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Gtari M, Maaoui R, Ghodhbane-Gtari F, Ben Slama K, Sbissi I. MAGs-centric crack: how long will, spore-positive Frankia and most Protofrankia, microsymbionts remain recalcitrant to axenic growth? Front Microbiol 2024; 15:1367490. [PMID: 39144212 PMCID: PMC11323853 DOI: 10.3389/fmicb.2024.1367490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 07/04/2024] [Indexed: 08/16/2024] Open
Abstract
Nearly 50 years after the ground-breaking isolation of the primary Comptonia peregrina microsymbiont under axenic conditions, efforts to isolate a substantial number of Protofrankia and Frankia strains continue with enduring challenges and complexities. This study aimed to streamline genomic insights through comparative and predictive tools to extract traits crucial for isolating specific Frankia in axenic conditions. Pangenome analysis unveiled significant genetic diversity, suggesting untapped potential for cultivation strategies. Shared metabolic strategies in cellular components, central metabolic pathways, and resource acquisition traits offered promising avenues for cultivation. Ecological trait extraction indicated that most uncultured strains exhibit no apparent barriers to axenic growth. Despite ongoing challenges, potential caveats, and errors that could bias predictive analyses, this study provides a nuanced perspective. It highlights potential breakthroughs and guides refined cultivation strategies for these yet-uncultured strains. We advocate for tailored media formulations enriched with simple carbon sources in aerobic environments, with atmospheric nitrogen optionally sufficient to minimize contamination risks. Temperature adjustments should align with strain preferences-28-29°C for Frankia and 32-35°C for Protofrankia-while maintaining an alkaline pH. Given potential extended incubation periods (predicted doubling times ranging from 3.26 to 9.60 days, possibly up to 21.98 days), patience and rigorous contamination monitoring are crucial for optimizing cultivation conditions.
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Affiliation(s)
- Maher Gtari
- Department of Biological and Chemical Engineering, USCR Molecular Bacteriology and Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Tunis, Tunisia
| | - Radhi Maaoui
- Department of Biological and Chemical Engineering, USCR Molecular Bacteriology and Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Tunis, Tunisia
| | - Faten Ghodhbane-Gtari
- Department of Biological and Chemical Engineering, USCR Molecular Bacteriology and Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Tunis, Tunisia
- Higher Institute of Biotechnology Sidi Thabet, University of La Manouba, Tunisia
| | - Karim Ben Slama
- LR Bioresources, Environment, and Biotechnology (LR22ES04), Higher Institute of Applied Biological Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Imed Sbissi
- LR Pastoral Ecology, Arid Regions Institute, University of Gabes, Medenine, Tunisia
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Anderson MD, Taylor DL, Olson K, Ruess RW. Composition of soil Frankia assemblages across ecological drivers parallels that of nodule assemblages in Alnus incana ssp. tenuifolia in interior Alaska. Ecol Evol 2024; 14:e11458. [PMID: 38979008 PMCID: PMC11229434 DOI: 10.1002/ece3.11458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 07/10/2024] Open
Abstract
In root nodule symbioses (RNS) between nitrogen (N)-fixing bacteria and plants, bacterial symbionts cycle between nodule-inhabiting and soil-inhabiting niches that exert differential selection pressures on bacterial traits. Little is known about how the resulting evolutionary tension between host plants and symbiotic bacteria structures naturally occurring bacterial assemblages in soils. We used DNA cloning to examine soil-dwelling assemblages of the actinorhizal symbiont Frankia in sites with long-term stable assemblages in Alnus incana ssp. tenuifolia nodules. We compared: (1) phylogenetic diversity of Frankia in soil versus nodules, (2) change in Frankia assemblages in soil versus nodules in response to environmental variation: both across succession, and in response to long-term fertilization with N and phosphorus, and (3) soil assemblages in the presence and absence of host plants. Phylogenetic diversity was much greater in soil-dwelling than nodule-dwelling assemblages and fell into two large clades not previously observed. The presence of host plants was associated with enhanced representation of genotypes specific to A. tenuifolia, and decreased representation of genotypes specific to a second Alnus species. The relative proportion of symbiotic sequence groups across a primary chronosequence was similar in both soil and nodule assemblages. Contrary to expectations, both N and P enhanced symbiotic genotypes relative to non-symbiotic ones. Our results provide a rare set of field observations against which predictions from theoretical and experimental work in the evolutionary ecology of RNS can be compared.
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Affiliation(s)
- M. D. Anderson
- Biology DepartmentMacalester CollegeSaint PaulMinnesotaUSA
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
| | - D. L. Taylor
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - K. Olson
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
| | - R. W. Ruess
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
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Yuan Y, Chen Z, Huang X, Wang F, Guo H, Huang Z, Yang H. Comparative analysis of nitrogen content and its influence on actinorhizal nodule and rhizospheric microorganism diversity in three Alnus species. Front Microbiol 2023; 14:1230170. [PMID: 38169791 PMCID: PMC10758417 DOI: 10.3389/fmicb.2023.1230170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Alnus spp. (alder) are typical nonleguminous nitrogen-fixing trees that have a symbiotic relationship with Frankia. To explore the differences in nitrogen-fixing microorganisms between three alders (A. cremastogyne, A. glutinosa, and A. formosana) with different chromosome ploidies, the community structure and compositional diversity of potential nitrogen-fixing microorganism in root nodules and rhizosphere soil were comparatively analyzed using 16S rRNA and nitrogenase (nifH) gene sequencing. The nitrogen contents in the root nodules and rhizosphere soil were also determined. The results showed that the contents of total nitrogen and nitrate nitrogen in the root nodules of the three alders are significantly higher than those in the rhizosphere soils, while the ammonium nitrogen content show the opposite trend. The family, genus, and species levels showed obviously differences between root nodules and rhizosphere soils, while there were no significant differences at the classification level between the three alders. At the phylum level, the dominant phyla from 16S rRNA and nifH gene data in the root nodules and rhizosphere soil of the three alders are phylum Actinomycetota and phylum Pseudomonadota, respectively. The LEfSe results showed that there are significant differences in the dominant groups in the root nodules and rhizosphere oil of the three alders. The relative abundances of dominant groups also showed obvious differences between the root nodules and rhizosphere soils of three alders. The relative abundances of Frankia and unclassified_Frankia in root nodules are obviously higher than those in rhizosphere soils, and their relative abundances in A. glutinosa root nodules are significantly higher than those in A. cremastogyne and A. formosana at the genus and species levels. The diversity of potential nitrogen-fixing microorganism from 16S rRNA and nifH gene data in the A. glutinosa root nodules and rhizosphere soils are all higher than those in A. cremastogyne and A. formosana. The results of functional prediction also showed that the OTUs for nitrogen fixation, nitrate respiration, and ureolysis in A. glutinosa root nodules are higher than those in the other two alders. Redundancy analysis revealed that the total nitrogen content mostly affects the Frankia community. Overall, there are significant differences in the community composition and structure of potential nitrogen-fixing microorganism in the root nodules and rhizosphere soils between the three alders. A. glutinosa showed a relatively stronger nitrogen fixation capacity than A. formosana and A. cremastogyne. The results help elucidates how the community structure and nitrogen-fixing ability of potential nitrogen-fixing microorganism differ between alder species and serve as a reference for applying Frankia to alder plantations.
