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Hu B, Flemetakis E, Liu Z, Hänsch R, Rennenberg H. Significance of nitrogen-fixing actinorhizal symbioses for restoration of depleted, degraded, and contaminated soil. TRENDS IN PLANT SCIENCE 2023; 28:752-764. [PMID: 37002002 DOI: 10.1016/j.tplants.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/09/2023] [Accepted: 03/09/2023] [Indexed: 06/17/2023]
Abstract
Atmospheric nitrogen (N2)-fixing legume trees are frequently used for the restoration of depleted, degraded, and contaminated soils. However, biological N2 fixation (BNF) can also be performed by so-called actinorhizal plants. Actinorhizal plants include a high diversity of woody species and therefore can be applied in a broad spectrum of environments. In contrast to N2-fixing legumes, the potential of actinorhizal plants for soil restoration remains largely unexplored. In this Opinion, we propose related basic research requirements for the characterization of environmental stress responses that determine the restoration potential of actinorhizal plants for depleted, degraded, and contaminated soils. We identify advantages and unexplored processes of actinorhizal plants and describe a mainly uncharted avenue of future research for this important group of plant species.
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Affiliation(s)
- Bin Hu
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, PR China.
| | - Emmanouil Flemetakis
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, PR China; Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Zhenshan Liu
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, PR China
| | - Robert Hänsch
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, PR China; Institute for Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, D-38106 Braunschweig, Germany.
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, PR China
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2
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Chetri SPK, Rahman Z, Thomas L, Lal R, Gour T, Agarwal LK, Vashishtha A, Kumar S, Kumar G, Kumar R, Sharma K. Paradigms of actinorhizal symbiosis under the regime of global climatic changes: New insights and perspectives. J Basic Microbiol 2022; 62:764-778. [PMID: 35638879 DOI: 10.1002/jobm.202200043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/17/2022] [Accepted: 05/14/2022] [Indexed: 11/05/2022]
Abstract
Nitrogen occurs as inert and inaccessible dinitrogen gaseous form (N2 ) in the atmosphere. Biological nitrogen fixation is a chief process that makes this dinitrogen (N2 ) accessible and bioavailable in the form of ammonium (NH4 + ) ions. The key organisms to fix nitrogen are certain prokaryotes, called diazotrophs either in the free-living form or establishing significant mutual relationships with a variety of plants. On such examples is ~95-100 MY old incomparable symbiosis between dicotyledonous trees and a unique actinobacterial diazotroph in diverse ecosystems. In this association, the root of the certain dicotyledonous tree (~25 genera and 225 species) belonging to three different taxonomic orders, Fagales, Cucurbitales, and Rosales (FaCuRo) known as actinorhizal trees can host a diazotroph, Frankia of order Frankiales. Frankia is gram-positive, branched, filamentous, sporulating, and free-living soil actinobacterium. It resides in the specialized, multilobed, and coralloid organs (lateral roots but without caps), the root nodules of actinorhizal tress. This review aims to provide systematic information on the distribution and the phylogenetic diversity of hosts from FaCuRo and their micro-endosymbionts (Frankia spp.), colonization mechanisms, and signaling pathways. We also aim to provide details on developmental and physiological imperatives for gene regulation and functional genomics of symbiosis, phenomenal restoration ecology, influences of contemporary global climatic changes, and anthropogenic impacts on plant-Frankia interactions for the functioning of ecosystems and the biosphere.
