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1. Identification and evolution of nsLTPs in the root nodule nitrogen fixation clade and molecular response of Frankia to AgLTP24

Author: Mélanie Gasser, Jean Keller, Pascale Fournier, Petar Pujic, Philippe Normand, and Hasna Boubakri
Subjects: Medicine, Science
Abstract: Abstract Non-specific lipid transfer proteins (nsLTPs) are antimicrobial peptides, involved in several plant biological processes including root nodule nitrogen fixation (RNF). Nodulating plants belonging to the RNF clade establish symbiosis with the nitrogen-fixing bacteria rhizobia (legumes symbiosis model) and Frankia (actinorhizal symbiosis model) leading to root nodule formation. nsLTPs are involved in processes active in early step of symbiosis and functional nodule in both models. In legumes, nsLTPs have been shown to regulate symbiont entry, promote root cortex infection, membrane biosynthesis, and improve symbiosis efficiency. More recently, a nsLTP, AgLTP24 has been described in the context of actinorhizal symbiosis between Alnus glutinosa and Frankia alni ACN14a. AgLTP24 is secreted at an early step of symbiosis on the deformed root hairs and targets the symbiont in the nitrogen-fixing vesicles in functional nodules. nsLTPs are involved in RNF, but their functions and evolutionary history are still largely unknown. Numerous putative nsLTPs were found up-regulated in functional nodules compared to non-infected roots in different lineages within the RNF clade. Here, results highlight that nodulating plants that are co-evolving with their nitrogen-fixing symbionts appear to have independently specialized nsLTPs for this interaction, suggesting a possible convergence of function, which opens perspectives to investigate nsLTPs functions in RNF.
Published: 2023
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2. A Nonspecific Lipid Transfer Protein with Potential Functions in Infection and Nodulation

Author: Mélanie Gasser, Nicole Alloisio, Pascale Fournier, Severine Balmand, Ons Kharrat, Joris Tulumello, Lorena Carro, Abdelaziz Heddi, Pedro Da Silva, Philippe Normand, Petar Pujic, and Hasna Boubakri
Subjects: Alnus glutinosa, antimicrobial peptide, Frankia, immunity, infection threads, nitrogen fixation, Microbiology, QR1-502, Botany, QK1-989
Abstract: The response of Alnus glutinosa to Frankia alni ACN14a is driven by several sequential physiological events from calcium spiking and root-hair deformation to the development of the nodule. Early stages of actinorhizal symbiosis were monitored at the transcriptional level to observe plant host responses to Frankia alni. Forty-two genes were significantly upregulated in inoculated compared with noninoculated roots. Most of these genes encode proteins involved in biological processes induced during microbial infection, such as oxidative stress or response to stimuli, but a large number of them are not differentially modulated or downregulated later in the process of nodulation. In contrast, several of them remained upregulated in mature nodules, and this included the gene most upregulated, which encodes a nonspecific lipid transfer protein (nsLTP). Classified as an antimicrobial peptide, this nsLTP was immunolocalized on the deformed root-hair surfaces that are points of contact for Frankia spp. during infection. Later in nodules, it binds to the surface of F. alni ACN14a vesicles, which are the specialized cells for nitrogen fixation. This nsLTP, named AgLTP24, was biologically produced in a heterologous host and purified for assay on F. alni ACN14a to identify physiological effects. Thus, the activation of the plant immunity response occurs upon first contact, while the recognition of F. alni ACN14a genes switches off part of the defense system during nodulation. AgLTP24 constitutes a part of the defense system that is maintained all along the symbiosis, with potential functions such as the formation of infection threads or nodule primordia to the control of F. alni proliferation. [Graphic: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Published: 2022
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3. The cadCA and cadB/DX operons are possibly induced in cadmium resistance mechanism by Frankia alni ACN14a

Author: Medhat Rehan, Ahmed Alhusays, Ahmed M. Serag, Hasna Boubakri, Petar Pujic, and Philippe Normand
Subjects: Bioremediation, Cadmium, Cadmium accumulation, Cadmium resistance, Frankia, Gene expression, Biotechnology, TP248.13-248.65, Biology (General), QH301-705.5
Abstract: Background: Cadmium (Cd2+) is one of the highly toxic heavy metals and is considered as a carcinogenic agent. Our aim was to confirm the ability of Frankia alni ACN14a to resist Cd2+ and to determine the genes involved in the resistance mechanism. Results: F. alni ACN14a and Frankia casuarinae CcI3 hyphae showed up to 10 and 22 times Cd2+ accumulation when exposed to 1 mM Cd2+, respectively. Scanning electron microscopy (SEM) exhibited a stable Cd2+ precipitate on the cell surface, and the increase in Cd2+ weight level reached 16.45% when evaluated with SEM-EDAX analysis. The following two potential Cd2+ operons were identified: 1. cadCA operon, which encodes a copper-transporting P-type ATPase A (cadA, FRAAL0989) and an ArsR family regulator (cadC, FRAAL0988), with 37- and 70-fold increase in their expression by qRT-PCR, respectively and 2. cadB/DX, which encodes a putative cobalt-zinc-cadmium resistance protein (cadD, FRAAL3628) and heavy metal-associated domain protein (cadX, FRAAL3626), with 22- and 16-fold upregulation when exposed to Cd2+ stress. Conclusions: Cd2+ tolerance by F. alni ACN14a involved efflux of Cd2+ outside the cells and binding it to the membrane surface. Our results indicate the existence of two cadmium-resistance mechanisms in Frankia strains, which support the idea of using them as a bioremediation agent.How to cite: Rehan M, Alhusays A, Serag AM, et al. The cadCA and cadB/DX operons are possibly induced in cadmium resistance mechanism by Frankia alni ACN14a. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.09.006.
Published: 2022
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4. Frankia alni Carbonic Anhydrase Regulates Cytoplasmic pH of Nitrogen-Fixing Vesicles

Author: Petar Pujic, Lorena Carro, Pascale Fournier, Jean Armengaud, Guylaine Miotello, Nathalie Dumont, Caroline Bourgeois, Xavier Saupin, Patrick Jame, Gabriela Vuletin Selak, Nicole Alloisio, and Philippe Normand
Subjects: homeostasis, acidity, symbiosis, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract: A phyloprofile of Frankia genomes was carried out to identify those genes present in symbiotic strains of clusters 1, 1c, 2 and 3 and absent in non-infective strains of cluster 4. At a threshold of 50% AA identity, 108 genes were retrieved. Among these were known symbiosis-associated genes such as nif (nitrogenase), and genes which are not know as symbiosis-associated genes such as can (carbonic anhydrase, CAN). The role of CAN, which supplies carbonate ions necessary for carboxylases and acidifies the cytoplasm, was thus analyzed by staining cells with pH-responsive dyes; assaying for CO2 levels in N-fixing propionate-fed cells (that require a propionate-CoA carboxylase to yield succinate-CoA), fumarate-fed cells and N-replete propionate-fed cells; conducting proteomics on N-fixing fumarate and propionate-fed cells and direct measurement of organic acids in nodules and in roots. The interiors of both in vitro and nodular vesicles were found to be at a lower pH than that of hyphae. CO2 levels in N2-fixing propionate-fed cultures were lower than in N-replete ones. Proteomics of propionate-fed cells showed carbamoyl-phosphate synthase (CPS) as the most overabundant enzyme relative to fumarate-fed cells. CPS combines carbonate and ammonium in the first step of the citrulline pathway, something which would help manage acidity and NH4+. Nodules were found to have sizeable amounts of pyruvate and acetate in addition to TCA intermediates. This points to CAN reducing the vesicles’ pH to prevent the escape of NH3 and to control ammonium assimilation by GS and GOGAT, two enzymes that work in different ways in vesicles and hyphae. Genes with related functions (carboxylases, biotin operon and citrulline-aspartate ligase) appear to have undergone decay in non-symbiotic lineages.
Published: 2023
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5. Microbial risk assessment of Nocardia cyriacigeorgica in polluted environments, case of urban rainfall water

Author: Florian Vautrin, Petar Pujic, Christian Paquet, Emmanuelle Bergeron, Delphine Mouniée, Thierry Marchal, Hélène Salord, Jeanne-Marie Bonnet, Benoit Cournoyer, Thierry Winiarski, Vanessa Louzier, and Veronica Rodriguez-Nava
Subjects: Nocardia, Opportunistic pathogen, Environment, Murine model of transient immunoparalysis, Urban pollution, Hsp65 metabarcoding, Biotechnology, TP248.13-248.65
Abstract: Urban Infiltration Basins (UIBs) are used to manage urban runoff transfers and feed aquifers. These UIBs can accumulate urban pollutants and favor the growth of potentially pathogenic biological agents as Nocardia. Objectives: To assess the spatio-temporal dynamics of pathogenic Nocardia in UIBs and to stablish phylogenetic relationships between clinical and UIB N. cyriacigeorgica strains. To assess pathogenicity associated with environmental N. cyriacigeorgica using an animal model, and to identify genetic elements that may be associated to its virulence. Methods: A well-characterized UIB in terms of chemical pollutants from Lyon area was used in this study during a whole year. Cultural and Next-Generation-Sequencing methods were used for Nocardia detection and typing. Clinical and environmental isolates phylogenetic relationships and virulences were compared with Multilocus-Sequence-Analysis study together with a murine model. Results: In autumn, N. cyriacigeorgica and N. nova were the pathogenic most prevalent species in the UIB. The complex N. abscessus/asiatica was also detected together with some other non-pathogenic species. The presence of pathogenic Nocardia was positively correlated to metallic trace elements. Up to 1.0 × 103 CFU/g sediment of N. cyriacigeorgica and 6 OTUs splited in two different phylogroups were retrieved and were close to clinical strains. The EML446 tested UIB isolate showed significant infectivity in mice with pulmonary damages similar to clinical clone (GUH-2). Conclusion: Hsp65 marker-based metabarcoding approach allowed detecting N. cyriacigeogica as the most abundant Nocardia pathogenic species in a UIB. Metal trace elements-polluted environments can be reservoirs of pathogenic Nocardia which may have a similar virulence to clinical strains.
Published: 2021
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6. Correction: Pujic et al. The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules. Microorganisms 2022, 10, 651

Author: Petar Pujic, Nicole Alloisio, Guylaine Miotello, Jean Armengaud, Danis Abrouk, Pascale Fournier, and Philippe Normand
Subjects: n/a, Biology (General), QH301-705.5
Abstract: The authors wish to make the following corrections to this paper [...]
Published: 2022
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7. Pseudomonas ST1 and Pantoea Paga Strains Cohabit in Olive Knots

Author: Gabriela Vuletin Selak, Marina Raboteg Božiković, Danis Abrouk, Marija Bolčić, Katja Žanić, Slavko Perica, Philippe Normand, and Petar Pujic
Subjects: host pathogen interaction, Pseudomonas ST1, Pantoea paga, galls, Olea europaea L., plant microbiome, Biology (General), QH301-705.5
Abstract: Two bacteria belonging to the Pseudomonas and Pantoea genera were isolated from olive knots. Both bacterial strains were omnipresent in this study’s olive orchard with high susceptibility of the autochthonous olive genotypes indicating coevolution of bacteria with host plants. Genomes of two endemic bacteria show conserved core genomes and genome plasticity. The Pseudomonas ST1 genome has conserved virulence-related genes including genes for quorum sensing, pilus, and flagella biosynthesis, two copies of indole acetic acid biosynthesis (IAA) operons, type I-VI secretions systems, and genes for alginate and levan biosynthesis. Development of knots depends only on the presence of the Pseudomonas ST1 strain which then allows Pantoea paga strain co-infection and cohabitation in developed knots. The two bacteria are sensitive to a large number of antimicrobials, antibiotics, H2O2, and Cu (II) salts that can be efficiently used in propagation of bacterial free olive cultivars.
Published: 2022
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8. The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules

Author: Petar Pujic, Nicole Alloisio, Guylaine Miotello, Jean Armengaud, Danis Abrouk, Pascale Fournier, and Philippe Normand
Subjects: omics, nitrogenase, hopanoids, actinorhizae, Biology (General), QH301-705.5
Abstract: Omics are the most promising approaches to investigate microbes for which no genetic tools exist such as the nitrogen-fixing symbiotic Frankia. A proteogenomic analysis of symbiotic Frankia alni was done by comparing those proteins more and less abundant in Alnus glutinosa nodules relative to N-replete pure cultures with propionate as the carbon source and ammonium as the nitrogen-source. There were 250 proteins that were significantly overabundant in nodules at a fold change (FC) ≥ 2 threshold, and 1429 with the same characteristics in in vitro nitrogen-replete pure culture. Nitrogenase, SuF (Fe–Su biogenesis) and hopanoid lipids synthesis determinants were the most overabundant proteins in symbiosis. Nitrogenase was found to constitute 3% of all Frankia proteins in nodules. Sod (superoxide dismutase) was overabundant, indicating a continued oxidative stress, while Kats (catalase) were not. Several transporters were overabundant including one for dicarboxylates and one for branched amino acids. The present results confirm the centrality of nitrogenase in the actinorhizal symbiosis.
Published: 2022
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9. Seed Paternity Analysis Using SSR Markers to Assess Successful Pollen Donors in Mixed Olive Orchards

Author: Gabriela Vuletin Selak, Alenka Baruca Arbeiter, Julián Cuevas, Slavko Perica, Petar Pujic, Marina Raboteg Božiković, and Dunja Bandelj
Subjects: Olea europaea L., cultivar ‘Oblica’, microsatellites, seed paternity assignment, cross-compatibility, self-incompatibility, Botany, QK1-989
Abstract: The olive tree (Olea europaea L.) is a wind-pollinated crop that exhibits an extreme alternate bearing habit. To improve fruit set, several methods have been used to determine the most successful compatible combinations of cultivars. In this study, priority is given to seed paternity analysis based on simple sequence repeats (SSRs), microsatellite markers used for the identification of potential pollen donors of cultivar ‘Oblica’ in a mixed olive orchard during two consecutive years. Seven microsatellite primers were successfully used to examine the paternity of olive embryos from ‘Oblica’ mother trees. Embryos were considered as a product of self-fertilization if only maternal alleles were present, but not a single case of self-fertilization was found among all the embryos analyzed. Two dominant pollen donors were not the closest nor the cultivars with the highest number of trees in the orchard, suggesting that cross-compatibility may have a key role in determining pollen donor success. In our earlier studies, pollen tube growth and fertilization success correlated with fruit set when controlled crosses between cultivars were performed; however, some discrepancy might appear compared to paternity analyses when mother trees have a free choice among different pollen sources from cultivars growing in their surroundings.
Published: 2021
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10. Actinorhizal Signaling Molecules: Frankia Root Hair Deforming Factor Shares Properties With NIN Inducing Factor

Author: Maimouna Cissoko, Valérie Hocher, Hassen Gherbi, Djamel Gully, Alyssa Carré-Mlouka, Seyni Sane, Sarah Pignoly, Antony Champion, Mariama Ngom, Petar Pujic, Pascale Fournier, Maher Gtari, Erik Swanson, Céline Pesce, Louis S. Tisa, Mame Oureye Sy, and Sergio Svistoonoff
Subjects: symbioses, nodulation factors, nodule inception, Casuarina, Alnus, Discaria, Plant culture, SB1-1110
Abstract: Actinorhizal plants are able to establish a symbiotic relationship with Frankia bacteria leading to the formation of root nodules. The symbiotic interaction starts with the exchange of symbiotic signals in the soil between the plant and the bacteria. This molecular dialog involves signaling molecules that are responsible for the specific recognition of the plant host and its endosymbiont. Here we studied two factors potentially involved in signaling between Frankia casuarinae and its actinorhizal host Casuarina glauca: (1) the Root Hair Deforming Factor (CgRHDF) detected using a test based on the characteristic deformation of C. glauca root hairs inoculated with F. casuarinae and (2) a NIN activating factor (CgNINA) which is able to activate the expression of CgNIN, a symbiotic gene expressed during preinfection stages of root hair development. We showed that CgRHDF and CgNINA corresponded to small thermoresistant molecules. Both factors were also hydrophilic and resistant to a chitinase digestion indicating structural differences from rhizobial Nod factors (NFs) or mycorrhizal Myc-LCOs. We also investigated the presence of CgNINA and CgRHDF in 16 Frankia strains representative of Frankia diversity. High levels of root hair deformation (RHD) and activation of ProCgNIN were detected for Casuarina-infective strains from clade Ic and closely related strains from clade Ia unable to nodulate C. glauca. Lower levels were present for distantly related strains belonging to clade III. No CgRHDF or CgNINA could be detected for Frankia coriariae (Clade II) or for uninfective strains from clade IV.
Published: 2018
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11. Virulence test using nematodes to prescreen Nocardia species capable of inducing neurodegeneration and behavioral disorders

Author: Claire Bernardin Souibgui, Anthony Zoropogui, Jeremy Voisin, Sebastien Ribun, Valentin Vasselon, Petar Pujic, Veronica Rodriguez-Nava, Patrick Belly, Benoit Cournoyer, and Didier Blaha
Subjects: Nocardia, C. elegans, Parkinson’s symptoms, Neuronal apoptosis, Rapid virulence test, Medicine, Biology (General), QH301-705.5
Abstract: Background Parkinson’s disease (PD) is a disorder characterized by dopaminergic neuron programmed cell death. The etiology of PD remains uncertain—some cases are due to selected genes associated with familial heredity, others are due to environmental exposure to toxic components, but over 90% of cases have a sporadic origin. Nocardia are Actinobacteria that can cause human diseases like nocardiosis. This illness can lead to lung infection or central nervous system (CNS) invasion in both immunocompromised and immunocompetent individuals. The main species involved in CNS are N. farcinica, N. nova, N. brasiliensis and N. cyriacigeorgica. Some studies have highlighted the ability of N. cyriacigeorgica to induce Parkinson’s disease-like symptoms in animals. Actinobacteria are known to produce a large variety of secondary metabolites, some of which can be neurotoxic. We hypothesized that neurotoxic secondary metabolite production and the onset of PD-like symptoms in animals could be linked. Methods Here we used a method to screen bacteria that could induce dopaminergic neurodegeneration before performing mouse experiments. Results The nematode Caenorhabditis elegans allowed us to demonstrate that Nocardia strains belonging to N. cyriacigeorgica and N. farcinica species can induce dopaminergic neurodegeneration. Strains of interest involved with the nematodes in neurodegenerative disorders were then injected in mice. Infected mice had behavioral disorders that may be related to neuronal damage, thus confirming the ability of Nocardia strains to induce neurodegeneration. These behavioral disorders were induced by N. cyriacigeorgica species (N. cyriacigeorgica GUH-2 and N. cyriacigeorgica 44484) and N. farcinica 10152. Discussion We conclude that C. elegans is a good model for detecting Nocardia strains involved in neurodegeneration. This model allowed us to detect bacteria with high neurodegenerative effects and which should be studied in mice to characterize the induced behavioral disorders and bacterial dissemination.
Published: 2017
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12. The Frankia alni Symbiotic Transcriptome

Author: Nicole Alloisio, Clothilde Queiroux, Pascale Fournier, Petar Pujic, Philippe Normand, David Vallenet, Claudine Médigue, Masatoshi Yamaura, Kentaro Kakoi, and Ken-ichi Kucho
Subjects: Microbiology, QR1-502, Botany, QK1-989
Abstract: The actinobacteria Frankia spp. are able to induce the formation of nodules on the roots of a large spectrum of actinorhizal plants, where they convert dinitrogen to ammonia in exchange for plant photosynthates. In the present study, transcriptional analyses were performed on nitrogen-replete free-living Frankia alni cells and on Alnus glutinosa nodule bacteria, using whole-genome microarrays. Distribution of nodule-induced genes on the genome was found to be mostly over regions with high synteny between three Frankia spp. genomes, while nodule-repressed genes, which were mostly hypothetical and not conserved, were spread around the genome. Genes known to be related to nitrogen fixation were highly induced, nif (nitrogenase), hup2 (hydrogenase uptake), suf (sulfur-iron cluster), and shc (hopanoids synthesis). The expression of genes involved in ammonium assimilation and transport was strongly modified, suggesting that bacteria ammonium assimilation was limited. Genes involved in particular in transcriptional regulation, signaling processes, protein drug export, protein secretion, lipopolysaccharide, and peptidoglycan biosynthesis that may play a role in symbiosis were also identified. We also showed that this Frankia symbiotic transcriptome was highly similar among phylogenetically distant plant families Betulaceae and Myricaceae. Finally, comparison with rhizobia transcriptome suggested that F. alni is metabolically more active in symbiosis than rhizobia.
Published: 2010
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13. Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant.

Author: Tomas Persson, Kai Battenberg, Irina V Demina, Theoden Vigil-Stenman, Brian Vanden Heuvel, Petar Pujic, Marc T Facciotti, Elizabeth G Wilbanks, Anna O'Brien, Pascale Fournier, Maria Antonia Cruz Hernandez, Alberto Mendoza Herrera, Claudine Médigue, Philippe Normand, Katharina Pawlowski, and Alison M Berry
Subjects: Medicine, Science
Abstract: 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 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 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 D. 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 α- and β-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.
Published: 2015
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14. Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style?

Author: Martha E Trujillo, Rodrigo Bacigalupe, Petar Pujic, Yasuhiro Igarashi, Patricia Benito, Raúl Riesco, Claudine Médigue, and Philippe Normand
Subjects: Medicine, Science
Abstract: Endophytic microorganisms live inside plants for at least part of their life cycle. According to their life strategies, bacterial endophytes can be classified as "obligate" or "facultative". Reports that members of the genus Micromonospora, Gram-positive Actinobacteria, are normal occupants of nitrogen-fixing nodules has opened up a question as to what is the ecological role of these bacteria in interactions with nitrogen-fixing plants and whether it is in a process of adaptation from a terrestrial to a facultative endophytic life. The aim of this work was to analyse the genome sequence of Micromonospora lupini Lupac 08 isolated from a nitrogen fixing nodule of the legume Lupinus angustifolius and to identify genomic traits that provide information on this new plant-microbe interaction. The genome of M. lupini contains a diverse array of genes that may help its survival in soil or in plant tissues, while the high number of putative plant degrading enzyme genes identified is quite surprising since this bacterium is not considered a plant-pathogen. Functionality of several of these genes was demonstrated in vitro, showing that Lupac 08 degraded carboxymethylcellulose, starch and xylan. In addition, the production of chitinases detected in vitro, indicates that strain Lupac 08 may also confer protection to the plant. Micromonospora species appears as new candidates in plant-microbe interactions with an important potential in agriculture and biotechnology. The current data strongly suggests that a beneficial effect is produced on the host-plant.
Published: 2014
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15. Draft Genomes of Frankia strains AiPa1 and AiPs1 Retrieved from Soil with Monocultures of Picea abies or Pinus sylvestris using Alnus incana as Capture Plant

Author: Philippe Normand, Petar Pujic, Danis Abrouk, Spandana Vemulapally, Trina Guerra, Camila Carlos-Shanley, and Dittmar Hahn
Published: 2023

16. Structure of surface polysaccharides affects symbiotic nitrogen fixation in Frankia alni ACN14a

Author: Ken-Ichi Kucho, Masahito Hashimoto, Philippe Normand, Pascale Fournier, and Petar Pujic
Subjects: Forestry
Abstract: Frankia spp. are nitrogen-fixing actinobacteria that establish root-nodule symbiosis with actinorhizal plants comprising more than 200 species in eight dicotyledonous families. From a cell population of Frankia alni strain ACN14a that had been subcultured for over 30 years, we identified two types of variants (types A and S) with a different colony appearance. Type A variants exhibited ambiguous, and type S variants exhibited sharp colony edges. The two types differed in molecular weight and monosaccharide composition of cell surface polysaccharides, which could be responsible for the differences in colony appearance. When inoculated to a host plant Alnus glutinosa, both types induced nodulation but plants infected with type S isolates showed much lower nitrogen fixation activity than those infected with type A isolates. Indeed, type S isolates developed fewer vesicles inside infected plant cells. These results suggest that surface polysaccharides of Frankia play important roles in symbiotic interactions with actinorhizal plants.
Published: 2022

17. Comparative Phylogenomics and Phylotranscriptomics Provide Insights into the Genetic Complexity of Nitrogen Fixing Root Nodule Symbiosis

