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1. Field Site-Specific Effects of an Azospirillum Seed Inoculant on Key Microbial Functional Groups in the Rhizosphere

Author

Sébastien Renoud, Jordan Vacheron, Danis Abrouk, Claire Prigent-Combaret, Laurent Legendre, Daniel Muller, and Yvan Moënne-Loccoz

Subjects
microbial functional group, PGPR, inoculation, nitrogen fixers, ACC deaminase producers, 4-diacetylphloroglucinol producers, Microbiology, QR1-502
Abstract

The beneficial effects of plant growth–promoting Rhizobacteria (PGPR) entail several interaction mechanisms with the plant or with other root-associated microorganisms. These microbial functions are carried out by multiple taxa within functional groups and contribute to rhizosphere functioning. It is likely that the inoculation of additional PGPR cells will modify the ecology of these functional groups. We also hypothesized that the inoculation effects on functional groups are site specific, similarly as the PGPR phytostimulation effects themselves. To test this, we assessed in the rhizosphere of field-grown maize the effect of seed inoculation with the phytostimulatory PGPR Azospirillum lipoferum CRT1 on the size and/or diversity of selected microbial functional groups important for plant growth, using quantitative polymerase chain reaction and/or Illumina MiSeq metabarcoding. The functional groups included bacteria able to fix nitrogen (a key nutrient for plant growth), producers of 1-aminocyclopropane-1-carboxylate (ACC) deaminase (which modulate ethylene metabolism in plant and stimulate root growth), and producers of 2,4-diacetylphloroglucinol (an auxinic signal enhancing root branching). To test the hypothesis that such ecological effects were site-specific, the functional groups were monitored at three different field sites, with four sampling times over two consecutive years. Despite poor inoculant survival, inoculation enhanced maize growth. It also increased the size of functional groups in the three field sites, at the maize six-leaf and flowering stages for diazotrophs and only at flowering stage for ACC deaminase and 2,4-diacetylphloroglucinol producers. Sequencing done in the second year revealed that inoculation modified the composition of diazotrophs (and of the total bacterial community) and to a lesser extent of ACC deaminase producers. This study revealed an ecological impact that was field specific (even though a few taxa were impacted in all fields) and of unexpected magnitude with the phytostimulatory Azospirillum inoculant, when considering microbial functional groups. Further methodological developments are needed to monitor additional functional groups important for soil functioning and plant growth under optimal or stress conditions.

Published
2022
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2. Microbiome Analysis of New, Insidious Cave Wall Alterations in the Apse of Lascaux Cave

Author

Lise Alonso, Thomas Pommier, Danis Abrouk, Mylène Hugoni, Van Tran Van, Guillaume Minard, Claire Valiente Moro, and Yvan Moënne-Loccoz

Subjects
Paleolithic caves, anthropization, cave alterations, microbial diversity, pigmented fungi, collembola, Biology (General), QH301-705.5
Abstract

Lascaux Cave is a UNESCO site that was closed to the public following wall surface alterations. Most black stains that had formed on wall surface are stable or receding, but a new type of alteration visually quite different (termed dark zones) developed in Lascaux’s Apse room in the last 15 years. Here, we tested the hypothesis that dark zones displayed a different microbial community than black stains previously documented in the same room, using metabarcoding (MiSeq sequencing). Indeed, dark zones, black stains and neighboring unstained parts displayed distinct microbial communities. However, similarly to what was observed in black stains, pigmented fungi such as Ochroconis (now Scolecobasidium) were more abundant and the bacteria Pseudomonas less abundant in dark zones than in unstained parts. The collembola Folsomia candida, which can disseminate microorganisms involved in black stain development, was also present on dark zones. Illumina sequencing evidenced Ochroconis (Scolecobasidium) in all collembola samples from dark zones, as in collembola from black stains. This study shows that the microbial properties of dark zones are peculiar, yet dark zones display a number of microbial resemblances with black stains, which suggests a possible role of collembola in promoting these two types of microbial alterations on wall surfaces.

Published
2022
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4. 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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5. 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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6. Effect of Inoculation Level on the Impact of the PGPR Azospirillum lipoferum CRT1 on Selected Microbial Functional Groups in the Rhizosphere of Field Maize

Author

Sébastien Renoud, Danis Abrouk, Claire Prigent-Combaret, Florence Wisniewski-Dyé, Laurent Legendre, Yvan Moënne-Loccoz, and Daniel Muller

Subjects
functional community, diazotrophs, nitrogen fixers, ACC deaminase producers, Biology (General), QH301-705.5
Abstract

The impact of inoculated plant growth-promoting rhizobacteria (PGPR) on its host physiology and nutrition depends on inoculum level. Whether the impact of the inoculated PGPR on the indigenous rhizosphere microbiota also varies with the PGPR inoculum level is unclear. Here, we tested this issue using the PGPR Azospirillum lipoferum CRT1—maize model system, where the initial seed inoculation is known to enhance maize growth and germination, and impacts the maize rhizomicrobiota, including microbial functional groups modulating plant growth. A. lipoferum CRT1 was added to the seeds at standard (105–6 cells.seed−1) or reduced (104–5 cells.seed−1) inoculation levels, in three fields. The effect of the two PGPR formulations was assessed on maize growth and on the nifH (nitrogen fixation), acdS (ACC deaminase activity) and phlD (2,4-diacetylphloroglucinol production) microbial functional groups. The size of the three functional groups was monitored by qPCR at the six-leaf stage and the flowering stage, and the diversity of the nifH and acdS functional groups (as well as the bacterial community) were estimated by MiSeq metabarcoding at the six-leaf stage. The results showed that the benefits of the reduced inoculant formulation were significant in two out of three fields, but different (often lower) than those of the standard formulation. The effects of formulations on the size of the three functional groups differed, and depended on field site and functional group. The reduced formulation had an impact on the diversity of nifH and acdS groups at one site, whereas the standard formulation had an impact at the two other sites. Inoculation significantly impacted the total bacterial community in the three fields, but only with the reduced formulation. In conclusion, the reduced inoculant formulation impacted the indigenous rhizosphere microbiota differently, but not less efficiently, than the standard formulation.

