scholarly journals Creation and multi-omics characterization of a genomically hybrid strain in the nitrogen-fixing symbiotic bacteriumSinorhizobium meliloti

2018 ◽  
Author(s):  
Alice Checcucci ◽  
George C. diCenzo ◽  
Veronica Ghini ◽  
Marco Bazzicalupo ◽  
Anke Becker ◽  
...  
Keyword(s):  
Precision Agriculture ◽  
Sinorhizobium Meliloti ◽  
Metabolic Flux ◽  
Symbiotic Bacterium ◽  
Biotechnological Applications ◽  
Bacterial Strains ◽  
Hybrid Strain ◽  
Single Genome ◽  
Symbiotic Phenotype ◽  
Multiple Strains

AbstractMany bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbour a multipartite genome composed by more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacteriumSinorhizobium meliloti. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donorS. melilotistrain to an acceptor strain. Thecis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extra-cellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modelling were employed forin silicoprediction of metabolic flux reorganization. Phenotypes of thecis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with thecis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.

Symbiotic phenotype of a membrane-bound glucose dehydrogenase mutant of Sinorhizobium meliloti

2008 ◽  
Vol 313 (1-2) ◽  
pp. 217-225 ◽  
Author(s):  
Cecilia E. Bernardelli ◽  
María F. Luna ◽  
María L. Galar ◽  
José L. Boiardi
Keyword(s):  
Sinorhizobium Meliloti ◽  
Glucose Dehydrogenase ◽  
Symbiotic Phenotype ◽  
Membrane Bound

scholarly journals Safety Evaluation of Multiple Strains ofLactobacillus plantarumandPediococcus pentosaceusin Wistar Rats Based on the Ames Test and a 28-Day Feeding Study

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Cheng-Chih Tsai ◽  
Sew-Fen Leu ◽  
Quan-Rong Huang ◽  
Lan-Chun Chou ◽  
Chun-Chih Huang
Keyword(s):  
Wistar Rats ◽  
Clinical Chemistry ◽  
Toxicity Study ◽  
Bacterial Strains ◽  
Oral Toxicity ◽  
Short Term ◽  
Mutagenic Potential ◽  
Multiple Strains

Three lactic acid bacterial strains,Lactobacillus plantarum, HK006, and HK109, andPediococcus pentosaceusPP31 exhibit probiotic potential as antiallergy agents, both in vitro and in vivo. However, the safety of these new strains requires evaluation when isolated from infant faeces or pickled cabbage. Multiple strains (HK006, HK109, and PP31) were subject to a bacterial reverse mutation assay and a short-term oral toxicity study. The powder product exhibited mutagenic potential inSalmonellaTyphimurium strains TA98 and TA1535 (with or without metabolic activation). In the short-term oral toxicity study, rats received a normal dosage of 390 mg/kg/d (approximately9×109 CFU/kg/d) or a high dosage of 1950 mg/kg/d (approximately4.5×1010 CFU/kg/d) for 28 d. No adverse effects were observed regarding the general condition, behaviour, growth, feed and water consumption, haematology, clinical chemistry indices, organ weights, or histopathologic analysis of the rats. These studies have demonstrated that the consumption of multiple bacterial strains is not associated with any signs of mutagenicity ofS.Typhimurium or toxicity in Wistar rats, even after consuming large quantities of bacteria.

scholarly journals Inoculation with Efficient Nitrogen Fixing and Indoleacetic Acid Producing Bacterial Microsymbiont Enhance Tolerance of the Model LegumeMedicago truncatulato Iron Deficiency

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Nadia Kallala ◽  
Wissal M’sehli ◽  
Karima Jelali ◽  
Zribi Kais ◽  
Haythem Mhadhbi
Keyword(s):  
Oxidative Stress ◽  
Iron Deficiency ◽  
Medicago Truncatula ◽  
Sinorhizobium Meliloti ◽  
Plant Biomass ◽  
High Growth ◽  
Fe Deficiency ◽  
Nitrogen Fixing ◽  
Bacterial Strains ◽  
Negative Effect

