 publications

(9 citation statements)

References 107 publications

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“…When in the endosymbiotic state, Rhizobium bacteroids reduce atmospheric nitrogen N 2 to ammonia, which is then exported to the plant for assimilation. In return, the plant host provides fixed carbon and other micro-nutrients to the bacteroids to sustain the symbiosis (Wielbo, 2012; Udvardi and Poole, 2013). The availability of symbiotically supplied nitrogen enables leguminous plants to satisfy their high nitrogen demands and, in part, contributed to the evolutionary success and diversification of the Leguminosae (Doyle and Luckow, 2003).…”

Section: Introductionmentioning

confidence: 99%

The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum

2016

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The free-living legume symbiont Rhizobium leguminosarum is of significant economic value because of its ability to provide fixed nitrogen to globally important leguminous food crops, such as peas and lentils. Discovery based research into the genetics and physiology of R. leguminosarum provides the foundational knowledge necessary for understanding the bacterium's complex lifestyle, necessary for augmenting its use in an agricultural setting. Transposon insertion sequencing (INSeq) facilitates high-throughput forward genetic screening at a genomic scale to identify individual genes required for growth in a specific environment. In this study we applied INSeq to screen the genome of R. leguminosarum bv. viciae strain 3841 (RLV3841) for genes required for growth on minimal mannitol containing medium. Results from this study were contrasted with a prior INSeq experiment screened on peptide rich media to identify a common set of functional genes necessary for basic physiology. Contrasting the two growth conditions indicated that approximately 10% of the chromosome was required for growth, under both growth conditions. Specific genes that were essential to singular growth conditions were also identified. Data from INSeq screening on mannitol as a sole carbon source were used to reconstruct a metabolic map summarizing growth impaired phenotypes observed in the Embden-Meyerhof-Parnas pathway, Entner-Doudoroff pathway, pentose phosphate pathway, and tricarboxylic acid cycle. This revealed the presence of mannitol dependent and independent metabolic pathways required for growth, along with identifying metabolic steps with isozymes or possible carbon flux by-passes. Additionally, genes were identified on plasmids pRL11 and pRL12 that are likely to encode functional activities important to the central physiology of RLV3841.

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Section: Introductionmentioning

confidence: 99%

The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum

2016

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“…Members in these genera share a unique relationship with plant hosts. Rhizobium , and Sinorhizobium are both able to enter into an endosymbiotic mutualism with certain species of leguminous plants, in which the Rhizobia fix atmospheric nitrogen into a biologically available form for the plant in return for fixed carbon and energy [ 26 ]. This symbiosis is particularly important in the context of agriculturally produced pulse crops, where the Rhizobium legume symbiosis affords farmers the ability to reduce the rate of synthetic nitrogen fertilizers application [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

Construction of a mariner-based transposon vector for use in insertion sequence mutagenesis in selected members of the Rhizobiaceae

Perry

Yost

2014

BMC Microbiol

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BackgroundThe Rhizobiaceae family of Gram-negative bacteria often engage in symbiosis with plants of economic importance. Historically, genetic studies to identify the function of individual genes, and characterize the biology of these bacteria have relied on the use of classical transposon mutagenesis. To increase the rate of scientific discovery in the Rhizobiaceae there is a need to adapt high-throughput genetic screens like insertion sequencing for use in this family of bacteria. Here we describe a Rhizobiaceae compatible MmeI-adapted mariner transposon that can be used with insertion sequencing for high-throughput genetic screening.ResultsThe newly constructed mariner transposon pSAM_Rl mutagenized R. leguminosarum, S. meliloti, and A. tumefaciens at a high frequency. In R. leguminosarum, mutant pools were generated that saturated 88% of potential mariner insertions sites in the genome. Analysis of the R. leguminosarum transposon insertion sequencing data with a previously described hidden Markov model-based method resulted in assignment of the contribution of all annotated genes in the R. leguminosarum 3841 genome for growth on a complex medium. Good concordance was observed between genes observed to be required for growth on the complex medium, and previous studies.ConclusionsThe newly described Rhizobiaceaee compatible mariner transposon insertion sequencing vector pSAM_Rl has been shown to mutagenize at a high frequency and to be an effective tool for use in high-throughput genetic screening. The construction and validation of this transposon insertion sequencing tool for use in the Rhizobiziaceae will provide an opportunity for researchers in the Rhizobiaceae community to use high-throughput genetic screening, allowing for significant increase in the rate of genetic discovery, particularly given the recent release of genome sequences from many Rhizobiaceae strains.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-014-0298-z) contains supplementary material, which is available to authorized users.

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“…Rhizobium etli CFN42 is able to establish a symbiotic relationship with the roots of Phaseolus vulgaris plants, forming nitrogen-fixing nodules. The ability to nodulate and fix nitrogen in association with leguminous plants is a characteristic shared by many rhizobial strains ( Gage, 2004 ; Wielbo, 2012 ; Quinto et al, 2014 ; Westhoek et al, 2017 ). This ability depends on the presence of a set of genes required for nodulation (nod) and nitrogen fixation (fix and nif).…”

Section: Introductionmentioning

confidence: 99%

Transfer of the Symbiotic Plasmid of Rhizobium etli CFN42 to Endophytic Bacteria Inside Nodules

et al. 2020

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Conjugative transfer is one of the mechanisms allowing diversification and evolution of bacteria. Rhizobium etli CFN42 is a bacterial strain whose habitat is the rhizosphere and is able to form nodules as a result of the nitrogen-fixing symbiotic relationship it may establish with the roots of Phaseolus vulgaris . R. etli CFN42 contains one chromosome and six large plasmids (pRet42a – pRet42f). Most of the genetic information involved in the establishment of the symbiosis is localized on plasmid pRet42d, named as the symbiotic plasmid (pSym). This plasmid is able to perform conjugation, using pSym encoded transfer genes controlled by the RctA/RctB system. Another plasmid of CFN42, pRet42a, has been shown to perform conjugative transfer not only in vitro , but also on the surface of roots and inside nodules, using other rhizobia as recipients. In addition to the rhizobia involved in the formation of nodules, these structures have been shown to contain endophytic bacteria from different genera and species. In this work, we have explored the conjugative transfer of the pSym (pRet42d) from R. etli CFN42 to endophytic bacteria as putative recipients, using as donor a CFN42 derivative labeled with GFP in the pRet42d and RFP in the chromosome. We were able to isolate some transconjugants, which inherit the GFP, but not the RFP marker. Some of them were identified, analyzed and evaluated for their ability to nodulate. We found transconjugants from genera such as Stenotrophomonas , Achromobacter , and Bacillus , among others. Although all the transconjugants carried the GFP marker, and nod, fix , and nif genes from pRet42d, not all were able to nodulate. Ultrastructure microscopy analysis showed some differences in the structure of the nodules of one of the transconjugants. A replicon of the size of pRet42d (371 Kb) could not be visualized in the transconjugants, suggesting that the pSym or a segment of the plasmid is integrated in the chromosome of the recipients. These findings strengthen the proposal that nodules constitute a propitious environment for exchange of genetic information among bacteria, in addition to their function as structures where nitrogen fixation and assimilation takes place.

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Rhizobial communities in symbiosis with legumes: genetic diversity, competition and interactions with host plants

Cited by 10 publications

References 107 publications

The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum

The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum

Construction of a mariner-based transposon vector for use in insertion sequence mutagenesis in selected members of the Rhizobiaceae

Transfer of the Symbiotic Plasmid of Rhizobium etli CFN42 to Endophytic Bacteria Inside Nodules

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