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Berckx F, Wibberg D, Brachmann A, Morrison C, Obaid NB, Blom J, Kalinowski J, Wall LG, Pawlowski K. Genome analysis and biogeographic distribution of the earliest divergent Frankia clade in the southern hemisphere. FEMS Microbiol Ecol 2024; 100:fiae042. [PMID: 38520167 DOI: 10.1093/femsec/fiae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/19/2024] [Accepted: 03/21/2024] [Indexed: 03/25/2024] Open
Abstract
Coriariaceae are a small plant family of 14-17 species and subspecies that currently have a global but disjunct distribution. All species can form root nodules in symbiosis with diazotrophic Frankia cluster-2 strains, which form the earliest divergent symbiotic clade within this bacterial genus. Studies on Frankia cluster-2 mostly have focused on strains occurring in the northern hemisphere. Except for one strain from Papua New Guinea, namely Candidatus Frankia meridionalis Cppng1, no complete genome of Frankia associated with Coriaria occurring in the southern hemisphere has been published thus far, yet the majority of the Coriariaceae species occur here. We present field sampling data of novel Frankia cluster-2 strains, representing two novel species, which are associated with Coriaria arborea and Coriaria sarmentosa in New Zealand, and with Coriaria ruscifolia in Patagonia (Argentina), in addition to identifying Ca. F. meridionalis present in New Zealand. The novel Frankia species were found to be closely related to both Ca. F. meridionalis, and a Frankia species occurring in the Philippines, Taiwan, and Japan. Our data suggest that the different Frankia cluster-2 species diverged early after becoming symbiotic circa 100 million years ago.
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Affiliation(s)
- Fede Berckx
- Department of Ecology, Environment and Plant Science, Stockholm University, 106 91 Stockholm, Sweden
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, 756 51 Uppsala, Sweden
| | | | - Andreas Brachmann
- LMU München, Faculty of Biology, Genetics, 82152 Planegg-Martinsried, Germany
| | - Ciara Morrison
- Department of Ecology, Environment and Plant Science, Stockholm University, 106 91 Stockholm, Sweden
| | - Nadia B Obaid
- Department of Ecology, Environment and Plant Science, Stockholm University, 106 91 Stockholm, Sweden
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | | | - Luis G Wall
- CONICET, National Council for Scientific and Technical Research, Argentina
- Department of Science and Technology, National University of Quilmes, B12876BXD Bernal, Argentina
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Science, Stockholm University, 106 91 Stockholm, Sweden
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2
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Nouioui I, Neumann-Schaal M, Pujic P, Fournier P, Normand P, Herrera-Belaroussi A, Vemulapally S, Guerra T, Hahn D. Frankia nepalensis sp. nov., a non-infective non-nitrogen-fixing isolate from root nodules of Coriaria nepalensis Wall. Int J Syst Evol Microbiol 2023; 73. [PMID: 38098135 DOI: 10.1099/ijsem.0.006199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
Strains CN4T, CN6, CN7 and CNm7 were isolated from root nodules of Coriaria nepalensis from Murree in Pakistan. They do not form root nodules on C. nepalensis nor on Alnus glutinosa although they deformed root hairs of Alnus. The colonies are bright red-pigmented, the strains form hyphae and sporangia but no N2-fixing vesicles and do not fix nitrogen in vitro. The peptidoglycan of strain CN4T contains meso-diaminopimelic acid; whole cell sugars consist of ribose, mannose, glucose, galactose and rhamnose. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown lipids represent the major polar lipids; MK-9(H4) and MK-9(H6) are the predominant menaquinones (>15 %), and iso-C16 : 0 and C17 : 1ω8c are the major fatty acids (>15 %). The results of comparative 16S rRNA gene sequence analyses indicated that strain CN4T is most closely related to Frankia saprophytica CN 3T. An MLSA phylogeny using amino acids sequences of AtpD, DnaA, FtsZ, Pgk and RpoB, assigned the strain to cluster 4 non-nodulating species, close to F. saprophytica CN 3T , Frankia asymbiotica M16386T and Frankia inefficax EuI1cT with 0.04 substitutions per site, while that value was 0.075 with other strains. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between CN4T and all species of the genus Frankia with validly published names were below the defined threshold for prokaryotic species demarcation, with dDDH and ANI values at or below 27.8 and 83.7 %, respectively. The four strains CN4T, CN6, CN7 and CNm7 had dDDH (98.6-99.6 %) and ANI values that grouped them as representing a single species. CN4T has a 10.76 Mb genome. CN4T was different from its close phylogenetic neighbours with validly published names in being red-pigmented, in having several lantibiotic-coding clusters, a carbon monoxide dehydrogenase cluster and a clustered regularly interspaced short palindromic repeats (CRISPR) cluster. The results of phenotypic, physiological and phylogenomic analyses confirmed the assignment of strain CN4T (=DSM 114740T = LMG 32595T) to a novel species, with CN4T as type strain, for which the name Frankia nepalensis sp. nov. is proposed.