The aim of this study was to assess the effect of symbiotic bacteria inoculation on the response ofMedicago truncatulagenotypes to iron deficiency. The present work was conducted on threeMedicago truncatulagenotypes: A17, TN8.20, and TN1.11. Three treatments were performed: control (C), direct Fe deficiency (DD), and induced Fe deficiency by bicarbonate (ID). Plants were nitrogen-fertilized (T) or inoculated with two bacterial strains:Sinorhizobium melilotiTII7 andSinorhizobium medicaeSII4. Biometric, physiological, and biochemical parameters were analyzed. Iron deficiency had a significant lowering effect on plant biomass and chlorophyll content in allMedicago truncatulagenotypes. TN1.11 showed the highest lipid peroxidation and leakage of electrolyte under iron deficiency conditions, which suggest that TN1.11 was more affected than A17 and TN8.20 by Fe starvation. Iron deficiency affected symbiotic performance indices of allMedicago truncatulagenotypes inoculated with bothSinorhizobiumstrains, mainly nodules number and biomass as well as nitrogen-fixing capacity. Nevertheless, inoculation withSinorhizobiumstrains mitigates the negative effect of Fe deficiency on plant growth and oxidative stress compared to nitrogen-fertilized plants. The highest auxin producing strain, TII7, preserves relatively high growth and root biomass and length when inoculated to TN8.20 and A17. On the other hand, both TII7 and SII4 strains improve the performance of sensitive genotype TN1.11 through reduction of the negative effect of iron deficiency on chlorophyll and plant Fe content. The bacterial inoculation improved Fe-deficient plant response to oxidative stress via the induction of the activities of antioxidant enzymes.

scholarly journals CRISpy-pop: a web tool for designing CRISPR/Cas9-driven genetic modifications in diverse populations

2020 ◽  
Author(s):  
Hayley R. Stoneman ◽  
Russell L. Wrobel ◽  
Michael Place ◽  
Michael Graham ◽  
David J. Krause ◽  
...  
Keyword(s):  
Web Application ◽  
Genomic Data ◽  
Model Organisms ◽  
Bacterial Strains ◽  
Rna Sequences ◽  
Guide Rna ◽  
Guide Rnas ◽  
Population Genomic ◽  
Current Implementation ◽  
Multiple Strains

AbstractCRISPR/Cas9 is a powerful tool for editing genomes, but design decisions are generally made with respect to a single reference genome. With population genomic data becoming available for an increasing number of model organisms, researchers are interested in manipulating multiple strains and lines. CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing for diverse yeast and bacterial strains. The current implementation designs and predicts the activity of guide RNAs against more than 1000 Saccharomyces cerevisiae genomes, including 167 strains frequently used in bioenergy research. Zymomonas mobilis, an increasingly popular bacterial bioenergy research model, is also supported. CRISpy-pop is available as a web application (https://CRISpy-pop.glbrc.org/) with an intuitive graphical user interface. CRISpy-pop also cross-references the human genome to allow users to avoid the selection of sgRNAs with potential biosafety concerns. Additionally, CRISpy-pop predicts the strain coverage of each guide RNA within the supported strain sets, which aids in functional population genetic studies. Finally, we validate how CRISpy-pop can accurately predict the activity of guide RNAs across strains using population genomic data.

scholarly journals Polychlorinated Biphenyl Rhizoremediation by Pseudomonas fluorescens F113 Derivatives, Using a Sinorhizobium meliloti nod System To Drive bph Gene Expression