Published
2022
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7. Diversifying Anaerobic Respiration Strategies to Compete in the Rhizosphere

Author

Solène M. Lecomte, Wafa Achouak, Danis Abrouk, Thierry Heulin, Xavier Nesme, and Feth el Zahar Haichar

Subjects
rhizosphere competence, anaerobic respiration, terminal electron acceptors, respiratory pathways, rhizobacteria, root colonization, Environmental sciences, GE1-350
Abstract

The rhizosphere is the interface between plant roots and soil where intense, varied interactions between plants and microbes influence plants' health and growth through their influence on biochemical cycles, such as the carbon, nitrogen, and iron cycles. The rhizosphere is also a changing environment where oxygen can be rapidly limited and anaerobic zones can be established. Microorganisms successfully colonize the rhizosphere when they possess specific traits referred to as rhizosphere competence. Anaerobic respiration flexibility contributes to the rhizosphere competence of microbes. Indeed, a wide range of compounds that are available in the rhizosphere can serve as alternative terminal electron acceptors during anaerobic respiration such as nitrates, iron, carbon compounds, sulfur, metalloids, and radionuclides. In the presence of multiple terminal electron acceptors in a complex environment such as the rhizosphere and in the absence of O2, microorganisms will first use the most energetic option to sustain growth. Anaerobic respiration has been deeply studied, and the genes involved in anaerobic respiration have been identified. However, aqueous environment and paddy soils are the most studied environments for anaerobic respiration, even if we provide evidence in this review that anaerobic respiration also occurs in the plant rhizosphere. Indeed, we provide evidence by performing a BLAST analysis on metatranscriptomic data that genes involved in iron, sulfur, arsenate and selenate anaerobic respiration are expressed in the rhizosphere, underscoring that the rhizosphere environment is suitable for the establishment of anaerobic respiration. We thus focus this review on current research concerning the different types of anaerobic respiration that occur in the rhizosphere. We also discuss the flexibility of anaerobic respiration as a fundamental trait for the microbial colonization of roots, environmental and ecological adaptation, persistence and bioremediation in the rhizosphere. Anaerobic respiration appears to be a key process for the functioning of an ecosystem and interactions between plants and microbes.

Published
2018
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8. Exploring the Diversity of Fungal DyPs in Mangrove Soils to Produce and Characterize Novel Biocatalysts

Author

Amal Ben Ayed, Geoffroy Saint-Genis, Laurent Vallon, Dolores Linde, Annick Turbé-Doan, Mireille Haon, Marianne Daou, Emmanuel Bertrand, Craig B. Faulds, Giuliano Sciara, Martino Adamo, Roland Marmeisse, Sophie Comtet-Marre, Pierre Peyret, Danis Abrouk, Francisco J. Ruiz-Dueñas, Cyril Marchand, Mylène Hugoni, Patricia Luis, Tahar Mechichi, and Eric Record

Subjects
lignocellulose degrading enzymes, dye-decolorizing peroxidases, heterologous expression, dye decolorization, marine fungus, mangrove, Biology (General), QH301-705.5
Abstract

The functional diversity of the New Caledonian mangrove sediments was examined, observing the distribution of fungal dye-decolorizing peroxidases (DyPs), together with the complete biochemical characterization of the main DyP. Using a functional metabarcoding approach, the diversity of expressed genes encoding fungal DyPs was investigated in surface and deeper sediments, collected beneath either Avicennia marina or Rhizophora stylosa trees, during either the wet or the dry seasons. The highest DyP diversity was observed in surface sediments beneath the R. stylosa area during the wet season, and one particular operational functional unit (OFU1) was detected as the most abundant DyP isoform. This OFU was found in all sediment samples, representing 51–100% of the total DyP-encoding sequences in 70% of the samples. The complete cDNA sequence corresponding to this abundant DyP (OFU 1) was retrieved by gene capture, cloned, and heterologously expressed in Pichia pastoris. The recombinant enzyme, called DyP1, was purified and characterized, leading to the description of its physical–chemical properties, its ability to oxidize diverse phenolic substrates, and its potential to decolorize textile dyes; DyP1 was more active at low pH, though moderately stable over a wide pH range. The enzyme was very stable at temperatures up to 50 °C, retaining 60% activity after 180 min incubation. Its ability to decolorize industrial dyes was also tested on Reactive Blue 19, Acid Black, Disperse Blue 79, and Reactive Black 5. The effect of hydrogen peroxide and sea salt on DyP1 activity was studied and compared to what is reported for previously characterized enzymes from terrestrial and marine-derived fungi.

Published
2021
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10. Wheat genome architecture influences interactions with phytobeneficial microbial functional groups in the rhizosphere

Author

Cécile Gruet, Danis Abrouk, Andreas Börner, Daniel Muller, and Yvan Moënne‐Loccoz

Subjects
Physiology, Plant Science
Abstract

Wheat has undergone a complex evolutionary history, which led to allopolyploidization and the hexaploid bread wheat Triticum aestivum. However, the significance of wheat genomic architecture for beneficial plant-microbe interactions is poorly understood, especially from a functional standpoint. In this study, we tested the hypothesis that wheat genomic architecture was an overriding factor determining root recruitment of microorganisms with particular plant-beneficial traits. We chose five wheat species representing genomic profiles AA (Triticum urartu), BB {SS} (Aegilops speltoides), DD (Aegilops tauschii), AABB (Triticum dicoccon) and AABBDD (Triticum aestivum) and assessed by qPCR their ability to interact with free-nitrogen fixers, 1-aminocyclopropane-1-carboxylate deaminase producers, 2,4-diacetylphloroglucinol producers and auxin producers via the phenylpyruvate decarboxylase pathway, in combination with Illumina MiSeq metabarcoding analysis of N fixers (and of the total bacterial community). We found that the abundance of the microbial functional groups could fluctuate according to wheat genomic profile, as did the total bacterial abundance. N fixer diversity and total bacterial diversity were also influenced significantly by wheat genomic profile. Often, rather similar results were obtained for genomes DD (Ae. tauschii) and AABBDD (T. aestivum), pointing for the first time that the D genome could be particularly important for wheat-bacteria interactions. This article is protected by copyright. All rights reserved.