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Affiliation(s)
- Imen Nouioui
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Petar Pujic
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Pascale Fournier
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Philippe Normand
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Aude Herrera-Belaroussi
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Spandana Vemulapally
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Trina Guerra
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
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3
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Gtari M. Taxogenomic status of phylogenetically distant Frankia clusters warrants their elevation to the rank of genus: A description of Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov. as three novel genera within the family Frankiaceae. Front Microbiol 2022; 13:1041425. [PMID: 36425027 PMCID: PMC9680954 DOI: 10.3389/fmicb.2022.1041425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
The genus Frankia is at present the sole genus in the family Frankiaceae and encompasses filamentous, sporangia-forming actinomycetes principally isolated from root nodules of taxonomically disparate dicotyledonous hosts named actinorhizal plants. Multiple independent phylogenetic analyses agree with the division of the genus Frankia into four well-supported clusters. Within these clusters, Frankia strains are well defined based on host infectivity range, mode of infection, morphology, and their behaviour in culture. In this study, phylogenomics, overall genome related indices (OGRI), together with available data sets for phenotypic and host-plant ranges available for the type strains of Frankia species, were considered. The robustness and the deep radiation observed in Frankia at the subgeneric level, fulfilling the primary principle of phylogenetic systematics, were strengthened by establishing genome criteria for new genus demarcation boundaries. Therefore, the taxonomic elevation of the Frankia clusters to the rank of the genus is proposed. The genus Frankia should be revised to encompass cluster 1 species only and three novel genera, Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov., are proposed to accommodate clusters 2, 3, and 4 species, respectively. New combinations for validly named species are also provided.
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Affiliation(s)
- Maher Gtari
- USCR Bactériologie Moléculaire & Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Tunis, Tunisia
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4
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Carlos-Shanley C, Guerra T, Hahn D. Draft genomes of non-nitrogen-fixing Frankia strains. J Genomics 2021; 9:68-75. [PMID: 34703504 PMCID: PMC8542509 DOI: 10.7150/jgen.65429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/14/2021] [Indexed: 12/04/2022] Open
Abstract
In this study, we describe the genomes of two novel candidate species of non-nitrogen fixing Frankia that were isolated from the root nodules of Coriaria nepalensis and Alnus glutinosa, genospecies CN and Ag, respectively. Comparative genomic analyses revealed that both genospecies lack genes essential for nitrogen-fixation and possess genes involved in the degradation of plant cell walls. Additionally, we found distinct biosynthetic gene clusters in each genospecies. The availability of these genomes will contribute to the study of the taxonomy and evolution of actinorhizal symbioses.
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Affiliation(s)
- Camila Carlos-Shanley
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Trina Guerra
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
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5
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Herrera-Belaroussi A, Normand P, Pawlowski K, Fernandez MP, Wibberg D, Kalinowski J, Brachmann A, Berckx F, Lee N, Blom J, Pozzi AC, Fournier P, Bethencourt L, Dubost A, Abrouk D, Sellstedt A. Candidatus Frankia nodulisporulans sp. nov., an Alnus glutinosa-infective Frankia species unable to grow in pure culture and able to sporulate in-planta. Syst Appl Microbiol 2020; 43:126134. [PMID: 33059155 DOI: 10.1016/j.syapm.2020.126134] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 11/16/2022]
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.
