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Pascale Fournier - One of the best experts on this subject based on the ideXlab platform.
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Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa.
International journal of systematic and evolutionary microbiology, 2018Co-Authors: Philippe Normand, Imen Nouioui, Petar Pujic, Pascale Fournier, Audrey Dubost, Guillaume Schwob, Hans-peter Klenk, Agnès Nguyen, Danis Abrouk, Aude Herrera-belaroussiAbstract:Strain ARgP5T, an actinobacterium isolated from a root nodule present on an Alnus incana subspecies rugosa shrub growing in Quebec City, Canada, was the subject of polyphasic taxonomic studies to clarify its status within the genus Frankia . 16S rRNA gene sequence similarities and ANI values between ARgP5T and type strains of species of the genus Frankia with validly published names were 98.8 and 82 % or less, respectively. The in silico DNA G+C content was 72.4 mol%. ARgP5T is characterised by the presence of meso-A2pm, galactose, glucose, mannose, rhamnose (trace), ribose and xylose as whole-organism hydrolysates; MK-9(H8) as predominant menaquinone; diphosphatidylglycerol, phosphatidylinositol and phosphatidylglycerol as polar lipids and iso-C16 : 0 and C17 : 1ω8c as major fatty acids. The proteomic results confirmed the distinct position of ARgP5T from its closest neighbours in Frankia cluster 1. ARgP5T was found to be infective on two alder (Alnus glutinosa and Alnusalnobetula subsp. crispa) and on one bayberry (Morella pensylvanica) species and to fix nitrogen in symbiosis and in pure culture. On the basis of phylogenetic (16S rRNA gene sequence), genomic, proteomic and phenotypic results, strain ARgP5T (=DSM 45898=CECT 9033) is considered to represent a novel species within the genus Frankia for which the name Frankia canadensis sp. nov., is proposed.
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Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host
2016Co-Authors: Tomas Persson, Pascale Fournier, Kai Battenberg, Irina V. Demina, Theoden Vigil-stenman, Maria Antonia, Cruz Hern, Alberto Mendoza, Claudine MédigueAbstract:Frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with acti-norhizal plants. Phylogenetically, symbiotic Frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. The strains of cluster II which form symbioses with actinorhizal Rosales and Cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. The genome of the first representative of this cluster, Candidatus Frankia datiscae Dg1 (Dg1), a microsymbiont of Datisca glomerata, was recently sequenced. A phylogenetic analysis of 50 different housekeeping genes of Dg1 and three published Frankia genomes showed that cluster II is basal among the symbiotic Frankia clusters. Detailed analysis showed that nodules of D. glomerata, independent of the origin of the inoculum, contain several closely related cluster II Frankia operational taxonomic units. Actinorhizal plants and legumes both belong to the nitrogen-fixing plant clade, and bacterial signaling in both groups involves the common sym
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in planta sporulation phenotype a major life history trait to understand the evolution of alnus infective Frankia strains
Environmental Microbiology, 2015Co-Authors: Adrien C Pozzi, Imen Nouioui, Pascale Fournier, Hector H Bautistaguerrero, Laetitia Cotingalvan, Regis PepinAbstract:Two major types of Frankia strains are usually recognized, based on the ability to sporulate in-planta: spore-positive (Sp+) and spore-negative (Sp-). We carried out a study of Sp+ and Sp- Frankia strains based on nodules collected on Alnus glutinosa, Alnus incana and Alnus viridis. The nodules were phenotyped using improved histology methods, and endophytic Frankia strain genotype was determined using a multilocus sequence analysis approach. An additional sampling was done to assess the relation between Sp+ phenotype frequency and genetic diversity of Frankia strains at the alder stand scale. Our results revealed that (i) Sp+ and Sp- Alnus-infective Frankia strains are genetically different even when sampled from the same alder stand and the same host-plant species; (ii) there are at least two distinct phylogenetic lineages of Sp+ Frankia that cluster according to the host-plant species and without regard of geographic distance and (iii) genetic diversity of Sp+ strains is very low at the alder stand scale compared with Sp- strains. Difference in evolutionary history and genetic diversity between Sp+ and Sp- Frankia allows us to discuss the possible ecological role of in-planta sporulation.