Published
2022

11. Genomic Insights of Alnus-Infective Frankia Strains Reveal Unique Genetic Features and New Evidence on Their Host-Restricted Lifestyle

Author

Sandra Kim Tiam, Hasna Boubakri, Lorine Bethencourt, Danis Abrouk, Pascale Fournier, and Aude Herrera-Belaroussi

Subjects
Frankia, actinorhizal symbiosis, Genetics, agmatine deiminase, in planta sporulation, genome reduction, Genetics (clinical), HUP, gas vesicles
Abstract

The present study aimed to use comparative genomics to explore the relationships between Frankia and actinorhizal plants using a data set made of 33 Frankia genomes. The determinants of host specificity were first explored for “Alnus-infective strains” (i.e., Frankia strains belonging to Cluster Ia). Several genes were specifically found in these strains, including an agmatine deiminase which could possibly be involved in various functions as access to nitrogen sources, nodule organogenesis or plant defense. Within “Alnus-infective strains”, Sp+ Frankia genomes were compared to Sp− genomes in order to elucidate the narrower host specificity of Sp+ strains (i.e., Sp+ strains being capable of in planta sporulation, unlike Sp− strains). A total of 88 protein families were lost in the Sp+ genomes. The lost genes were related to saprophytic life (transcriptional factors, transmembrane and secreted proteins), reinforcing the proposed status of Sp+ as obligatory symbiont. The Sp+ genomes were also characterized by a loss of genetic and functional paralogs, highlighting a reduction in functional redundancy (e.g., hup genes) or a possible loss of function related to a saprophytic lifestyle (e.g., genes involved in gas vesicle formation or recycling of nutrients).

Published
2023
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15. 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

16. 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

17. Datamining and functional environmental genomics reassess the phylogenetics and functional diversity of fungal monosaccharide transporters

Author

Roland Marmeisse, Danis Abrouk, Delphine Melayah, Laurent Vallon, Sabine Zimmermann, Florian Barbi, Marc Lemaire, Patricia Luis, Carmen Guerrero-Galán, Laurence Fraissinet-Tachet, Jeanne Doré, 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), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Microbiologie, adaptation et pathogénie (MAP), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), and CNRS-INSU ECCO Microbien programINRA metaprogramme M2E (project Metascreen)

Subjects
Protein family, Rhamnose, [SDV]Life Sciences [q-bio], Mannose, Xylose, Applied Microbiology and Biotechnology, 03 medical and health sciences, chemistry.chemical_compound, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Phylogeny, ComputingMilieux_MISCELLANEOUS, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Metatranscriptomics, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Fungal protein, environmental genomics, Ascomycota, biology, 030306 microbiology, Monosaccharides, metatranscriptomics 22 23, sugar transporters, Fungi, Membrane Transport Proteins, Biological Transport, General Medicine, biology.organism_classification, Yeast, Glucose, Biochemistry, chemistry, Galactose, Metagenomics, Biotechnology
Abstract

International audience; Sugar transporters are essential components of carbon metabolism and have been extensively studied to control sugar uptake by yeasts and filamentous fungi used in fermentation processes. Based on published information on characterized fungal sugar porters, we show that this protein family encompasses phylogenetically distinct clades. While several clades encompass transporters that seemingly specialized on specific "sugar-related" molecules (e.g., myo-inositol, charged sugar analogs), others include mostly either mono- or di/oligosaccharide low-specificity transporters. To address the issue of substrate specificity of sugar transporters, that protein primary sequences do not fully reveal, we screened "multi-species" soil eukaryotic cDNA libraries for mannose transporters, a sugar that had never been used to select transporters. We obtained 19 environmental transporters, mostly from Basidiomycota and Ascomycota. Among them, one belonged to the unusual "Fucose H+ Symporter" family, which is only known in Fungi for a rhamnose transporter in Aspergillus niger. Functional analysis of the 19 transporters by expression in yeast and for two of them in Xenopus laevis oocytes for electrophysiological measurements indicated that most of them showed a preference for D-mannose over other tested D-C6 (glucose, fructose, galactose) or D-C5 (xylose) sugars. For the several glucose and fructose-negative transporters, growth of the corresponding recombinant yeast strains was prevented on mannose in the presence of one of these sugars that may act by competition for the binding site. Our results highlight the potential of environmental genomics to figure out the functional diversity of key fungal protein families and that can be explored in a context of biotechnology. KEY POINTS: • Most fungal sugar transporters accept several sugars as substrates. • Transporters, belonging to 2 protein families, were isolated from soil cDNA libraries. • Environmental transporters featured novel substrate specificities.

Published
2021

18. Implications of carbon catabolite repression for plant–microbe interactions

Author

Theophile Franzino, Hasna Boubakri, Tomislav Cernava, Danis Abrouk, Wafa Achouak, Sylvie Reverchon, William Nasser, Feth el Zahar Haichar, Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Chromatine et Régulation de la Pathogénie bactérienne (CRP), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), 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), Graz University of Technology [Graz] (TU Graz), 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), and ANR-18-CE32-0005,DIORE,Régulation de la dénitrification par la nature des exsudats racinaires(2018)

Subjects
Catabolite Repression, Bacteria, integumentary system, fungi, Fungi, Cell Biology, Plant Science, carbon catabolite repression, Biochemistry, CCR, Carbon, carbon utilization, [SDE]Environmental Sciences, rhizosphere, Molecular Biology, substrate-use preferences, Biotechnology, plant-microbe interaction
Abstract

International audience; Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.

