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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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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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Ktari A, Nouioui I, Furnholm T, Swanson E, Ghodhbane-Gtari F, Tisa LS, Gtari M. Permanent draft genome sequence of Frankia sp. NRRL B-16219 reveals the presence of canonical nod genes, which are highly homologous to those detected in Candidatus Frankia Dg1 genome. Stand Genomic Sci 2017; 12:51. [PMID: 28878862 PMCID: PMC5584510 DOI: 10.1186/s40793-017-0261-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/22/2017] [Indexed: 01/24/2023] Open
Abstract
Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219 is closely related to "Frankia discariae" with a 16S rRNA gene similarity of 99.78%. Because of the lack of genetic tools for Frankia, our understanding of the bacterial signals involved during the plant infection process and the development of actinorhizal root nodules is very limited. Since the first three Frankia genomes were sequenced, additional genome sequences covering more diverse strains have helped provide insight into the depth of the pangenome and attempts to identify bacterial signaling molecules like the rhizobial canonical nod genes. The genome sequence of Frankia sp. strain NRRL B-16219 was generated and assembled into 289 contigs containing 8,032,739 bp with 71.7% GC content. Annotation of the genome identified 6211 protein-coding genes, 561 pseudogenes, 1758 hypothetical proteins and 53 RNA genes including 4 rRNA genes. The NRRL B-16219 draft genome contained genes homologous to the rhizobial common nodulation genes clustered in two areas. The first cluster contains nodACIJH genes whereas the second has nodAB and nodH genes in the upstream region. Phylogenetic analysis shows that Frankia nod genes are more deeply rooted than their sister groups from rhizobia. PCR-sequencing suggested the widespread occurrence of highly homologous nodA and nodB genes in microsymbionts of field collected Ceanothus americanus.
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Affiliation(s)
- Amir Ktari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Imen Nouioui
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Teal Furnholm
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 289 Rudman Hall, 46 college Road, Durham, NH 03824-2617 USA
| | - Erik Swanson
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 289 Rudman Hall, 46 college Road, Durham, NH 03824-2617 USA
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Louis S Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 289 Rudman Hall, 46 college Road, Durham, NH 03824-2617 USA
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
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Nguyen TV, Wibberg D, Battenberg K, Blom J, Vanden Heuvel B, Berry AM, Kalinowski J, Pawlowski K. An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH. BMC Genomics 2016; 17:796. [PMID: 27729005 PMCID: PMC5059922 DOI: 10.1186/s12864-016-3140-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/28/2016] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The ability to establish root nodule symbioses is restricted to four different plant orders. Soil actinobacteria of the genus Frankia can establish a symbiotic relationship with a diverse group of plants within eight different families from three different orders, the Cucurbitales, Fagales and Rosales. Phylogenetically, Frankia strains can be divided into four clusters, three of which (I, II, III) contain symbiotic strains. Members of Cluster II nodulate the broadest range of host plants with species from four families from two different orders, growing on six continents. Two Cluster II genomes were sequenced thus far, both from Asia. RESULTS In this paper we present the first Frankia cluster II genome from North America (California), Dg2, which represents a metagenome of two major and one minor strains. A phylogenetic analysis of the core genomes of 16 Frankia strains shows that Cluster II the ancestral group in the genus, also ancestral to the non-symbiotic Cluster IV. Dg2 contains the canonical nod genes nodABC for the production of lipochitooligosaccharide Nod factors, but also two copies of the sulfotransferase gene nodH. In rhizobial systems, sulfation of Nod factors affects their host specificity and their stability. CONCLUSIONS A comparison with the nod gene region of the previously sequenced Dg1 genome from a Cluster II strain from Pakistan shows that the common ancestor of both strains should have contained nodABC and nodH. Phylogenetically, Dg2 NodH proteins are sister to rhizobial NodH proteins. A glnA-based phylogenetic analysis of all Cluster II strains sampled thus far supports the hypothesis that Cluster II Frankia strains came to North America with Datisca glomerata following the Madrean-Tethyan pattern.
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Affiliation(s)
- Thanh Van Nguyen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany
| | - Kai Battenberg
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, 35392, Giessen, Germany
| | | | - Alison M Berry
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden.