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Alnus peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing Frankia
The ISME Journal, 2015Co-Authors: Lorena Carro, Petar Pujic, Pascale Fournier, Nicole Alloisio, Hasna Boubakri, Anne E Hay, Franck Poly, Philippe François, Peter MergaertAbstract:Actinorhizal plant growth in pioneer ecosystems depends on the symbiosis with the nitrogen-fixing actinobacterium Frankia cells that are housed in special root organs called nodules. Nitrogen fixation occurs in differentiated Frankia cells known as vesicles. Vesicles lack a pathway for assimilating ammonia beyond the glutamine stage and are supposed to transfer reduced nitrogen to the plant host cells. However, a mechanism for the transfer of nitrogen-fixation products to the plant cells remains elusive. Here, new elements for this metabolic exchange are described. We show that Alnus glutinosa nodules express defensin-like peptides, and one of these, Ag5, was found to target Frankia vesicles. In vitro and in vivo analyses showed that Ag5 induces drastic physiological changes in Frankia , including an increased permeability of vesicle membranes. A significant release of nitrogen-containing metabolites, mainly glutamine and glutamate, was found in N_2-fixing cultures treated with Ag5. This work demonstrates that the Ag5 peptide is central for Frankia physiology in nodules and uncovers a novel cellular function for this large and widespread defensin peptide family.
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Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant
PLoS ONE, 2015Co-Authors: Tomas Persson, Brian Vanden Heuvel, Kai Battenberg, Irina V. Demina, Theoden Vigil-stenman, M. T. Facciotti, E. G. Wilbanks, A. O'brien, Pascale FournierAbstract:Frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. Phylogenetically, symbiotic Frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. The strains of cluster II which form symbioses with actinorhizal Rosales and Cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. The genome of the first representative of this cluster, Candidatus Frankia datiscae Dg1 (Dg1), a microsymbiont of Datisca glomerata, was recently sequenced. A phylogenetic analysis of 50 different housekeeping genes of Dg1 and three published Frankia genomes showed that cluster II is basal among the symbiotic Frankia clusters. Detailed analysis showed that nodules of Datisca glomerata, independent of the origin of the inoculum, contain several closely related cluster II Frankia operational taxonomic units. Actinorhizal plants and legumes both belong to the nitrogen-fixing plant clade, and bacterial signaling in both groups involves the common symbiotic pathway also used by arbuscular mycorrhizal fungi. However, so far, no molecules resembling rhizobial Nod factors could be isolated from Frankia cultures. Alone among Frankia genomes available to date, the genome of Dg1 contains the canonical nod genes nodA, nodB and nodC known from rhizobia, and these genes are arranged in two operons which are expressed in Datisca glomerata nodules. Furthermore, Frankia Dg1 nodC was able to partially complement a Rhizobium leguminosarum A34 nodC::Tn5 mutant. Phylogenetic analysis showed that Dg1 Nod proteins are positioned at the root of both alpha- and beta-rhizobial NodABC proteins. NodA-like acyl transferases were found across the phylum Actinobacteria, but among Proteobacteria only in nodulators. Taken together, our evidence indicates an Actinobacterial origin of rhizobial Nod factors.
Louis S. Tisa - One of the best experts on this subject based on the ideXlab platform.
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permanent draft genome sequence of Frankia sp nrrl b 16219 reveals the presence of canonical nod genes which are highly homologous to those detected in candidatus Frankia dg1 genome
Standards in Genomic Sciences, 2017Co-Authors: A. Ktari, Imen Nouioui, Faten Ghodhbanegtari, Teal Furnholm, Erik Swanson, Louis S. TisaAbstract:Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219 is closely related to “Frankia discariae” with a 16S rRNA gene similarity of 99.78%. Because of the lack of genetic tools for Frankia, our understanding of the bacterial signals involved during the plant infection process and the development of actinorhizal root nodules is very limited. Since the first three Frankia genomes were sequenced, additional genome sequences covering more diverse strains have helped provide insight into the depth of the pangenome and attempts to identify bacterial signaling molecules like the rhizobial canonical nod genes. The genome sequence of Frankia sp. strain NRRL B-16219 was generated and assembled into 289 contigs containing 8,032,739 bp with 71.7% GC content. Annotation of the genome identified 6211 protein-coding genes, 561 pseudogenes, 1758 hypothetical proteins and 53 RNA genes including 4 rRNA genes. The NRRL B-16219 draft genome contained genes homologous to the rhizobial common nodulation genes clustered in two areas. The first cluster contains nodACIJH genes whereas the second has nodAB and nodH genes in the upstream region. Phylogenetic analysis shows that Frankia nod genes are more deeply rooted than their sister groups from rhizobia. PCR-sequencing suggested the widespread occurrence of highly homologous nodA and nodB genes in microsymbionts of field collected Ceanothus americanus.