2005 ◽  
Vol 71 (5) ◽  
pp. 2687-2694 ◽  
Author(s):  
Marta Villacieros ◽  
Clare Whelan ◽  
Martina Mackova ◽  
Jesper Molgaard ◽  
María Sánchez-Contreras ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pseudomonas Fluorescens ◽  
Sinorhizobium Meliloti ◽  
Polychlorinated Biphenyl ◽  
Expression System ◽  
Single Copy ◽  
Bacterial Strains ◽  
High Level Expression ◽  
High Level ◽  
Biodegradation Genes

ABSTRACT Rhizoremediation of organic chemicals requires high-level expression of biodegradation genes in bacterial strains that are excellent rhizosphere colonizers. Pseudomonas fluorescens F113 is a biocontrol strain that was shown to be an excellent colonizer of numerous plant rhizospheres, including alfalfa. Although a derivative of F113 expressing polychlorinated biphenyl (PCB) biodegradation genes (F113pcb) has been reported previously, this strain shows a low level of bph gene expression, limiting its rhizoremediation potential. Here, a high-level expression system was designed from rhizobial nod gene regulatory relays. Nod promoters were tested in strain F113 by using β-galactosidase transcriptional fusions. This analysis showed that nodbox 4 from Sinorhizobium meliloti has a high level of expression in F113 that is dependent on an intact nodD1 gene. A transcriptional fusion of a nodbox cassette containing the nodD1 gene and nodbox 4 fused to a gfp gene was expressed in the alfalfa rhizosphere. The bph operon from Burkholderia sp. strain LB400 was cloned under the control of the nodbox cassette and was inserted as a single copy into the genome of F113, generating strain F113L::1180. This new genetically modified strain has a high level of BphC activity and grows on biphenyl as a sole carbon and energy source at a growth rate that is more than three times higher than that of F113pcb. Degradation of PCBs 3, 4, 5, 17, and 25 was also much faster in F113L::1180 than in F113pcb. Finally, the modified strain cometabolized PCB congeners present in Delor103 better than strain LB400, the donor of the bph genes used.

Isolation, bioassay and characterisation of Xenorhabdus sp. SY5, a highly virulent symbiotic bacterium of an entomopathogenic nematode isolated from China

Nematology ◽  
2013 ◽  
Vol 15 (2) ◽  
pp. 153-163 ◽  
Author(s):  
Huan Wang ◽  
Hui Dong ◽  
Haitao Qian ◽  
Runxi Xia ◽  
Bin Cong
Keyword(s):  
Growth Inhibition ◽  
Insecticidal Activity ◽  
Entomopathogenic Nematode ◽  
Symbiotic Bacterium ◽  
Symbiotic Bacteria ◽  
Toxin Gene ◽  
Agricultural Pests ◽  
Bacterial Strains ◽  
Biological Pest Control ◽  
Highly Virulent

The entomopathogenic nematodes (EPN), together with their symbiotic bacteria, are obligate and lethal parasites of insects and are applied as biological approaches to pest management. In this paper, we isolated 122 strains of symbiotic bacteria from 23 EPN isolates that were gathered in various soils containing different vegetations from different regions of China. All these isolated bacterial strains showed oral insecticidal activity and/or growth inhibition to the larvae of Ostrinia furnacalis. Among these strains, Xenorhabdus sp. SY5 exhibited high insecticidal activity to O. furnacalis, Plutella xylostella, Mythimna separata, Laphygma exigua and Tenebrio molitor, all of which are important agricultural pests. Xenorhabdus sp. SY5 was isolated from EPN Steinernema sp. SY5. Through DEAE-52 column chromatography, seven toxins were purified from X. sp. SY5. Bioassay results showed that all seven toxins had, to a certain extent, insecticidal activity and/or growth inhibition to O. furnacalis, T. molitor, P. xylostella, M. separata and L. exigua. Our data also showed that each of these toxins had different insecticidal activity and/or growth inhibition against different insect species. The partial toxin gene sequence of X. sp. SY5 was determined, and its deduced amino acid sequence only showed 75, 66 and 65% identities to homologues of EPN symbiotic bacteria Photorhabdus luminescens, Xenorhabdus nematophila and Yersinia mollaretii, respectively. These results suggested that strain SY5 is a highly virulent EPN symbiotic bacterial strain that has a potential value for biological pest control.