Published
2022

19. Effect of Inoculation Level on the Impact of the PGPR

Author

Sébastien, Renoud, Danis, Abrouk, Claire, Prigent-Combaret, Florence, Wisniewski-Dyé, Laurent, Legendre, Yvan, Moënne-Loccoz, and Daniel, Muller

Abstract

The impact of inoculated plant growth-promoting rhizobacteria (PGPR) on its host physiology and nutrition depends on inoculum level. Whether the impact of the inoculated PGPR on the indigenous rhizosphere microbiota also varies with the PGPR inoculum level is unclear. Here, we tested this issue using the PGPR

Published
2021

20. Field Site-Specific Effects of an

Author

Sébastien, Renoud, Jordan, Vacheron, Danis, Abrouk, Claire, Prigent-Combaret, Laurent, Legendre, Daniel, Muller, and Yvan, Moënne-Loccoz

Abstract

The beneficial effects of plant growth-promoting Rhizobacteria (PGPR) entail several interaction mechanisms with the plant or with other root-associated microorganisms. These microbial functions are carried out by multiple taxa within functional groups and contribute to rhizosphere functioning. It is likely that the inoculation of additional PGPR cells will modify the ecology of these functional groups. We also hypothesized that the inoculation effects on functional groups are site specific, similarly as the PGPR phytostimulation effects themselves. To test this, we assessed in the rhizosphere of field-grown maize the effect of seed inoculation with the phytostimulatory PGPR

Published
2021

22. Small-Scale Variability in Bacterial Community Structure in Different Soil Types

Author

Jean Thioulouse, Claire Prigent-Combaret, Naoise Nunan, Geneviève L. Grundmann, Deborah Goffner, Jean M.F. Martins, Mylène Hugoni, Audrey Dubost, Danis Abrouk, 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 d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Swedish University of Agricultural Sciences (SLU), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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 des Géosciences de l’Environnement (IGE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Environnement, Santé, Sociétés (ESS), Centre National de la Recherche Scientifique (CNRS), EC2CO MicrobiEn AO2012779949French National Research Agency (ANR) ANR-11LABX-0010, Unité Mixte Internationale 'Environnement Santé Sociétés' (ESS), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Ecology and Environmental sciences, IEES-Paris, Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Unité de Neurobiologie des canaux Ioniques et de la Synapse (UNIS - Inserm U1072), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and EC2CO MicrobiEn AO2012779949French National Research Agency (ANR)ANR-11LABX-0010

Subjects
0301 basic medicine, 030106 microbiology, Soil Science, Biology, Spatial distribution, Generalist and specialist species, Ecological strategies, 03 medical and health sciences, Soil, Microbial ecology, RNA, Ribosomal, 16S, Ecosystem, Ecology, Evolution, Behavior and Systematics, Spatial organization, Soil Microbiology, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Ecology, Community, Microbiota, Spatial scale, Community structure, Biodiversity, 15. Life on land, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Bacterial diversity, Spatial ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.

Published
2021

23. Proposal of 'Candidatus Frankia alpina', the uncultured symbiont of Alnus alnobetula and A. incana that forms spore-containing nitrogen-fixing root nodules

Author

Pascale Fournier, Adrien C. Pozzi, Danis Abrouk, Maria P. Fernandez, Audrey Dubost, Philippe Normand, Lorine Bethencourt, Aude Herrera-Belaroussi, Hector H. Bautista-Guerrero, Guillaume Schwob, 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), FR BioEnVis, and Université de Lyon

Subjects
NJ, food.ingredient, Root nodule, spores, [SDV]Life Sciences [q-bio], Frankia, Biology, Myrica, Microbiology, Actinobacteria, Myricaceae, 03 medical and health sciences, food, Botany, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, 030306 microbiology, fungi, average nucleotide identity, General Medicine, alder, 15. Life on land, Alnus alnobetula, biology.organism_classification, ML, neighbour-joining, Symbiotic. Abbreviations: ANI, Nitrogen fixation, Candidatus, maximum-likelihood, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

The members of the genus Frankia are, with a few exceptions, a group of nitrogen-fixing symbiotic actinobacteria that nodulate mostly woody dicotyledonous plants belonging to three orders, eight families and 23 genera of pioneer dicots. These bacteria have been characterized phylogenetically and grouped into four molecular clusters. One of the clusters, cluster 1 contains strains that induce nodules on Alnus spp. (Betulaceae), Myrica spp., Morella spp. and Comptonia spp. (Myricaceae) that have global distributions. Some of these strains produce not only hyphae and vesicles, as other cluster 1 strains do, but also numerous sporangia in their host symbiotic tissues, hence their phenotype being described as spore-positive (Sp+). While Sp+ strains have resisted repeated attempts at cultivation, their genomes have recently been characterized and found to be different from those of all described species, being markedly smaller than their phylogenetic neighbours. We thus hereby propose to create a 'Candidatus Frankia alpina' species for some strains present in nodules of Alnus alnobetula and A. incana that grow in alpine environments at high altitudes or in subarctic environments at high latitudes.