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Genomic, transcriptomic, and proteomic approaches towards understanding the molecular mechanisms of salt tolerance in Frankia strains isolated from Casuarina trees
BMC Genomics, 2017Co-Authors: Rediet Oshone, Mariama Ngom, Feixia Chu, Samira Mansour, Antony Champion, Mame Ourèye Sy, Louis S. TisaAbstract:BackgroundSoil salinization is a worldwide problem that is intensifying because of the effects of climate change. An effective method for the reclamation of salt-affected soils involves initiating plant succession using fast growing, nitrogen fixing actinorhizal trees such as the Casuarina. The salt tolerance of Casuarina is enhanced by the nitrogen-fixing symbiosis that they form with the actinobacterium Frankia. Identification and molecular characterization of salt-tolerant Casuarina species and associated Frankia is imperative for the successful utilization of Casuarina trees in saline soil reclamation efforts. In this study, salt-tolerant and salt-sensitive Casuarina associated Frankia strains were identified and comparative genomics, transcriptome profiling, and proteomics were employed to elucidate the molecular mechanisms of salt and osmotic stress tolerance.ResultsSalt-tolerant Frankia strains (CcI6 and Allo2) that could withstand up to 1000 mM NaCl and a salt-sensitive Frankia strain (CcI3) which could withstand only up to 475 mM NaCl were identified. The remaining isolates had intermediate levels of salt tolerance with MIC values ranging from 650 mM to 750 mM. Comparative genomic analysis showed that all of the Frankia isolates from Casuarina belonged to the same species (Frankia casuarinae). Pangenome analysis revealed a high abundance of singletons among all Casuarina isolates. The two salt-tolerant strains contained 153 shared single copy genes (most of which code for hypothetical proteins) that were not found in the salt-sensitive(CcI3) and moderately salt-tolerant (CeD) strains. RNA-seq analysis of one of the two salt-tolerant strains (Frankia sp. strain CcI6) revealed hundreds of genes differentially expressed under salt and/or osmotic stress. Among the 153 genes, 7 and 7 were responsive to salt and osmotic stress, respectively. Proteomic profiling confirmed the transcriptome results and identified 19 and 8 salt and/or osmotic stress-responsive proteins in the salt-tolerant (CcI6) and the salt-sensitive (CcI3) strains, respectively.ConclusionGenetic differences between salt-tolerant and salt-sensitive Frankia strains isolated from Casuarina were identified. Transcriptome and proteome profiling of a salt-tolerant strain was used to determine molecular differences correlated with differential salt-tolerance and several candidate genes were identified. Mechanisms involving transcriptional and translational regulation, cell envelop remodeling, and previously uncharacterized proteins appear to be important for salt tolerance. Physiological and mutational analyses will further shed light on the molecular mechanism of salt tolerance in Casuarina associated Frankia isolates.
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Frankia inefficax sp. nov., an actinobacterial endophyte inducing ineffective, non nitrogen-fixing, root nodules on its actinorhizal host plants
Antonie van Leeuwenhoek, 2017Co-Authors: Imen Nouioui, Louis S. Tisa, Faten Ghodhbane-gtari, Manfred Rohde, Maria Carmen Montero-calasanz, Hans-peter KlenkAbstract:Strain EuI1c^T is the first actinobacterial endophyte isolated from Elaeagnus umbellata that was shown to be infective on members of Elaeagnaceae and Morella but lacking the ability to form effective root nodules on its hosts. The strain can be easily distinguished from strains of other Frankia species based on its inability to produce vesicles, the specialized thick-walled structures where nitrogen fixation occurs. Chemotaxonomically, strain EuI1c^T contains phosphatidylinositol, diphosphatidylglycerol, two glycophospholipids and phosphatidylglycerol as phospholipids. The whole cell sugars were composed of glucose, galactose, mannose, ribose, rhamnose and fucose as diagnostic sugars of the species. Major fatty acids were iso -C_16:0, C_17:1 ω 8c and C_15:0 and C_17:0 and the predominant menaquinones were MK-9(H_6), MK-9(H_8) and MK-9(H_4). Analysis of the 16S rRNA gene sequence of strain EuI1c^T showed 97, 97.4 and 97.9% identity with Frankia elaeagni DSM 46783^T, Frankia casuarinae DSM 45818^T and Frankia alni DSM 45986^T, respectively. Digital DNA:DNA hybridizations with type strains of the three Frankia species with validly/effectively published names are significantly below 70%. These results warrant distinction of EuI1c^T (= DSM 45817^T = CECT 9037^T) as the type strain of a novel species designated Frankia inefficax sp. nov.
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Permanent Draft Genome Sequence of Frankia sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equisetifolia
Genome announcements, 2016Co-Authors: Timothy D’angelo, Rediet Oshone, Stephen Simpson, Krystalynne Morris, Feseha Abebe-akele, W. Kelley Thomas, Louis S. TisaAbstract:ABSTRACT Frankia sp. strain BR is a member of Frankia lineage Ic and is able to reinfect plants of the Casuarinaceae family. Here, we report a 5.2-Mbp draft genome sequence with a G+C content of 70.0% and 4,777 candidate protein-encoding genes.