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Affiliation(s)
- Yuwei Yuan
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Zhi Chen
- Sichuan Key Laboratory of Ecological Restoration and Conservation for Forest and Wetland, Sichuan Academy of Forestry, Chengdu, China
| | - Xin Huang
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Fang Wang
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Hongying Guo
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Zhen Huang
- Sichuan Key Laboratory of Ecological Restoration and Conservation for Forest and Wetland, Sichuan Academy of Forestry, Chengdu, China
| | - Hanbo Yang
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
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Nouioui I, Ghodhbane-Gtari F, Jando M, Klenk HP, Gtari M. Frankia colletiae sp. nov., a nitrogen-fixing actinobacterium isolated from Colletia cruciata. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748481 DOI: 10.1099/ijsem.0.005656] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A nitrogen-fixing actinobacterium strain (Cc1.17T) isolated from a root nodule of Colletia cruciata was subjected to polyphasic taxonomic studies. The strain was characterized by the presence of meso-diaminopimelic acid in its peptidoglycan, galactose, glucose, mannose, rhamnose, ribose and xylose as cell-wall sugars, phosphatidylinositol, diphosphatidylglycerol, glycophospholipids, phosphatidylglycerol, glycophospholipid and uncharacterized lipids as its polar lipids, and C16 : 0, iso-C16 : 0, C17 : 1 ω9 and C18 : 1 ω9 as major fatty acids (>10 %). Strain Cc1.17T showed 16S rRNA gene sequence similarities of 97.4-99.8 % to validly named Frankia species. Phylogenetic trees based on 16S rRNA gene and genome sequences placed strain Cc1.17T in a new lineage within the genus Frankia. Digital DNA-DNA hybridization and average nucleotide identity values between strain Cc1.17T and its closest phylogenomic neighbours were well below the thresholds recommended for prokaryotic species delineation. Therefore, strain Cc1.17T (=DSM 43829T=CECT 9313T) merits recognition as the type strain of a new species for which the name Frankia colletiae sp. nov. is proposed.
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Affiliation(s)
- Imen Nouioui
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Faten Ghodhbane-Gtari
- Institut Supérieur de Biotechnologie de Sidi Thabet, Université La Manouba, Manouba, Tunisia.,USCR Bactériologie Moléculaire & génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, 1080 Tunis Cedex, Tunisia
| | - Marlen Jando
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Maher Gtari
- USCR Bactériologie Moléculaire & génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, 1080 Tunis Cedex, Tunisia
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Nouioui I, Ghodhbane-Gtari F, Pötter G, Klenk HP, Goodfellow M. Novel species of Frankia, Frankia gtarii sp. nov. and Frankia tisai sp. nov., isolated from a root nodule of Alnus glutinosa. Syst Appl Microbiol 2023; 46:126377. [PMID: 36379075 DOI: 10.1016/j.syapm.2022.126377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022]
Abstract
The status of four Frankia strains isolated from a root nodule of Alnus glutinosa was established in a polyphasic study. Taxogenomics and phenotypic features show that the isolates belong to the genus Frankia. All four strains form extensively branched substrate mycelia, multilocular sporangia, vesicles, lack aerial hyphae, but contain meso-diaminopimelic acid as the diamino acid of the peptidoglycan, galactose, glucose, mannose, ribose, xylose and traces of rhamnose as cell wall sugars, iso-C16:0 as the predominant fatty acid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol as the major polar lipids, have comparable genome sizes to other cluster 1, Alnus-infective strains with structural and accessory genes associated with nitrogen fixation. The genome sizes of the isolates range from 7.0 to 7.7 Mbp and the digital DNA G + C contents from 71.3 to 71.5 %. The four sequenced genomes are rich in biosynthetic gene clusters predicted to express for novel specialized metabolites, notably antibiotics. 16S rRNA gene and whole genome sequence analyses show that the isolates fall into two lineages that are closely related to the type strains of Frankia alni and Frankia torreyi. All of these taxa are separated by combinations of phenotypic properties and by digital DNA:DNA hybridization scores which indicate that they belong to different genomic species. Based on these results, it is proposed that isolates Agncl-4T and Agncl-10, and Agncl-8T and Agncl-18, be recognised as Frankia gtarii sp. nov. and Frankia tisai sp. nov. respectively, with isolates Agncl-4T (=DSM 107976T = CECT 9711T) and Agncl-8T (=DSM 107980T = CECT 9715T) as the respective type strains.
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Affiliation(s)
- Imen Nouioui
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
| | - Faten Ghodhbane-Gtari
- Institut Supérieur de Biotechnologie de Sidi Thabet, Université de La Manouba, Tunisia; USCR Bactériologie Moléculaire & Génomique, Institut National des Sciences Appliquées & de Technologie, Université de Carthage, Tunisia
| | - Gabriele Pötter
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne NE1 7RU, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne NE1 7RU, UK
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6
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Swanson E, Sbissi I, Ktari A, Cherif-Silini H, Ghodhbane-Gtari F, Tisa LS, Gtari M. Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere. Front Microbiol 2022; 13:1027317. [PMID: 36439809 PMCID: PMC9684332 DOI: 10.3389/fmicb.2022.1027317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/21/2022] [Indexed: 11/12/2022] Open
Abstract
The actinorhizal plant, Coriaria myrtifolia, is a neurotoxic plant species endemic to the western Mediterranean area, which forms a nitrogen-fixing symbiosis with members of Frankia cluster 2. Contrarily to other Frankia clusters, the occurrence and mode of dispersal for infective cluster 2 units outside of the host plant rhizosphere remains controversial. The present study was designed to investigate the structure of the microbiomes of C. myrtifolia phytosphere, rhizosphere, and soil samples extending outward linearly up to 1 km. Results showed that the epiphyte and endophyte communities were not significantly different from each other for most of the plant tissues. The communities associated with the below-ground tissues (nodule and root) were significantly different from those found on the above-ground tissues (fruit, leaves, and stems) and had a higher community richness. Coriaria myrtifolia phytomicrobiomes were dominated by Cyanobacteria for leaf, stem, and fruit while Actinobacteria and Proteobacteria were dominant in the root and nodule organelles. The nodule, a special niche for nitrogen fixation, was mainly inhabited by Frankia but contained several non-Frankia bacteria. Beside Frankia cluster 2, the presence of clusters 1, 4, and large numbers of cluster 3 strains have been detected in nodules, roots, and rhizospheres of C. myrtifolia. Despite Frankia being found in all plots using plant trapping bioassays with C. myrtifolia seedlings, Frankia cluster 2 was not detected in soil metagenomes showing the limits of detection by this approach. This result also suggests that in the absence of appropriate host plant species, Frankia cluster 2 has a reduced number of infective units present in the soil outward from the rhizosphere.
