Strain identifier

BacDive ID: 140636

Type strain: Yes

Species: Actinorhabdospora filicis

Strain Designation: K12-0408

Strain history: <- NBRC; NBRC 111897 <- A. Matsumoto, Kitasato Inst., Tokyo, Japan; K12-0408

NCBI tax ID(s): 1785913 (species)

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General

@ref: 64815

BacDive-ID: 140636

DSM-Number: 108652

keywords: 16S sequence, Bacteria, aerobe, Gram-positive

description: Actinorhabdospora filicis K12-0408 is an aerobe, Gram-positive bacterium that builds an aerial mycelium and was isolated from rhizosphere soils of fern plants.

NCBI tax id

  • NCBI tax id: 1785913
  • Matching level: species

strain history

  • @ref: 64815
  • history: <- NBRC; NBRC 111897 <- A. Matsumoto, Kitasato Inst., Tokyo, Japan; K12-0408

doi: 10.13145/bacdive140636.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Actinorhabdospora
  • species: Actinorhabdospora filicis
  • full scientific name: Actinorhabdospora filicis Mingma et al. 2016

@ref: 64815

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micromonosporales

family: Micromonosporaceae

genus: Actinorhabdospora

species: Actinorhabdospora filicis

full scientific name: Actinorhabdospora filicis Mingma et al. 2016

strain designation: K12-0408

type strain: yes

Morphology

cell morphology

  • @ref: 43070
  • gram stain: positive
  • motility: no

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium namefurther description
43070yesAerial myceliumwhiteISP2forms long chains of cylindrical spores (more than 10 spores per chain) with smooth surfaces
43070yesSubstrate mycelialight yellow to pale yellowISP2

pigmentation

@refproductionname
43070nodiffusible pigments
43070noMelanin pigments

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43070Nutrient agar (NA)yes
43070PDAyes
43070Czapek's agaryes
43070ISP4yes
64815CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
64815GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
64815NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
64815ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
43070positivegrowth22-30
64815positivegrowth28

culture pH

  • @ref: 43070
  • ability: positive
  • type: growth
  • pH: 6.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43070
  • oxygen tolerance: aerobe

halophily

  • @ref: 43070
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4307017632nitrate-reduction
43070casein+degradation
430705291gelatin+degradation
4307053426tween 80+degradation
4307016708adenine-degradation
4307017057cellobiose-degradation
4307017368hypoxanthine-degradation
4307028017starch-degradation
4307015318xanthine-degradation
4307017057cellobiose+carbon source
4307012936D-galactose+carbon source
4307017234glucose+carbon source
4307036218beta-lactose+carbon source
4307017306maltose+carbon source
4307016024D-mannose+carbon source
4307033942ribose+carbon source
4307048095(-)-D-fructose+/-carbon source
4307015963ribitol-carbon source
4307030849L-arabinose-carbon source
4307017268myo-inositol-carbon source
4307016899D-mannitol-carbon source
4307028053melibiose-carbon source
4307016634raffinose-carbon source
43070(-)-D-rhamnose-carbon source
4307027922sorbose-carbon source
4307017992sucrose-carbon source
4307017151xylitol-carbon source
4307018222xylose-carbon source
4307017057cellobiose+builds acid from
4307017234glucose+builds acid from
4307017306maltose+builds acid from
4307016024D-mannose+builds acid from

metabolite production

  • @ref: 43070
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
43070urease-3.5.1.5
43070acid phosphatase+3.1.3.2
43070esterase (C 4)+
43070esterase Lipase (C 8)+
43070alpha-fucosidase+3.2.1.51
43070alpha-galactosidase+3.2.1.22
43070beta-galactosidase+3.2.1.23
43070alpha-glucosidase+3.2.1.20
43070beta-glucosidase+3.2.1.21
43070leucine aminopeptidase+3.4.1.1
43070phosphoamidase+3.9.1.1
43070trypsin+3.4.21.4
43070valine aminopeptidase+
43070alkaline phosphatase-3.1.3.1
43070alpha-chymotrypsin-3.4.21.1
43070cystine aminopeptidase-3.4.11.3
43070N-acetyl-beta-glucosaminidase-3.2.1.52
43070beta-glucuronidase-3.2.1.31
43070lipase (C 14)-
43070alpha-mannosidase-3.2.1.24

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43070C17:05.4
    43070C15:0 iso9.8
    43070C15:0 anteiso6.5
    43070C16:0 iso5.1
    43070C16:0 iso 2OH3.1
    43070C17:0 iso5.8
    43070C17:0 iso 2OH2
    43070C17:0 anteiso23.3
    43070anteiso-C17:0 2-OH17.9
    4307010-methyl C17:05.75
    4307010-methyl C18:02.19
  • type of FA analysis: whole cell analysis
  • incubation medium: YD broth
  • agar/liquid: liquid
  • incubation temperature: 27
  • incubation time: 8
  • software version: Sherlock 6.0
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43070rhizosphere soils of fern (pteridophyte) plantsFussa and Hamura city, located in Tokyo prefecture, JapanJapanJPNAsia
64815rhizosphere soil of fernFussa, TokyoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_14280.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_7358;97_8828;98_10825;99_14280&stattab=map
  • Last taxonomy: Actinorhabdospora filicis subclade
  • 16S sequence: LC120802
  • Sequence Identity:
  • Total samples: 1575
  • soil counts: 1280
  • aquatic counts: 23
  • animal counts: 120
  • plant counts: 152

Safety information

risk assessment

  • @ref: 64815
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64815
  • description: Actinorhabdospora filicis gene for 16S ribosomal RNA, partial sequence
  • accession: LC120802
  • length: 1450
  • database: nuccore
  • NCBI tax ID: 1785913

GC content

  • @ref: 43070
  • GC-content: 69.6
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 64815

culture collection no.: NBRC 111897, TBRC 5327, DSM 108652

straininfo link

  • @ref: 96763
  • straininfo: 404696

literature

  • topic: Phylogeny
  • Pubmed-ID: 27169368
  • title: Actinorhabdospora filicis gen. nov., sp. nov., a new member of the family Micromonosporaceae.
  • authors: Mingma R, Tanaka K, Omura S, Takahashi Y, Matsumoto A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001145
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Japan, Micromonosporaceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43070Ratchanee Mingma, Kazuki Tanaka, Satoshi Omura, Yoko Takahashi and Atsuko MatsumotoActinorhabdospora filicis gen. nov., sp. nov., a new member of the family Micromonosporaceae10.1099/ijsem.0.001145IJSEM 66: 3071-3077 201627169368
64815Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-108652Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108652)
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/
96763Reimer, 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-ID404696.1