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Affiliation(s)
| | - Zeeshanur Rahman
- Department of Botany, Zakir Husain Delhi College, University of Delhi, New Delhi, Delhi, India
| | - Lebin Thomas
- Department of Botany, Hansraj College, University of Delhi, New Delhi, Delhi, India
| | - Ratan Lal
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Tripti Gour
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Lokesh Kumar Agarwal
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Akanksha Vashishtha
- Department of Plant Protection, CCS University, Meerut, Uttar Pradesh, India
| | - Sachin Kumar
- Department of Botany, Shri Venkateshwara College, University of Delhi, New Delhi, Delhi, India
| | - Gaurav Kumar
- Department of Environmental Studies, PGDAV College, University of Delhi, New Delhi, Delhi, India
| | - Rajesh Kumar
- Department of Botany, Hindu College, University of Delhi, New Delhi, Delhi, India
| | - Kuldeep Sharma
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
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3
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Sarkar I, Sen G, Bhattacharyya S, Gtari M, Sen A. Inter-cluster competition and resource partitioning may govern the ecology of Frankia. Arch Microbiol 2022; 204:326. [PMID: 35576077 DOI: 10.1007/s00203-022-02910-0] [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] [Received: 12/18/2021] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/25/2022]
Abstract
Microbes live in a complex communal ecosystem. The structural complexity of microbial community reflects diversity, functionality, as well as habitat type. Delineation of ecologically important microbial populations along with exploration of their roles in environmental adaptation or host-microbe interaction has a crucial role in modern microbiology. In this scenario, reverse ecology (the use of genomics to study ecology) plays a pivotal role. Since the co-existence of two different genera in one small niche should maintain a strict direct interaction, it will be interesting to utilize the concept of reverse ecology in this scenario. Here, we exploited an 'R' package, the RevEcoR, to resolve the issue of co-existing microbes which are proven to be a crucial tool for identifying the nature of their relationship (competition or complementation) persisting among them. Our target organism here is Frankia, a nitrogen-fixing actinobacterium popular for its genetic and host-specific nature. According to their plant host, Frankia has already been sub-divided into four clusters C-I, C-II, C-III, and C-IV. Our results revealed a strong competing nature of CI Frankia. Among the clusters of Frankia studied, the competition index between C-I and C-III was the largest. The other interesting result was the co-occurrence of C-II and C-IV groups. It was revealed that these two groups follow the theory of resource partitioning in their lifestyle. Metabolic analysis along with their differential transporter machinery validated our hypothesis of resource partitioning among C-II and C-IV groups.
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Affiliation(s)
- I Sarkar
- Bioinformatics Facility, University of North Bengal, Siliguri, West Bengal, India
- Department of Botany, University of North Bengal, Siliguri, West Bengal, India
| | - G Sen
- Bioinformatics Facility, University of North Bengal, Siliguri, West Bengal, India
| | - S Bhattacharyya
- Biswa Bangla Genome Centre, Univ. of North Bengal, Siliguri, West Bengal, India
| | - M Gtari
- Unité de Bactériologie Moléculaire and Génomique, Département de Génie Biologique and Chimique, Institut National Des Sciences Appliquéeset de Technologie, Université de Carthage, Carthage, Tunisia
| | - A Sen
- Bioinformatics Facility, University of North Bengal, Siliguri, West Bengal, India.
- Biswa Bangla Genome Centre, Univ. of North Bengal, Siliguri, West Bengal, India.
- Department of Botany, University of North Bengal, Siliguri, West Bengal, India.
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4
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Maity PJ, Pawlowski K. Anthropogenic influences on the distribution of the Casuarina-Frankia symbiosis. Symbiosis 2021. [DOI: 10.1007/s13199-021-00765-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Belaid K, Swanson E, Carré-Mlouka A, Hocher V, Svistoonoff S, Gully D, Simpson S, Morris K, Thomas WK, Amrani S, Tisa LS, Gherbi H. Draft Genome Sequence of the Symbiotic Frankia sp. strain B2 isolated from root nodules of Casuarina cunninghamiana found in Algeria. J Genomics 2020; 8:11-15. [PMID: 32064004 PMCID: PMC7019079 DOI: 10.7150/jgen.38461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/22/2019] [Indexed: 11/05/2022] Open
Abstract
Frankia sp. strain B2 was isolated from Casuarina cunninghamiana nodules. Here, we report the 5.3-Mbp draft genome sequence of Frankia sp. strain B2 with a G+C content of 70.1 % and 4,663 candidate protein-encoding genes. Analysis of the genome revealed the presence of high numbers of secondary metabolic biosynthetic gene clusters.