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Affiliation(s)
- Erik Swanson
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Imed Sbissi
- LR Ecologie Pastorale, Institut des Régions Arides, Médenine, Tunisia
| | - Amir Ktari
- USCR Bactériologie Moléculaire and Génomique, Institut National des Sciences Appliquées and de Technologie, Université de Carthage, Tunis Cedex, Tunisia
| | - Hafsa Cherif-Silini
- LR Microbiologie Appliquée, Département de Microbiologie, Faculté des Sciences Naturelles et de la Vie, Université Ferhat Abbas, Sétif, Algeria
| | - Faten Ghodhbane-Gtari
- USCR Bactériologie Moléculaire and Génomique, Institut National des Sciences Appliquées and de Technologie, Université de Carthage, Tunis Cedex, Tunisia
- Institut Supérieur de Biotechnologie de Sidi Thabet, Université de La Manouba, Biotechnopôle, Sidi Thabet, Sidi Thabet, Tunisia
| | - Louis S. Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- *Correspondence: Louis S. Tisa,
| | - Maher Gtari
- USCR Bactériologie Moléculaire and Génomique, Institut National des Sciences Appliquées and de Technologie, Université de Carthage, Tunis Cedex, Tunisia
- Maher Gtari,
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7
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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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Gueddou A, Sbissi I, Louati M, Ghodhbane-Gtari F, Cherif-Silini H, Gtari M. Root Nodule Microsymbionts of Native Coriaria myrtifolia in Algeria. Microbiol Insights 2022; 15:11786361221133794. [PMID: 36325108 PMCID: PMC9619857 DOI: 10.1177/11786361221133794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022] Open
Abstract
Coriaria myrtifolia occurs as natural flora of warm temperate
climates of northern Algeria which commonly found in hedges, forest and ravine
edges. This actinorhizal species was known to establish a mutualistic symbiosis
with members of phylogenetic cluster 2 (including strains associated to
Coriaria spp., Ceanothus,
Datiscaceae, and Dryadoideae) within the
genus Frankia. Attempts to isolate C.
myrtifolia microsymbionts from native plants growing in 4 locations
in Algeria permitted to only recover asymbiotic Frankia strains
(unable to reestablish nodulation and to fix nitrogen) from phylogenetic cluster
4 and several non-Frankia actinobacteria including members of
Micrococcus, Micromonospora, Nocardia, Plantactinospora,
and Streptomyces genera. The biodiversity of
Frankia microsymbionts of C. myrtifolia
root nodules was assessed using PCR-amplification followed by partial nucleotide
sequencing of glnA1 (glutamine synthetase type 1) gene. On the
12 different glnA1 gene sequences obtained in this study, 9
were detected for the first time, and were mainly closelyrelated to
Mediterranean genotypes previously described in the Grand Maghreb countries
(Morocco and Tunisia) and in Europe (France) but without clear separations from
other cluster 2 genotypes.
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Affiliation(s)
- Abdellatif Gueddou
- USCR Bactériologie Moléculaire &
Génomique, Institut National des Sciences Appliquées et de Technologie, Université
de Carthage, Tunisia
| | - Imed Sbissi
- LR Ecologie Pastorale, Institut des
Régions Arides, Médenine, Tunisia
| | - Moussa Louati
- USCR Bactériologie Moléculaire &
Génomique, Institut National des Sciences Appliquées et de Technologie, Université
de Carthage, Tunisia
| | - Faten Ghodhbane-Gtari
- USCR Bactériologie Moléculaire &
Génomique, Institut National des Sciences Appliquées et de Technologie, Université
de Carthage, Tunisia,Institut Supérieur de Biotechnologie de
Sidi Thabet, Université la Manouba, Tunisia
| | - Hafsa Cherif-Silini
- LR Microbiologie Appliquée, FNLS,
Université Ferhat Abbas Alegria, Sétif, Alegria
| | - Maher Gtari
- USCR Bactériologie Moléculaire &
Génomique, Institut National des Sciences Appliquées et de Technologie, Université
de Carthage, Tunisia,Maher Gtari, Universite de Carthage,
Institut National des Sciences Appliquées et de Technologie Centre Urbain Nord
BP 676-1080 Tunis Cedex, Tunis, 1054, Tunisia.
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Mohr JF, Gama S, Roy S, Bellenger JP, Plass W, Wichard T. Hydroxypyridinones in nitrogen-fixing bacterial cultures: A metal buffer for molybdenum and simulation of natural conditions. METALLOMICS : INTEGRATED BIOMETAL SCIENCE 2022; 14:6650223. [PMID: 35881466 DOI: 10.1093/mtomcs/mfac055] [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: 05/29/2022] [Accepted: 07/11/2022] [Indexed: 11/12/2022]
Abstract
Organic matter regulates the availability of important trace elements in aquatic and terrestrial ecosystems by acting as a source and container for microbes. To overcome the limitation of trace elements, nitrogen-fixing bacteria, for example, release low-molecular-weight chelators (metallophores), which scavenge the essential cofactors of the nitrogenase, iron and molybdenum, via complexation and subsequent uptake. The formation of metallophores is triggered by limiting conditions, which must be replicated in the laboratory in order to study metallophores as a mediator in metal cycling. While EDTA-based buffer systems for metal cations are well established, there is limited knowledge regarding the buffering of oxoanions such as molybdate in a bacterial growth medium. To mimic the availability of molybdenum in nature under laboratory conditions, this study created a Mo-buffer system for bacterial growth media of the model organisms Azotobacter vinelandii and Frankia sp. CH37. We investigated selected hydroxypyridinones (HPs) as potential molybdenum-chelating agents, determining the amount required for efficient molybdenum complexation by calculating speciation plots of the various candidate complexes in artificial growth media at various pH values. The Mo-maltol system was identified as an ideal, non-toxic molybdenum-buffer system. In the presence of the Mo-maltol system, the growth of Frankia sp. was limited under diazotrophic conditions, whereas A. vinelandii could acquire molybdenum through the release of protochelin and subsequent molybdenum uptake. The study paves the way for unravelling molybdenum recruitment and homeostasis under limiting conditions in bacteria.
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Affiliation(s)
- Jan Frieder Mohr
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Sofia Gama
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
- Department of Analytical Chemistry, Faculty of Chemistry, University of Białystok, Białystok, Poland
| | - Sébastien Roy
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Philippe Bellenger
- Centre SÈVE, Département de Chimie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Winfried Plass
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Thomas Wichard
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
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Alnus glutinosa seedlings grown following co-inoculation with Frankia torreyi strain CpI1 and Frankia asymbiotica strain NRRL B-16386. Symbiosis 2022. [DOI: 10.1007/s13199-022-00845-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Genome Sequence of Frankia sp. Strain CH37, a Metallophore-Producing, Nitrogen-Fixing Actinobacterium Isolated from the Sea Buckthorn, Hippophae rhamnoides (Elaeagnaceae). Microbiol Resour Announc 2020; 9:9/50/e01184-20. [PMID: 33303668 PMCID: PMC7729416 DOI: 10.1128/mra.01184-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We report the genome sequence of Frankia sp. strain CH37, a filamentous nitrogen-fixing soil-dwelling Gram-positive bacterium and hyper-producer of metal-complexing organic ligands (metallophores) isolated from the sea buckthorn (Hippophae rhamnoides). The 9.7-Mbp sequence, obtained using PacBio technology, harbors 7,766 predicted coding sequences, including gene clusters for metallophore production. We report the genome sequence of Frankia sp. strain CH37, a filamentous nitrogen-fixing soil-dwelling Gram-positive bacterium and hyperproducer of metal-complexing organic ligands (metallophores) isolated from the sea buckthorn (Hippophae rhamnoides). The 9.7-Mbp sequence, obtained using PacBio technology, harbors 7,766 predicted coding sequences, including gene clusters for metallophore production.