Author: Yu Zhang, Yuan Fu, Wenfei Xian, Xiuli Li, Yong Feng, Fengjiao Bu, Yan Shi, Shiyu Chen, Robin van Velzen, Alison M. Berry, Marco G. Salgado, Hui Liu, Tingshuang Yi, Pascale Fournier, Nicole Alloisio, Petar Pujic, Hasna Boubakri, M. Eric Schranz, Pierre-Marc Delaux, Gane Ka-shu Wong, Valerie Hocher, Sergio Svistoonoff, Hassen Gherbi, Ertao Wang, Wouter Kohlen, Luis G. Wall, Martin Parniske, Katharina Pawlowski, Normand Philippe, Jeffrey J. Doyle, and Shifeng Cheng
Abstract: Plant root nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. It is widely accepted that nodulation originated through the assembly of modules recruited from existing functions, such as mycorrhizal symbiosis, polar growth, and lateral root development. Because nodulating species are scattered within the NFNC, the number of times nodulation has evolved or has been lost has been a matter of considerable speculation. This interesting evolutionary question has practical implications concerning the ease with which nodulation might be engineered in non-nodulating crop plants. Nodulating species share many commonalities, due either to divergence from a common ancestor over 100 million years ago or to convergence or deep homology following independent origins over that same time period. In either case, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation—what must be acquired or cannot be lost for a functional symbiosis—and what the latitude is for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here we present new information across the spectrum of nodulating groups. We find no evidence for convergence at the level of amino acid residues or gene family expansion across the NFNC. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor, NIN, as a master regulator of nodulation, and identify key mutations affecting its function across the NFNC. We find that nodulation genes are over-represented among orthologous gene groups (OGs) present in the NFNC common ancestor, but that lineage-specific OGs play major roles in nodulation. We identified over 900,000 conserved noncoding elements (CNEs), of which over 300,000 were unique to NFNC species. A significant proportion of these are associated with nodulation-related genes and thus are candidates for transcriptional regulators.
Published: 2023

18. Roots of the xerophyte Panicum turgidum host a cohort of ionizing-radiation-resistant biotechnologically-valuable bacteria

Author: Haïtham Sghaier, Rania Ouertani, Sihem Guesmi, Afef Najjari, Kais Ghedira, Ameur Cherif, Marwa Jabberi, Philippe Normand, Petar Pujic, National Institute of Agronomy, Tunis,Tunisia, Centre National des Sciences et Technologies Nucléaires [Tunisie] (CNSTN), Université de Tunis El Manar (UTM), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP), Université de la Manouba [Tunisie] (UMA), and Université de Carthage - University of Carthage
Subjects: QH301-705.5, Panicum turgidum, Metataxonomic, Radioresistant, Biology, Dessiccation, Ionizing radiation, 03 medical and health sciences, Xerophyte, métataxonomique, Botany, Desiccation, Biology (General), Radiorésistant, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Profils métaboliques, 030306 microbiology, Host (biology), Approche culturelle, Culture approach, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Panicum turgide, Metabolic profiles, Cohort, General Agricultural and Biological Sciences, Bacteria
Abstract: International audience; Les communautés bactériennes associées aux racines dePanicum turgide, exposés à des conditions arides, ont été investis-associée à une combinaison d'approches culturelles et métataxonomiques. Technologie traditionnelle basée sur la culture-ont été utilisées et 32 isolats de racines irradiées ont été identifiés comme appartenant àActinobactéries, Bacteroidetes, Firmicutes et Proteobacteria embranchements. Quatre souches actinobactériennes ont étéRésistant aux rayonnements ionisants (IR) :Microbactériesp. PT8 (4,8 kGy (kGy)),Microcoquesp.PT11 (4,4 kGy),Kocuria rhizophilaPT10 (2,9 kGy) etPromicromonospora paniciPT9T(2,6 kGy), basésur le Ddixdose nécessaire pour une réduction de 90 % des unités formant colonies (UFC). Concernant l'enquêtedes communautés microbiennesin situ, analyses métataxonomiques de la diversité des microorganismes résistants aux IRassociée aux racines irradiées a révélé une dominance marquée des Actinobactéries (46,6%) etProtéobactéries (31,5%) par rapport aux Bacteroidetes (4,6%) et Firmicutes (3,2%). Irradiation gamma nonn'ont fait que modifier la structure des communautés bactériennes, mais ont également affecté leurs propriétés fonctionnelles.Des analyses comparatives des profils métaboliques ont indiqué l'induction de plusieurs voies liées à l'adaptation.au stress oxydatif dans les racines irradiées, comme la réparation de l'ADN, la synthèse de métabolites secondaires, la réactionenzymes atténuant les espèces oxygénées (ROS),etc. P. turgidumest emblématique des plantes adaptées au désert.Jusqu'à présent, aucun autre travail n'a porté sur le profil microbien des racines irradiées de cexérophyte.
Published: 2022

19. Draft Genomes of Symbiotic Frankia Strains AgB32 and AgKG'84/4 from Root Nodules of Alnus Glutinosa growing under Contrasted Environmental Conditions

Author: Philippe Normand, Petar Pujic, Danis Abrouk, Spandana Vemulapally, Trina Guerra, Camila Carlos-Shanley, and Dittmar Hahn
Published: 2022

20. Draft Genomes of Nitrogen-fixing Frankia Strains Ag45/Mut15 and AgPM24 Isolated from Root Nodules of Alnus Glutinosa

Author: Philippe Normand, Petar Pujic, Danis Abrouk, Spandana Vemulapally, Trina Guerra, Camila Carlos-Shanley, and Dittmar Hahn
Published: 2022

21. Draft Genome of Frankia sp. Strain R82, an Isolate from Root Nodules of Myrica gale

Author: Philippe Normand, Petar Pujic, Danis Abrouk, Spandana Vemulapally, Trina Guerra, Camila Carlos-Shanley, and Dittmar Hahn
Subjects: Immunology and Microbiology (miscellaneous), Genetics, Molecular Biology
Abstract: The Frankia sp. strain R82 genome is described as representative of a novel candidate species within Frankia cluster 1, as indicated by average nucleotide identity (ANI) analyses, with its closest relatives being Frankia nodulisporulans AgTrs and strains Ag45/Mut15 and AgPM24 (86% identity).
Published: 2022

22. A non specific Lipid Transfer Protein with potential functions in infection and nodulation

Author: Mélanie Gasser, Nicole Alloisio, Pascale Fournier, Severine Balmand, Ons Kharrat, Joris Tulumello, Lorena Carro, Abdelaziz Heddi, Pedro Da Silva, Philippe Normand, Petar Pujic, Hasna Boubakri, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université de Lyon, Unité de recherche Génétique Microbienne (UGM), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Physiology, Nitrogen Fixation, [SDV]Life Sciences [q-bio], Frankia, General Medicine, Symbiosis, Plant Roots, Agronomy and Crop Science
Abstract: The response of Alnus glutinosa to Frankia alni ACN14a is driven by several sequential physiological events from calcium spiking and root-hair deformation to the development of the nodule. Early stages of actinorhizal symbiosis were monitored at the transcriptional level to observe plant host responses to Frankia alni. Forty-two genes were significantly upregulated in inoculated compared with noninoculated roots. Most of these genes encode proteins involved in biological processes induced during microbial infection, such as oxidative stress or response to stimuli, but a large number of them are not differentially modulated or downregulated later in the process of nodulation. In contrast, several of them remained upregulated in mature nodules, and this included the gene most upregulated, which encodes a nonspecific lipid transfer protein (nsLTP). Classified as an antimicrobial peptide, this nsLTP was immunolocalized on the deformed root-hair surfaces that are points of contact for Frankia spp. during infection. Later in nodules, it binds to the surface of F. alni ACN14a vesicles, which are the specialized cells for nitrogen fixation. This nsLTP, named AgLTP24, was biologically produced in a heterologous host and purified for assay on F. alni ACN14a to identify physiological effects. Thus, the activation of the plant immunity response occurs upon first contact, while the recognition of F. alni ACN14a genes switches off part of the defense system during nodulation. AgLTP24 constitutes a part of the defense system that is maintained all along the symbiosis, with potential functions such as the formation of infection threads or nodule primordia to the control of F. alni proliferation. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Published: 2022

23. Draft Genomes of

Author: Philippe, Normand, Petar, Pujic, Danis, Abrouk, Spandana, Vemulapally, Trina, Guerra, Camila, Carlos-Shanley, and Dittmar, Hahn
Abstract: The genomes of two nitrogen-fixing
Published: 2022

24. The non-specific Lipid Transfer Protein (nsLTP) is involved at early and late stages of symbiosis between Alnus glutinosa and Frankia alni

Author: Melanie Gasser, Séverine Balmand, Aziz Heddi, Petar Pujic, Pascale Fournier, Philippe Normand, Ons Kharrat, Hasna Boubakri, Joris Tulumello, Nicole Alloisio, and Pedro Da Silva
Subjects: Frankia alni, Alnus glutinosa, biology, Symbiosis, Frankia, Primordium, Root hair, biology.organism_classification, Plant lipid transfer proteins, Fold change, Cell biology
Abstract: SummaryAlnus glutinosa response to Frankia alni is driven by several sequential physiological modifications that include calcium spiking, root hair deformation, penetration, induction of primordium, formation and growth of nodule. Here, we have conducted a transcriptomic study to analyse plant responses to Frankia alni at early stages of symbiosis establishment.Forty-two genes were significantly activated by either with a Frankia culture supernatant or with living cells separated from the roots by a dialysis membrane permitted to identify plant genes which expression changes upon early contact with Frankia. Most of these genes encode biological processes, including oxidative stress and response to stimuli. The most upregulated gene is the non-specific lipid transfer protein (nsLTP) encoding gene with a fold change of 141. Physiological experiments showed that nsLTP increases Frankia nitrogen fixation at sub-lethal concentration. Immunohistochemistry experiments conducted at an early infection stage indicated that nsLTP protein is localized at the deformed root hair region after Frankia inoculation and later in nodules, precisely around bacterial vesicles. Taken together, these results suggest that nsLTP acts at early and late stages of symbiosis, probably by increasing nitrogen uptake by Frankia.
Published: 2021

25. Draft genome sequence of Promicromonospora panici sp. nov., a novel ionizing-radiation-resistant actinobacterium isolated from roots of the desert plant Panicum turgidum

Author: Imen Nouioui, Petar Pujic, Hans-Peter Klenk, Haïtham Sghaier, Kais Ghedira, Sihem Guesmi, Philippe Normand, Audrey Dubost, Ameur Cherif, José Mariano Igual, Afef Najjari, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universite Lyon 1, CNRS UMR 5557, Ecologie Microbienne (France), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), Institut National Agronomique de Tunisie (INAT), Centre National des Sciences et Technologies Nucléaires [Tunisie] (CNSTN), Newcastle University [Newcastle], Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Université de Tunis El Manar (UTM), Laboratoire de Bioinformatique, biomathématiques, biostatistiques (BIMS) (LR11IPT09), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Université de Tunis El Manar (UTM), Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA), Spanish National Research Council (CSIC), Université de la Manouba [Tunisie] (UMA), This work was performed under the auspices of Université Lyon 1, CNRS UMR 5557, Écologie Microbienne (France) and the National Center for Nuclear Sciences and Technology CNSTN (Tunisia) and in the ambit of the BIODESERT research program of the LR11-ES31 (BVBGR, ISBST, University of Manouba). The LABGeM (CEA/Genoscope & CNRS UMR8030), the France Génomique and French Bioinformatics Institute national infrastructures (funded as part of Investissement d'Avenir program managed by Agence Nationale pour la Recherche, contracts ANR-10-INBS-09 and ANR-11-INBS-0013) are acknowledged for support within the MicroScope annotation platform., Igual, José Mariano [0000-0002-5080-0378], and Igual, José Mariano
Subjects: DNA, Bacterial, food.ingredient, Tunisia, Hypha, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Panicum, Microbiology, Genome, Plant Roots, Ionizing-radiation resistant, 03 medical and health sciences, food, Microbial ecology, Promicromonospora panici, RNA, Ribosomal, 16S, Radiation, Ionizing, Botany, Promicromonospora, Phylogeny, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Base Composition, 030306 microbiology, Strain (biology), Fatty Acids, Nucleic Acid Hybridization, General Medicine, Sequence Analysis, DNA, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Ksar Ghilane oasis, Bacterial Typing Techniques, Actinobacteria, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Oxidative stress, Panicum turgidum, Genome sequence, Molecular Medicine, Microbial genetics, Polyphasic taxonomy, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: 4 tablas y 4 figuras., A novel strain of the genus Promicromonospora, designated PT9T, was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9T is aerobic, non-spore-forming, Gram- positive actinomycete that produces branched hyphae and forms white to yellowish-white colonies. Chemotaxonomic features, including fatty acids, whole cell sugars and polar lipid profles, support the assignment of PT9T to the genus Promicromonospora. The genomic relatedness indexes based on DNA-DNA hybridization and average nucleotide identity values revealed a signifcant genomic divergence between strain PT9T and all sequenced type strains of the taxon. Phylogenomic analysis showed that isolate PT9T was most closely related to Promicromonospora soli CGMCC 4.7398T. Phenotypic and phylogenomic analyses suggest that isolate PT9T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora panici sp. nov. is proposed. The type strain is PT9T (LMG 31103T= DSM 108613T).The isolate PT9T is an ionizing-radiation-resistant actinobacterium (D10 value=2.6 kGy), with resistance to desiccation and hydrogen peroxide. The complete genome sequence of PT9T consists of 6,582,650 bps with 71.2% G+C content and 6291 protein-coding sequences. This genome will help to decipher the microbial genetic bases for ionizing-radiation resistance mechanisms including the response to oxidative stress., This work was performed under the auspices of Université Lyon 1, CNRS UMR 5557, Écologie Microbienne (France) and the National Center for Nuclear Sciences and Technology CNSTN (Tunisia) and in the ambit of the BIODESERT research program of the LR11-ES31 (BVBGR, ISBST, University of Manouba). The LABGeM (CEA/Genoscope & CNRS UMR8030), the France Génomique and French Bioinformatics Institute national infrastructures (funded as part of Investissement d'Avenir program managed by Agence Nationale pour la Recherche, contracts ANR-10-INBS-09 and ANR-11-INBS-0013) are acknowledged for support within them MicroScope annotation platform.
Published: 2021