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Affiliation(s)
- Kathia Belaid
- Laboratoire de Biologie du Sol, Faculté des Sciences Biologiques, Université des Sciences et de la Technologies Houari Boumediene (USTHB), BP32 El Alia - Bab Ezzouar Algiers, Algeria.,Laboratoire des Symbioses Tropicales et Méditerranéennes (IRD/INRA/CIRAD/Université de Montpellier/Supagro), 34398 Montpellier Cedex 5, France
| | - Erik Swanson
- University of New Hampshire, 46 College Rd., Durham, New Hampshire, USA, 03824-2617
| | - Alyssa Carré-Mlouka
- Laboratoire des Symbioses Tropicales et Méditerranéennes (IRD/INRA/CIRAD/Université de Montpellier/Supagro), 34398 Montpellier Cedex 5, France.,Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM) UMR 7245 CNRS-MNHN), Museum national d'Histoire naturelle, Centre National de la Recherche Scientifique (CNRS), CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Valérie Hocher
- Laboratoire des Symbioses Tropicales et Méditerranéennes (IRD/INRA/CIRAD/Université de Montpellier/Supagro), 34398 Montpellier Cedex 5, France
| | - Sergio Svistoonoff
- Laboratoire des Symbioses Tropicales et Méditerranéennes (IRD/INRA/CIRAD/Université de Montpellier/Supagro), 34398 Montpellier Cedex 5, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes (IRD/INRA/CIRAD/Université de Montpellier/Supagro), 34398 Montpellier Cedex 5, France
| | - Stephen Simpson
- University of New Hampshire, 46 College Rd., Durham, New Hampshire, USA, 03824-2617
| | - Krystalynne Morris
- University of New Hampshire, 46 College Rd., Durham, New Hampshire, USA, 03824-2617
| | - W Kelley Thomas
- University of New Hampshire, 46 College Rd., Durham, New Hampshire, USA, 03824-2617
| | - Said Amrani
- Laboratoire de Biologie du Sol, Faculté des Sciences Biologiques, Université des Sciences et de la Technologies Houari Boumediene (USTHB), BP32 El Alia - Bab Ezzouar Algiers, Algeria
| | - Louis S Tisa
- University of New Hampshire, 46 College Rd., Durham, New Hampshire, USA, 03824-2617
| | - Hassen Gherbi
- Laboratoire des Symbioses Tropicales et Méditerranéennes (IRD/INRA/CIRAD/Université de Montpellier/Supagro), 34398 Montpellier Cedex 5, France
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6
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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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7
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Béthencourt L, Boubakri H, Taib N, Normand P, Armengaud J, Fournier P, Brochier-Armanet C, Herrera-Belaroussi A. Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation. Res Microbiol 2019; 170:202-213. [PMID: 31018159 DOI: 10.1016/j.resmic.2019.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 10/27/2022]
Abstract
Sporulation is a microbial adaptive strategy to resist inhospitable conditions for vegetative growth and to disperse to colonise more favourable environments. This microbial trait is widespread in Actinobacteria. Among them, Frankia strains are able to differentiate sporangia in pure culture, while others can sporulate even when in symbiosis with sporulation occurring within host cells. The molecular determinants controlling Frankia sporulation have not been yet described. In order to highlight, for the first time, the molecular players potentially involved in Frankia sporulation, we conducted (i) a comparison of protein contents between Frankia spores and hyphae and (ii) a comparative genomic analysis of Frankia proteomes with sporulating and non-sporulating Actinobacteria. Among the main results, glycogen-metabolism related proteins, as well as oxidative stress response and protease-like proteins were overdetected in hyphae, recalling lytic processes that allow Streptomyces cells to erect sporogenic hyphae. Several genes encoding transcriptional regulators, including GntR-like, appeared up-regulated in spores, as well as tyrosinase, suggesting their potential role in mature spore metabolism. Finally, our results highlighted new proteins potentially involved in Frankia sporulation, including a pyrophosphate-energized proton pump and YaaT, described as involved in the phosphorelay allowing sporulation in Bacillus subtilis, leading us to discuss the role of a phosphorelay in Frankia sporulation.
