Strain identifier

BacDive ID: 13288

Type strain: Yes

Species: Crossiella cryophila

Strain Designation: TS-1980

Strain history: CIP <- 2001, IFO <- Y. Okami: strain TS-1980

NCBI tax ID(s): 43355 (species)

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General

@ref: 11492

BacDive-ID: 13288

DSM-Number: 44230

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic

description: Crossiella cryophila TS-1980 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 43355
  • Matching level: species

strain history

@refhistory
11492<- NRRL <- IFO <- Y. Okami, TS-1980
67770IFO 14475 <-- Y. Okami TS-1980.
118801CIP <- 2001, IFO <- Y. Okami: strain TS-1980

doi: 10.13145/bacdive13288.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Crossiella
  • species: Crossiella cryophila
  • full scientific name: Crossiella cryophila corrig. (Labeda and Lechevalier 1989) Labeda 2001

  • synonyms

    • @ref: 20215
    • synonym: Saccharothrix cryophilis

@ref: 11492

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Crossiella

species: Crossiella cryophila

full scientific name: Crossiella cryophila (Labeda and Lechevalier 1989) Labeda 2001

strain designation: TS-1980

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.353
69480100positive
118801nopositivefilament-shaped

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
20024Bright yellow10-14 daysISP 2
20024Colorless10-14 daysISP 3
20024Colorless10-14 daysISP 4
20024Colorless10-14 daysISP 5
20024Colorless10-14 daysISP 6
20024Colorless10-14 daysISP 7
1188011

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20024yesAerial MyceliumWhiteISP 2
20024yesAerial MyceliumWhiteISP 3
20024yesAerial MyceliumWhiteISP 4
20024yesAerial MyceliumWhiteISP 5
20024yesAerial MyceliumWhiteISP 6
20024yesAerial MyceliumWhiteISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11492GYM 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
20024ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20024ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20024ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20024ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20024ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20024ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
33627MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
118801CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11492positivegrowth28mesophilic
20024positiveoptimum25mesophilic
33627positivegrowth30mesophilic
67770positivegrowth28mesophilic
118801positivegrowth25-30mesophilic
118801nogrowth10psychrophilic
118801nogrowth37mesophilic
118801nogrowth41thermophilic
118801nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118801
  • oxygen tolerance: obligate aerobe

spore formation

@refspore descriptionspore formationconfidence
20024Formation of spore chains (rectiflixibilis), spore surface smoothyes
69481yes100
69480yes100

compound production

  • @ref: 11492
  • compound: dopsisamine

halophily

@refsaltgrowthtested relationconcentration
20024NaClpositivemaximum2.5 %
118801NaClpositivegrowth0-2 %
118801NaClnogrowth4 %
118801NaClnogrowth6 %
118801NaClnogrowth8 %
118801NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
11880116947citrate-carbon source
1188014853esculin+hydrolysis
118801606565hippurate-hydrolysis
11880117632nitrate+reduction
11880116301nitrite-reduction
11880117632nitrate-respiration

antibiotic resistance

  • @ref: 118801
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refmetaboliteproductionChebi-ID
67770dopsisamineyes
68368acetoinyes15688
68368indoleno35581
68368hydrogen sulfideno16136
118801indoleno35581

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11880115688acetoin-
11880117234glucose-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
118801oxidase-
118801beta-galactosidase+3.2.1.23
118801alcohol dehydrogenase-1.1.1.1
118801gelatinase+
118801amylase+
118801DNase-
118801caseinase+3.4.21.50
118801catalase+1.11.1.6
118801tween esterase-
118801gamma-glutamyltransferase+2.3.2.2
118801lecithinase-
118801lipase-
118801lysine decarboxylase-4.1.1.18
118801ornithine decarboxylase-4.1.1.17
118801phenylalanine ammonia-lyase-4.3.1.24
118801protease-
118801tryptophan deaminase-
118801urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin+3.4.21.4
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20024+-+-++++++++++++++-
118801++--++-+-++-----+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20024+++++-+--++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118801+++++-+--++----+--++-+--+-+-----++-----+-------------------+--+----------+-+---++-----+---+++++--++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11492soilJapanJPNAsia
67770SoilJapanJPNAsiaShosenkyo, Yamanashi Pref.
118801Environment, SoilJapanJPNAsiaShosenkyo

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_92100.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37995;97_48342;98_63421;99_92100&stattab=map
  • Last taxonomy: Crossiella cryophila subclade
  • 16S sequence: AF114806
  • Sequence Identity:
  • Total samples: 299
  • soil counts: 163
  • aquatic counts: 16
  • animal counts: 46
  • plant counts: 74

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
114921Risk group (German classification)
200241German classification
1188011Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Crossiella cryophila strain NRRL B-16238 16S ribosomal RNA gene, partial sequence
  • accession: AF114806
  • length: 1499
  • database: ena
  • NCBI tax ID: 43355

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Crossiella cryophila DSM 44230GCA_014204915contigncbi43355
66792Crossiella cryophila strain DSM 4423043355.3wgspatric43355
66792Crossiella cryophila DSM 442302870600976draftimg43355

GC content

  • @ref: 11492
  • GC-content: 71.4
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes89.185no
anaerobicno98.967no
halophileno87.021no
spore-formingyes94.041yes
glucose-utilyes88.594no
aerobicyes93.573no
flagellatedno97.233no
thermophileno98.166yes
motileno93.103no
glucose-fermentno90.616no

External links

@ref: 11492

culture collection no.: DSM 44230, ATCC 51143, IFO 14475, JCM 9111, NBRC 14475, NCIMB 13187, NRRL B-16238, CGMCC 4.1710, CIP 107132, IMSNU 21335, KCTC 9391, VKM Ac-1965

straininfo link

  • @ref: 82489
  • straininfo: 42826

literature

  • topic: Phylogeny
  • Pubmed-ID: 11491360
  • title: Crossiella gen. nov., a new genus related to Streptoalloteichus.
  • authors: Labeda DP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-4-1575
  • year: 2001
  • mesh: Actinomycetales/*classification/*genetics/metabolism/ultrastructure, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Microscopy, Electron, Scanning, Phylogeny, Species Specificity
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11492Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44230)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44230
20024Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44230.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33627Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4534
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82489Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42826.1StrainInfo: A central database for resolving microbial strain identifiers
118801Curators of the CIPCollection of Institut Pasteur (CIP 107132)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107132