26. Ionizing-radiation-resistant Kocuria rhizophila PT10 isolated from the Tunisian Sahara xerophyte Panicum turgidum: Polyphasic characterization and proteogenomic arsenal

Author: Ameur Cherif, Haïtham Sghaier, Guylaine Miotello, Afef Najjari, Jean Armengaud, Kais Ghedira, Sihem Guesmi, José Mariano Igual, Phillippe Normand, Hans-Peter Klenk, Audrey Dubost, Petar Pujic, Imen Nouioui, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universite Lyon 1 UMR 5557Ecologie Microbienne (France) National Center for Nuclear Sciences and Technologies CNSTN (MESRS, Tunisia) BIODESERT research program (BVBGR, ISBST, University of Manouba (MESRS, Tunisia) LR11-ES31LABGeM (CEA/Genoscope CNRS) UMR8030, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), Université de Lyon, Igual, José Mariano [0000-0002-5080-0378], and Igual, José Mariano
Subjects: 0106 biological sciences, Ionizing radiation, Kocuria rhizophila, In silico, Panicum turgidum, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Panicum, 01 natural sciences, Genome, Radiation Tolerance, Ionizing radiations, Microbiology, 03 medical and health sciences, Xerophyte, Bacterial Proteins, Genetics, Desiccation, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Secondary metabolites, biology.organism_classification, Oxidative stres, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Gamma Rays, Genes, Bacterial, Oxidative stress, Proteome, 010606 plant biology & botany, Micrococcaceae
Abstract: 14 páginas, 5 tablas, 4 figuras, A new strain belonging to the genus Kocuria, designed PT10, was isolated from irradiated roots of the xerophyte Panicum turgidum. Isolate PT10 is a Gram-positive, coccoid, aerobic and ionizing-radiation (IR)-resistant acti-nobacterium. PT10 has shown an ability to survive under extreme conditions, such as gamma irradiation, desiccation and high concentration of hydrogen peroxide. Phenotypic, chemotaxonomic and comparative genome analyses support the assignment of strain PT10 (LMG 31102 =DSM 108617) as Kocuria rhizophila. The complete genome sequence of PT10 consists of one chromosome (2,656,287 bps), with a 70.7% G +C content and comprises 2481 protein-coding sequences. A total of 1487 proteins were identified by LC-MS/MS profiling. In silico analyses revealed that the proteome of the oxidation-tolerant PT10 possesses several features explaining its IR-resistant phenotype and many adaptive pathways implicated in response to environmental pressures — desiccation, cold, reactive oxygen species and other stressors., This work was performed under the auspices of Université Lyon 1, UMR 5557, Ecologie Microbienne (France) and the National Center for Nuclear Sciences and Technologies CNSTN (MESRS, Tunisia) and in the ambit of the BIODESERT research program of the LR11-ES31 (BVBGR, ISBST, University of Manouba (MESRS, Tunisia). The LABGeM (CEA/ Genoscope & CNRS UMR8030), the France G ́enomique and French Bioinformatics Institute national infrastructures (funded as part of Investissement d’Avenir program managed by Agence Nationale pour la Recherche, contracts ANR-10-INBS-09 and ANR-11-INBS-0013) are acknowledged for support within the MicroScope annotation platform. We thank Betty Bigai, Corinne Sannaire and platform Genomique Environnementale PGE, UMR CNRS 5557 for technical support
Published: 2021

27. Roots of the xerophyte

Author: Sihem, Guesmi, Afef, Najjari, Petar, Pujic, Kais, Ghedira, Rania, Ouertani, Marwa, Jabberi, Ameur, Cherif, Philippe, Normand, and Haïtham, Sghaier
Abstract: Bacterial communities associated with roots of
Published: 2020

28. Microbial risk assessment of

Author: Florian, Vautrin, Petar, Pujic, Christian, Paquet, Emmanuelle, Bergeron, Delphine, Mouniée, Thierry, Marchal, Hélène, Salord, Jeanne-Marie, Bonnet, Benoit, Cournoyer, Thierry, Winiarski, Vanessa, Louzier, and Veronica, Rodriguez-Nava
Subjects: Murine model of transient immunoparalysis, Hsp65 metabarcoding, Environment, Urban pollution, Nocardia, ComputingMethodologies_COMPUTERGRAPHICS, Research Article, Opportunistic pathogen
Abstract: Graphical abstract, Highlights • Urban infiltration basins are a reservoir of a high diversity of Nocardia encompassing both pathogenic and not-pathogenic species. • Relative abundance of pathogenic Nocardia species presents a positive correlation with metal trace elements. • High infraspecific variability within N. cyriacigeorgica, forming three phylogroups. • Environmental N. cyriacigeorgica strains may be as virulent as clinical GUH-2 strain. • hsp65 marker can be used by metabarcoding approach for assessment of environmental Nocardia biodiversity., Urban Infiltration Basins (UIBs) are used to manage urban runoff transfers and feed aquifers. These UIBs can accumulate urban pollutants and favor the growth of potentially pathogenic biological agents as Nocardia. Objectives To assess the spatio-temporal dynamics of pathogenic Nocardia in UIBs and to stablish phylogenetic relationships between clinical and UIB N. cyriacigeorgica strains. To assess pathogenicity associated with environmental N. cyriacigeorgica using an animal model, and to identify genetic elements that may be associated to its virulence. Methods A well-characterized UIB in terms of chemical pollutants from Lyon area was used in this study during a whole year. Cultural and Next-Generation-Sequencing methods were used for Nocardia detection and typing. Clinical and environmental isolates phylogenetic relationships and virulences were compared with Multilocus-Sequence-Analysis study together with a murine model. Results In autumn, N. cyriacigeorgica and N. nova were the pathogenic most prevalent species in the UIB. The complex N. abscessus/asiatica was also detected together with some other non-pathogenic species. The presence of pathogenic Nocardia was positively correlated to metallic trace elements. Up to 1.0 × 103 CFU/g sediment of N. cyriacigeorgica and 6 OTUs splited in two different phylogroups were retrieved and were close to clinical strains. The EML446 tested UIB isolate showed significant infectivity in mice with pulmonary damages similar to clinical clone (GUH-2). Conclusion Hsp65 marker-based metabarcoding approach allowed detecting N. cyriacigeogica as the most abundant Nocardia pathogenic species in a UIB. Metal trace elements-polluted environments can be reservoirs of pathogenic Nocardia which may have a similar virulence to clinical strains.
Published: 2020

29. Genome Sequences of Three Nocardia cyriacigeorgica Strains and One Nocardia asteroides Strain

Author: Emmanuelle Bergeron, Christophe Martin, Petar Pujic, Veronica Rodriguez-Nava, Thierry Winiarski, Florian Vautrin, Benoit Cournoyer, Vanessa Louzier, Danis Abrouk, Audrey Dubost, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE), Observatoire Français des Nocardioses [Hôpital de la Croix-Rousse, CHU-HCL] (Institut des Agents Infectieux - IAI), Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL)-Centre de Biologie et Pathologie Nord [Hôpital de la Croix-Rousse, CHU-HCL], Agressions Pulmonaires et Circulatoires dans le Sepsis - UR (APCSé), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), The LABGeM (CEA/Genoscope and CNRS UMR8030), the France Génomique, and The French Institute of Bioinformatics (funded as part of the Investissement d’Avenir program managed by the Agence Nationale pour la Recherche, contracts ANR-10-INBS-09, ANR-11-INBS-0013) are all thanked for their support to the MicroScope annotation platform., ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-11-INBS-0013/11-INBS-0013,ReNaBi-IFB,Institut français de bioinformatique(2011), ANR-17-CE04-0010,INFILTRON,Dispositif INFILTRON pour une évaluation des fonctions infiltration & filtration des sols urbains dans un contexte de gestion des eaux pluviales(2017), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), Cournoyer, Benoit, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Infrastructures - Institut français de bioinformatique - - IFB (ex Renabi-IFB)2011 - ANR-11-INBS-0013 - INBS - VALID, Dispositif INFILTRON pour une évaluation des fonctions infiltration & filtration des sols urbains dans un contexte de gestion des eaux pluviales - - INFILTRON2017 - ANR-17-CE04-0010 - AAPG2017 - VALID, Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre de Biologie et Pathologie Nord [Hôpital de la Croix-Rousse, CHU-HCL]-Hôpital de la Croix-Rousse [CHU - HCL], and Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL)
Subjects: [SDE] Environmental Sciences, 0301 basic medicine, 030106 microbiology, Biology, Genome, Microbiology, 03 medical and health sciences, Immunology and Microbiology (miscellaneous), nocardia astéroïdes, cellule souche, Genetics, NOCARDIA CYRIACIGEORGICA, Molecular Biology, integumentary system, Strain (biology), Microbiology and Parasitology, Genome Sequences, Nocardia, bacterial infections and mycoses, Pathogenicity, biology.organism_classification, Microbiologie et Parasitologie, facteur de pathogénicité, séquence du génome, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, 030104 developmental biology, [SDE]Environmental Sciences, bacteria, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: We report four draft genome sequences of Nocardia spp. The strains are the Nocardia cyriacigeorgica DSM 44484 pathogenic type strain; two environmental isolates, Nocardia cyriacigeorgica EML446 and EML1456; and the Nocardia asteroides ATCC 19247 nonpathogenic type strain, with estimated genome sizes of 6.3 to 6.8 Mb. The study of these isolates will provide insight into physiology, evolution, and pathogenicity of Nocardia spp.
Published: 2019

30. Genome sequence of pseudomonas sp. strain ST1, isolated fromo Olive (Olea europaea L.) knot galls in croatia

Author: Philippe Normand, Petar Pujic, Katja Žanić, Slavko Perica, Pascale Fournier, Gabriela Vuletin Selak, Marina Raboteg, Audrey Dubost, Danis Abrouk, Institute for Adriatic Crops and Karst Reclamation, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Split-Dalmatia County grant, Unity Through Knowledge Fund, collaboration grant 2017 within the Research Cooperability Program 10/17, French government, Agency for Mobility and EU Programmes, Embassy of the French Republic, and French National Research Agency (ANR) ANR-10-INBS-09 ANR-11-INBS-0013
Subjects: Whole genome sequencing, 0303 health sciences, biology, 030306 microbiology, olive, Pseudomonas sp. Strain ST1, genome sequence, [SDV]Life Sciences [q-bio], Pseudomonas, Ribosomal RNA, croatie, biology.organism_classification, DNA sequencing, pseudomonas, séquence du génome, 03 medical and health sciences, Immunology and Microbiology (miscellaneous), Olea, Botany, Transfer RNA, Genetics, Molecular Biology, Gene, Genome size, olea europaea, 030304 developmental biology
Abstract: We report the genome sequence of a Pseudomonas sp. strain isolated from olive knot galls. The genome size is 6.101 Mbp with a G+C content of 58%. A total of 6,137 coding DNA sequences (CDS) were predicted, including 52 tRNA and 4 rRNA genes.
Published: 2019