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Affiliation(s)
- Lorine Béthencourt
- Écologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne, 69622 Cedex, France
| | - Hasna Boubakri
- Écologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne, 69622 Cedex, France
| | - Najwa Taib
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
| | - Philippe Normand
- Écologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne, 69622 Cedex, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Bagnols sur Cèze, F-30207, France
| | - Pascale Fournier
- Écologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne, 69622 Cedex, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
| | - Aude Herrera-Belaroussi
- Écologie 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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8
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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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9
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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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10
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Mansour S, Swanson E, McNutt Z, Pesce C, Harrington K, Abebe-Alele F, Simpson S, Morris K, Thomas WK, Tisa LS. Permanent Draft Genome sequence for Frankia sp . strain CcI49, a Nitrogen-Fixing Bacterium Isolated from Casuarina cunninghamiana that Infects Elaeagnaceae. J Genomics 2017; 5:119-123. [PMID: 28943973 PMCID: PMC5607709 DOI: 10.7150/jgen.22138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/31/2017] [Indexed: 01/22/2023] Open
Abstract
Frankia sp. strain CcI49 was isolated from Casuarina cunninghamiana nodules. However the strain was unable to re-infect Casuarina, but was able to infect other actinorhizal plants including Elaeagnaceae. Here, we report the 9.8-Mbp draft genome sequence of Frankia sp. strain CcI49 with a G+C content of 70.5 % and 7,441 candidate protein-encoding genes. Analysis of the genome revealed the presence of a bph operon involved in the degradation of biphenyls and polychlorinated biphenyls.
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Affiliation(s)
| | - Erik Swanson
- University of New Hampshire, Durham, New Hampshire, USA
| | | | - Céline Pesce
- University of New Hampshire, Durham, New Hampshire, USA
| | | | | | | | | | | | - Louis S Tisa
- University of New Hampshire, Durham, New Hampshire, USA
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11
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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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12
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Oshone R, Ngom M, Chu F, Mansour S, Sy MO, Champion A, Tisa LS. Genomic, transcriptomic, and proteomic approaches towards understanding the molecular mechanisms of salt tolerance in Frankia strains isolated from Casuarina trees. BMC Genomics 2017; 18:633. [PMID: 28821232 PMCID: PMC5563000 DOI: 10.1186/s12864-017-4056-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/11/2017] [Indexed: 11/10/2022] Open
Abstract
Background Soil salinization is a worldwide problem that is intensifying because of the effects of climate change. An effective method for the reclamation of salt-affected soils involves initiating plant succession using fast growing, nitrogen fixing actinorhizal trees such as the Casuarina. The salt tolerance of Casuarina is enhanced by the nitrogen-fixing symbiosis that they form with the actinobacterium Frankia. Identification and molecular characterization of salt-tolerant Casuarina species and associated Frankia is imperative for the successful utilization of Casuarina trees in saline soil reclamation efforts. In this study, salt-tolerant and salt-sensitive Casuarina associated Frankia strains were identified and comparative genomics, transcriptome profiling, and proteomics were employed to elucidate the molecular mechanisms of salt and osmotic stress tolerance. Results Salt-tolerant Frankia strains (CcI6 and Allo2) that could withstand up to 1000 mM NaCl and a salt-sensitive Frankia strain (CcI3) which could withstand only up to 475 mM NaCl were identified. The remaining isolates had intermediate levels of salt tolerance with MIC values ranging from 650 mM to 750 mM. Comparative genomic analysis showed that all of the Frankia isolates from