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Affiliation(s)
- Aude Herrera-Belaroussi
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France.
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Maria P Fernandez
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Daniel Wibberg
- The Center for Biotechnology CeBiTec, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- The Center for Biotechnology CeBiTec, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Andreas Brachmann
- Biocenter of the LMU Munich, Genetics Section, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Fede Berckx
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Natuschka Lee
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden
| | - Jochen Blom
- Bioinformatics & Systems Biology, Justus-Liebig-University, 35392 Giessen, Hesse, Germany
| | - Adrien C Pozzi
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Lorine Bethencourt
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Danis Abrouk
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Anita Sellstedt
- Department of Plant Physiology, UPSC, Umeå University, 90187 Umeå, Sweden.
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6
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Pozzi ACM, Herrera-Belaroussi A, Schwob G, Bautista-Guerrero HH, Bethencourt L, Fournier P, Dubost A, Abrouk D, Normand P, Fernandez MP. Proposal of ' Candidatus Frankia alpina', the uncultured symbiont of Alnus alnobetula and A. incana that forms spore-containing nitrogen-fixing root nodules. Int J Syst Evol Microbiol 2020; 70:5453-5459. [PMID: 32910750 DOI: 10.1099/ijsem.0.004433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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.
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Affiliation(s)
- Adrien C Meynier Pozzi
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Aude Herrera-Belaroussi
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Guillaume Schwob
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Hector H Bautista-Guerrero
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Lorine Bethencourt
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Pascale Fournier
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Danis Abrouk
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Philippe Normand
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Maria P Fernandez
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
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7
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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8
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Berckx F, Wibberg D, Kalinowski J, Pawlowski K. The Peptidoglycan Biosynthesis Gene murC in Frankia: Actinorhizal vs. Plant Type. Genes (Basel) 2020; 11:genes11040432. [PMID: 32316316 PMCID: PMC7231273 DOI: 10.3390/genes11040432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/30/2020] [Accepted: 04/08/2020] [Indexed: 11/16/2022] Open
Abstract
Nitrogen-fixing Actinobacteria of the genus Frankia can be subdivided into four phylogenetically distinct clades; members of clusters one to three engage in nitrogen-fixing root nodule symbioses with actinorhizal plants. Mur enzymes are responsible for the biosynthesis of the peptidoglycan layer of bacteria. The four Mur ligases,MurC, MurD, MurE, and MurF, catalyse the addition of a short polypeptide to UDP-N-acetylmuramic acid. Frankia strains of cluster-2 and cluster-3 contain two copies of murC, while the strains of cluster-1 and cluster-4 contain only one. Phylogenetically, the protein encoded by the murC gene shared only by cluster-2 and cluster-3, termed MurC1, groups with MurC proteins of other Actinobacteria. The protein encoded by the murC gene found in all Frankia strains, MurC2, shows a higher similarity to the MurC proteins of plants than of Actinobacteria. MurC2 could have been either acquired via horizontal gene transfer or via gene duplication and convergent evolution, while murC1 was subsequently lost in the cluster-1 and cluster-4 strains. In the nodules induced by the cluster-2 strains, the expression levels of murC2 were significantly higher than those of murC1. Thus, there is clear sequence divergence between both types of Frankia MurC, and Frankia murC1 is in the process of being replaced by murC2, indicating selection in favour of murC2. Nevertheless, protein modelling showed no major structural differences between the MurCs from any phylogenetic group examined.