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permanent draft genome sequence for Frankia sp strain ei5c a single spore isolate of a nitrogen fixing actinobacterium isolated from the root nodules of elaeagnus angustifolia
Genome Announcements, 2016Co-Authors: Timothy Dangelo, Rediet Oshone, Feseha Abebeakele, Stephen Simpson, Krystalynne Morris, Kelley W Thomas, Louis S. TisaAbstract:ABSTRACT Frankia sp. strain EI5c is a member of Frankia lineage III, which is able to reinfect plants of the Eleagnaceae, Rhamnaceae, Myricaceae, and Gymnostoma, as well as the genus Alnus. Here, we report the 6.6-Mbp draft genome sequence of Frankia sp. strain EI5c with a G+C content of 72.14 % and 5,458 candidate protein-encoding genes.
Maher Gtari - One of the best experts on this subject based on the ideXlab platform.
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Frankia soli sp. nov., an actinobacterium isolated from soil beneath Ceanothus jepsonii.
International journal of systematic and evolutionary microbiology, 2020Co-Authors: Maher Gtari, Faten Ghodhbane-gtari, Imen NouiouiAbstract:Actinobacterial strain CjT was directly isolated from soil beneath Ceanothus jepsonii growing in the USA. The strain formed cell structures typical of the genus Frankia including extensive hyphae, vesicles and sporangia, and it effectively nodulated members of the actinorhizal Colletieae, Elaeagnaceae and Myricaceae. The whole-cell hydrolysate of strain CjT was rich in meso-diaminopimelic acid and galactose, glucose, mannose, xylose, ribose and a trace of rhamnose. Tbe polar lipid profile contained phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and glycophospholipid. The menaquinone was predominantly MK-9(H4). The fatty acid profile predominantly consisted of C17 : 1ω8c, iso-C16 : 0, C15:0, C16 : 0 and C17 : 0. A multilocus sequence analysis phylogeny based on atp1, ftsZ, dnaK, gyrA and secA gene sequences positioned the strain within Elaeagnaceae- and Colletieae -nodulating species together with Frankia elaeagni DSM 46783T, Frankia discariae DSM 46785T and Frankia irregularis DSM 45899T. Pairwise 16S rRNA gene sequence similarities showed that strain CjT was most closely related to F. discariae DSM 46785T (99.78 %) while their digital DNA–DNA hybridization value was 41.1 %. Based on the overall analyses, strain CjT (=DSM 100623T=CECT 9041T) warrants classification as the type strain of a novel species, for which the name Frankia soli sp. nov. is proposed.
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Frankia nodulating Alnus glutinosa and Casuarinaceae in Tunisia
2015Co-Authors: Maher Gtari, Lorenzo Brusetti, Daniele Daffonchio, M E Aouani, Abdellatif BoudabousAbstract:Abstract- The capacity of some Tunisian soils to induce nodulation on Casuarina spp. and Alnus glutinosa was investigated through survey at fields and by plant-trapping bioassay. Frankia nodules were detected only in the north of Tunisia in some experimental forest sta-tions for Casuarinaceae, and in natural endemic A. glutinosa stands. Frankia genetic diver-sity was assessed by PCR-RFLP of nifD-K region and, for Casuarinaceae, also of 16S-23S rDNA internal transcribed spacers, amplified from DNA directly extracted from root nod-ules. Restriction patterns showed that one and two haplotypes of Frankia colonise Casuar-inaceae and A. glutinosa, respectively. Frankia in nodules of Casuarinaceae were found to be closely related to the group 1 of Casuarinaceae nodulating strains previously identified in Australia, corroborating the hypothesis of a recent introduction of these strains into Tunisia, probably with their hosts
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Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains
Scientific Reports, 2015Co-Authors: Maher Gtari, Faten Ghodhbane-gtari, Imed Sbissi, I. Nouioui, A. Ktari, K. Hezbri, W. Mimouni, A. Ayari, T. Yamanaka, Philippe NormandAbstract:The repeated failures reported in cultivating some microbial lineages are a major challenge in microbial ecology and probably linked, in the case of Frankia microsymbionts to atypical patterns of auxotrophy. Comparative genomics of the so far uncultured cluster-2 Candidatus Frankia datiscae Dg1, with cultivated Frankiae has revealed genome reduction, but no obvious physiological impairments. A direct physiological assay on nodule tissues from Coriaria myrtifolia infected with a closely-related strain permitted the identification of a requirement for alkaline conditions. A high pH growth medium permitted the recovery of a slow-growing actinobacterium. The strain obtained, called BMG5.1, has short hyphae, produced diazovesicles in nitrogen-free media, and fulfilled Koch's postulates by inducing effective nodules on axenically grown Coriaria spp. and Datisca glomerata. Analysis of the draft genome confirmed its close proximity to the Candidatus Frankia datiscae Dg1 genome with the absence of 38 genes (trehalose synthase, fumarylacetoacetase, etc) in BMG5.1 and the presence of 77 other genes (CRISPR, lanthionine synthase, glutathione synthetase, catalase, Na+/H+ antiporter, etc) not found in Dg1. A multi-gene phylogeny placed the two cluster-2 strains together at the root of the Frankia radiation.