Casuarina belonged to the same species (Frankia casuarinae). Pangenome analysis revealed a high abundance of singletons among all Casuarina isolates. The two salt-tolerant strains contained 153 shared single copy genes (most of which code for hypothetical proteins) that were not found in the salt-sensitive(CcI3) and moderately salt-tolerant (CeD) strains. RNA-seq analysis of one of the two salt-tolerant strains (Frankia sp. strain CcI6) revealed hundreds of genes differentially expressed under salt and/or osmotic stress. Among the 153 genes, 7 and 7 were responsive to salt and osmotic stress, respectively. Proteomic profiling confirmed the transcriptome results and identified 19 and 8 salt and/or osmotic stress-responsive proteins in the salt-tolerant (CcI6) and the salt-sensitive (CcI3) strains, respectively. Conclusion Genetic differences between salt-tolerant and salt-sensitive Frankia strains isolated from Casuarina were identified. Transcriptome and proteome profiling of a salt-tolerant strain was used to determine molecular differences correlated with differential salt-tolerance and several candidate genes were identified. Mechanisms involving transcriptional and translational regulation, cell envelop remodeling, and previously uncharacterized proteins appear to be important for salt tolerance. Physiological and mutational analyses will further shed light on the molecular mechanism of salt tolerance in Casuarina associated Frankia isolates. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4056-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rediet Oshone
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, 46 College Rd, Durham, NH, 03824-2617, USA
| | - Mariama Ngom
- Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux, Centre de Recherche de Bel-Air, Dakar, Sénégal.,Laboratoire Campus de Biotechnologies Végétales, Département de Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Sénégal.,Laboratoire Commun de Microbiologie Institut de Recherche pour le Développement/Institut Sénégalais de Recherches Agricoles/Université Cheikh Anta Diop, Centre de Recherche de Bel-Air, Dakar, Sénégal
| | - Feixia Chu
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, 46 College Rd, Durham, NH, 03824-2617, USA
| | - Samira Mansour
- Faculty of Science, Suez Canal University, Ismalia, Egypt
| | - Mame Ourèye Sy
- Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux, Centre de Recherche de Bel-Air, Dakar, Sénégal.,Laboratoire Campus de Biotechnologies Végétales, Département de Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Sénégal
| | - Antony Champion
- Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux, Centre de Recherche de Bel-Air, Dakar, Sénégal.,UMR DIADE, Institut de Recherche pour le Développement, Montpellier, France
| | - Louis S Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, 46 College Rd, Durham, NH, 03824-2617, USA.
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Pesce C, Swanson E, Simpson S, Morris K, Thomas WK, Tisa LS, Sellstedt A. Draft Genome Sequence of the Symbiotic Frankia Sp. Strain KB5 Isolated from Root Nodules of Casuarina equisetifolia. J Genomics 2017; 5:64-67. [PMID: 28698736 PMCID: PMC5504825 DOI: 10.7150/jgen.20887] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/29/2017] [Indexed: 01/27/2023] Open
Abstract
Frankia sp. strain KB5 was isolated from Casuarina equisetifolia and previous studies have shown both nitrogenase and uptake hydrogenase activities under free-living conditions. Here, we report 5.5-Mbp draft genome sequence with a G+C content of 70.03 %, 4,958 candidate protein-encoding genes, and 2 rRNA operons.
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Affiliation(s)
- Céline Pesce
- University of New Hampshire, Durham, New Hampshire, USA
| | - Erik Swanson
- University of New Hampshire, Durham, New Hampshire, USA
| | | | | | | | - Louis S Tisa
- University of New Hampshire, Durham, New Hampshire, USA
| | - Anita Sellstedt
- UPSC, Department of Plant physiology, Umeå University, S-90187 Umeå, Sweden
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14
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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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15
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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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