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12
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Mansour S, Swanson E, Pesce C, Simpson S, Morris K, Thomas WK, Tisa LS. Draft Genome Sequences for the Frankia sp. strains CgS1, CcI156 and CgMI4, Nitrogen-Fixing Bacteria Isolated from Casuarina sp. in Egypt. J Genomics 2020; 8:84-88. [PMID: 33029225 PMCID: PMC7532629 DOI: 10.7150/jgen.51181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/05/2020] [Indexed: 02/04/2023] Open
Abstract
Frankia sp. strains CgS1, CcI156 and CgMI4 were isolated from Casuarina glauca and C. cunninghamiana nodules. Here, we report the 5.26-, 5.33- and 5.20-Mbp draft genome sequences of Frankia sp. strains CgS1, CcI156 and CgMI4, respectively. Analysis of the genome revealed the presence of high numbers of secondary metabolic biosynthetic gene clusters.
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Affiliation(s)
- Samira Mansour
- Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Erik Swanson
- University of New Hampshire, Durham, New Hampshire, USA
| | - Céline Pesce
- University of New Hampshire, Durham, New Hampshire, USA.,Present address: HM Clause, Davis, California, USA
| | | | | | | | - Louis S Tisa
- University of New Hampshire, Durham, New Hampshire, USA
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13
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Draft Genome Sequence for
Frankia
sp. Strain BMG5.11, a Nitrogen-Fixing Bacterium Isolated from Elaeagnus angustifolia. Microbiol Resour Announc 2020; 9:9/37/e00824-20. [PMID: 32912917 PMCID: PMC7484076 DOI: 10.1128/mra.00824-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Frankia sp. strain BMG5.11, which was isolated from Elaeagnus angustifolia nodules, is able to infect other actinorhizal plants, including Elaeagnaceae, Rhamnaceae, Colletieae, Gymnostoma, and Myricaceae. Here, we report the 11.3-Mbp draft genome sequence of Frankia sp. strain BMG5.11, with a G+C content of 69.9% and 9,926 candidate protein-encoding genes. Frankia sp. strain BMG5.11, which was isolated from Elaeagnus angustifolia nodules, is able to infect other actinorhizal plants, including Elaeagnaceae, Rhamnaceae, Colletieae, Gymnostoma, and Myricaceae. Here, we report the 11.3-Mbp draft genome sequence of Frankia sp. strain BMG5.11, with a G+C content of 69.9% and 9,926 candidate protein-encoding genes.
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14
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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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15
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Gtari M, Ghodhbane-Gtari F, Nouioui I. Frankia soli sp. nov., an actinobacterium isolated from soil beneath Ceanothus jepsonii. Int J Syst Evol Microbiol 2019; 70:1203-1209. [PMID: 31829914 DOI: 10.1099/ijsem.0.003899] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Actinobacterial strain CjT was directly isolated from soil beneath Ceanothus jepsonii growing in the USA. The strain formed cell structures typical of the genus Frankia including extensive hyphae, vesicles and sporangia, and it effectively nodulated members of the actinorhizal Colletieae, Elaeagnaceae and Myricaceae. The whole-cell hydrolysate of strain CjT was rich in meso-diaminopimelic acid and galactose, glucose, mannose, xylose, ribose and a trace of rhamnose. Tbe polar lipid profile contained phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and glycophospholipid. The menaquinone was predominantly MK-9(H4). The fatty acid profile predominantly consisted of C17 : 1ω8c, iso-C16 : 0, C15:0, C16 : 0 and C17 : 0. A multilocus sequence analysis phylogeny based on atp1, ftsZ, dnaK, gyrA and secA gene sequences positioned the strain within Elaeagnaceae- and Colletieae-nodulating species together with Frankia elaeagni DSM 46783T, Frankia discariae DSM 46785T and Frankia irregularis DSM 45899T. Pairwise 16S rRNA gene sequence similarities showed that strain CjT was most closely related to F. discariae DSM 46785T (99.78 %) while their digital DNA-DNA hybridization value was 41.1 %. Based on the overall analyses, strain CjT (=DSM 100623T=CECT 9041T) warrants classification as the type strain of a novel species, for which the name Frankia soli sp. nov. is proposed.
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Affiliation(s)
- Maher Gtari
- Unité de Bactériologie Moléculaire et Génomique, Université Carthage (INSAT), Centre Urbain Nord, BP 676-1080 Tunis Cedex, Tunisia
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST), 2092, Tunis, Tunisia.,Unité de Bactériologie Moléculaire et Génomique, Université Carthage (INSAT), 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
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16
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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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17
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Nouioui I, Cortés-albayay C, Carro L, Castro JF, Gtari M, Ghodhbane-Gtari F, Klenk HP, Tisa LS, Sangal V, Goodfellow M. Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus Frankia. Front Microbiol 2019; 10:1457. [PMID: 31333602 PMCID: PMC6624747 DOI: 10.3389/fmicb.2019.01457] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
This study was designed to determine the plant growth promoting (PGP) potential of members of the genus Frankia. To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the Frankia genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (trpD), anthranilate synthases, and aminases (trpA and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (nif operon except for atypical Frankia) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in Frankia cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of Frankia casuarinae, F. inefficax, F. irregularis, and F. saprophytica. In short, these in silico genome analyses provide an insight into the PGP abilities of Frankia strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in Frankia strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that Frankia may have novel molecular mechanisms for cytokinin biosynthesis.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Carlos Cortés-albayay
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca, Spain
| | - Jean Franco Castro
- The Chilean Collection of Microbial Genetic Resources (CChRGM), Instituto de Investigaciones Agropecuarias (INIA) – Quilamapu, Chillán, Chile
| | - Maher Gtari
- Institut National des Sciences Appliquées et de Technologie, Université de Carthage Centre Urbain Nord, Tunis, Tunisia
| | - Faten Ghodhbane-Gtari
- Institut National des Sciences Appliquées et de Technologie, Université de Carthage Centre Urbain Nord, Tunis, Tunisia
- Laboratoire Microorganismes et Biomolécules Actives, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Louis S. Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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18
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Contrasted evolutionary constraints on carbohydrate active enzymes (CAZymes) in selected Frankia strains. Antonie van Leeuwenhoek 2018; 112:115-125. [PMID: 30291576 DOI: 10.1007/s10482-018-1173-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/29/2018] [Indexed: 10/28/2022]
Abstract
Carbohydrate active enzymes (CAZymes) are capable of breaking complex polysaccharides into simpler form. In plant-host-associated microorganisms CAZymes are known to be involved in plant cell wall degradation. However, the biology and evolution of Frankia CAZymes are largely unknown. In the present study, we took a genomic approach to evaluate the presence and putative roles of CAZymes in Frankia. The CAZymes were found to be potentially highly expressed (PHX) proteins and contained more aromatic amino acids, which increased their biosynthetic energy cost. These energy rich amino acids were present in the active sites of CAZymes aiding in their carbohydrate binding capacity. Phylogenetic and evolutionary analyses showed that, in Frankia strains with the capacity to nodulate host plants, CAZymes were evolving slower than the other PHX genes, whereas similar genes from non-nodulating (or ineffectively nodulating) Frankia strains showed little variation in their evolutionary constraints compared to other PHX genes. Thus, the present study revealed the persistence of a strong purifying selection on CAZymes of Frankia indicating their crucial role.