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draft genome sequence of Frankia sp strain thr a nitrogen fixing actinobacterium isolated from the root nodules of casuarina cunninghamiana grown in egypt
Genome Announcements, 2014Co-Authors: Sheldon G Hurst, Rediet Oshone, Feseha Abebeakele, Krystalynne Morris, Kelley W Thomas, Faten Ghodhbanegtari, A. Ktari, Karima Salem, Samira R Mansour, Maher GtariAbstract:Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.3-Mbp draft genome sequence for Frankia sp. stain Thr, a nitrogen-fixing actinobacterium isolated from root nodules of Casuarina cunninghamiana collected in Egypt.
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genetic diversity among elaeagnus compatible Frankia strains and sympatric related nitrogen fixing actinobacteria revealed by nifh sequence analysis
Soil Biology & Biochemistry, 2007Co-Authors: Maher Gtari, Abdenaceur Hassen, Lorenzo Brusetti, Daniele Daffonchio, Diego Mora, Abdellatif BoudabousAbstract:Elaeagnus compatible Frankia isolates from Tunisian soil have been previously clustered with Frankia, colonizing Elaeagnaceae and Rhamnaceae in two different phylogenetic subgroups, while strain BMG5.6 was described as a new lineage closely related to Frankia and Micromonospora genera. In this study we further assess the diversity of captured Frankia and the relationship with BMG5.6-like actinobacteria, by using nifH gene sequences. Using PCR-RFLP screening on DNA extracted from lobe nodules, additional microsymbionts sharing BMG5.6 features have been detected proving a widespread occurrence of these actinobacteria in Elaeagnus root nodules. Neighbour-Joining trees of Frankia nifH sequences were consistent with previously published 16S rRNA and GlnII phylogenetic trees. Although four main clades could be discerned, actinobacterial strain BMG5.6 was clustered with Frankia strains isolated from Elaeagnus. The present study underscored the emanation of new diazotrophic taxon isolated from actinorhizal nodules occupying intermediate taxonomic position between Frankia and Micromonospora. Moreover, its aberrant position in nifH phylogeny should open network investigations on the natural history of nitrogen-fixing gene among actinobacteria.
Imen Nouioui - One of the best experts on this subject based on the ideXlab platform.
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Frankia soli sp. nov., an actinobacterium isolated from soil beneath Ceanothus jepsonii.
International journal of systematic and evolutionary microbiology, 2020Co-Authors: Maher Gtari, Faten Ghodhbane-gtari, Imen NouiouiAbstract:Actinobacterial strain CjT was directly isolated from soil beneath Ceanothus jepsonii growing in the USA. The strain formed cell structures typical of the genus Frankia including extensive hyphae, vesicles and sporangia, and it effectively nodulated members of the actinorhizal Colletieae, Elaeagnaceae and Myricaceae. The whole-cell hydrolysate of strain CjT was rich in meso-diaminopimelic acid and galactose, glucose, mannose, xylose, ribose and a trace of rhamnose. Tbe polar lipid profile contained phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and glycophospholipid. The menaquinone was predominantly MK-9(H4). The fatty acid profile predominantly consisted of C17 : 1ω8c, iso-C16 : 0, C15:0, C16 : 0 and C17 : 0. A multilocus sequence analysis phylogeny based on atp1, ftsZ, dnaK, gyrA and secA gene sequences positioned the strain within Elaeagnaceae- and Colletieae -nodulating species together with Frankia elaeagni DSM 46783T, Frankia discariae DSM 46785T and Frankia irregularis DSM 45899T. Pairwise 16S rRNA gene sequence similarities showed that strain CjT was most closely related to F. discariae DSM 46785T (99.78 %) while their digital DNA–DNA hybridization value was 41.1 %. Based on the overall analyses, strain CjT (=DSM 100623T=CECT 9041T) warrants classification as the type strain of a novel species, for which the name Frankia soli sp. nov. is proposed.
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Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa.
