Strain identifier

BacDive ID: 131722

Type strain: Yes

Species: Frankia alni

Strain Designation: ACN14a, ULQ010201401

Strain history: <- M. Gtari, University of Tunis El Manar, Tunisia; ACN14a <- P. Normand, University Claude Bernard Lyon

NCBI tax ID(s): 1859 (species)

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General

@ref: 23518

BacDive-ID: 131722

DSM-Number: 45986

keywords: genome sequence, 16S sequence, Bacteria, aerobe, heterotroph, spore-forming, mesophilic, Gram-positive

description: Frankia alni ACN14a is an aerobe, heterotroph, spore-forming bacterium that was isolated from root nodule of Alnus viridis ssp. crispa.

NCBI tax id

  • NCBI tax id: 1859
  • Matching level: species

strain history

  • @ref: 23518
  • history: <- M. Gtari, University of Tunis El Manar, Tunisia; ACN14a <- P. Normand, University Claude Bernard Lyon

doi: 10.13145/bacdive131722.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Frankiales
  • family: Frankiaceae
  • genus: Frankia
  • species: Frankia alni
  • full scientific name: Frankia alni (Woronin 1866) Von Tubeuf 1895 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Schinzia alni
    20215Frankia subtilis

@ref: 23518

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Frankiaceae

genus: Frankia

species: Frankia alni

full scientific name: Frankia alni (Woronin 1866) Von Tubeuf 1895 emend. Nouioui et al. 2016

strain designation: ACN14a, ULQ010201401

type strain: yes

Morphology

cell morphology

  • @ref: 25097
  • gram stain: positive

colony morphology

  • @ref: 25097
  • colony color: white
  • medium used: BAP (basic propionate) medium with ammonium chloride

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_45986_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45986_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45986_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45986_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45986_5.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45986_6.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45986_7.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
23518BAP+ MEDIUM FOR FRANKIA (DSMZ Medium 1536)yeshttps://mediadive.dsmz.de/medium/1536Name: BAP+ MEDIUM FOR FRANKIA (DSMZ Medium 1536) Composition: KH2PO4 0.95 g/l K2HPO4 0.6 g/l Na-propionate 0.48 g/l NH4Cl 0.27 g/l MgSO4 x 7 H2O 0.025 g/l Citric acid 0.01 g/l Eisencitrat 0.01 g/l CaCl2 x 2 H2O 0.01 g/l H3BO3 0.00286 g/l MnCl2 x 4 H2O 0.00181 g/l Pyridoxine hydrochloride 0.0005 g/l Nicotinic acid 0.0005 g/l ZnSO4 x 7 H2O 0.00022 g/l Thiamine HCl 0.0001 g/l CuSO4 x 5 H2O 8e-05 g/l Na2MoO4 x 2 H2O 2.5e-05 g/l CoSO4 x 7 H2O 1e-06 g/l Distilled water
25097liquid BAP (basic propionate) mediumyes
25097BAP (basic propionate) mediumyes
23518MODIFIED BAP+ (PSA) MEDIUM FOR FRANKIA (DSMZ Medium 1660)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1660.pdf

culture temp

@refgrowthtypetemperaturerange
23518positivegrowth28mesophilic
25097positiveoptimum28mesophilic