31. Whole-Genome Sequence of a Pantoea sp. Strain Isolated from an Olive (Olea europaea L.) Knot

Author: Marina Raboteg, Audrey Dubost, Gabriela Vuletin Selak, Philippe Normand, Petar Pujic, Danis Abrouk, Katja Žanić, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: [SDV]Life Sciences [q-bio], Genome, DNA sequencing, 03 medical and health sciences, Immunology and Microbiology (miscellaneous), Genetics, 14. Life underwater, Pantoea sp. paga, total genome sequence, olea europaea, Molecular Biology, Genome size, Gene, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, biology, 030306 microbiology, Microbiology and Parasitology, Pantoea, Genome Sequences, Ribosomal RNA, biology.organism_classification, Microbiologie et Parasitologie, Olive trees, séquence du génome
Abstract: Here, we present the total genome sequence of Pantoea sp. strain paga, a plant-associated bacterium isolated from knots present on olive trees grown on the Adriatic Coast. The genome size of Pantoea sp. paga is 5.08 Mb, with a G+C content of 54%. The genome contains 4,776 predicted coding DNA sequences (CDSs), including 70 tRNA genes and 1 ribosomal operon. Obtained genome sequence data will provide insight on the physiology, ecology, and evolution of Pantoea spp.
Published: 2019

32. Omics of the early molecular dialogue between Frankia alni and Alnus glutinosa and the cellulase synton

Author: Haïtham Sghaier, David Roche, Jean Armengaud, Petar Pujic, Guylaine Miotello, Alison M. Berry, Nicole Alloisio, Pascale Fournier, Philippe Normand, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), French National Research Agency (ANR) ANR-13-BSV7-0013-03 ANR-10-BLAN-1708, and Universite de Lyon
Subjects: Frankia alni, 0303 health sciences, biology, 030306 microbiology, Operon, [SDV]Life Sciences [q-bio], Frankia, ATP-binding cassette transporter, Cellulase, biology.organism_classification, Microbiology, Streptomyces, Actinobacteria, 03 medical and health sciences, Alnus glutinosa, Biochemistry, biology.protein, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: International audience; The early Frankia-Alnus symbiotic molecular exchanges were analyzed in detail by protein and RNA omics. For this, Frankia cells were placed in the presence of Alnus roots but separated by a dialysis membrane for 64 h. The bacterial cells were then harvested and analyzed by high-throughput proteomics and transcriptomics (RNA-seq). The most upregulated gene clusters were found to be the potassium transporter operon kdp and an ABC transporter operon of uncharacterized function. The most upregulated proteins were found to be acyl dehydrogenases and the potassium transporter Kdp. These suggest a preadaptation to the impending stresses linked to the penetration into isotonic host tissues and a possible rearrangement of the membrane. Another cluster among the 60 most upregulated ones that comprised two cellulases and a cellulose synthase was conserved among the Frankia and other actinobacteria such as Streptomyces. Cellulase activity was detected on CMC all along the length of the root but not away from it. Frankia alni ACN14a was found to be unable to respire or grow on glucose as sole carbon source. The cellulose synthase was found active at the tip of hyphae in response to Alnus root exudates, resulting in a calcofluor stained tip.
Published: 2019

33. Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa

Author: Danis Abrouk, Guillaume Schwob, Aude Herrera-Belaroussi, Hans-Peter Klenk, Philippe Normand, Joël F. Pothier, Agnès Nguyen, Audrey Dubost, Pascale Fournier, Maria P. Fernandez, Imen Nouioui, Petar Pujic, Valentin Pflüger, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: DNA, Bacterial, 0301 basic medicine, Root nodule, nodule, [SDV]Life Sciences [q-bio], Frankia, Subspecies, Alnus, Plant Roots, Microbiology, 03 medical and health sciences, Morella, Symbiosis, RNA, Ribosomal, 16S, Botany, Phospholipids, Phylogeny, Ecology, Evolution, Behavior and Systematics, Base Composition, Alnus incana, Phylogenetic tree, biology, Fatty Acids, Quebec, Nucleic Acid Hybridization, Vitamin K 2, Sequence Analysis, DNA, General Medicine, 570: Biologie, 16S ribosomal RNA, biology.organism_classification, symbiosis, Bacterial Typing Techniques, Alnus glutinosa, 030104 developmental biology, nitrogen fixation
Abstract: Strain ARgP5(T), 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 ARgP5(T) 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%. ARgP5(T) is characterised by the presence of meso-A(2)pm, galactose, glucose, mannose, rhamnose (trace), ribose and xylose as whole-organism hydrolysates; MK-9(H-8) as predominant menaquinone; diphosphatidylglycerol, phosphatidylinositol and phosphatidylglycerol as polar lipids and iso-C-16 : 0 and C-17 : 1 omega 8c as major fatty acids. The proteomic results confirmed the distinct position of ARgP5(T) from its closest neighbours in Frankia cluster 1. ARgP5(T) 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 ARgP5(T) (= 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.
Published: 2018

34. Actinorhizal Signaling Molecules

Author: Maimouna, Cissoko, Valérie, Hocher, Hassen, Gherbi, Djamel, Gully, Alyssa, Carré-Mlouka, Seyni, Sane, Sarah, Pignoly, Antony, Champion, Mariama, Ngom, Petar, Pujic, Pascale, Fournier, Maher, Gtari, Erik, Swanson, Céline, Pesce, Louis S, Tisa, Mame Oureye, Sy, and Sergio, Svistoonoff
Subjects: Plant Science, symbioses, nodule inception, Discaria, Casuarina, Alnus, nodulation factors, Original Research
Abstract: Actinorhizal plants are able to establish a symbiotic relationship with Frankia bacteria leading to the formation of root nodules. The symbiotic interaction starts with the exchange of symbiotic signals in the soil between the plant and the bacteria. This molecular dialog involves signaling molecules that are responsible for the specific recognition of the plant host and its endosymbiont. Here we studied two factors potentially involved in signaling between Frankia casuarinae and its actinorhizal host Casuarina glauca: (1) the Root Hair Deforming Factor (CgRHDF) detected using a test based on the characteristic deformation of C. glauca root hairs inoculated with F. casuarinae and (2) a NIN activating factor (CgNINA) which is able to activate the expression of CgNIN, a symbiotic gene expressed during preinfection stages of root hair development. We showed that CgRHDF and CgNINA corresponded to small thermoresistant molecules. Both factors were also hydrophilic and resistant to a chitinase digestion indicating structural differences from rhizobial Nod factors (NFs) or mycorrhizal Myc-LCOs. We also investigated the presence of CgNINA and CgRHDF in 16 Frankia strains representative of Frankia diversity. High levels of root hair deformation (RHD) and activation of ProCgNIN were detected for Casuarina-infective strains from clade Ic and closely related strains from clade Ia unable to nodulate C. glauca. Lower levels were present for distantly related strains belonging to clade III. No CgRHDF or CgNINA could be detected for Frankia coriariae (Clade II) or for uninfective strains from clade IV.
Published: 2018

35. The PEG-responding desiccome of the alder microsymbiont Frankia alni

Author: Kais Ghedira, Philippe Normand, Haïtham Sghaier, Emna Harigua-Souiai, Cherif Ben Hamda, Jean Armengaud, Ikram Guizani, Petar Pujic, Sihem Guesmi, Guylaine Miotello, Pascale Fournier, Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP), Laboratoire d'Epidémiologie Moléculaire et de Pathologie Expérimentale Appliquée aux Maladies Infectieuses (LR11IPT04), Université de Tunis El Manar (UTM)-Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Faculté des Sciences de Bizerte [Université de Carthage], Université de Carthage - University of Carthage, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre National des Sciences et Technologies Nucléaires [Tunisie] (CNSTN), INAT Laboratoire Recherche-Développement Sciences et Technologie de l'Eau (INAT-LRSTE), Université de Carthage - University of Carthage-INAT, Laboratoire Innovations technologiques pour la Détection et le Diagnostic (LI2D), Service de Pharmacologie et Immunoanalyse (SPI), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Médicaments et Technologies pour la Santé (MTS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biotechnology and Bio-Geo Resources Valorization, Sidi Thabet Technopark (LR11ES31), This work was supported by the Tunisian National Center for Nuclear Sciences and Technology (CNSTN), the Institut Pasteur de Tunis (Tunis) and the Ministry of Higher Education and Scientific Research in Tunisia., Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Institut Pasteur de Tunis-Réseau International des Instituts Pasteur ( RIIP ), Laboratoire d'Epidémiologie Moléculaire et de Pathologie Expérimentale Appliquée aux Maladies Infectieuses ( LR11IPT04 ), Institut Pasteur de Tunis-Université Tunis El Manar ( UTM ) -Réseau International des Instituts Pasteur ( RIIP ), Faculté des Sciences de Bizerte, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre National des Sciences et Technologies Nucléaires [Tunisie] ( CNSTN ), INAT Laboratoire Recherche-Développement Sciences et Technologie de l'Eau ( INAT-LRSTE ), Carthage University-INAT, Laboratoire Innovations technologiques pour la Détection et le Diagnostic ( LI2D ), Service de Pharmacologie et Immunoanalyse ( SPI ), Département Médicaments et Technologies pour la Santé ( DMTS ), Direction de Recherche Fondamentale (CEA) ( DRF (CEA) ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) ( DRF (CEA) ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Département Médicaments et Technologies pour la Santé ( DMTS ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Sidi Thabet Technopark ( LR11ES31 ), Université Tunis El Manar (UTM)-Institut Pasteur de Tunis, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Médicaments et Technologies pour la Santé (MTS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: 0301 basic medicine, Models, Molecular, Proteomics, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, [ SDV.BV.BOT ] Life Sciences [q-bio]/Vegetal Biology/Botanics, Microorganism, [SDV]Life Sciences [q-bio], 030106 microbiology, Frankia, Large-conductance mechanosensitive channel, lcsh:Medicine, Article, Ion Channels, Polyethylene Glycols, 03 medical and health sciences, Symbiosis, Bacterial Proteins, Osmotic Pressure, Stress, Physiological, Tandem Mass Spectrometry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:Science, 2. Zero hunger, Frankia alni, Multidisciplinary, biology, [ SDV ] Life Sciences [q-bio], Chemistry, lcsh:R, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, 030104 developmental biology, Biochemistry, Nitrogen fixation, Solvents, lcsh:Q, Actinorhizal plant, Mechanoreceptors, Bacteria
Abstract: International audience; Actinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser. A total of 2,052 proteins were detected and quantified. Under osmotic stress, PEG-grown F. alni cells increased the abundance of envelope-associated proteins like ABC transporters, mechano-sensitive ion channels and Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated (cas) components. Conjointly, dispensable pathways, like nitrogen fixation, aerobic respiration and homologous recombination, were markedly down-regulated. Molecular modelling and docking simulations suggested that the PEG is acting on Frankia partly by filling the inner part of an up-regulated osmotic-stress large conductance mechanosensitive channel. Actinobacteria belonging to the genus Frankia do establish nitrogen-fixing nodular symbiosis with the roots of 23 angiosperm genera that are collectively called " actinorhizals " 1. These plants form root nodules in which Frankia fixes nitrogen, thus permitting them to thrive in pioneer soils poor in nitrogen and organic matter, such as glacial moraines, lava fields, forest burnouts or anthropogenic sites such as mine spoils or hydrodam dykes 2. Frankia establishes a symbiotic association with the roots of several dicotyledonous plants. The different Frankia lineages form a coherent cluster at the root of the aerobic actinobacteria phylum 3 , and F. alni in particular establishes symbiosis with alder (Alnus) and bayberry (Morella) species 4. The interaction has evolved over several million years with a sophisticated dialogue that does not imply acy-lated N-acetyl-glucosamine oligomeric Nod factors 5. The Frankia determinants of symbiosis are still poorly known, which is for the most part due to the lack of a genetic transformation system. Transcriptomics has shown genes coding for nitrogenase (nif), hydrogenase uptake (hup), hopanoids (shc, hpn), iron-sulfur (suf) clusters as among the most up-regulated 6. Proteomics has also been used to analyze the symbiosis 7 to identify up-regulated peptides and it has shown the presence of Nif, Hup, Suf, Hop proteins as expected but also several transporters, regulators and various proteins involved in stress responses.
Published: 2018

36. Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis

Author: Qiang Gao, Xun Xu, Marco G. Salgado, Philippe Normand, Sergio Svistoonoff, Henk W. M. Hilhorst, Martin Parniske, Wouter Kohlen, Gane Ka-Shu Wong, Yuhu Liang, Jean Keller, Yuda Purwana Roswanjaya, Yue Song, Xiaodong Fang, Jeff J. Doyle, Alison M. Berry, Yuan Fu, Nicole Alloisio, Leandro Imanishi, Jean-Michel Ané, Xin Liu, Matthew B. Crook, Jing Qu, Yan Xu, Benjamin Billault-Penneteau, Pierre-Marc Delaux, Katharina Pawlowski, Shifeng Cheng, Shixu He, Dominique Lauressergues, Shanyun Xu, Kai Battenberg, Valérie Hocher, Klaus F. X. Mayer, Hassen Gherbi, Petar Pujic, Huanming Yang, Luis Gabriel Wall, Georg Haberer, Manuel Spannagl, Maximilian Griesmann, Yue Chang, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Shenzhen Municipal Government of China [JCYJ20150529150409546, JCYJ20150831201643396], Swedish Research Council Vetenskapsradet [VR 2012-03061], German Ministry of Education and Research grant [031A536], Deutsche Forschungsgemeinschaft Project [SFB924], National Science Foundation [NSF 1237936, 1546742], French National Research Agency [ANR-12-BSV7-0007-02], USDA [NIFA 2015-67014-22849, NIFA590 CA-D-PLS-2173-H], ECOS-SUD [A13B03], National University of Quilmes, Argentina [PUNQ 1411/15], NWO-VENI [863.15.010], Alberta Innovates Technology Futures (AITF) Innovates Centres of Research Excellence (iCORE), European Project: 340904,EC:FP7:ERC,ERC-2013-ADG,EVOLVINGNODULES(2014), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Ludwig Maximilian University [Munich] (LMU), Beijing Genomics Institute [Shenzhen] (BGI), Institute of Virology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Helmholtz Zentrum München = German Research Center for Environmental Health, Weber State University, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional de Quilmes (UNQ), Wageningen University and Research [Wageningen] (WUR), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), University of California [Davis] (UC Davis), and University of California (UC)
Subjects: 0301 basic medicine, Nodule (geology), Root nodule, [SDV]Life Sciences [q-bio], MESH: Genetics, Phylogenomics, Laboratorium voor Plantenfysiologie, Clade, MESH: Phylogeny, MESH: Nitrogen, MESH: Evolution, Molecular, Phylogeny, 2. Zero hunger, Multidisciplinary, MESH: Symbiosis, MESH: Genomics, SYMBIOSIS, food and beverages, Fabaceae, Genomics, MESH: Root Nodules, Plant, LEGUMES, Nitrogen fixation, Laboratory of Molecular Biology, Root Nodules, Plant, CIENCIAS NATURALES Y EXACTAS, Laboratory of Plant Physiology, Genome, Plant, Nitrogen, NITROGEN FIXATION, Biology, engineering.material, Bacterial Physiological Phenomena, Ciencias Biológicas, Evolution, Molecular, 03 medical and health sciences, Symbiosis, Phylogenetics, Nitrogen Fixation, Botany, Life Science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Laboratorium voor Moleculaire Biologie, Ciencias de las Plantas, Botánica, fungi, 15. Life on land, 030104 developmental biology, MESH: Bacterial Physiological Phenomena, engineering, EPS, ACTINORHIZA, MESH: Fabaceae
Abstract: The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of 10 plant species covering the diversity of nodule morphotypes, bacterial symbionts, and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION in 10 of 13 genomes of nonnodulating species within this clade. The discovery that multiple independent losses shaped the present-day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so-far-underestimated selection pressure against this symbiosis. Fil: Griesmann, Maximilian. Ludwig Maximilians Universitat; Alemania Fil: Chang, Yue. No especifíca; Fil: Liu, Xin. No especifíca; Fil: Song, Yue. No especifíca; Fil: Haberer, Georg. Helmholtz Center Munich; Alemania Fil: Crook, Matthew B.. Weber State University; Estados Unidos Fil: Billault-Penneteau, Benjamin. Ludwig Maximilians Universitat; Alemania Fil: Lauressergues, Dominique. Université de Toulouse; Francia Fil: Keller, Jean. Université de Toulouse; Francia Fil: Imanishi, Leandro Ezequiel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Roswanjaya, Yuda Purwana. University of Agriculture Wageningen; Países Bajos Fil: Kohlen, Wouter. University of Agriculture Wageningen; Países Bajos Fil: Pujic, Petar. Université de Lyon; Francia Fil: Battenberg, Kai. University of California at Davis; Estados Unidos Fil: Alloisio, Nicole. No especifíca; Fil: Liang, Yuhu. No especifíca; Fil: Hilhorst, Henk. No especifíca; Fil: Salgado, Marco G.. Stockholms Universitet; Suecia Fil: Hocher, Valerie. Université Montpellier II; Francia Fil: Gherbi, Hassen. Université Montpellier II; Francia Fil: Svistoonoff, Sergio. Université Montpellier II; Francia Fil: Doyle, Jeff J.. Cornell University; Estados Unidos Fil: He, Shixu. No especifíca; Fil: Xu, Yan. China National Genebank; China Fil: Xu, Shanyun. China National Genebank; China Fil: Qu, Jing. China National Genebank; China Fil: Gao, Qiang. No especifíca; Fil: Fang, Xiaodong. No especifíca; Fil: Fu, Yuan. China National Genebank; China Fil: Normand, Philippe. Universite Lyon 2; Francia Fil: Berry, Alison M.. University of California at Davis; Estados Unidos Fil: Wall, Luis Gabriel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Ané, Jean Michel. University of Wisconsin; Estados Unidos Fil: Pawlowski, Katharina. Stockholms Universitet; Suecia Fil: Xu, Xun. China National Genebank; China Fil: Yang, Huanming. James D. Watson Institute Of Genome Sciences; China Fil: Spannagl, Manuel. Helmholtz Center Munich German Research Center For Environmental Health; Alemania Fil: Mayer, Klaus F.X.. Helmholtz Center Munich German Research Center For Environmental Health; Alemania Fil: Wong, Gane Ka-Shu. University of Alberta; Canadá Fil: Parniske, Martin. Ludwig Maximilians Universitat; Alemania Fil: Delaux, Pierre Marc. No especifíca; Fil: Cheng, Shifeng. China National Genebank; China
Published: 2018

37. Molecular response to nitrogen starvation by Frankia alni ACN14a revealed by transcriptomics and functional analysis with a fosmid library in Escherichia coli

Author: Petar Pujic, Tristan Lurthy, Hasna Boubakri, Stéphanie Anchisi, Pascale Fournier, Alise J. Ponsero, Philippe Normand, Nicole Alloisio, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), French national program EC2CO-Biohefect/Ecodyn/Dril/Micro-biEn AO 2015, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: 0301 basic medicine, Nitrogen, [SDV]Life Sciences [q-bio], 030106 microbiology, Alnus, medicine.disease_cause, nitrogen stress, Microbiology, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Escherichia coli, medicine, Symbiosis, Molecular Biology, Gene Library, Nitrite reductase, Frankia alni, biology, Strain (chemistry), Gene Expression Regulation, Bacterial, General Medicine, biology.organism_classification, Fosmid, Biochemistry, chemistry, fosmid library, nitrogen fixation, Nitrogen fixation, Frankia, DNA
Abstract: The transcriptome of Frankia alni strain ACN14a was compared between in vitro ammonium-replete (N-replete) and ammonium-free dinitrogen-fixing (N-fixing) conditions using DNA arrays. A Welch-test (p \\textless 0.05) revealed significant upregulation of 252 genes under N-fixing vs. N-replete (fold-change (FC) >= 2), as well as significant downregulation of 48 other genes (FC
Published: 2018

38. Generation of a cluster-free Streptomyces albus chassis strains for improved heterologous expression of secondary metabolite clusters

Author: Birgit Rosenkränzer, Petar Pujic, Suvd Nadmid, Philippe Normand, Andriy Luzhetskyy, Maksym Myronovskyi, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: 0301 basic medicine, Metabolite, [SDV]Life Sciences [q-bio], 030106 microbiology, Heterologous, Gene Expression, Bioengineering, Secondary metabolite, Applied Microbiology and Biotechnology, Streptomyces, 03 medical and health sciences, chemistry.chemical_compound, Gene cluster, medicine, Gene, Streptomyces albus, ComputingMilieux_MISCELLANEOUS, Genetics, biology, Chromosomes, Bacterial, biology.organism_classification, 030104 developmental biology, chemistry, Multigene Family, Heterologous expression, Microorganisms, Genetically-Modified, Biotechnology, medicine.drug
Abstract: Natural products are a rich source of potential drugs for many applications. Discovery of natural products through the activation of cryptic gene clusters encoding their biosynthetic pathways, engineering of those biosynthetic pathways and optimization of production yields often rely on the expression of these gene clusters in suitable heterologous host strains. Streptomyces albus J1074 provides high success rates of heterologous cluster expression with high levels of metabolite production, rapid growth and amenability to genetic manipulations. Here, we report the construction of S. albus chassis strains optimized for the discovery of natural products through heterologous expression of secondary metabolite clusters. 15 clusters encoding secondary metabolite biosynthetic pathways were deleted in the chromosome of S. albus Del14. This strain provides a substantially improved compound detection limit, owing to the lack of native secondary metabolites. Furthermore, the production yield of natural products heterologously expressed in S. albus Del14 was higher than in commonly used S. albus J1074 and S. coelicolor hosts. S. albus strains B2P1 and B4 were generated by introduction of additional phage phiC31 attB sites into the chromosome of S. albus Del14, allowing integration of up to four copies of a heterologous gene cluster. Amplification of gene clusters in the chromosome of the constructed strains further improved production yields of the encoded compounds. One cryptic cluster from Streptomyces spp. and two clusters from distantly related Frankia spp. strains were successfully activated in these new chassis strains, leading to the isolation of a new compound fralnimycin.
Published: 2018

39. Bacterial‐induced calcium oscillations are common to nitrogen‐fixing associations of nodulating legumes and non‐legumes

Author: Emma Granqvist, Jongho Sun, J. Allan Downie, Petar Pujic, Richard J. Morris, René Geurts, Rik Op den Camp, Lionel Hill, Giles E. D. Oldroyd, Philippe Normand, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), BBSRC [BB/J004553/1], European Research Council, John Innes Foundation, NWO [VICI 865.13.001], and Oldroyd, Giles E. D.
Subjects: Microinjections, Symbiotic signalling, Physiology, [SDV]Life Sciences [q-bio], Calcium oscillations, Frankia, nodosité racinaire, Plant Science, nitrogen‐fixing clade, Nodulation, Sinorhizobium fredii, Plant Root Nodulation, Rhizobia, Nod factor, Nitrogen-fixing clade, Bacterial Proteins, protéine bactérienne, Nitrogen Fixation, Botany, Laboratorium voor Moleculaire Biologie, Calcium Signaling, Phylogeny, Frankia alni, Vegetal Biology, calcium, Bacteria, Rapid Report, EPS-1, biology, Research, Parasponia, Fabaceae, 15. Life on land, Actinorhizal, Legumes, biology.organism_classification, actinorhizal, calcium oscillations, legumes, nitrogen-fixing, clade, nodulation, symbiotic signalling, fixation de l'azote, Rapid Reports, Laboratory of Molecular Biology, Actinorhizal plant, Biologie végétale
Abstract: * Plants that form root-nodule symbioses are within a monophyletic \textquoteleftnitrogen-fixing' clade and associated signalling processes are shared with the arbuscular mycorrhizal symbiosis. Central to symbiotic signalling are nuclear-associated oscillations in calcium ions (Ca2+), occurring in the root hairs of several legume species in response to the rhizobial Nod factor signal. * In this study we expanded the species analysed for activation of Ca2+ oscillations, including nonleguminous species within the nitrogen-fixing clade. * We showed that Ca2+ oscillations are a common feature of legumes in their association with rhizobia, while Cercis, a non-nodulating legume, does not show Ca2+ oscillations in response to Nod factors from Sinorhizobium fredii NGR234. Parasponia andersonii, a nonlegume that can associate with rhizobia, showed Nod factor-induced calcium oscillations to S. fredii NGR234 Nod factors, but its non-nodulating sister species, Trema tomentosa, did not. Also within the nitrogen-fixing clade are actinorhizal species that associate with Frankia bacteria and we showed that Alnus glutinosa induces Ca2+ oscillations in root hairs in response to exudates from Frankia alni, but not to S. fredii NGR234 Nod factors. * We conclude that the ability to mount Ca2+ oscillations in response to symbiotic bacteria is a common feature of nodulating species within the nitrogen-fixing clade.
Published: 2015