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19
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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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20
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Kucho KI, Tobita H, Ikebe M, Shibata M, Imaya A, Kabeya D, Saitoh T, Okamoto T, Ono K, Morisada K. Frankia communities at revegetating sites in Mt. Ontake, Japan. Antonie van Leeuwenhoek 2018; 112:91-99. [PMID: 30155663 DOI: 10.1007/s10482-018-1151-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/25/2018] [Indexed: 11/24/2022]
Abstract
In 1984 at Mt. Ontake in Japan, an earthquake caused a devastating landslide, and as a result, the vegetation on the south slope of the mountain was completely eliminated. In higher elevation (2000 m) areas, revegetation has not yet been completed even 30 years after the landslide. Revegetation progress throughout the area was heterogeneous. In the partially revegetated areas, actinorhizal plant species such as Alnus maximowiczii and Alnus matsumurae have been found. In the present study, we investigated the Frankia communities in the higher-elevation area using sequence analysis of the amplified nifH (dinitrogenase reductase) gene from nodule and soil samples collected in the disturbed region, undisturbed forest, and in the boundary between the disturbed region and the undisturbed forest. Phylogenetic analysis of partial nifH sequences revealed the presence of six clusters, each of which consisted of highly similar (> 99%) sequences. Four clusters showed significant sequence similarity to Frankia (three Alnus- and a Casuarina-infecting strains). Diversity in the Frankia community was relatively low-only one or two clusters were detected in a site. At most of the sampling sites, a dominant cluster in a nodule coincided with that in rhizosphere soil, indicating that community structure in the rhizosphere is a primary factor that determines occupancy in a nodule. No significant difference in community structure was observed between plant species. Diversity in the Frankia community varied depending on revegetation progress. Cluster A, which was the most dominant in the disturbed region, was likely to have invaded from undisturbed forest.
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Affiliation(s)
- Ken-Ichi Kucho
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, 890-0065, Japan.
| | - Hiroyuki Tobita
- Department of Plant Ecology, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, 305-8687, Japan
| | - Mari Ikebe
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, 890-0065, Japan
| | - Mitsue Shibata
- Department of Forest Vegetation, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, 305-8687, Japan
| | - Akihiro Imaya
- Forestry Division, Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Daisuke Kabeya
- Department of Plant Ecology, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, 305-8687, Japan
| | - Tomoyuki Saitoh
- Tohoku Research Center, Forestry and Forest Products Research Institute, 2-25 Nabeyashiki, Shimokuriyagawa, Morioka, Iwate, 020-0123, Japan
| | - Toru Okamoto
- Kansai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, 612-0855, Japan
| | - Kenji Ono
- Tohoku Research Center, Forestry and Forest Products Research Institute, 2-25 Nabeyashiki, Shimokuriyagawa, Morioka, Iwate, 020-0123, Japan
| | - Kazuhito Morisada
- Department of Forest Soil, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, 305-8687, Japan
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21
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Draft genome sequence of the symbiotic Frankia sp. strain BMG5.30 isolated from root nodules of Coriaria myrtifolia in Tunisia. Antonie van Leeuwenhoek 2018; 112:67-74. [PMID: 30069723 DOI: 10.1007/s10482-018-1138-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/27/2018] [Indexed: 12/28/2022]
Abstract
Frankia sp. strain BMG5.30 was isolated from root nodules of a Coriaria myrtifolia seedling on soil collected in Tunisia and represents the second cluster 2 isolate. Frankia sp. strain BMG5.30 was able to re-infect C. myrtifolia generating root nodules. Here, we report its 5.8-Mbp draft genome sequence with a G + C content of 70.03% and 4509 candidate protein-encoding genes.
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22
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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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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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24
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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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25
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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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26
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Nouioui I, Gueddou A, Ghodhbane-Gtari F, Rhode M, Gtari M, Klenk HP. Frankia asymbiotica sp. nov., a non-infective actinobacterium isolated from Morella californica root nodule. Int J Syst Evol Microbiol 2017; 67:4897-4901. [PMID: 28918775 DOI: 10.1099/ijsem.0.002153] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The taxonomic status of strain M16386T, a nitrogen-fixing but non-nodulating isolate from Morella californica, was established on the basis of a polyphasic approach. The strain grows as branched hyphae, with vesicles and non-motile productive multilocular sporangia. It metabolizes short fatty acids, TCA cycle intermediates and carbohydrates as carbon sources, and fixes nitrogen in the absence of combined nitrogen source in the growth media. Chemotaxonomic traits of strain M16386T are consistent with its affiliation to the genus Frankia. The characteristic diamino acid in the cell wall is meso-diaminopimelic acid. Strain M16386T contains phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, glycophospholipid and phospholipid as polar lipids; MK-9(H4) and MK-9(H6) as the predominant menaquinones; iso-C16 : 0 and C17 : 1ω8c as major fatty acids; and galactose, glucose, mannose, rhamnose and ribose as whole-cell sugars. Strain M16386T showed 98.2 % 16S rRNA gene sequence similarity with its closest phylogenetic neighbour, Frankia inefficaxDSM 45817T. Based on these results, strain M16386T (=DSM 100626T=CECT 9040T) is designated the type strain of a novel species of the genus Frankia,for which the name Frankia asymbiotica sp. nov. is proposed.
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Affiliation(s)
- Imen Nouioui
- School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Abdellatif Gueddou
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Manfred Rhode
- Central Facility for Microscopy, HZI-Helmholtz Centre for Infection Research, Inhoffenstraße7, 38124 Braunschweig, Germany
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
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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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Permanent Draft Genome Sequence for Frankia sp. Strain Cc1.17, a Nitrogen-Fixing Actinobacterium Isolated from Root Nodules of Colletia cruciata. GENOME ANNOUNCEMENTS 2017; 5:5/24/e00530-17. [PMID: 28619804 PMCID: PMC5473273 DOI: 10.1128/genomea.00530-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Frankia sp. strain Cc1.17 is a member of the Frankia lineage 3, the organisms of which are able to reinfect plants of the Eleagnaceae, Rhamnaceae, and Myricaceae families and the genera Gynmnostoma and Alnus. Here, we report the 8.4-Mbp draft genome sequence, with a G+C content of 72.14% and 6,721 candidate protein-coding genes.