scholarly journals Bioactive Cytokinins Are Selectively Secreted by Sinorhizobium meliloti Nodulating and Nonnodulating Strains

2013 ◽  
Vol 26 (10) ◽  
pp. 1225-1231 ◽  
Author(s):  
Anna Kisiala ◽  
Carole Laffont ◽  
R. J. Neil Emery ◽  
Florian Frugier
Keyword(s):  
Sinorhizobium Meliloti ◽  
Root Nodule ◽  
System Development ◽  
Lateral Roots ◽  
Extracellular Polysaccharide ◽  
Bacterial Strains ◽  
Symbiotic Interaction ◽  
Root System Development ◽  
Liquid Chromatography Tandem Mass ◽  
Meliloti Strain

Bacteria present in the rhizosphere of plants often synthesize phytohormones, and these signals can consequently affect root system development. In legumes, plants adapt to nitrogen starvation by forming lateral roots as well as a new organ, the root nodule, following a symbiotic interaction with bacteria collectively referred to as rhizobia. As cytokinin (CK) phytohormones were shown to be necessary and sufficient to induce root nodule organogenesis, the relevance of CK production by symbiotic rhizobia was questioned. In this study, we analyzed quantitatively, by liquid chromatography-tandem mass spectrometry, the production of 25 forms of CK in nine rhizobia strains belonging to four different species. All bacterial strains were able to synthesize a mix of CK, and bioactive forms of CK, such as iP, were notably found to be secreted in bacterial culture supernatants. Use of a mutant affected in extracellular polysaccharide (EPS) production revealed a negative correlation of EPS production with the ability to secrete CK. In addition, analysis of a nonnodulating Sinorhizobium meliloti strain revealed a similar pattern of CK production and secretion when compared with a related nodulating strain. This indicates that bacterially produced CK are not sufficient to induce symbiotic nodulation.

scholarly journals Roles for Riboflavin in the Sinorhizobium-Alfalfa Association

2002 ◽  
Vol 15 (5) ◽  
pp. 456-462 ◽  
Author(s):  
Guoping Yang ◽  
T. V. Bhuvaneswari ◽  
Cecillia M. Joseph ◽  
Maria D. King ◽  
Donald A. Phillips
Keyword(s):  
Sinorhizobium Meliloti ◽  
Root Colonization ◽  
Defined Medium ◽  
Control Strain ◽  
Linkage Groups ◽  
Bacterial Strains ◽  
Riboflavin Production ◽  
E Coli ◽  
Alfalfa Root ◽  
Riboflavin Synthesis

Genes contributing to riboflavin production in Sinorhizobium meliloti were identified, and bacterial strains that overproduce this vitamin were constructed to characterize how additional riboflavin affects interactions between alfalfa (Medicago sativa) and S. meliloti. Riboflavin-synthesis genes in S. meliloti were found in three separate linkage groups and designated as ribBA, ribDribC, and ribH for their similarities to Escherichia coli genes. The ribBA and ribC loci complemented corresponding E. coli rib mutants. S. meliloti cells containing extra copies of ribBA released 10 to 20% more riboflavin than a control strain but grew at similar rates in a defined medium lacking riboflavin. Cells carrying extra copies of ribBA colonized roots to densities that were 55% higher than that of a control strain. No effect of extra rib genes was detected on alfalfa grown in the absence or presence of combined N. These results support the importance of extracellular riboflavin for alfalfa root colonization by S. meliloti and are consistent with the hypothesis that this molecule benefits bacteria indirectly through an effect on the plant.

scholarly journals Specific Host-Responsive Associations Between Medicago truncatula Accessions and Sinorhizobium Strains