International journal of systematic and evolutionary microbiology, 2018Co-Authors: Philippe Normand, Imen Nouioui, Petar Pujic, Pascale Fournier, Audrey Dubost, Guillaume Schwob, Hans-peter Klenk, Agnès Nguyen, Danis Abrouk, Aude Herrera-belaroussiAbstract:Strain ARgP5T, an actinobacterium isolated from a root nodule present on an Alnus incana subspecies rugosa shrub growing in Quebec City, Canada, was the subject of polyphasic taxonomic studies to clarify its status within the genus Frankia . 16S rRNA gene sequence similarities and ANI values between ARgP5T and type strains of species of the genus Frankia with validly published names were 98.8 and 82 % or less, respectively. The in silico DNA G+C content was 72.4 mol%. ARgP5T is characterised by the presence of meso-A2pm, galactose, glucose, mannose, rhamnose (trace), ribose and xylose as whole-organism hydrolysates; MK-9(H8) as predominant menaquinone; diphosphatidylglycerol, phosphatidylinositol and phosphatidylglycerol as polar lipids and iso-C16 : 0 and C17 : 1ω8c as major fatty acids. The proteomic results confirmed the distinct position of ARgP5T from its closest neighbours in Frankia cluster 1. ARgP5T was found to be infective on two alder (Alnus glutinosa and Alnusalnobetula subsp. crispa) and on one bayberry (Morella pensylvanica) species and to fix nitrogen in symbiosis and in pure culture. On the basis of phylogenetic (16S rRNA gene sequence), genomic, proteomic and phenotypic results, strain ARgP5T (=DSM 45898=CECT 9033) is considered to represent a novel species within the genus Frankia for which the name Frankia canadensis sp. nov., is proposed.
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permanent draft genome sequence of Frankia sp nrrl b 16219 reveals the presence of canonical nod genes which are highly homologous to those detected in candidatus Frankia dg1 genome
Standards in Genomic Sciences, 2017Co-Authors: A. Ktari, Imen Nouioui, Faten Ghodhbanegtari, Teal Furnholm, Erik Swanson, Louis S. TisaAbstract:Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219 is closely related to “Frankia discariae” with a 16S rRNA gene similarity of 99.78%. Because of the lack of genetic tools for Frankia, our understanding of the bacterial signals involved during the plant infection process and the development of actinorhizal root nodules is very limited. Since the first three Frankia genomes were sequenced, additional genome sequences covering more diverse strains have helped provide insight into the depth of the pangenome and attempts to identify bacterial signaling molecules like the rhizobial canonical nod genes. The genome sequence of Frankia sp. strain NRRL B-16219 was generated and assembled into 289 contigs containing 8,032,739 bp with 71.7% GC content. Annotation of the genome identified 6211 protein-coding genes, 561 pseudogenes, 1758 hypothetical proteins and 53 RNA genes including 4 rRNA genes. The NRRL B-16219 draft genome contained genes homologous to the rhizobial common nodulation genes clustered in two areas. The first cluster contains nodACIJH genes whereas the second has nodAB and nodH genes in the upstream region. Phylogenetic analysis shows that Frankia nod genes are more deeply rooted than their sister groups from rhizobia. PCR-sequencing suggested the widespread occurrence of highly homologous nodA and nodB genes in microsymbionts of field collected Ceanothus americanus.
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Frankia coriariae sp nov an infective and effective microsymbiont isolated from coriaria japonica
International Journal of Systematic and Evolutionary Microbiology, 2017Co-Authors: Imen Nouioui, Faten Ghodhbanegtari, Manfred Rohde, Hans-peter KlenkAbstract:The taxonomic description of a nitrogen-fixing actinobacterium, strain BMG5.1T, as a novel species within the genus Frankia was based on a polyphasic approach. The strain was isolated from the root nodules of Coriaria japonica, and it fulfilled Koch’s postulates by inducing effective nodules on Coriaria spp. and Datisca spp. Based on phenotypic and chemotaxonomic features, strain BMG5.1T is distinguishable from all other species of the genus Frankia . It is characterized by the presence of phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol and glycophospholipids in its polar lipids; galactose, glucose, mannose and a trace of ribose as cellular sugars; meso-diaminopimelic acid as cell-wall peptidoglycan; C18 : 1ω9c as major fatty acid (>30 %); and MK-9(H6) (44.7 %) as predominant isoprenolog (>30 %). The 16S rRNA gene sequence similarities and the digital DNA–DNA hybridization values between the described novel strain and strains of the other species of the genus Frankia correspond to a range of 97–98.4 % and 22.1–24 %, respectively. The DNA G+C content is 70.2 mol%. On the basis of these results, strain BMG5.1T (=CECT 9032T=DSM 100624T) is proposed as the type strain of a novel species of the genus Frankia , named Frankia coriariae sp. nov.