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Affiliation(s)
- Fede Berckx
- Department of Ecology, Environment, and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden;
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
| | - Katharina Pawlowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
- Correspondence: ; Tel.: +46-8-16-3772; Fax: +46-8-16-5525
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9
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Huisman R, Geurts R. A Roadmap toward Engineered Nitrogen-Fixing Nodule Symbiosis. PLANT COMMUNICATIONS 2020; 1:100019. [PMID: 33404552 PMCID: PMC7748023 DOI: 10.1016/j.xplc.2019.100019] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/06/2019] [Accepted: 12/27/2019] [Indexed: 05/26/2023]
Abstract
In the late 19th century, it was discovered that legumes can establish a root nodule endosymbiosis with nitrogen-fixing rhizobia. Soon after, the question was raised whether it is possible to transfer this trait to non-leguminous crops. In the past century, an ever-increasing amount of knowledge provided unique insights into the cellular, molecular, and genetic processes controlling this endosymbiosis. In addition, recent phylogenomic studies uncovered several genes that evolved to function specifically to control nodule formation and bacterial infection. However, despite this massive body of knowledge, the long-standing objective to engineer the nitrogen-fixing nodulation trait on non-leguminous crop plants has not been achieved yet. In this review, the unsolved questions and engineering strategies toward nitrogen-fixing nodulation in non-legume plants are discussed and highlighted.
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Affiliation(s)
- Rik Huisman
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Rene Geurts
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
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10
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Nguyen TV, Wibberg D, Vigil-Stenman T, Berckx F, Battenberg K, Demchenko KN, Blom J, Fernandez MP, Yamanaka T, Berry AM, Kalinowski J, Brachmann A, Pawlowski K. Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster: They Come in Teams. Genome Biol Evol 2019; 11:2273-2291. [PMID: 31368478 PMCID: PMC6735867 DOI: 10.1093/gbe/evz153] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 11/14/2022] Open
Abstract
Frankia strains induce the formation of nitrogen-fixing nodules on roots of actinorhizal plants. Phylogenetically, Frankia strains can be grouped in four clusters. The earliest divergent cluster, cluster-2, has a particularly wide host range. The analysis of cluster-2 strains has been hampered by the fact that with two exceptions, they could never be cultured. In this study, 12 Frankia-enriched metagenomes of Frankia cluster-2 strains or strain assemblages were sequenced based on seven inoculum sources. Sequences obtained via DNA isolated from whole nodules were compared with those of DNA isolated from fractionated preparations enhanced in the Frankia symbiotic structures. The results show that cluster-2 inocula represent groups of strains, and that strains not represented in symbiotic structures, that is, unable to perform symbiotic nitrogen fixation, may still be able to colonize nodules. Transposase gene abundance was compared in the different Frankia-enriched metagenomes with the result that North American strains contain more transposase genes than Eurasian strains. An analysis of the evolution and distribution of the host plants indicated that bursts of transposition may have coincided with niche competition with other cluster-2 Frankia strains. The first genome of an inoculum from the Southern Hemisphere, obtained from nodules of Coriaria papuana in Papua New Guinea, represents a novel species, postulated as Candidatus Frankia meridionalis. All Frankia-enriched metagenomes obtained in this study contained homologs of the canonical nod genes nodABC; the North American genomes also contained the sulfotransferase gene nodH, while the genome from the Southern Hemisphere only contained nodC and a truncated copy of nodB.
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Affiliation(s)
- Thanh Van Nguyen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Germany
| | | | - Fede Berckx
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis
| | - Kirill N Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Gießen, Germany
| | - Maria P Fernandez
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université Lyon I, Villeurbanne Cedex, France
| | | | - Alison M Berry
- Department of Plant Sciences, University of California, Davis
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Germany
| | - Andreas Brachmann
- Biocenter, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
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11
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Flandrois JP, Brochier-Armanet C, Briolay J, Abrouk D, Schwob G, Normand P, Fernandez MP. Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon. Res Microbiol 2019; 170:280-287. [PMID: 31279085 DOI: 10.1016/j.resmic.2019.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 05/02/2019] [Accepted: 06/25/2019] [Indexed: 11/28/2022]
Abstract
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 systematics 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 ribosomal 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.
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Affiliation(s)
- Jean-Pierre Flandrois
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France.
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France.
| | - Jérôme Briolay
- Université de Lyon, Université Lyon 1, DTAMB, Villeurbanne, France.
| | - Danis Abrouk
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, INRA, UMR1418, Laboratoire d'Écologie Microbienne, Villeurbanne, France.
| | - Guillaume Schwob
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, INRA, UMR1418, Laboratoire d'Écologie Microbienne, Villeurbanne, France.