Published
2020

24. Proposal of '

Author

Adrien C Meynier, Pozzi, Aude, Herrera-Belaroussi, Guillaume, Schwob, Hector H, Bautista-Guerrero, Lorine, Bethencourt, Pascale, Fournier, Audrey, Dubost, Danis, Abrouk, Philippe, Normand, and Maria P, Fernandez

Subjects
Magnoliopsida, Nitrogen Fixation, Frankia, Alnus, Root Nodules, Plant, Symbiosis, Phylogeny, Bacterial Typing Techniques
Abstract

The members of the genus

Published
2020

25. Candidatus Frankia nodulisporulans sp. nov., an Alnus glutinosa-infective Frankia species unable to grow in pure culture and able to sporulate in-planta

Author

Andreas Brachmann, Adrien C. Pozzi, Lorine Bethencourt, Philippe Normand, Natuschka M. Lee, Jörn Kalinowski, Pascale Fournier, Fede Berckx, Anita Sellstedt, Maria P. Fernandez, Jochen Blom, Katharina Pawlowski, Daniel Wibberg, Aude Herrera-Belaroussi, Danis Abrouk, Audrey Dubost, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
DNA, Bacterial, Root nodule, Hypha, Frankia, Sp plus Frankia strains, Alnus, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, RNA, Ribosomal, 16S, Botany, In-planta sporulation, Frankia-Alnus symbiosis, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, Sweden, 0303 health sciences, biology, 030306 microbiology, Sporangium, Comparative genomics, fungi, Sequence Analysis, DNA, biology.organism_classification, 16S ribosomal RNA, Bacterial Typing Techniques, Alnus glutinosa, GenBank, Candidatus, France, Root Nodules, Plant, Hydrogenasee, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

We describe a new Frankia species, for three non-isolated strains obtained from Alnus glutinosa in France and Sweden, respectively. These strains can nodulate several Alnus species (A. glutinosa, A. incana, A. alnobetula), they form hyphae, vesicles and sporangia in the root nodule cortex but have resisted all attempts at isolation in pure culture. Their genomes have been sequenced, they are significantly smaller than those of other Alnus-infective species (5Mb instead of 7.5Mb) and are very closely related to one another (ANI of 100%). The name Candidatus Frankia nodulisporulans is proposed. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and draft genome sequences reported in this study for AgTrS, AgUmASt1 and AgUmASH1 are MT023539/LR778176/LR778180 and NZ_CADCWS000000000.1/CADDZU010000001/CADDZW010000001, respectively. Copyright © 2020 Elsevier GmbH. All rights reserved.

Published
2020

26. Author Correction: Complex ecological interactions of Staphylococcus aureus in tampons during menstruation

Author

Samuel Barreto, Michèle Bes, Gery Lamblin, Jean-Philippe Rasigade, Anne Tristan, Daniel Muller, Tristan Ferry, Y. Gillet, François Golfier, Claire Prigent-Combaret, Jean Thioulouse, Danis Abrouk, Gerard Lina, Isaline Jacquemond, Audrey Dubost, Anaëlle Muggeo, Pierre Adrien Bolze, and Claude Alexandre Gustave

Subjects
Adult, Staphylococcus aureus, lcsh:Medicine, medicine.disease_cause, Microbiology, Young Adult, RNA, Ribosomal, 16S, Medicine, DNA Barcoding, Taxonomic, Humans, lcsh:Science, Author Correction, Menstrual Hygiene Products, Multidisciplinary, Bacteria, business.industry, Microbiota, lcsh:R, Staphylococcal Infections, During menstruation, Shock, Septic, Menstruation, Vagina, lcsh:Q, Female, business, Tampon
Abstract

Menstrual toxic shock syndrome (mTSS) is a severe disease that occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock toxin 1 and who use tampons. The aim of the present study was to determine the impact of the composition of vaginal microbial communities on tampon colonisation by S. aureus during menses. We analysed the microbiota in menstrual fluids extracted from tampons from 108 healthy women and 7 mTSS cases. Using culture, S. aureus was detected in menstrual fluids of 40% of healthy volunteers and 100% of mTSS patients. Between class analysis of culturomic and 16S rRNA gene metabarcoding data indicated that the composition of the tampons' microbiota differs according to the presence or absence of S. aureus and identify discriminating genera. However, the bacterial communities of tampon fluid positive for S. aureus did not cluster together. No difference in tampon microbiome richness, diversity, and ecological distance was observed between tampon vaginal fluids with or without S. aureus, and between healthy donors carrying S. aureus and mTSS patients. Our results show that the vagina is a major niche of. S. aureus in tampon users and the composition of the tampon microbiota control its virulence though more complex interactions than simple inhibition by lactic acid-producing bacterial species.

Published
2020

27. Genome Sequence of

Author

Gabriela, Vuletin Selak, Marina, Raboteg, Pascale, Fournier, Audrey, Dubost, Danis, Abrouk, Katja, Žanić, Slavko, Perica, Philippe, Normand, and Petar, Pujić

Subjects
Genome Sequences
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

28. Complex ecological interactions of Staphylococcus aureus in tampons during menstruation

Author

Michèle Bes, Gery Lamblin, Jean Thioulouse, Audrey Dubost, François Golfier, Isaline Jacquemond, Daniel Muller, Anne Tristan, Samuel Barreto, Yves Gillet, Danis Abrouk, Claude Alexandre Gustave, Tristan Ferry, Jean-Philippe Rasigade, Anaëlle Muggeo, Gerard Lina, Pierre Adrien Bolze, Claire Prigent-Combaret, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Femme Mère Enfant [CHU - HCL] (HFME), Hospices Civils de Lyon (HCL), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Centre National de Reference des Staphylocoques, Université de Lyon, Hôpital de la Croix-Rousse [CHU - HCL], 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), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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 quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), 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), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de Chirurgie Gynécologique Oncologique et Obstétrique [CHU Lyon Sud], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Service de Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse - HCL], LABEX ECOFECT of Universite de Lyon within the programme 'Investissements d'Avenir' ANR-11-LABX-0048, ANR-11-IDEX-0007, 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 National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Davoine, Laure-Hélène, Service de Chirurgie Gynécologique et Oncologique – Obstétrique [CHU Lyon Sud], Service des Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse, CHU-HCL], 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
staphylococcus aureus, 0301 basic medicine, [SDV.IMM] Life Sciences [q-bio]/Immunology, [SDV]Life Sciences [q-bio], femme, 030106 microbiology, microbiome, Virulence, Severe disease, lcsh:Medicine, Biology, [SDV.MHEP.GEO]Life Sciences [q-bio]/Human health and pathology/Gynecology and obstetrics, medicine.disease_cause, Article, Microbiology, 03 medical and health sciences, microbiote, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Microbiome, lcsh:Science, ComputingMilieux_MISCELLANEOUS, cycle menstruel, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, communauté microbienne, Multidisciplinary, lcsh:R, Toxic shock syndrome, santé humaine, medicine.disease, During menstruation, equipment and supplies, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, medicine.anatomical_structure, Staphylococcus aureus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Vagina, [SDV.IMM]Life Sciences [q-bio]/Immunology, lcsh:Q, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Tampon
Abstract