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Frankia inefficax sp. nov., an actinobacterial endophyte inducing ineffective, non nitrogen-fixing, root nodules on its actinorhizal host plants
Antonie van Leeuwenhoek, 2017Co-Authors: Imen Nouioui, Louis S. Tisa, Faten Ghodhbane-gtari, Manfred Rohde, Maria Carmen Montero-calasanz, Hans-peter KlenkAbstract:Strain EuI1c^T is the first actinobacterial endophyte isolated from Elaeagnus umbellata that was shown to be infective on members of Elaeagnaceae and Morella but lacking the ability to form effective root nodules on its hosts. The strain can be easily distinguished from strains of other Frankia species based on its inability to produce vesicles, the specialized thick-walled structures where nitrogen fixation occurs. Chemotaxonomically, strain EuI1c^T contains phosphatidylinositol, diphosphatidylglycerol, two glycophospholipids and phosphatidylglycerol as phospholipids. The whole cell sugars were composed of glucose, galactose, mannose, ribose, rhamnose and fucose as diagnostic sugars of the species. Major fatty acids were iso -C_16:0, C_17:1 ω 8c and C_15:0 and C_17:0 and the predominant menaquinones were MK-9(H_6), MK-9(H_8) and MK-9(H_4). Analysis of the 16S rRNA gene sequence of strain EuI1c^T showed 97, 97.4 and 97.9% identity with Frankia elaeagni DSM 46783^T, Frankia casuarinae DSM 45818^T and Frankia alni DSM 45986^T, respectively. Digital DNA:DNA hybridizations with type strains of the three Frankia species with validly/effectively published names are significantly below 70%. These results warrant distinction of EuI1c^T (= DSM 45817^T = CECT 9037^T) as the type strain of a novel species designated Frankia inefficax sp. nov.
Philippe Normand - One of the best experts on this subject based on the ideXlab platform.
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Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa.
International journal of systematic and evolutionary microbiology, 2018Co-Authors: Philippe Normand, Imen Nouioui, Petar Pujic, Pascale Fournier, Audrey Dubost, Guillaume Schwob, Hans-peter Klenk, Agnès Nguyen, Danis Abrouk, Aude Herrera-belaroussiAbstract:Strain ARgP5T, an actinobacterium isolated from a root nodule present on an Alnus incana subspecies rugosa shrub growing in Quebec City, Canada, was the subject of polyphasic taxonomic studies to clarify its status within the genus Frankia . 16S rRNA gene sequence similarities and ANI values between ARgP5T and type strains of species of the genus Frankia with validly published names were 98.8 and 82 % or less, respectively. The in silico DNA G+C content was 72.4 mol%. ARgP5T is characterised by the presence of meso-A2pm, galactose, glucose, mannose, rhamnose (trace), ribose and xylose as whole-organism hydrolysates; MK-9(H8) as predominant menaquinone; diphosphatidylglycerol, phosphatidylinositol and phosphatidylglycerol as polar lipids and iso-C16 : 0 and C17 : 1ω8c as major fatty acids. The proteomic results confirmed the distinct position of ARgP5T from its closest neighbours in Frankia cluster 1. ARgP5T was found to be infective on two alder (Alnus glutinosa and Alnusalnobetula subsp. crispa) and on one bayberry (Morella pensylvanica) species and to fix nitrogen in symbiosis and in pure culture. On the basis of phylogenetic (16S rRNA gene sequence), genomic, proteomic and phenotypic results, strain ARgP5T (=DSM 45898=CECT 9033) is considered to represent a novel species within the genus Frankia for which the name Frankia canadensis sp. nov., is proposed.
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Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of the Order Rhamnales
Genome Announcements, 2016Co-Authors: Imen Nouioui, Philippe Normand, Faten Ghodhbane-gtari, Maria P. Fernandez, Markus Göker, Marcel Huntemann, Alicia Clum, Manoj PillayAbstract:Frankia sp. strain G2 was originally isolated from Casuarina equisetifolia and is characterized by its ability to nodulate actinorhizal plants of the Rhamnales order, but not its original host. It represents one of the largest Frankia genomes so far sequenced (9.5 Mbp).
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Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains
Scientific Reports, 2015Co-Authors: Maher Gtari, Faten Ghodhbane-gtari, Imed Sbissi, I. Nouioui, A. Ktari, K. Hezbri, W. Mimouni, A. Ayari, T. Yamanaka, Philippe NormandAbstract:The repeated failures reported in cultivating some microbial lineages are a major challenge in microbial ecology and probably linked, in the case of Frankia microsymbionts to atypical patterns of auxotrophy. Comparative genomics of the so far uncultured cluster-2 Candidatus Frankia datiscae Dg1, with cultivated Frankiae has revealed genome reduction, but no obvious physiological impairments. A direct physiological assay on nodule tissues from Coriaria myrtifolia infected with a closely-related strain permitted the identification of a requirement for alkaline conditions. A high pH growth medium permitted the recovery of a slow-growing actinobacterium. The strain obtained, called BMG5.1, has short hyphae, produced diazovesicles in nitrogen-free media, and fulfilled Koch's postulates by inducing effective nodules on axenically grown Coriaria spp. and Datisca glomerata. Analysis of the draft genome confirmed its close proximity to the Candidatus Frankia datiscae Dg1 genome with the absence of 38 genes (trehalose synthase, fumarylacetoacetase, etc) in BMG5.1 and the presence of 77 other genes (CRISPR, lanthionine synthase, glutathione synthetase, catalase, Na+/H+ antiporter, etc) not found in Dg1. A multi-gene phylogeny placed the two cluster-2 strains together at the root of the Frankia radiation.