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, INRA, UMR1418, Laboratoire d'Écologie Microbienne, Villeurbanne, France.
| | - Maria P Fernandez
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, INRA, UMR1418, Laboratoire d'Écologie Microbienne, Villeurbanne, France.
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12
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Billault-Penneteau B, Sandré A, Folgmann J, Parniske M, Pawlowski K. Dryas as a Model for Studying the Root Symbioses of the Rosaceae. FRONTIERS IN PLANT SCIENCE 2019; 10:661. [PMID: 31214211 PMCID: PMC6558151 DOI: 10.3389/fpls.2019.00661] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/02/2019] [Indexed: 05/28/2023]
Abstract
The nitrogen-fixing root nodule symbiosis is restricted to four plant orders: Fabales (legumes), Fagales, Cucurbitales and Rosales (Elaeagnaceae, Rhamnaceae, and Rosaceae). Interestingly all of the Rosaceae genera confirmed to contain nodulating species (i.e., Cercocarpus, Chamaebatia, Dryas, and Purshia) belong to a single subfamily, the Dryadoideae. The Dryas genus is particularly interesting from an evolutionary perspective because it contains closely related nodulating (Dryas drummondii) and non-nodulating species (Dryas octopetala). The close phylogenetic relationship between these two species makes Dryas an ideal model genus to study the genetic basis of nodulation by whole genome comparison and classical genetics. Therefore, we established methods for plant cultivation, transformation and DNA extraction for these species. We optimized seed surface sterilization and germination methods and tested growth protocols ranging from pots and Petri dishes to a hydroponic system. Transgenic hairy roots were obtained by adapting Agrobacterium rhizogenes-based transformation protocols for Dryas species. We compared several DNA extraction protocols for their suitability for subsequent molecular biological analysis. Using CTAB extraction, reproducible PCRs could be performed, but CsCl gradient purification was essential to obtain DNA in sufficient purity for high quality de novo genome sequencing of both Dryas species. Altogether, we established a basic toolkit for the culture, transient transformation and genetic analysis of Dryas sp.
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Affiliation(s)
| | - Aline Sandré
- Institute of Genetics, Faculty of Biology, LMU Munich, Martinsried, Germany
| | - Jessica Folgmann
- Institute of Genetics, Faculty of Biology, LMU Munich, Martinsried, Germany
| | - Martin Parniske
- Institute of Genetics, Faculty of Biology, LMU Munich, Martinsried, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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13
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Demina IV, Maity PJ, Nagchowdhury A, Ng JLP, van der Graaff E, Demchenko KN, Roitsch T, Mathesius U, Pawlowski K. Accumulation of and Response to Auxins in Roots and Nodules of the Actinorhizal Plant Datisca glomerata Compared to the Model Legume Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2019; 10:1085. [PMID: 31608077 PMCID: PMC6773980 DOI: 10.3389/fpls.2019.01085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/09/2019] [Indexed: 05/13/2023]
Abstract
Actinorhizal nodules are structurally different from legume nodules and show a greater similarity to lateral roots. Because of the important role of auxins in lateral root and nodule formation, auxin profiles were examined in roots and nodules of the actinorhizal species Datisca glomerata and the model legume Medicago truncatula. The auxin response in roots and nodules of both species was analyzed in transgenic root systems expressing a beta-glucuronidase gene under control of the synthetic auxin-responsive promoter DR5. The effects of two different auxin on root development were compared for both species. The auxin present in nodules at the highest levels was phenylacetic acid (PAA). No differences were found between the concentrations of active auxins of roots vs. nodules, while levels of the auxin conjugate indole-3-acetic acid-alanine were increased in nodules compared to roots of both species. Because auxins typically act in concert with cytokinins, cytokinins were also quantified. Concentrations of cis-zeatin and some glycosylated cytokinins were dramatically increased in nodules compared to roots of D. glomerata, but not of M. truncatula. The ratio of active auxins to cytokinins remained similar in nodules compared to roots in both species. The auxin response, as shown by the activation of the DR5 promoter, seemed significantly reduced in nodules compared to roots of both species, suggesting the accumulation of auxins in cell types that do not express the signal transduction pathway leading to DR5 activation. Effects on root development were analyzed for the synthetic auxin naphthaleneacetic acid (NAA) and PAA, the dominant auxin in nodules. Both auxins had similar effects, except that the sensitivity of roots to PAA was lower than to NAA. However, while the effects of both auxins on primary root growth were similar for both species, effects on root branching were different: both auxins had the classical positive effect on root branching in M. truncatula, but a negative effect in D. glomerata. Such a negative effect of exogenous auxin on root branching has previously been found for a cucurbit that forms lateral root primordia in the meristem of the parental root; however, root branching in D. glomerata does not follow that pattern.