culture pH

  • @ref: 25097
  • ability: positive
  • type: growth
  • pH: 6.3-6.8

Physiology and metabolism

oxygen tolerance

  • @ref: 25097
  • oxygen tolerance: aerobe

nutrition type

@reftype
25097heterotroph
25097chemoorganotroph

spore formation

  • @ref: 25097
  • type of spore: spore
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2509717521(-)-quinic acid-carbon source
2509715588D-malate-carbon source
2509716651(S)-lactate-carbon source
25097645522-hydroxybutyrate-carbon source
25097167632-oxobutanoate-carbon source
25097309162-oxoglutarate-carbon source
25097370543-hydroxybutyrate-carbon source
25097739183-O-methyl-D-glucose-carbon source
25097181014-hydroxyphenylacetic acid-carbon source
2509713705acetoacetate-carbon source
2509773706bromosuccinate-carbon source
2509717057cellobiose-carbon source
2509718333D-arabitol-carbon source
2509729990D-aspartate-carbon source
2509715824D-fructose-carbon source
2509728847D-fucose-carbon source
2509712936D-galactose-carbon source
2509718024D-galacturonic acid-carbon source
2509730612D-glucarate-carbon source
250978391D-gluconate-carbon source
2509717634D-glucose-carbon source
2509715748D-glucuronate-carbon source
2509716899D-mannitol-carbon source
2509716024D-mannose-carbon source
2509716523D-serine-carbon source
2509717924D-sorbitol-carbon source
2509723652dextrin-carbon source
2509716537galactarate-carbon source
2509716865gamma-aminobutyric acid-carbon source
250975291gelatin-carbon source
2509728066gentiobiose-carbon source
2509732323glucuronamide-carbon source
2509717754glycerol-carbon source
2509770744glycine-proline-carbon source
2509773804glycyl L-aspartic acid-carbon source
2509717596inosine-carbon source
2509717268myo-inositol-carbon source
2509716977L-alanine-carbon source
2509716467L-arginine-carbon source
2509718287L-fucose-carbon source
2509717464L-galactonic acid gamma-lactone-carbon source
2509729985L-glutamate-carbon source
2509715971L-histidine-carbon source
2509718183L-pyroglutamic acid-carbon source
2509762345L-rhamnose-carbon source
2509717115L-serine-carbon source
2509717716lactose-carbon source
2509717306maltose-carbon source
2509728053melibiose-carbon source
2509774611methyl (R)-lactate-carbon source
2509737657methyl D-glucoside-carbon source
2509763154N-acetyl-beta-D-mannosamine-carbon source
2509728037N-acetylgalactosamine-carbon source
2509735418n-acetylneuraminate-carbon source
2509775273niaproof-carbon source
2509717309pectin-carbon source
2509716634raffinose-carbon source
2509762965sodium formate-carbon source
2509717164stachyose-carbon source
2509717992sucrose-carbon source
2509727082trehalose-carbon source
2509732528turanose-carbon source
2509715589L-malate+carbon source
2509778697D-fructose 6-phosphate+carbon source
2509714314D-glucose 6-phosphate+carbon source
2509716523D-serine+nitrogen source
2509771321fusidate+growth
2509732735guanidinium chloride+nitrogen source
2509748607lithium chloride+growth
2509751850methyl pyruvate+carbon source
2509775248potassium tellurite+growth
2509775229sodium bromate+growth
2509775228sodium lactate+growth

antibiotic resistance

@refChEBImetaboliteis antibioticis resistant
250976472lincomycinyesyes
25097100147nalidixic acidyesyes
2509750694minocyclineyesyes
2509728001vancomycinyesyes
2509753156polychlorobiphenylyesyes
2509717097biphenylyesyes

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture composition
23518root nodule of Alnus viridis ssp. crispaAlnus viridis ssp. crispaTadoussacCanadaCANNorth America
25097TadoussacBAP (basic propionate) mediumsupplemented with 0.5 mM NH4Cl as nitrogen source

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Root nodule

taxonmaps

  • @ref: 69479
  • File name: preview.99_1688.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_932;97_1084;98_1293;99_1688&stattab=map
  • Last taxonomy: Frankia
  • 16S sequence: KX674376
  • Sequence Identity:
  • Total samples: 512
  • soil counts: 339
  • aquatic counts: 53
  • animal counts: 79
  • plant counts: 41

Safety information

risk assessment

  • @ref: 23518
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23518
  • description: Frankia alni ACN14a strain ACN14A 16S ribosomal RNA gene, partial sequence
  • accession: KX674376
  • length: 1510
  • database: ena
  • NCBI tax ID: 326424

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Frankia alni ACN14a326424.15completepatric326424
66792Frankia alni ACN14a637000115completeimg326424
66792Frankia alni ACN14aGCA_000058485completencbi326424