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comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts
BMC Genomics, 2008Co-Authors: Juliana E Mastronunzio, Philippe NormandAbstract:Frankia sp. strains, the nitrogen-fixing facultative endosymbionts of actinorhizal plants, have long been proposed to secrete hydrolytic enzymes such as cellulases, pectinases, and proteases that may contribute to plant root penetration and formation of symbiotic root nodules. These or other secreted proteins might logically be involved in the as yet unknown molecular interactions between Frankia and their host plants. We compared the genome-based secretomes of three Frankia strains representing diverse host specificities. Signal peptide detection algorithms were used to predict the individual secretomes of each strain, and the set of secreted proteins shared among the strains, termed the core Frankia secretome. Proteins in the core secretome may be involved in the actinorhizal symbiosis. The Frankia genomes have conserved Sec (general secretory) and Tat (twin arginine translocase) secretion systems. The potential secretome of each Frankia strain comprised 4–5% of the total proteome, a lower percentage than that found in the genomes of other actinobacteria, legume endosymbionts, and plant pathogens. Hydrolytic enzymes made up only a small fraction of the total number of predicted secreted proteins in each strain. Surprisingly, polysaccharide-degrading enzymes were few in number, especially in strain CcI3, with more esterolytic, lipolytic and proteolytic enzymes having signal peptides. A total of 161 orthologous proteins belong to the core Frankia secretome. Of these, 52 also lack homologs in closely related actinobacteria, and are termed "Frankia- specific." The genes encoding these conserved secreted proteins are often clustered near secretion machinery genes. The predicted secretomes of Frankia sp. are relatively small and include few hydrolases, which could reflect adaptation to a symbiotic lifestyle. There are no well-conserved secreted polysaccharide-degrading enzymes present in all three Frankia genomes, suggesting that plant cell wall polysaccharide degradation may not be crucial to root infection, or that this degradation varies among strains. We hypothesize that the relative lack of secreted polysaccharide-degrading enzymes in Frankia reflects a strategy used by these bacteria to avoid eliciting host defense responses. The esterases, lipases, and proteases found in the core Frankia secretome might facilitate hyphal penetration through the cell wall, release carbon sources, or modify chemical signals. The core secretome also includes extracellular solute-binding proteins and Frankia-specific hypothetical proteins that may enable the actinorhizal symbiosis.
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Differential Frankia protein patterns induced by phenolic extracts from Myricaceae seeds
Physiologia Plantarum, 2007Co-Authors: Emilie Bagnarol, Philippe Normand, Jean Popovici, Nicole Alloisio, Joelle Marechal, Pierre Pujic, Maria FernandezAbstract:Two-dimensional gel electrophoresis was used to identify differentially displayed proteins expressed during the early symbiotic interactions between the bacterium Frankia and actinorhizal plants. Myricaceae, the most primitive actinorhizal family, was used as an experimental model to study specificity mechanisms because it includes species with either narrowor large specificity. Seed phenolic extracts from two Myricaceae species, Myrica gale, a narrow specificity host and Morella cerifera considered as a promiscuous host, were used to induce three Frankia strains ACN14a, M16467 and Ea112. The global protein pattern was altered by exposure to the plant extracts. The addition of 30 mg l21 of seed phenolic extracts provoked the inhibition of many protein biosynthesis whereas 1 and 10 mg l21 induced a global reprogramming of Frankia protein pattern. Changes in intensity of 115 spots in response to seed extracts were detected and analyzed by matrix-assisted laser desorption/ ionization time of flight mass spectrometry. Fifty proteins were efficiently identified with Frankia protein data banks deduced from the sequences of Frankia strains ACN14a and EaN1pec genomes. Differential proteins were involved in different metabolism pathways such as glycolysis and gluconeogenesis, transcription, fatty acids, carbohydrates, coenzymes and purines metabolisms. Chaperones biosynthesis and iron transport regulation, essential for nitrogen fixation, seem to be strain dependant. Several proteins possibly involved in the regulation of nodulation were also differentially expressed. The most obvious response was the upregulation of oxidative stress proteins such as FeSOD and Tellurium resistance proteins, suggesting a reorganization of Frankia metabolism to protect against host plant defense.