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Affiliation(s)
- Irina V. Demina
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Pooja Jha Maity
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Anurupa Nagchowdhury
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Jason L. P. Ng
- Division of Plant Science, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Eric van der Graaff
- Department of Plant Physiology, Karl-Franzens-Universität Graz, Graz, Austria
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint-Petersburg, Russia
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Thomas Roitsch
- Department of Plant Physiology, Karl-Franzens-Universität Graz, Graz, Austria
| | - Ulrike Mathesius
- Division of Plant Science, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- *Correspondence: Katharina Pawlowski,
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14
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Gtari M, Nouioui I, Sarkar I, Ghodhbane-Gtari F, Tisa LS, Sen A, Klenk HP. An update on the taxonomy of the genus Frankia Brunchorst, 1886, 174 AL. Antonie van Leeuwenhoek 2018; 112:5-21. [PMID: 30232679 DOI: 10.1007/s10482-018-1165-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/14/2018] [Indexed: 12/30/2022]
Abstract
Since the recognition of the name Frankia in the Approved Lists of bacterial names (1980), few amendments have been given to the genus description. Successive editions of Bergey's Manual of Systematics of Archaea and Bacteria have broadly conflicting suprageneric treatments of the genus without any advances for subgeneric classification. This review focuses on recent results from taxongenomics and phenoarray approaches to the positioning and the structuring of the genus Frankia. Based on phylogenomic analyses, Frankia should be considered the single member of the family Frankiaceae within the monophyletic order, Frankiales. A polyphasic strategy incorporating genome to genome data and omniLog® phenoarrays, together with classical approaches, has allowed the designation and an amended description of a type strain of the type species Frankia alni, and the recognition of at least 10 novel species covering symbiotic and non symbiotic taxa within the genus. Genome to phenome data will be shortly incorporated in the scheme for proposing novel species including those recalcitrant to isolation in axenic culture.
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Affiliation(s)
- Maher Gtari
- Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080, Tunis Cedex, Tunisia.
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Indrani Sarkar
- NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri, 734013, India
| | - Faten Ghodhbane-Gtari
- Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080, Tunis Cedex, Tunisia.,Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisia
| | - Louis S Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH, 03824-2617, USA
| | - Arnab Sen
- NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri, 734013, India
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
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15
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Normand P, Nouioui I, Pujic P, Fournier P, Dubost A, Schwob G, Klenk HP, Nguyen A, Abrouk D, Herrera-Belaroussi A, Pothier JF, Pflüger V, Fernandez MP. Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa. Int J Syst Evol Microbiol 2018; 68:3001-3011. [PMID: 30059001 DOI: 10.1099/ijsem.0.002939] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Strain ARgP5T, an actinobacterium isolated from a root nodule present on an Alnus incana subspecies rugosa shrub growing in Quebec City, Canada, was the subject of polyphasic taxonomic studies to clarify its status within the genus Frankia. 16S rRNA gene sequence similarities and ANI values between ARgP5T and type strains of species of the genus Frankiawith validly published names were 98.8 and 82 % or less, respectively. The in silico DNA G+C content was 72.4 mol%. ARgP5T is characterised by the presence of meso-A2pm, galactose, glucose, mannose, rhamnose (trace), ribose and xylose as whole-organism hydrolysates; MK-9(H8) as predominant menaquinone; diphosphatidylglycerol, phosphatidylinositol and phosphatidylglycerol as polar lipids and iso-C16 : 0 and C17 : 1ω8c as major fatty acids. The proteomic results confirmed the distinct position of ARgP5T from its closest neighbours in Frankiacluster 1. ARgP5T was found to be infective on two alder (Alnus glutinosa and Alnusalnobetula subsp. crispa) and on one bayberry (Morella pensylvanica) species and to fix nitrogen in symbiosis and in pure culture. On the basis of phylogenetic (16S rRNA gene sequence), genomic, proteomic and phenotypic results, strain ARgP5T (=DSM 45898=CECT 9033) is considered to represent a novel species within the genus Frankia for which the name Frankia canadensis sp. nov., is proposed.