Menstrual toxic shock syndrome (mTSS) is a severe disease that occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock toxin 1 and who use tampons. The aim of the present study was to determine the impact of the composition of vaginal microbial communities on tampon colonisation by S. aureus during menses. We analysed the microbiota in menstrual fluids extracted from tampons from 108 healthy women and 7 mTSS cases. Using culture, S. aureus was detected in menstrual fluids of 40% of healthy volunteers and 100% of mTSS patients. Between class analysis of culturomic and 16S rRNA gene metabarcoding data indicated that the composition of the tampons’ microbiota differs according to the presence or absence of S. aureus and identify discriminating genera. However, the bacterial communities of tampon fluid positive for S. aureus did not cluster together. No difference in tampon microbiome richness, diversity, and ecological distance was observed between tampon vaginal fluids with or without S. aureus, and between healthy donors carrying S. aureus and mTSS patients. Our results show that the vagina is a major niche of. S. aureus in tampon users and the composition of the tampon microbiota control its virulence though more complex interactions than simple inhibition by lactic acid-producing bacterial species.

Published
2018

29. Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon

Author

Philippe Normand, Céline Brochier-Armanet, Guillaume Schwob, Jean-Pierre Flandrois, Danis Abrouk, Jérôme Briolay, Maria P. Fernandez, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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 de Lyon, 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), Fondation Verots, Ministry of Higher Education & Scientific Research (MHESR), 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, Spectinomycin, Operon, Ribosomal proteins, Computational biology, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, Genome, Polymerase Chain Reaction, 03 medical and health sciences, Ribosomal protein, RNA, Ribosomal, 16S, medicine, Spectinomycin operon, Molecular Biology, Gene, Phylogeny, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Phylogenetic tree, Base Sequence, 030306 microbiology, General Medicine, Sequence Analysis, DNA, Housekeeping gene, Anti-Bacterial Agents, Genes, Bacterial, Prokaryote systematics, Frankia, Long range PCR, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, medicine.drug
Abstract

International audience; The taxonomic assignment of uncultured prokaryotes to known taxa is a major challenge in microbial systematics. This relies usually on the phylogenetic analysis of the ribosomal small subunit RNA or a few housekeeping genes. Recent works have disclosed ribosomal proteins as valuable markers for system-atics and, due to the boom in complete genome sequencing, their use has become widespread. Yet, in the case of uncultured strains, for which complete genome sequences cannot be easily obtained, sequencing many markers is complicated and time consuming. Taking the advantage of the organization of ribo-somal protein coding genes in large gene clusters, we amplified a 32 kb conserved region encompassing the spectinomycin (spc) operon using long range PCR from isolated and from uncultured nodular endophytic Frankia strains. The phylogenetic analysis of the 27 ribosomal protein genes contained in this region provided a robust phylogenetic tree consistent with phylogenies based on larger set of markers, indicating that this subset of ribosomal proteins contains enough phylogenetic signal to address systematic issues. This work shows that using long range PCR could break down the barrier preventing the use of ribosomal proteins as phylogenetic markers when complete genome sequences cannot be easily obtained.

Published
2019

30. 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

31. Draft genome sequences for three unisolated

Author

Lorine, Bethencourt, Florian, Vautrin, Najwa, Taib, Audrey, Dubost, Lucia, Castro-Garcia, Olivier, Imbaud, Danis, Abrouk, Pascale, Fournier, Jérôme, Briolay, Agnès, Nguyen, Philippe, Normand, Maria P, Fernandez, Céline, Brochier-Armanet, and Aude, Herrera-Belaroussi

Subjects
Short Research Paper, AgTrS, AiOr, fungi, Frankia, AvVan
Abstract

Actinobacteria from genus Frankia are able to form symbiotic associations with actinorhizal plants including alders. Among them, Sp+ strains are characterized by their ability to differentiate numerous sporangia inside host plant cells (unlike “Sp-” strains unable of in-planta sporulation). Here, we report the first genome sequences of three unisolated Sp+ strains: AgTrS, AiOr and AvVan obtained from Alnus glutinosa, A. incana and A. alnobetula (previously known as viridis), respectively (with genome completeness estimated at more than 98%). They represent new Frankia species based on Average Nucleotide Identity (ANI) calculations, and the smallest Alnus-infective Frankia genomes so far sequenced (~5 Mbp), with 5,178, 6,192 and 5,751 candidate protein-encoding genes for AgTrS, AiOr and AvVan, respectively.

Published
2019

32. 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

33. 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

34. Draft genome sequences for three unisolated Alnus -infective Frankia Sp+ strains, AgTrS, AiOr and AvVan, the first sequenced Frankia strains able to sporulate in-planta

Author

Jérôme Briolay, Maria P. Fernandez, Aude Herrera-Belaroussi, Céline Brochier-Armanet, Najwa Taib, Audrey Dubost, Olivier Imbaud, Lucia Castro-Garcia, Pascale Fournier, Danis Abrouk, Florian Vautrin, Philippe Normand, Agnès Nguyen, Lorine Bethencourt, 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), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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 de Lyon, 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), 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), 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
Genetics, 0303 health sciences, biology, 030306 microbiology, Sporangium, [SDV]Life Sciences [q-bio], AiOr, Frankia, fungi, biology.organism_classification, Genome, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Actinobacteria, Spore, 03 medical and health sciences, Alnus glutinosa, AgTrS, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Actinorhizal plant, AvVan, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

International audience; Actinobacteria from genus Frankia are able to form symbiotic associations with actinorhizal plants including alders. Among them, Sp+ strains are characterized by their ability to differentiate numerous sporangia inside host plant cells (unlike "Sp-" strains unable of in-planta sporulation). Here, we report the first genome sequences of three unisolated Sp+ strains: AgTrS, AiOr and AvVan obtained from Alnus glutinosa, A. incana and A. alnobetula (previously known as viridis), respectively (with genome completeness estimated at more than 98%). They represent new Frankia species based on Average Nucleotide Identity (ANI) calculations, and the smallest Alnus-infective Frankia genomes so far sequenced (~5 Mbp), with 5,178, 6,192 and 5,751 candidate protein-encoding genes for AgTrS, AiOr and AvVan, respectively.