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29
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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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30
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Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
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31
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Ben Tekaya S, Ganesan AS, Guerra T, Dawson JO, Forstner MRJ, Hahn D. Sybr Green- and TaqMan-Based Quantitative PCR Approaches Allow Assessment of the Abundance and Relative Distribution of Frankia Clusters in Soils. Appl Environ Microbiol 2017; 83:e02833-16. [PMID: 27986724 PMCID: PMC5311412 DOI: 10.1128/aem.02833-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/09/2016] [Indexed: 11/20/2022] Open
Abstract
The nodule-forming actinobacterial genus Frankia can generally be divided into 4 taxonomic clusters, with clusters 1, 2, and 3 representing nitrogen-fixing strains of different host infection groups and cluster 4 representing atypical, generally non-nitrogen-fixing strains. Recently, quantitative PCR (qPCR)-based quantification methods have been developed for frankiae of clusters 1 and 3; however, similar approaches for clusters 2 and 4 were missing. We amended a database of partial 23S rRNA gene sequences of Frankia strains belonging to clusters 1 and 3 with sequences of frankiae representing clusters 2 and 4. The alignment allowed us to design primers and probes for the specific detection and quantification of these Frankia clusters by either Sybr Green- or TaqMan-based qPCR. Analyses of frankiae in different soils, all obtained from the same region in Illinois, USA, provided similar results, independent of the qPCR method applied, with abundance estimates of 10 × 105 to 15 × 105 cells (g soil)-1 depending on the soil. Diversity was higher in prairie soils (native, restored, and cultivated), with frankiae of all 4 clusters detected and those of cluster 4 dominating, while diversity in soils under Alnus glutinosa, a host plant for cluster 1 frankiae, or Betula nigra, a related nonhost plant, was restricted to cluster 1 and 3 frankiae and generally members of subgroup 1b were dominating. These results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees.IMPORTANCE Root nodule formation by the actinobacterium Frankia is host plant specific and largely, but not exclusively, correlates with assignments of strains to specific clusters within the genus. Due to the lack of adequate detection and quantification tools, studies on Frankia have been limited to clusters 1 and 3 and generally excluded clusters 2 and 4. We have developed tools for the detection and quantification of clusters 2 and 4, which can now be used in combination with those developed for clusters 1 and 3 to retrieve information on the ecology of all clusters delineated within the genus Frankia Our initial results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees.
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Affiliation(s)
| | | | - Trina Guerra
- Texas State University, Department of Biology, San Marcos, Texas, USA
| | - Jeffrey O Dawson
- University of Illinois at Urbana-Champaign, Department of Natural Resources and Environmental Sciences, Urbana, Illinois, USA
| | | | - Dittmar Hahn
- Texas State University, Department of Biology, San Marcos, Texas, USA
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32
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Nouioui I, Del Carmen Montero-Calasanz M, Ghodhbane-Gtari F, Rohde M, Tisa LS, Klenk HP, Gtari M. Frankia discariae sp. nov.: an infective and effective microsymbiont isolated from the root nodule of Discaria trinervis. Arch Microbiol 2017; 199:641-647. [PMID: 28105505 DOI: 10.1007/s00203-017-1337-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/01/2017] [Accepted: 01/04/2017] [Indexed: 10/20/2022]
Abstract
Strain BCU110501T was the first isolate reported to fulfill Koch's postulates by inducing effective nodules on its host plant of origin Discaria trinervis (Rhalmnaceae). Based on 16S rRNA gene sequence similarities, the strain was found to be most closely related to the type strain of Frankia elaeagni DSM 46783T (98.6%) followed by F. alni DSM 45986T (98.2%), F. casuarinae DSM 45818T (97.8%) and F. inefficacies DSM 45817T (97.8%). Digital DNA:DNA hybridizations (dDDH) between strain BCU110501Tand the type strains of other Frankia species were clearly below the cutoff point of 70%. The G+C content of DNA is 72.36%. The cell wall of strain BCU110501T contained meso-diaminopimelic acid and the cell sugars were galactose, glucose, mannose, xylose and ribose. Polar lipids were phosphatidylinositol (PI), diphosphatidylglycerol (DPG), glycophospholipid (GPL1-3), phosphatidylglycerol (PG) and an unknown lipid (L). The major fatty acids of strain BCU110501T consisted of iso-C16:0, C17:1 w8c and C16:0. Major menaquinones were MK9 (H4), MK9 (H6) and MK9 (H2). Based on these analyses, strain BCU110501T (=DSM 46785T=CECT 9042T) should be classified as the type strain of a novel Frankia species, for which the name Frankia discariae sp. nov. is proposed.
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Affiliation(s)
- Imen Nouioui
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092, Tunis, Tunisia.,School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
| | | | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092, Tunis, Tunisia
| | - Manfred Rohde
- HZI-Helmholtz Centre for Infection Research, Inhoffenstraße7, 38124, Brunswick, Germany
| | - 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
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092, Tunis, Tunisia.
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33
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Frankia inefficax sp. nov., an actinobacterial endophyte inducing ineffective, non nitrogen-fixing, root nodules on its actinorhizal host plants. Antonie van Leeuwenhoek 2016; 110:313-320. [PMID: 27830471 DOI: 10.1007/s10482-016-0801-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/03/2016] [Indexed: 10/20/2022]
Abstract
Strain EuI1cT is the first actinobacterial endophyte isolated from Elaeagnus umbellata that was shown to be infective on members of Elaeagnaceae and Morella but lacking the ability to form effective root nodules on its hosts. The strain can be easily distinguished from strains of other Frankia species based on its inability to produce vesicles, the specialized thick-walled structures where nitrogen fixation occurs. Chemotaxonomically, strain EuI1cT contains phosphatidylinositol, diphosphatidylglycerol, two glycophospholipids and phosphatidylglycerol as phospholipids. The whole cell sugars were composed of glucose, galactose, mannose, ribose, rhamnose and fucose as diagnostic sugars of the species. Major fatty acids were iso-C16:0, C17:1 ω8c and C15:0 and C17:0 and the predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). Analysis of the 16S rRNA gene sequence of strain EuI1cT showed 97, 97.4 and 97.9% identity with Frankia elaeagni DSM 46783T, Frankia casuarinae DSM 45818T and Frankia alni DSM 45986T, respectively. Digital DNA:DNA hybridizations with type strains of the three Frankia species with validly/effectively published names are significantly below 70%. These results warrant distinction of EuI1cT (= DSM 45817T = CECT 9037T) as the type strain of a novel species designated Frankia inefficax sp. nov.