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D'Angelo T, Oshone R, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. Permanent Draft Genome Sequence of Frankia sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equisetifolia. GENOME ANNOUNCEMENTS 2016; 4:e01000-16. [PMID: 27635010 PMCID: PMC5026450 DOI: 10.1128/genomea.01000-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 12/19/2022]
Abstract
Frankia sp. strain BR is a member of Frankia lineage Ic and is able to reinfect plants of the Casuarinaceae family. Here, we report a 5.2-Mbp draft genome sequence with a G+C content of 70.0% and 4,777 candidate protein-encoding genes.
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Affiliation(s)
| | - Rediet Oshone
- University of New Hampshire, Durham, New Hampshire, USA
| | | | | | | | | | - Louis S Tisa
- University of New Hampshire, Durham, New Hampshire, USA
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Permanent Draft Genome Sequence for Frankia sp. Strain EI5c, a Single-Spore Isolate of a Nitrogen-Fixing Actinobacterium, Isolated from the Root Nodules of Elaeagnus angustifolia. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00660-16. [PMID: 27389275 PMCID: PMC4939792 DOI: 10.1128/genomea.00660-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Frankia sp. strain EI5c is a member of Frankia lineage III, which is able to reinfect plants of the Eleagnaceae, Rhamnaceae, Myricaceae, and Gymnostoma, as well as the genus Alnus. Here, we report the 6.6-Mbp draft genome sequence of Frankia sp. strain EI5c with a G+C content of 72.14 % and 5,458 candidate protein-encoding genes.
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Permanent Draft Genome Sequence of Frankia sp. Strain Allo2, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Allocasuarina. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00388-16. [PMID: 27198023 PMCID: PMC4888991 DOI: 10.1128/genomea.00388-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Frankia sp. strain Allo2 is a member of Frankia lineage Ib, which is able to reinfect plants of the Casuarinaceae family, and exhibits a high level of salt tolerance compared to other isolates. Here, we report the 5.3-Mbp draft genome sequence of Frankia sp. strain Allo2 with a G+C content of 70.0% and 4,224 candidate protein-encoding genes.
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Ngom M, Oshone R, Hurst SG, Abebe-Akele F, Simpson S, Morris K, Sy MO, Champion A, Thomas WK, Tisa LS. Permanent Draft Genome Sequence for Frankia sp. Strain CeD, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equistifolia Grown in Senegal. GENOME ANNOUNCEMENTS 2016; 4:e00265-16. [PMID: 27056238 PMCID: PMC4824271 DOI: 10.1128/genomea.00265-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 11/29/2022]
Abstract
Frankiastrain CeD is a member ofFrankialineage Ib that is able to reinfect plants of theCasuarinafamilies. Here, we report a 5.0-Mbp draft genome sequence with a G+C content of 70.1% and 3,847 candidate protein-encoding genes.
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Affiliation(s)
- Mariama Ngom
- University of New Hampshire, Durham, New Hampshire, USA Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal Département de Biologie Végétale, Laboratoire Campus de Biotechnologies Végétales, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Dakar-Fann, Sénégal Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Centre de Recherche de Bel Air, Dakar, Sénégal
| | - Rediet Oshone
- University of New Hampshire, Durham, New Hampshire, USA
| | | | | | | | | | - Mame Ourèye Sy
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal Département de Biologie Végétale, Laboratoire Campus de Biotechnologies Végétales, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Dakar-Fann, Sénégal
| | - Antony Champion
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Centre de Recherche de Bel Air, Dakar, Sénégal Institut de Recherche pour le Développement (IRD), UMR DIADE, Montpellier, France
| | | | - Louis S Tisa
- University of New Hampshire, Durham, New Hampshire, USA
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Permanent Draft Genome Sequences for Two Variants of Frankia sp. Strain CpI1, the First Frankia Strain Isolated from Root Nodules of Comptonia peregrina. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01588-15. [PMID: 26769948 PMCID: PMC4714129 DOI: 10.1128/genomea.01588-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Frankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able to reinfect plants of the Betulaceae and Myricaceae families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes for CpI1-S and CpI1-P, respectively.
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