2017 ◽  
Vol 30 (5) ◽  
pp. 399-409 ◽  
Author(s):  
Théophile Kazmierczak ◽  
Marianna Nagymihály ◽  
Florian Lamouche ◽  
Quentin Barrière ◽  
Ibtissem Guefrachi ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Sinorhizobium Meliloti ◽  
Root Nodules ◽  
Nodule Formation ◽  
Bacterial Strains ◽  
Symbiotic Efficiency ◽  
Model Legume ◽  
Functional Studies ◽  
Multiple Parameters ◽  
Nitrogen Fixation Activity

Legume plants interact with rhizobia to form nitrogen-fixing root nodules. Legume-rhizobium interactions are specific and only compatible rhizobia and plant species will lead to nodule formation. Even within compatible interactions, the genotype of both the plant and the bacterial symbiont will impact on the efficiency of nodule functioning and nitrogen-fixation activity. The model legume Medicago truncatula forms nodules with several species of the Sinorhizobium genus. However, the efficiency of these bacterial strains is highly variable. In this study, we compared the symbiotic efficiency of Sinorhizobium meliloti strains Sm1021, 102F34, and FSM-MA, and Sinorhizobium medicae strain WSM419 on the two widely used M. truncatula accessions A17 and R108. The efficiency of the interactions was determined by multiple parameters. We found a high effectiveness of the FSM-MA strain with both M. truncatula accessions. In contrast, specific highly efficient interactions were obtained for the A17-WSM419 and R108-102F34 combinations. Remarkably, the widely used Sm1021 strain performed weakly on both hosts. We showed that Sm1021 efficiently induced nodule organogenesis but cannot fully activate the differentiation of the symbiotic nodule cells, explaining its weaker performance. These results will be informative for the selection of appropriate rhizobium strains in functional studies on symbiosis using these M. truncatula accessions, particularly for research focusing on late stages of the nodulation process.

scholarly journals l-Canavanine Made by Medicago sativa Interferes with Quorum Sensing in Sinorhizobium meliloti

2005 ◽  
Vol 187 (24) ◽  
pp. 8427-8436 ◽  
Author(s):  
Neela D. Keshavan ◽  
Puneet K. Chowdhary ◽  
Donovan C. Haines ◽  
Juan E. González
Keyword(s):  
Quorum Sensing ◽  
Medicago Sativa ◽  
Sinorhizobium Meliloti ◽  
Signal Molecules ◽  
Bacterial Strains ◽  
Signal Molecule ◽  
Gram Negative ◽  
Bacterial Quorum Sensing ◽  
Bacterial Quorum ◽  
Regulated Gene Expression

ABSTRACT Sinorhizobium meliloti is a gram-negative soil bacterium, capable of establishing a nitrogen-fixing symbiosis with its legume host, alfalfa (Medicago sativa). Quorum sensing plays a crucial role in this symbiosis, where it influences the nodulation process and the synthesis of the symbiotically important exopolysaccharide II (EPS II). S. meliloti has three quorum-sensing systems (Sin, Tra, and Mel) that use N-acyl homoserine lactones as their quorum-sensing signal molecule. Increasing evidence indicates that certain eukaryotic hosts involved in symbiotic or pathogenic relationships with gram-negative bacteria produce quorum-sensing-interfering (QSI) compounds that can cross-communicate with the bacterial quorum-sensing system. Our studies of alfalfa seed exudates suggested the presence of multiple signal molecules capable of interfering with quorum-sensing-regulated gene expression in different bacterial strains. In this work, we choose one of these QSI molecules (SWI) for further characterization. SWI inhibited violacein production, a phenotype that is regulated by quorum sensing in Chromobacterium violaceum. In addition, this signal molecule also inhibits the expression of the S. meliloti exp genes, responsible for the production of EPS II, a quorum-sensing-regulated phenotype. We identified this molecule as l-canavanine, an arginine analog, produced in large quantities by alfalfa and other legumes.

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