40. Micromonospora is a normal occupant of actinorhizal nodules

Author: Petar Pujic, Martha E. Trujillo, Lorena Carro, Philippe Normand, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Universidad de Salamanca, and French National Research Agency (ANR)Spanish GovernmentSpanish Government MEC CGL2009-07287
Subjects: DNA, Bacterial, Root nodule, [SDV]Life Sciences [q-bio], Frankia, Biology, Myrica, Alnus, Fagaceae, Micromonospora, Micromonospora lupini, General Biochemistry, Genetics and Molecular Biology, Microbiology, 03 medical and health sciences, Nitrogen Fixation, Coriaria, Antibiosis, Hippophae, Botany, Rosales, Symbiosis, Phylogeny, 030304 developmental biology, 0303 health sciences, Elaeagnaceae, 030306 microbiology, Elaeagnus, General Medicine, biology.organism_classification, Culture Media, Cucurbitaceae, Root Nodules, Plant, General Agricultural and Biological Sciences, Actinorhizal plant
Abstract: Actinorhizal plants have been found in eight genera belonging to three orders (Fagales, Rosales and Cucurbitales). These all bear root nodules inhabited by bacteria identified as the nitrogen-fixing actinobacterium Frankia. These nodules all have a peripheral cortex with enlarged cells filled with Frankia hyphae and vesicles. Isolation in pure culture has been notoriously difficult, due in a large part to the growth of fast-growing contaminants where, it was later found, Frankia was slow-growing. Many of these contaminants, which were later found to be Micromonospora, were obtained from Casuarina and Coriaria. Our study was aimed at determining if Micromonospora were also present in other actinorhizal plants. Nodules from Alnus glutinosa, Alnus viridis, Coriaria myrtifolia, Elaeagnus x ebbingei, Hippophae rhamnoides, Myrica gale and Morella pensylvanica were tested and were all found to contain Micromonospora isolates. These were found to belong to mainly three species: Micromonospora lupini, Micromonospora coriariae and Micromonospora saelicesensis. Micromonospora isolates were found to inhibit some Frankia strains and to be innocuous to other strains.
Published: 2013

41. Structural and gene expression analyses of uptake hydrogenases and other proteins involved in nitrogenase protection in Frankia

Author: Anita Sellstedt, Kerstin Richau, Petar Pujic, R. L. Kudahettige, N. P. Kudahettige, Umeå University, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Carl Tryggers Foundation, Sweden French National Research Agency (ANR)National Centre for Scientific Research, France French National Research Agency (ANR), and Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA, Bacterial, Models, Molecular, Hydrogenase, Hypha, [SDV]Life Sciences [q-bio], Frankia, General Biochemistry, Genetics and Molecular Biology, Microbiology, Hemoglobins, 03 medical and health sciences, hopanoids, Bacterial Proteins, Nitrogen Fixation, RNA, Ribosomal, 16S, Nitrogenase, Gene expression, hyphae, Symbiosis, Intramolecular Transferases, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Molecular nitrogen, biology, 030306 microbiology, fungi, food and beverages, Gene Expression Regulation, Bacterial, General Medicine, Plants, biology.organism_classification, haemoglobin, Isoenzymes, Oxygen, Oxidative Stress, Protein Subunits, Root Nodules, Plant, General Agricultural and Biological Sciences, Actinorhizal plant, Bacteria, Hydrogen
Abstract: International audience; The actinorhizal bacterium Frankia expresses nitrogenase and can therefore convert molecular nitrogen into ammonia and the by-product hydrogen. However, nitrogenase is inhibited by oxygen. Consequently, Frankia and its actinorhizal hosts have developed various mechanisms for excluding oxygen from their nitrogen-containing compartments. These include the expression of oxygen-scavenging uptake hydrogenases, the formation of hopanoid-rich vesicles, enclosed by multi-layered hopanoid structures, the lignification of hyphal cell walls, and the production of haemoglobins in the symbiotic nodule. In this work, we analysed the expression and structure of the so-called uptake hydrogenase (Hup), which catalyses the in vivo dissociation of hydrogen to recycle the energy locked up in this 'waste' product. Two uptake hydrogenase syntons have been identified in Frankia: synton 1 is expressed under free-living conditions while synton 2 is expressed during symbiosis. We used qPCR to determine synton 1 hup gene expression in two Frankia strains under aerobic and anaerobic conditions. We also predicted the 3D structures of the Hup protein subunits based on multiple sequence alignments and remote homology modelling. Finally, we performed BLAST searches of genome and protein databases to identify genes that may contribute to the protection of nitrogenase against oxygen in the two Frankia strains. Our results show that in Frankia strain ACN14a, the expression patterns of the large (HupL1) and small (HupS1) uptake hydrogenase subunits depend on the abundance of oxygen in the external environment. Structural models of the membrane-bound hydrogenase subunits of ACN14a showed that both subunits resemble the structures of known [NiFe] hydrogenases (Volbeda et al. 1995), but contain fewer cysteine residues than the uptake hydrogenase of the Frankia DC12 and Eu1c strains. Moreover, we show that all of the investigated Frankia strains have two squalene hopane cyclase genes (shc1 and shc2). The only exceptions were CcI3 and the symbiont of Datisca glomerata, which possess shc1 but not shc2. Four truncated haemoglobin genes were identified in Frankia ACN14a and Eu1f, three in CcI3, two in EANpec1 and one in the Datisca glomerata symbiont (Dg).
Published: 2013

42. Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes

Author: Hans-Peter Klenk, Karima Hezbri, Abdellatif Boudabous, Jean Armengaud, Arnab Sen, Petar Pujic, Faten Ghodhbane-Gtari, Maher Gtari, Philippe Normand, Louis S. Tisa, Daniele Daffonchio, Haïtham Sghaier, National Institute for Nuclear Science and Technology, Institut Supérieur de Biotechnologie de Sidi Thabet (ISBST), Laboratory Microorganismes and Biomolecular Activ, Université Tunis El Manar (UTM), Université de Carthage - University of Carthage, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Department of Botany, National University of Ireland [Galway] (NUI Galway), Biology and Environment Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Department of Food Environmental and Nutritional Sciences, (DeFENS), University of Milan, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire (UNH), School Biology, Newcastle University, EU project BIODESERT (European Community's Seventh Framework Programme CSA-SA REGPOT-2) 245746, Université de la Manouba [Tunisie] (UMA)-Université de la Manouba [Tunisie] (UMA), Université de Tunis El Manar (UTM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Institut Supérieur de Biotechnologie de Sidi Thabet ( ISBST ), Université Tunis El-Manar, Université de Carthage, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), National University of Ireland [Galway] ( NUI Galway ), King Abdullah University of Science and Technology ( KAUST ), Department of Molecular Cellular and Biomedical Science, and University of New Hampshire ( UNH )
Subjects: 0301 basic medicine, Proteomics, Geologic Sediments, [SDV]Life Sciences [q-bio], 030106 microbiology, Biology, Microbiology, Genome, Mass Spectrometry, Actinobacteria, 03 medical and health sciences, Microbial ecology, sable, Actinomycetales, genome, Ecology, Evolution, Behavior and Systematics, Geodermatophilaceae, Genetics, [ SDV ] Life Sciences [q-bio], sahara, Biodiversity, biology.organism_classification, Adaptation, Physiological, Environmental biotechnology, Evolutionary biology, silica, Proteome, biomarker, Original Article, Adaptation, escherichia coli, biomarqueur, Chromatography, Liquid
Abstract: The Geodermatophilaceae are unique model systems to study the ability to thrive on or within stones and their proteogenomes (referring to the whole protein arsenal encoded by the genome) could provide important insight into their adaptation mechanisms. Here we report the detailed comparative genome analysis of Blastococcus saxobsidens (Bs), Modestobacter marinus (Mm) and Geodermatophilus obscurus (Go) isolated respectively from the interior and the surface of calcarenite stones and from desert sandy soils. The genome-scale analysis of Bs, Mm and Go illustrates how adaptation to these niches can be achieved through various strategies including ` molecular tinkering/ opportunism' as shown by the high proportion of lost, duplicated or horizontally transferred genes and ORFans. Using high-throughput discovery proteomics, the three proteomes under unstressed conditions were analyzed, highlighting the most abundant biomarkers and the main protein factors. Proteomic data corroborated previously demonstrated stone-related ecological distribution. For instance, these data showed starvation-inducible, biofilm-related and DNA-protection proteins as signatures of the microbes associated with the interior, surface and outside of stones, respectively.
Published: 2016

43. Physiological effects of major up-regulated Alnus glutinosa peptides on Frankia sp. ACN14a

Author: Pascale Fournier, Lorena Carro, Nicole Alloisio, Abdelaziz Heddi, Philippe Normand, Franck Poly, Marjolaine Rey, Hasna Boubakri, Petar Pujic, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), School of Biology, IE University, Centre National de la Recherche Scientifique ( CNRS ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon, Biologie Fonctionnelle, Insectes et Interactions ( BF2I ), Institut National de la Recherche Agronomique ( INRA ) -Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Université de Lyon-Institut National des Sciences Appliquées ( INSA ), ANR [BugsInACell ANR-13-BSV7-0013-03], FR41 BioEnvironnement et Sante (Lyon), MEC from the Spanish government, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: 0106 biological sciences, 0301 basic medicine, Lysis, [SDV]Life Sciences [q-bio], Frankia, Peptide, Alnus, phylogeny, 01 natural sciences, Microbiology, Plant Root Nodulation, Plant Roots, Bacterial Adhesion, Defensins, 03 medical and health sciences, Oxygen Consumption, phylogénie, Soil Microbiology, Plant Proteins, chemistry.chemical_classification, biology, [ SDV ] Life Sciences [q-bio], fungi, Meristem, biology.organism_classification, In vitro, symbiosis, peptide, Amino acid, Alnus glutinosa, acide aminé, 030104 developmental biology, chemistry, nitrogen fixation, fixation de l'azote, Nitrogen fixation, symbiose, amino acid, defensin, respiration, 010606 plant biology & botany
Abstract: Supplementary Material; Alnus glutinosa has been shown previously to synthesize, in response to nodulation by Frankia sp. ACN14a, an array of peptides called Alnus symbiotic up-regulated peptides (ASUPs). In a previous study one peptide (Ag5) was shown to bind to Frankia nitrogen-fixing vesicles and to modify their porosity. Here we analyse four other ASUPs, alongside Ag5, to determine whether they have different physiological effects on in vitro grown Frankia sp. ACN14a. The five studied peptides were shown to have different effects on nitrogen fixation, respiration, growth, the release of ions and amino acids, as well as on cell clumping and cell lysis. The mRNA abundance for all five peptides was quantified in symbiotic nodules and one (Ag11) was found to be more abundant in the meristem part of the nodule. These findings point to some peptides having complementary effects on Frankia cells.
Published: 2016

44. Contrasted resistance of stone-dwelling Geodermatophilaceae species to stresses known to give rise to reactive oxygen species

