Strain identifier

BacDive ID: 131723

Type strain: Yes

Species: Frankia casuarinae

Strain Designation: Ccl3, HFP020203, HFPCcl3

Strain history: <- L. Tisa, Univ. of New Hampshire, USA; Ccl3 <- D. Benson <- Torrey laboratory <- Z. Zhang, Harvard University

NCBI tax ID(s): 106370 (species)

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General

@ref: 23519

BacDive-ID: 131723

DSM-Number: 45818

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

description: Frankia casuarinae Ccl3 is an aerobe, heterotroph, spore-forming bacterium that forms circular colonies and was isolated from Casuarina cunninghamiana root nodules.

NCBI tax id

  • NCBI tax id: 106370
  • Matching level: species

strain history

  • @ref: 23519
  • history: <- L. Tisa, Univ. of New Hampshire, USA; Ccl3 <- D. Benson <- Torrey laboratory <- Z. Zhang, Harvard University

doi: 10.13145/bacdive131723.20230509.8.1

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 casuarinae
  • full scientific name: Frankia casuarinae Nouioui et al. 2016

@ref: 23519

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Frankiaceae

genus: Frankia

species: Frankia casuarinae

full scientific name: Frankia casuarinae Nouioui et al. 2016

strain designation: Ccl3, HFP020203, HFPCcl3

type strain: yes

Morphology

cell morphology

  • @ref: 25097
  • gram stain: positive

colony morphology

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

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25097BAP (basic propionate) mediumyes
23519DPM MEDIUM (DSMZ Medium 737)yeshttps://mediadive.dsmz.de/medium/737Name: DPM MEDIUM (DSMZ Medium 737) Composition: Na-propionate 1.2 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.1 g/l Na2-EDTA 0.013608 g/l CaCl2 x 2 H2O 0.01 g/l FeSO4 x 7 H2O 0.009972 g/l H3BO3 0.00286 g/l MnCl2 x 4 H2O 0.00181 g/l ZnSO4 x 7 H2O 0.00022 g/l CuSO4 x 5 H2O 8e-05 g/l CoCl2 2.5e-05 g/l Na2MoO4 x 2 H2O 2.5e-05 g/l Distilled water
23519BAP+ 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

culture temp

@refgrowthtypetemperaturerange
25097positiveoptimum28mesophilic
23519positivegrowth28mesophilic

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
2509715589L-malate-carbon source
25097309162-oxoglutarate-carbon source
25097370543-hydroxybutyrate-carbon source
25097739183-O-methyl-D-glucose-carbon source
2509773706bromosuccinate-carbon source
2509717057cellobiose-carbon source
2509718333D-arabitol-carbon source
2509729990D-aspartate-carbon source
2509715824D-fructose-carbon source
2509778697D-fructose 6-phosphate-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
2509714314D-glucose 6-phosphate-carbon source
2509715748D-glucuronate-carbon source
2509716899D-mannitol-carbon source
2509716024D-mannose-carbon source
2509716523D-serine-nitrogen source
2509716523D-serine-carbon source
2509717924D-sorbitol-carbon source
2509723652dextrin-carbon source
2509716537galactarate-carbon source
2509716865gamma-aminobutyric acid-carbon source
250975291gelatin-carbon source
2509732323glucuronamide-carbon source
2509717754glycerol-carbon source
2509770744glycine-proline-carbon source
2509773804glycyl L-aspartic acid-carbon source
2509732735guanidinium chloride-nitrogen 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
2509748607lithium chloride-growth
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
2509775229sodium bromate-growth
2509762965sodium formate-carbon source
2509717164stachyose-carbon source
2509717992sucrose-carbon source
2509727082trehalose-carbon source
2509732528turanose-carbon source
25097645522-hydroxybutyrate+carbon source
25097167632-oxobutanoate+carbon source
25097181014-hydroxyphenylacetic acid+carbon source
2509730089acetate+carbon source
2509713705acetoacetate+carbon source
2509717968butyrate+carbon source
2509771321fusidate+carbon source
2509771321fusidate+growth
2509728066gentiobiose+carbon source
2509751850methyl pyruvate+carbon source
2509775248potassium tellurite+carbon source
2509775248potassium tellurite+growth
2509717272propionate+carbon source
2509775228sodium lactate+carbon source
2509775228sodium lactate+growth
2509753423tween 40+carbon source

antibiotic resistance

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

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture composition
23519Casuarina cunninghamiana root nodulesCasuarina cunninghamianaPetersham, MAUSAUSANorth America
25097Casuarina cunninghamianaFloridaUSAUSANorth AmericaBAP (basic propionate) mediumsupplemented with 0.5 mM NH4Cl as nitrogen source

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1636.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_932;97_1084;98_1293;99_1636&stattab=map
  • Last taxonomy: Frankia casuarinae
  • 16S sequence: KX674375
  • Sequence Identity:
  • Total samples: 229
  • soil counts: 156
  • aquatic counts: 24
  • animal counts: 35
  • plant counts: 14

Safety information

risk assessment

  • @ref: 23519
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23519
  • description: Frankia casuarinae strain CcI3 16S ribosomal RNA gene, partial sequence
  • accession: KX674375
  • length: 1512
  • database: ena
  • NCBI tax ID: 106370

GC content

@refGC-contentmethod
2509770.1
2351970.1sequence analysis

External links

@ref: 23519

culture collection no.: DSM 45818, CECT 9043

straininfo link

  • @ref: 90114
  • straininfo: 403303

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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

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
23519Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45818Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45818)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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/
90114Reimer, 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-ID403303.1