Published
2019

35. 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

36. Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size

Author

Maria P. Fernandez, Frédéric Menu, Aude Herrera-Belaroussi, Sophie S. Abby, Danis Abrouk, Adrien C. Pozzi, Philippe Normand, Hector H. Bautista-Guerrero, 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), Génomique et Évolution des Microorganismes (TIMC-IMAG-GEM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-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 Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-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 Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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), Modèles, Dynamiques, Corpus (MoDyCo), Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS), National Center for Scientific Research (CNRS) EC2CO, Mexico-France ECOS program, research cluster FR41 BioEnviS, Ministry of Higher Education and Research (France), CONACYT (Mexico), 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 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), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0301 basic medicine, DNA, Bacterial, Sequence analysis, 030106 microbiology, Frankia, Locus (genetics), genomospecies, Alnus, Applied Microbiology and Biotechnology, Microbiology, Genome, diversity, 03 medical and health sciences, taxonomy, Phylogenetics, RNA, Ribosomal, 16S, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], evolution, MLSA phylogeny, Amplified Fragment Length Polymorphism Analysis, Symbiosis, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Phylogeny, frankia, biology, Base Sequence, Myricaceae, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Bacterial taxonomy, Sequence Analysis, DNA, rpoB, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Genetic divergence, 030104 developmental biology, Evolutionary biology, Root Nodules, Plant, Multilocus Sequence Typing
Abstract

International audience; Diazotrophic Actinobacteria of the genus Frankia represent a challenge to classical bacterial taxonomy as they include many unculturable strains. As a consequence, we still have a poor understanding of their diversity, evolution and biogeography. In this study, a Multi-Locus Sequence Analysis (MLSA) using atpD, dnaA, ftsZ, pgk, and rpoB loci was done on a large set of cultured and uncultured strains, compared to 16S rRNA and correlated to Average Nucleotide Identity (ANI) from available Frankia genomes. MLSA provided a robust resolution of Frankia genus phylogeny and clarified the status of unresolved species and complex of species. The robustness of single-gene topologies and their congruence with the MLSA tree were tested. Lateral Gene Transfers (LGT) were few and scattered, suggesting they had no impact on the concatenate topology. The pgk marker - providing the longest sequence, highest mean genetic divergence and least occurrence of LGT - was used to survey an unequalled number of Alnus-infective Frankia - mainly uncultured strains from a broad range of host-species and geographic origins. This marker allowed reliable Single-Locus Strain Typing (SLST) below the species level, revealed an undiscovered taxonomical diversity, and highlighted the effect of cultivation, sporulation phenotype and host plant species on symbiont richness, diversity and phylogeny.

Published
2018

37. Efficiency and sensitivity of the digital droplet PCR for the quantification of antibiotic resistance genes in soils and organic residues

Author

Sylvie Nazaret, Danis Abrouk, Elisabeth Brothier, Laura Cavé, Edmond Hien, Panignimyandé Salomon Bouda, 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), Research Group on Environmental Multi-Resistance and Efflux Pump, Ecole Nationale Vétérinaire de Lyon (ENVL), IBIO - Plateforme de bio-imagerie en sciences médicales, Université de Lyon, Centre National de la Recherche Scientifique (CNRS), UMR Ecologie et Sols, Université de Ouagadougou, CNRS, ADEME, Campus France, IRD, 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), Université Joseph Ki-Zerbo [Ouagadougou] (UJZK), 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 ), Ecole Nationale Vétérinaire de Lyon ( ENVL ), Université de Lyon (COMUE), and Centre National de la Recherche Scientifique ( CNRS )

Subjects
0301 basic medicine, DNA, Bacterial, sol, [SDV]Life Sciences [q-bio], 030106 microbiology, Gene Dosage, résistance aux antibiotiques, Computational biology, Biology, Applied Microbiology and Biotechnology, Polymerase Chain Reaction, Sensitivity and Specificity, 03 medical and health sciences, chemistry.chemical_compound, Soil, pcr, Drug Resistance, Bacterial, Digital polymerase chain reaction, Environmental DNA, Copy-number variation, antibiotic resistance gene, sensibilité, Gene, Soil Microbiology, résidu organique, [ SDV ] Life Sciences [q-bio], organic residue, use efficiency, General Medicine, sensitivity, Molecular biology, genomic DNA, 030104 developmental biology, efficacité, chemistry, Genes, Bacterial, resistance to antibiotics, Low copy number, digital droplet PCR, DNA, Biotechnology, Antibiotic resistance genes
Abstract

Droplet digital PCR (ddPCR) allows absolute quantification and tolerance to inhibitors and has been proposed as the method of choice to overcome limitations of qPCR. The aim of this study was to evaluate ddPCR and qPCR performances to detect low copy number and copy number variation of antibiotic resistance genes (sul1 and qnrB genes encoding for resistance to sulfonamides and quinolones, respectively) using bacterial genomic DNA (gDNA) and metagenomic DNA extracted from soil and organic residue samples. With gDNA, qPCR showed a better range of quantification but the lower limit of quantification was at 15 copies of qnrB target vs. 1.6 in ddPCR. In the presence of background DNA or inhibitors, we observed a high loss of sensitivity in qPCR and an overestimation of target sequences. When using high amount of environmental DNA templates (70 ng per reaction), ddPCR was still allowing accurate quantification without adding PCR facilitator (i.e., T4 Gene 32 protein). Sensitivity to detect copy number variation was tenfold higher in ddPCR than in qPCR. Finally, the advantages of using ddPCR in environmental studies were confirmed with the quantification of sul1 and qnrB in soils, manures, or urban wastes.