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34
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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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35
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Nouioui I, Ghodhbane-Gtari F, Montero-Calasanz MDC, Göker M, Meier-Kolthoff JP, Schumann P, Rohde M, Goodfellow M, Fernandez MP, Normand P, Tisa LS, Klenk HP, Gtari M. Proposal of a type strain for Frankia alni (Woronin 1866) Von Tubeuf 1895, emended description of Frankia alni, and recognition of Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov. Int J Syst Evol Microbiol 2016; 66:5201-5210. [PMID: 27624710 DOI: 10.1099/ijsem.0.001496] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Before the establishment of pure cultures, the species Frankia alni, 'Frankia casuarinae' and 'Frankia elaeagni' were proposed to encompass all causal agents of the nitrogen-fixing root nodules of dicotyledonous plants from the genera Alnus, Casuarina or Elaeagnus. The sole Frankia species with a validly published name, the type species F. alni, was described by Woronin (1866) as present in the root of alder. Until now no type strain has been designated for F. alni, even though the absence of a type strain has seriously inhibited the application of modern taxonomic methods to the genus Frankia. Thus, we propose that strain ACN14aT, isolated in pure culture from Alnus viridis ssp. crispa with morphological properties matching the original description of F. alni, be recognized as the type strain of this species according to Rule 18f of the International Code of Nomenclature of Bacteria. We compared ACN14aT to two strains, CcI3T and BMG5.12T, isolated from Casuarina cunninghamiana and Elaeagnus angustifolia, respectively, based on chemotaxonomy, phenotype microarray data and molecular data retrieved from genome sequences. All three tested strains grew as branched hyphae, produced vesicles and multilocular sporangia containing non-motile spores and metabolized short fatty acids, TCA-cycle intermediates and carbohydrates. Chemotaxonomically, the three strains were indistinguishable with respect to phospholipids (phosphatidylinositol, diphosphatidylglycerol, glycophospholipids and phosphatidylglycerol) and cell-sugar composition (glucose, mannose, ribose, rhamnose, galactose and xylose, with the latter two being diagnostic for the genus). The major fatty acids identified in all three strains were iso-C16 : 0, C17 : 1ω8c, C15 : 0, C17 : 0 and C16 : 0. ACN14aT and BMG5.12T also shared C15 : 1ω6c, while C18 : 1ω9c was found to be unique to BMG5.12T. The major menaquinones identified in all three novel type strains were MK-9(H8), MK-9(H6) and MK-9(H4). MK-9(H2) was shared by ACN14aT and BMG5.12T, while MK-10(H4) and MK-8(H4) were only found in BMG5.12T. Analysis of 16S rRNA gene sequences showed 98.1-98.9 % identity between strains ACN14aT, CcI3T and BMG5.12T. Digital DNA-DNA hybridization values between the three type strains were well below 70 %. These results confirm the separation of the strains into three distinct species, Frankia alni, Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov. Thus, we propose ACN14aT (=DSM 45986T=CECT 9034T), CcI3T (=DSM 45818T=CECT 9043T) and BMG5.12T (=DSM 46783T=CECT 9031T) as the respective type strains.
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Affiliation(s)
- Imen Nouioui
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia.,School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | | | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, HZI - Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Michael Goodfellow
- School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Maria P Fernandez
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMRA1418, Cedex, 69622 Villeurbanne Cedex, France
| | - Philippe Normand
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMRA1418, Cedex, 69622 Villeurbanne Cedex, France
| | - 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
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
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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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Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of the Order Rhamnales. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00437-16. [PMID: 27231368 PMCID: PMC4882949 DOI: 10.1128/genomea.00437-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Frankia sp. strain G2 was originally isolated from Casuarina equisetifolia and is characterized by its ability to nodulate actinorhizal plants of the Rhamnales order, but not its original host. It represents one of the largest Frankia genomes so far sequenced (9.5 Mbp).
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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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Genomic approaches toward understanding the actinorhizal symbiosis: an update on the status of the Frankia genomes. Symbiosis 2016. [DOI: 10.1007/s13199-016-0390-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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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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Permanent Draft Genome Sequence of Frankia sp. Strain AvcI1, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Alnus viridis subsp. crispa Grown in Canada. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01511-15. [PMID: 26722013 PMCID: PMC4698390 DOI: 10.1128/genomea.01511-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Frankia strain AvcI1, isolated from root nodules of Alnus viridis subsp. crispa, is a member of Frankia lineage Ia, which is able to reinfect plants of the Betulaceae and Myricaceae families. Here, we report a 7.7-Mbp draft genome sequence with a G+C content of 72.41% and 6,470 candidate protein-encoding genes.
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Permanent Draft Genome Sequence of Frankia sp. Strain ACN1ag, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Alnus glutinosa. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01483-15. [PMID: 26679592 PMCID: PMC4683237 DOI: 10.1128/genomea.01483-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Frankia strain ACN1ag is a member of Frankia lineage Ia, which are able to re-infect plants of the Betulaceae and Myricaceae families. Here, we report a 7.5-Mbp draft genome sequence with a G+C content of 72.35% and 5,687 candidate protein-encoding genes.
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44
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Draft Genome Sequence of Frankia sp. Strain DC12, an Atypical, Noninfective, Ineffective Isolate from Datisca cannabina. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00889-15. [PMID: 26251504 PMCID: PMC4541282 DOI: 10.1128/genomea.00889-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Frankia sp. strain DC12, isolated from root nodules of Datisca cannabina, is a member of the fourth lineage of Frankia, which is unable to reinfect actinorhizal plants. Here, we report its 6.88-Mbp high-quality draft genome sequence, with a G+C content of 71.92% and 5,858 candidate protein-coding genes.
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45
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Persson T, Battenberg K, Demina IV, Vigil-Stenman T, Vanden Heuvel B, Pujic P, Facciotti MT, Wilbanks EG, O'Brien A, Fournier P, Cruz Hernandez MA, Mendoza Herrera A, Médigue C, Normand P, Pawlowski K, Berry AM. Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant. PLoS One 2015; 10:e0127630. [PMID: 26020781 PMCID: PMC4447401 DOI: 10.1371/journal.pone.0127630] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/16/2015] [Indexed: 11/18/2022] Open
Abstract
Frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. Phylogenetically, symbiotic frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. The strains of cluster II which form symbioses with actinorhizal Rosales and Cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. The genome of the first representative of this cluster, Candidatus Frankia datiscae Dg1 (Dg1), a microsymbiont of Datisca glomerata, was recently sequenced. A phylogenetic analysis of 50 different housekeeping genes of Dg1 and three published Frankia genomes showed that cluster II is basal among the symbiotic Frankia clusters. Detailed analysis showed that nodules of D. glomerata, independent of the origin of the inoculum, contain several closely related cluster II Frankia operational taxonomic units. Actinorhizal plants and legumes both belong to the nitrogen-fixing plant clade, and bacterial signaling in both groups involves the common symbiotic pathway also used by arbuscular mycorrhizal fungi. However, so far, no molecules resembling rhizobial Nod factors could be isolated from Frankia cultures. Alone among Frankia genomes available to date, the genome of Dg1 contains the canonical nod genes nodA, nodB and nodC known from rhizobia, and these genes are arranged in two operons which are expressed in D. glomerata nodules. Furthermore, Frankia Dg1 nodC was able to partially complement a Rhizobium leguminosarum A34 nodC::Tn5 mutant. Phylogenetic analysis showed that Dg1 Nod proteins are positioned at the root of both α- and β-rhizobial NodABC proteins. NodA-like acyl transferases were found across the phylum Actinobacteria, but among Proteobacteria only in nodulators. Taken together, our evidence indicates an Actinobacterial origin of rhizobial Nod factors.