GC content

@refGC-contentmethod
2509772.8
2351872.8sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes88.724yes
anaerobicno98.335yes
halophileno97.469no
spore-formingyes75.891no
glucose-utilyes71.949yes
motileno94.057no
flagellatedno98.264no
aerobicyes88.008yes
thermophileno98.895yes
glucose-fermentno94.127no

External links

@ref: 23518

culture collection no.: DSM 45986, CECT 9034

straininfo link

  • @ref: 90113
  • straininfo: 405251

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics17151343Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DRGenome Res10.1101/gr.57984072006DNA Transposable Elements, DNA, Bacterial, Evolution, Molecular, Frankia/*genetics, Gene Deletion, Gene Duplication, *Genome, Bacterial, Geography, Magnoliopsida/*microbiology, Molecular Sequence Data, Nitrogen Fixation, Phylogeny, Plant Roots/microbiology, Prophages, Sequence Analysis, DNA, *SymbiosisPhylogeny
Metabolism19101977Biosynthetic gene cluster of cetoniacytone A, an unusual aminocyclitol from the endosymbiotic Bacterium Actinomyces sp. Lu 9419.Wu X, Flatt PM, Xu H, Mahmud TChembiochem10.1002/cbic.2008005272009Actinomyces/*genetics/*metabolism, Amino Acid Sequence, Antineoplastic Agents/*metabolism, Cyclohexanones/*metabolism, Frankia/genetics, Gene Expression, Gene Silencing, Genome, Bacterial, Metals/metabolism, Molecular Sequence Data, Multigene Family/*genetics, Racemases and Epimerases/chemistry/genetics/metabolism, Sequence Analysis, DNAGenetics
Phylogeny19440980The phylogeny of uptake hydrogenases in Frankia.Leul M, Normand P, Sellstedt AInt Microbiolim23061182009Bacterial Proteins/*classification, Frankia/*enzymology/genetics, Genome, Bacterial, Geography, Hydroxyproline/classification, Nitrogen Fixation, Oxidoreductases/*classification, PhylogenyEnzymology
Phylogeny20445637The genus Micromonospora is widespread in legume root nodules: the example of Lupinus angustifolius.Trujillo ME, Alonso-Vega P, Rodriguez R, Carro L, Cerda E, Alonso P, Martinez-Molina EISME J10.1038/ismej.2010.552010Bacterial Proteins/genetics, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fabaceae/*microbiology, In Situ Hybridization, Lupinus/*microbiology, Micromonospora/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nitrogen Fixation, Phylogeny, Polymorphism, Genetic, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, SpainGenetics
Enzymology22159868Lectin genes in the Frankia alni genome.Pujic P, Fournier P, Alloisio N, Hay AE, Marechal J, Anchisi S, Normand PArch Microbiol10.1007/s00203-011-0770-12011Alnus/microbiology, Cloning, Molecular, Escherichia coli/genetics, Frankia/*genetics, *Genes, Bacterial, Genome, Bacterial, Lectins/*genetics, Phylogeny, Root Nodules, Plant/microbiology, Streptomyces/genetics, Symbiosis/geneticsGenetics
Metabolism24676750Degradation of atrazine by Frankia alni ACN14a: gene regulation, dealkylation, and dechlorination.Rehan M, Kluge M, Franzle S, Kellner H, Ullrich R, Hofrichter MAppl Microbiol Biotechnol10.1007/s00253-014-5665-z2014Atrazine/*metabolism, Biotransformation, Carbon/metabolism, Chlorine/metabolism, Chromatography, High Pressure Liquid, Computational Biology, Dealkylation, Frankia/genetics/growth & development/*metabolism, Gene Expression Profiling, *Gene Expression Regulation, Bacterial, Mass Spectrometry, Multigene Family, Nitrogen/metabolism, Real-Time Polymerase Chain Reaction
Phylogeny27624710Proposal 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.Nouioui I, Ghodhbane-Gtari F, Montero-Calasanz MDC, Goker M, Meier-Kolthoff JP, Schumann P, Rohde M, Goodfellow M, Fernandez MP, Normand P, Tisa LS, Klenk HP, Gtari MInt J Syst Evol Microbiol10.1099/ijsem.0.0014962016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Frankia/*classification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome
Phylogeny27830471Frankia inefficax sp. nov., an actinobacterial endophyte inducing ineffective, non nitrogen-fixing, root nodules on its actinorhizal host plants.Nouioui I, Ghodhbane-Gtari F, Del Carmen Montero-Calasanz M, Rohde M, Tisa LS, Gtari M, Klenk HPAntonie Van Leeuwenhoek10.1007/s10482-016-0801-72016Bacterial Typing Techniques, Carbohydrates/analysis, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Endophytes/*classification/genetics/*isolation & purification/metabolism, Fatty Acids/analysis, Frankia/*classification/genetics/*isolation & purification/metabolism, *Nitrogen Fixation, Phospholipids/analysis, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, *Soil Microbiology, Species Specificity, Symbiosis, Tracheophyta/microbiologyEnzymology
Metabolism29378337Molecular response to nitrogen starvation by Frankia alni ACN14a revealed by transcriptomics and functional analysis with a fosmid library in Escherichia coli.Lurthy T, Alloisio N, Fournier P, Anchisi S, Ponsero A, Normand P, Pujic P, Boubakri HRes Microbiol10.1016/j.resmic.2017.12.0022018Alnus/microbiology, Bacterial Proteins/genetics/metabolism, Escherichia coli/*genetics/metabolism, Frankia/*genetics/physiology, Gene Expression Regulation, Bacterial, Gene Library, Nitrogen/*metabolism, Symbiosis, TranscriptomeTranscriptome
Phylogeny30030730Frankia torreyi sp. nov., the first actinobacterium of the genus Frankia Brunchorst 1886, 174(AL) isolated in axenic culture.Nouioui I, Ghodhbane-Gtari F, Jando M, Tisa LS, Klenk HP, Gtari MAntonie Van Leeuwenhoek10.1007/s10482-018-1131-82018Axenic Culture, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Frankia/classification/genetics/*isolation & purification/metabolism, Myricaceae/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiologyMetabolism
30917411Omics of the early molecular dialogue between Frankia alni and Alnus glutinosa and the cellulase synton.Pujic P, Alloisio N, Fournier P, Roche D, Sghaier H, Miotello G, Armengaud J, Berry AM, Normand PEnviron Microbiol10.1111/1462-2920.146062019
31608043A Stable Genetic Transformation System and Implications of the Type IV Restriction System in the Nitrogen-Fixing Plant Endosymbiont Frankia alni ACN14a.Gifford I, Vance S, Nguyen G, Berry AMFront Microbiol10.3389/fmicb.2019.022302019
Metabolism34684801A Promiscuous Halogenase for the Derivatization of Flavonoids.Kolling D, Stierhof M, Lasch C, Myronovskyi M, Luzhetskyy AMolecules10.3390/molecules262062202021Bacterial Proteins/chemistry/genetics/*metabolism, Biocatalysis, Drug Discovery, Flavonoids/chemistry/*metabolism, Frankia/enzymology/genetics, Genes, Bacterial, *Halogenation, Molecular Docking Simulation, Oxidoreductases/chemistry/genetics/*metabolism, Recombinant Proteins/chemistry/genetics/metabolism, Substrate SpecificityEnzymology
36102948A Nonspecific Lipid Transfer Protein with Potential Functions in Infection and Nodulation.Gasser M, Alloisio N, Fournier P, Balmand S, Kharrat O, Tulumello J, Carro L, Heddi A, Da Silva P, Normand P, Pujic P, Boubakri HMol Plant Microbe Interact10.1094/MPMI-06-22-0131-R2022

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
23518Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45986Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45986)
25097I. G.-G. Nouioui, F.,Montero-Calasanz, M. D.,Göker, M.,Meier-Kolthoff, J. P.,Schumann, P.,Rohde, M.,Goodfellow, M.,Fernandez, M. P.,Normand, P.,Tisa, L. S.,Klenk, H. P.,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. nov10.1099/ijsem.0.001496IJSEM 66: 5201-5210 201627624710
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66793Mukherjee et al.GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life10.1038/nbt.3886 35: 676-683 201728604660
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90113Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405251.1