Author: Jérôme Gury, Elena Crotti, Maher Gtari, Radhi Maaoui, Daniele Daffonchio, Rabeb Boujmil, Petar Pujic, Imen Essoussi, Philippe Normand, Bessem Chouaia, Abdellatif Boudabous, Lorenzo Brusetti, Haïtham Sghaier, Laboratoire Microorganismes et Biomolecules Actives, Université Tunis El Manar (UTM), Unite de Microbiologie et de Biologie Moleculaire, CNSTN, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Faculty of Science and Technology, Free University of Bozen-Bolzano, Dipartimento di Scienze e Tecnologie Alimentarie Microbiologiche (DISTAM), Università degli studi di Milano [Milano], Université de Tunis El Manar (UTM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Università degli Studi di Milano [Milano] (UNIMI), Université Tunis El Manar ( UTM ), Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux ( IPREM ), Université de Pau et des Pays de l'Adour ( UPPA ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), University of Bozen/Bolzano, and Dipartimento di Scienze e Tecnologie Alimentarie Microbiologiche ( DISTAM )
Subjects: Settore BIO/07 - Ecologia, Biotope, Ultraviolet Rays, Niche, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, reactive oxygen species-generating stresses, Settore BIO/19 - Microbiologia Generale, medicine.disease_cause, Applied Microbiology and Biotechnology, Microbiology, Actinobacteria, 03 medical and health sciences, Stress, Physiological, Metals, Heavy, Actinomycetales, Botany, medicine, heavy metals, Ecosystem, Soil Microbiology, Geodermatophilaceae, 030304 developmental biology, chemistry.chemical_classification, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Reactive oxygen species, Gamma radiation, Heavy metals, Ionizing radiation, Reactive oxygen species-generating stresses, UV, Ecology, Dehydration, biology, Mediterranean Region, 030306 microbiology, gamma radiation, 15. Life on land, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Oxidative Stress, chemistry, Gamma Rays, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ionizing radiation, Reactive Oxygen Species, Desiccation, Soil microbiology, Oxidative stress
Abstract: Stones in arid environments are inhabited by actinobacteria of the family Geodermatophilaceae like the genera Blastococcus and Modestobacter frequently isolated from altered calcarenites. Their habitat requires adaptation to light-induced and other stresses that generate reactive oxygen species. Here, we show that representative members of the species Blastococcus saxobsidens , Geodermatophilus obscurus , and Modestobacter multiseptatus are differentially adapted to stresses associated with arid environments. Whereas B. saxobsidens was found to be sensitive to gamma radiation (D10 = 900 Gy; 10% survival at 900 Gy), M. multiseptatus was moderately (D10 = 6000 Gy) and G. obscurus was highly tolerant (D10 = 9000 Gy). A difference in resistance to high-frequency (λ value = 254 nm) UV was shown by B. saxobsidens , M. multiseptatus , and G. obscurus , being sensitive, tolerant, and highly tolerant (D10 of 6, 900, and > 3500 kJ m−2, respectively). Tolerance to desiccation, mitomycin C and hydrogen peroxide correlated with the ionizing radiation and UV resistance profiles of the three species and were correlated with the pigments synthesized. Resistance to heavy metals/metalloids did not follow the same pattern, with resistance to Ag2+ and Pb2+ being similar for B. saxobsidens , M. multiseptatus , and G. obscurus , whereas resistance to ![Graphic][1] , Cr2+, or Cu2+ was greater for B. saxobsidens than for the other two species. The stress resistance profiles of M. multiseptatus and B. saxobsidens were reflected in different calcarenite colonization patterns. While M. multiseptatus was predominantly isolated from the first two millimeters of stone surface, B. saxobsidens was predominantly isolated from the deeper part of the stone where it is better protected from sun irradiation, suggesting that the response to light- and desiccation-induced oxidative stress is an important driver for niche colonization in the stone biotope. [1]: /embed/inline-graphic-1.gif
Published: 2012

45. Virulence test using nematodes to prescreen Nocardia species capable of inducing neurodegeneration and behavioral disorders

Author: Claire, Bernardin-Souibgui, primary, Anthony, Zoropogui, additional, Jeremy, Voisin, additional, Sebastien, Ribun, additional, Valentin, Vasselon, additional, Petar, Pujic, additional, Veronica, Rodriguez-Nava, additional, Patrick, Belly, additional, Benoit, Cournoyer, additional, and Blaha, Didier, additional
Published: 2017
Full Text: View/download PDF

46. The N-metabolites of roots and actinorhizal nodules from Alnus glutinosa and Datisca glomerata: can D. glomerata change N-transport forms when nodulated?

Author: Alison M. Berry, Tomas Persson, Thanh Van Nguyen, Philippe Normand, Petar Pujic, Katharina Pawlowski, Nicole Alloisio, Department of Ecology Environment and Plant Science, Stockholm University, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS )
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Frankia, nitrogen-fixation, actinorrhiza, arginine, 01 natural sciences, 03 medical and health sciences, Symbiosis, métabolite, Botany, Datisca glomerata, chemistry.chemical_classification, frankia, [ SDV ] Life Sciences [q-bio], biology, fungi, Xylem, food and beverages, actinorhiza, biology.organism_classification, root, actinorhize, Amino acid, gamma-aminobutyrate (GABA), racine, Alnus glutinosa, 030104 developmental biology, Biochemistry, chemistry, fixation de l'azote, citrulline, Nitrogen fixation, General Agricultural and Biological Sciences, Actinorhizal plant, 010606 plant biology & botany
Abstract: To gain more insight in nitrogen metabolism in actinorhizal nodules, a comparison between the N metabolite profiles in roots vs. nodules was initiated for one host plant from the best-examined order of actinorhizal plants, Fagales, A. glutinosa (Betulaceae), a temperate tree, and one host plant from the Cucurbitales order, Datisca glomerata (Datiscaceae). For both symbioses, the symbiotic transcriptomes have been published and can be used to assess the expression of genes representing specific metabolic pathways in nodules. The amino acid profiles of roots in this study suggest that A. glutinosa transported aspartate, glutamate and citrulline in the xylem, a combination of nitrogenous solutes not published previously for this species. The amino acid profiles of D. glomerata roots depended on whether the plants were nodulated or grown on nitrate; roots of nodulated plants contained increased amounts of arginine. Although bacterial transcriptome data showed no symbiotic auxotrophy for branched chain amino acids (leucine, isoleucine, valine) in either symbiosis, D. glomerata nodules contained comparatively high levels of these amino acids. This might represent a response to osmotic stress.
Published: 2015

47. Organic acids metabolism in Frankia alni

Author: Lorena Carro, Pascale Fournier, Petar Pujic, Hasna Boubakri, Nicole Alloisio, Tomas Persson, Katharina Pawlowski, Philippe Normand, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), School Biology, Newcastle University, Department Ecology Environment and Plant Sciece, Stockholm University, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: 0106 biological sciences, 0301 basic medicine, Membrane permeability, [SDV]Life Sciences [q-bio], Frankia, vésicule, dicarboxylate, 01 natural sciences, Microbiology, 03 medical and health sciences, Citrate synthase, propionate, métabolisme, vesicle, chemistry.chemical_classification, Frankia alni, organic acid, frankia, biology, [ SDV ] Life Sciences [q-bio], Metabolism, biology.organism_classification, Citric acid cycle, 030104 developmental biology, Biochemistry, chemistry, nitrogen fixation, acide organique, biology.protein, Propionate, General Agricultural and Biological Sciences, respiration, 010606 plant biology & botany, Organic acid
Abstract: Trophic exchanges constitute the bases of the symbiosis between the nitrogen-fixing actinomycete Frankia and its host plant Alnus, but the identity of the compounds exchanged is still poorly known. In the current work, previously published transcriptomic studies of Alnus nodules and of symbiotic Frankia were reexamined for TCA cycle related genes. The bacterial TCA enzyme genes were all upregulated, especially the succinyl-CoA synthase and the citrate synthase while on the plant side, none was significantly modified in nodules relative to non-inoculated roots. A preliminary metabolomics approach permitted to see that citrate, 2-oxoglutarate, succinate, malate and fumarate were all more abundant (FC (Fold change) = 5-70) in mature nitrogen-fixing nodules than in roots. In the evaluation of the uptake and metabolism of these organic acids, a significant change was observed in the morphology of nitrogen fixing vesicles in vitro: the dicarboxylates malate, succinate and fumarate induced the formation of larger vesicles than was the case with propionate. Moreover, the production of spores was also modified depending on the organic acid present. The assays showed that most C4 dicarboxylates were taken up while C6 tricarboxylates were not and citrate even partially blocked catabolism of reserve carbon. Tests were performed to determine if the change in membrane permeability induced by Ag5, a peptide previously shown to modify the membranes of Frankia, increased the uptake of specific organic acids. No effect was observed with citrate while an increase in nitrogen fixation was seen with propionate.
Published: 2015

48. Alnus peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing Frankia

Author: Valérie Hocher, Petar Pujic, Lorena Carro, Nicole Alloisio, Pascale Fournier, Séverine Balmand, Franck Poly, Anne E Hay, Philippe Normand, Marjolaine Rey, Philippe François, Hasna Boubakri, Abdelaziz Heddi, Peter Mergaert, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Intéractions Plantes-Bactéries (PBI), Département Microbiologie (Dpt Microbio), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, ANR ([Sesam ANR-10-BLAN-1708], [BugsInACell ANR-13-BSV7-0013-03]), FR BioEnvironment and Health (Lyon), MEC postdoctoral fellowship from the Spanish government to LC (Programa Nacional de Movilidad de Recursos Humanos del Plan Nacional de I-D+i), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Diversité, adaptation, développement des plantes ( DIADE ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), Intéractions Plantes-Bactéries ( PBI ), Département Microbiologie ( Dpt Microbio ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Biologie Fonctionnelle, Insectes et Interactions ( BF2I ), Institut National de la Recherche Agronomique ( INRA ) -Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), and Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Université de Lyon-Institut National des Sciences Appliquées ( INSA )
Subjects: Nitrogen, [SDV]Life Sciences [q-bio], Frankia, Biology, Alnus, Plant Roots, Microbiology, Defensins, 03 medical and health sciences, Symbiosis, Ammonia, Nitrogen Fixation, Nitrogenase, Botany, Ecology, Evolution, Behavior and Systematics, Plant Proteins, 030304 developmental biology, 0303 health sciences, [ SDV ] Life Sciences [q-bio], 030306 microbiology, Vesicle, Cell Membrane, fungi, Microarray Analysis, biology.organism_classification, Plant cell, Glutamine, Alnus glutinosa, Biochemistry, Nitrogen fixation, Original Article, Actinorhizal plant, Porosity
Abstract: International audience; 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 N2-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.
Published: 2015

49. Adaptations of Prokaryotes to Their Biotopes and to Physicochemical Conditions in Natural or Anthropized Environments

Author: Pierre Caumette, Philippe Normand, Petar Pujic, Philippe Goulas, Florence Wisniewski-Dyé, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Jean-Claude Bertrand, Pierre Caumette, Philippe Lebaron, Robert Matheron, Philippe Normand, Télesphore Sime-Ngando, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), and Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Biotope, Morphology, Glycosylation, Physiology, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Signal transduction, Adaptability, 03 medical and health sciences, Antibiosis, Fitness, Selective advantage, Homeostasis, Adaptation, 030304 developmental biology, media_common, Phase variation, 0303 health sciences, biology, 030306 microbiology, 15. Life on land, biology.organism_classification, Protein modification, Quorum sensing, Metabolism, 13. Climate action, Evolutionary biology, Posttranslational modification, Transcription, Bacteria
Abstract: International audience; Microorganisms to Physicochemical Conditions…?> live in a constantly changing environment and must modify their physiology and morphology to cope with these changes. The main systems for molecular adaptation to modifications of environmental conditions and the behavioral responses of prokaryotes in various habitats, excluding extreme habitats, are discussed. The main regulation systems that are described are transcription, signal transduction, and protein modifications. Three specialized systems are also presented in details: quorum sensing, phase variation, and antibiosis. Quorum sensing allows bacteria to trigger some responses when their density is high enough to permit the function to be successful. Phase variation is an adaptive process by which a bacterial subpopulation undergoes frequent, usually reversible phenotypic changes resulting from genetic or epigenetic alterations, allowing rapid modification of the cells physiology. Antibiosis is the ability to synthesize molecules that will impact other taxa and eventually provide a selective advantage to which some microbes respond by resisting to these molecules.Finally are described the physiological responses to various environmental parameters such as temperature, oxidants, salinity, acidity, pressure, desiccation, and how this translates in different biotopes such as soil, water bodies, sediments, biofilms, mats, air, and manmade biotopes.
Published: 2015

50. The Frankia alni Symbiotic Transcriptome

Author: Nicole Alloisio, Ken-ichi Kucho, Petar Pujic, Philippe Normand, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Graduate School of Science and Engineering, Kagoshima University, Frans J. de Bruijn, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: 0106 biological sciences, 0303 health sciences, 03 medical and health sciences, [SDV]Life Sciences [q-bio], 01 natural sciences, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience
Published: 2015

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