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Affiliation(s)
- Philippe Normand
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Imen Nouioui
- 2Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia.,3School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Petar Pujic
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Pascale Fournier
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Audrey Dubost
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Guillaume Schwob
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Hans-Peter Klenk
- 3School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | | | - Danis Abrouk
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Aude Herrera-Belaroussi
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Joël F Pothier
- 5Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland
| | | | - Maria P Fernandez
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
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16
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Nouioui I, Ghodhbane-Gtari F, Jando M, Tisa LS, Klenk HP, Gtari M. Frankia torreyi sp. nov., the first actinobacterium of the genus Frankia Brunchorst 1886, 174 AL isolated in axenic culture. Antonie van Leeuwenhoek 2018; 112:57-65. [PMID: 30030730 DOI: 10.1007/s10482-018-1131-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/12/2018] [Indexed: 11/30/2022]
Abstract
Strain CpI1T was, in 1978, the first isolate of the genus Frankia to be obtained from Comptonia peregrina root nodules. In this study, a polyphasic approach was performed to identify the taxonomic position of strain CpI1T among the members of the genus Frankia. The strain contains meso-diaminopimelic acid as the diagnostic diamino acid and galactose, glucose, mannose, rhamnose, ribose and xylose as cell wall sugars. The polar lipids were found to consist of phosphatidylinositol, diphosphatidylglycerol, glycophospholipids, phosphatidylglycerol, an aminophospholipid and unidentified phospholipids and lipids. The predominant menaquinone was identified as MK-9 (H8), while the major fatty acid are iso-C16:0 and C17:1ω 8c. The 16S rRNA gene sequence identity varies from 97.4 to 99.6% with the type strains of currently described Frankia species. Phylogenetic analyses based on 16S rRNA gene sequences and multi-locus sequence analysis (MLSA) using atp1, ftsZ, dnaK, gyrA and secA gene sequences showed that strain CpI1T is closely related to Frankia alni ACN14aT. The genome size of strain CpI1T is 7.6 Mb with a digital DNA G+C content of 72.4%. Digital DNA:DNA hybridization (values between strain CpI1T and its close phylogenetic relative F. alni ACN14aT was 44.1%, well below the threshold of 70% for distinguishing between bacterial genomic species. Based on the phenotypic, phylogenetic and genomic data, strain CpI1T (= DSM44263T = CECT9035T) warrants classification as the type strain of a novel species, for which the name Frankia torreyi sp. nov. is proposed.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST), 2092, Tunis, Tunisia.,Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080, Tunis Cedex, Tunisia
| | - Marlen Jando
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Brunswick, Germany
| | - Louis S Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, USA
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Maher Gtari
- Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080, Tunis Cedex, Tunisia.