Published
2016

38. Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov

Author

Vincent Daubin, Philippe Normand, Danis Abrouk, Alison M. Berry, Isaac Gifford, Arnab Sen, Assam University, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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), 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), Uniformed Services University of the Health Sciences (USUHS), Department of Plant Sciences [Davis, CA], University of California [Davis] (UC Davis), University of California-University of California, Institute of Microelectronics (NCSR), 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 de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -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 ), Armed Forces Radiobiology Research Institute, University of California [Davis] ( UC Davis ), Institute of Microelectronics ( NCSR ), 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), Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), and University of California (UC)-University of California (UC)

Subjects
DNA, Bacterial, MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, [SDV]Life Sciences [q-bio], Molecular Sequence Data, MESH : Genome, Bacterial, Concatenation, MESH : Actinobacteria, MESH: Genome, Bacterial, Microbiology, Genome, Tree (descriptive set theory), MESH : RNA, Ribosomal, 23S, Phylogenetics, RNA, Ribosomal, 16S, Botany, MESH : DNA, Bacterial, MESH: Phylogeny, Phylogeny, Ecology, Evolution, Behavior and Systematics, Geodermatophilaceae, MESH: Molecular Sequence Data, [ SDV ] Life Sciences [q-bio], Phylogenetic tree, biology, MESH : Phylogeny, Sequence Analysis, DNA, General Medicine, biology.organism_classification, MESH: RNA, Ribosomal, 23S, MESH: DNA, Bacterial, Actinobacteria, MESH : RNA, Ribosomal, 16S, Nakamurellaceae, Kocuria, MESH: RNA, Ribosomal, 16S, RNA, Ribosomal, 23S, Evolutionary biology, Genome, Bacterial, MESH : Sequence Analysis, DNA, MESH: Actinobacteria
Abstract

The phylogeny of the class Actinobacteria remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies based on the number of lateral gene transfers (LGT) needed to explain the diversity of histories among gene trees for a set of genomes. We used 100 completely sequenced genomes representing 35 families and 17 orders of the class Actinobacteria and evaluated eight different hypotheses for their phylogeny, including one based on a concatenate of 54 conserved proteins present in single copy in all these genomes, trees based on 16S and 23S rRNA gene sequences or their concatenation, and a tree based on the concatenation of MLSA genes (encoding AtpI, GyrA, FtsZ, SecA and DnaK). We used Prunier to infer the number of LGT in 579 proteins (different from those used to build the concatenated tree) present in at least 70 species, using the different hypothetical species trees as references. The best tree, with the lowest number of lateral transfers, was the one based on the concatenation of 54 proteins. In that tree, the orders Bifidobacteriales , Coriobacteriales , ‘Coryneb acteriales’, ‘Micromonosporales’, ‘Propionibacteriales’, ‘Pseudonocardiales’, Streptomycetales and ‘Streptosporangiales’ were recovered while the orders ‘Frankiales’ and Micrococcales were not. It is thus proposed that the order ‘Frankiales’, which has an effectively but not validly published name, be split into Frankiales ord. nov. (type family Frankiaceae ), Geodermatophilales ord. nov. ( Geodermatophilaceae ), Acidothermales ord. nov. ( Acidothermaceae ) and Nakamurellales ord. nov. ( Nakamurellaceae ). The order Micrococcales should also be split into Micrococcales (genera Kocuria , Rothia , Micrococcus , Arthrobacter , Tropheryma , Microbacterium , Leifsonia and Clavibacter ), Cellulomonales ( Beutenbergia , Cellulomonas , Xylanimonas , Jonesia and Sanguibacter ) and Brachybacteriales ( Brachybacterium ) but the formal proposal for this will have to wait until more genomes become available for a significant proportion of strains in this order.

Published
2014

39. Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

Author

Daniel Muller, Malek Shams, Céline Lavire, Christine Oger-Desfeux, Xavier Nesme, Jessica Baude, Laurent Guéguen, Ludovic Vial, Denis Costechareyre, Tony Campillo, Danis Abrouk, Vincent Daubin, Florent Lassalle, Florence Hommais, David Chapulliot, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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), 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), Microbiologie, adaptation et pathogénie (MAP), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Pôle Rhône-Alpin de BioInformatique [Lyon] (PRABI), Université de Lyon-Université de Lyon, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), 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 de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -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 ), Microbiologie, adaptation et pathogénie ( MAP ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), PRABI, 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
AD-HOC-COMMITTEE, EVOLUTIONARY BIOLOGY, Adaptation, Biological, Agrobacterium, Genome, C58, bacterial species, GENETICS & HEREDITY, Research Articles, Phylogeny, Genetics, bactérie, évolution biologique, 0303 health sciences, biology, TI PLASMIDS, Ecology, Genomovar, Genomics, FAMILY, BACTERIA, Life Sciences & Biomedicine, Species complex, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], GENES, Genetic Speciation, Molecular Sequence Data, linear chromosome, bacterial evolution, Evolution, Molecular, 03 medical and health sciences, 0603 Evolutionary Biology, Bacterial Proteins, phylogénie, ecological niche, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Ecological niche, 0604 Genetics, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, écologie microbienne, Science & Technology, 030306 microbiology, biology.organism_classification, EVOLUTION, SP NOV, RHIZOBIUM-LEGUMINOSARUM, Agrobacterium tumefaciens, Hypothetical species, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, FERULIC ACID, Genome, Bacterial, Developmental Biology
Abstract

International audience; The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome--one on the circular chromosome and six on the linear chromosome--suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species.

Published
2011

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