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Affiliation(s)
- Tomas Persson
- Department of Ecology, Environment and Plant Sciences, Lilla Frescati, Stockholm University, 106 91, Stockholm, Sweden
| | - Kai Battenberg
- Department of Plant Sciences, University of California Davis, Davis, California, 95616, United States of America
| | - Irina V. Demina
- Department of Ecology, Environment and Plant Sciences, Lilla Frescati, Stockholm University, 106 91, Stockholm, Sweden
| | - Theoden Vigil-Stenman
- Department of Ecology, Environment and Plant Sciences, Lilla Frescati, Stockholm University, 106 91, Stockholm, Sweden
| | - Brian Vanden Heuvel
- Department of Biology, Colorado State University, Pueblo, Colorado, 81001, United States of America
| | - Petar Pujic
- Université Lyon 1, Université Lyon, CNRS, Ecologie Microbienne UMR5557, 69622, Villeurbanne Cedex, France
| | - Marc T. Facciotti
- Department of Biomedical Engineering, University of California Davis, Davis, California, 95616, United States of America
- UC Davis Genome Center, University of California Davis, Davis, California, 95616, United States of America
| | - Elizabeth G. Wilbanks
- UC Davis Genome Center, University of California Davis, Davis, California, 95616, United States of America
| | - Anna O'Brien
- UC Davis Genome Center, University of California Davis, Davis, California, 95616, United States of America
| | - Pascale Fournier
- Université Lyon 1, Université Lyon, CNRS, Ecologie Microbienne UMR5557, 69622, Villeurbanne Cedex, France
| | | | - Alberto Mendoza Herrera
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710, Reynosa, Tamaulipas, Mexico
| | | | - Philippe Normand
- Université Lyon 1, Université Lyon, CNRS, Ecologie Microbienne UMR5557, 69622, Villeurbanne Cedex, France
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Lilla Frescati, Stockholm University, 106 91, Stockholm, Sweden
| | - Alison M. Berry
- Department of Plant Sciences, University of California Davis, Davis, California, 95616, United States of America
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Põlme S, Bahram M, Kõljalg U, Tedersoo L. Global biogeography of Alnus-associated Frankia actinobacteria. THE NEW PHYTOLOGIST 2014; 204:979-988. [PMID: 25124146 DOI: 10.1111/nph.12962] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/03/2014] [Indexed: 06/03/2023]
Abstract
Macroecological patterns of microbes have received relatively little attention until recently. This study aimed to disentangle the determinants of the global biogeographic community of Alnus-associated actinobacteria belonging to the Frankia alni complex. By determining a global sequence similarity threshold for the nitrogenase reductase (nifH) gene, we separated Frankia into operational taxonomic units (OTUs) and tested the relative effects of Alnus phylogeny, geographic relatedness, and climatic and edaphic variables on community composition at the global scale. Based on the optimal nifH gene sequence similarity threshold of 99.3%, we distinguished 43 Frankia OTUs from root systems of 22 Alnus species on four continents. Host phylogeny was the main determinant of Frankia OTU-based community composition, but there was no effect on the phylogenetic structure of Frankia. Biogeographic analyses revealed the strongest cross-continental links over the Beringian land bridge. Despite the facultative symbiotic nature of Frankia, phylogenetic relations among Alnus species play a prominent role in structuring root-associated Frankia communities and their biogeographic patterns. Our results suggest that Alnus species exert strong phylogenetically determined selection pressure on compatible Actinobacteria.
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Affiliation(s)
- Sergei Põlme
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., 51005, Tartu, Estonia; Natural History Museum of Tartu University, 46 Vanemuise Street, 51014, Tartu, Estonia
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Draft Genome Sequence of Frankia sp. Strain BMG5.23, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina glauca Grown in Tunisia. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00520-14. [PMID: 24874687 PMCID: PMC4038892 DOI: 10.1128/genomea.00520-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.27-Mbp draft genome sequence for Frankia sp. strain BMG5.23, a salt-tolerant nitrogen-fixing actinobacterium isolated from root nodules of Casuarina glauca collected in Tunisia.
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48
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Hurst SG, Oshone R, Ghodhbane-Gtari F, Morris K, Abebe-Akele F, Thomas WK, Ktari A, Salem K, Mansour S, Gtari M, Tisa LS. Draft Genome Sequence of Frankia sp. Strain Thr, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina cunninghamiana Grown in Egypt. GENOME ANNOUNCEMENTS 2014; 2:e00493-14. [PMID: 24855310 PMCID: PMC4031348 DOI: 10.1128/genomea.00493-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/06/2014] [Indexed: 11/20/2022]
Abstract
Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.3-Mbp draft genome sequence for Frankia sp. stain Thr, a nitrogen-fixing actinobacterium isolated from root nodules of Casuarina cunninghamiana collected in Egypt.
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Affiliation(s)
| | - Rediet Oshone
- University of New Hampshire, Durham, New Hampshire, USA
| | | | | | | | | | - Amir Ktari
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université Carthage (INSAT), Campus Universitaire, Tunis, Tunisia
| | - Karima Salem
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université Carthage (INSAT), Campus Universitaire, Tunis, Tunisia
| | - Samira Mansour
- Botany Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | | | - Louis S Tisa
- University of New Hampshire, Durham, New Hampshire, USA
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Absence of cospeciation between the uncultured Frankia microsymbionts and the disjunct actinorhizal Coriaria species. BIOMED RESEARCH INTERNATIONAL 2014; 2014:924235. [PMID: 24864264 PMCID: PMC4016943 DOI: 10.1155/2014/924235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 01/21/2023]
Abstract
Coriaria is an actinorhizal plant that forms root nodules in symbiosis with nitrogen-fixing actinobacteria of the genus Frankia. This symbiotic association has drawn interest because of the disjunct geographical distribution of Coriaria in four separate areas of the world and in the context of evolutionary relationships between host plants and their uncultured microsymbionts. The evolution of Frankia-Coriaria symbioses was examined from a phylogenetic viewpoint using multiple genetic markers in both bacteria and host-plant partners. Total DNA extracted from root nodules collected from five species: C. myrtifolia, C. arborea, C. nepalensis, C. japonica, and C. microphylla, growing in the Mediterranean area (Morocco and France), New Zealand, Pakistan, Japan, and Mexico, respectively, was used to amplify glnA gene (glutamine synthetase), dnaA gene (chromosome replication initiator), and the nif DK IGS (intergenic spacer between nifD and nifK genes) in Frankia and the matK gene (chloroplast-encoded maturase K) and the intergenic transcribed spacers (18S rRNA-ITS1-5.8S rRNA-ITS2-28S rRNA) in Coriaria species. Phylogenetic reconstruction indicated that the radiations of Frankia strains and Coriaria species are not congruent. The lack of cospeciation between the two symbiotic partners may be explained by host shift at high taxonomic rank together with wind dispersal and/or survival in nonhost rhizosphere.
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Tisa LS, Beauchemin N, Gtari M, Sen A, Wall LG. What stories can the Frankia genomes start to tell us? J Biosci 2013; 38:719-26. [DOI: 10.1007/s12038-013-9364-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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