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17
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Nouioui I, Ghodhbane-Gtari F, Rhode M, Sangal V, Klenk HP, Gtari M. Frankia irregularis sp. nov., an actinobacterium unable to nodulate its original host, Casuarina equisetifolia, but effectively nodulates members of the actinorhizal Rhamnales. Int J Syst Evol Microbiol 2018; 68:2883-2914. [PMID: 30010524 DOI: 10.1099/ijsem.0.002914] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A red pigmented actinobacterium designated G2T, forming extremely branched vegetative hyphae, vesicles and mutilocular sporangia, was isolated from Casuarina equisetifolia nodules. The strain failed to nodulate its original host plant but effectively nodulated members of actinorhizal Rhamnales. The taxonomic position of G2T was determined using a polyphasic approach. The peptidoglycan of the strain contained meso-diaminopimelic acid as diagnostic diamino acid, galactose, glucose, mannose, rhamnose, ribose and xylose. The polar lipid pattern consisted of phosphatidylinositol (PI), diphosphatidylglycerol (DPG), glycophospholipids (GPL1-2), phosphatidylglycerol (PG), aminophospholipid (APL) and unknown lipids (L). The predominant menaquinones were MK-9 (H4) and MK-9 (H6) while the major fatty acids were iso-C16 : 0, C17 : 1ω8c and C15 : 0. The size of the genome of G2T was 9.5 Mb and digital DNA G+C content was 70.9 %. The 16S rRNA gene showed 97.4-99.5 % sequence identity with the type strains of species of the genus Frankia. Digital DNA -DNA hybridisation (dDDH) values between G2T and its nearest phylogenetic neighbours Frankia elaeagniand Frankia discariaewere below the threshold of 70 %. On the basis of these results, strain G2T (=DSM 45899T=CECT 9038T) is proposed to represent the type strain of a novel species Frankia irregularis sp. nov.
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Affiliation(s)
- Imen Nouioui
- 1School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Faten Ghodhbane-Gtari
- 2Laboratoire Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université Tunis El Manar, 2092 Tunis, Tunisia
| | - Manfred Rhode
- 3Central Facility for Microscopy, HZI-Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Vartul Sangal
- 4Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Hans-Peter Klenk
- 1School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Maher Gtari
- 5Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080 Tunis Cedex, Tunisia
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18
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Pozzi AC, Bautista-Guerrero HH, Abby SS, Herrera-Belaroussi A, Abrouk D, Normand P, Menu F, Fernandez MP. 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. Syst Appl Microbiol 2018; 41:311-323. [DOI: 10.1016/j.syapm.2018.03.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 03/08/2018] [Accepted: 03/10/2018] [Indexed: 10/17/2022]
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19
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Lurthy T, Alloisio N, Fournier P, Anchisi S, Ponsero A, Normand P, Pujic P, Boubakri H. Molecular response to nitrogen starvation by Frankia alni ACN14a revealed by transcriptomics and functional analysis with a fosmid library in Escherichia coli. Res Microbiol 2018; 169:90-100. [PMID: 29378337 DOI: 10.1016/j.resmic.2017.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/21/2017] [Accepted: 12/06/2017] [Indexed: 12/20/2022]
Abstract
The transcriptome of Frankia alni strain ACN14a was compared between in vitro ammonium-replete (N-replete) and ammonium-free dinitrogen-fixing (N-fixing) conditions using DNA arrays. A Welch-test (p < 0.05) revealed significant upregulation of 252 genes under N-fixing vs. N-replete (fold-change (FC) ≥ 2), as well as significant downregulation of 48 other genes (FC ≤ 0.5). Interestingly, there were 104 Frankia genes upregulated in vitro that were also significantly upregulated in symbiosis with Alnus glutinosa, while the other 148 genes were not, showing that the physiology of in vitro fixation is markedly different from that under symbiotic conditions. In particular,in vitro fixing cells were seen to upregulate genes identified as coding for a nitrite reductase, and amidases that were not upregulated in symbiosis. Confirmatory assays for nitrite reductase showed that Frankia indeed reduced nitrite and used it as a nitrogen source. An Escherichia coli fosmid clone carrying the nirB region was able to grow better in the presence of 5 mM nitrite than without it, confirming the function of the genome region. The physiological pattern that emerges shows that Frankia undergoes nitrogen starvation that induces a molecular response different from that seen in symbiosis.
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Affiliation(s)
- Tristan Lurthy
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Nicole Alloisio
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Pascale Fournier
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Stéphanie Anchisi
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Alise Ponsero
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Philippe Normand
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France.
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