Strain identifier

BacDive ID: 11308

Type strain: Yes

Species: Collimonas fungivorans

Strain history: CIP <- 2005, W. de Boer, Netherlands Inst. Ecol., Heteren, Netherlands: strain Ter6

NCBI tax ID(s): 158899 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6913

BacDive-ID: 11308

DSM-Number: 17622

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Collimonas fungivorans CCUG 48868 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from dune soil with Marram grass tussocks.

NCBI tax id

  • NCBI tax id: 158899
  • Matching level: species

strain history

@refhistory
6913<- W. de Boer, Centre for Terrest. Ecology, Heteren; Ter6
374452005, W. de Boer, Netherlands Inst. Ecol., Heteren, Netherlands: strain Ter6
67772de Boer W, NIOO - KNAW, Centre for Terrestrial Ecology
119491CIP <- 2005, W. de Boer, Netherlands Inst. Ecol., Heteren, Netherlands: strain Ter6

doi: 10.13145/bacdive11308.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Collimonas
  • species: Collimonas fungivorans
  • full scientific name: Collimonas fungivorans De Boer et al. 2004

@ref: 6913

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Collimonas

species: Collimonas fungivorans

full scientific name: Collimonas fungivorans de Boer et al. 2004

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30085negative1.5 µm0.4 µmrod-shapedyes
119491negativerod-shapedno

pigmentation

  • @ref: 30085
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6913COLLIMONAS MEDIUM (DSMZ Medium 1035)yeshttps://mediadive.dsmz.de/medium/1035Name: COLLIMONAS MEDIUM (DSMZ Medium 1035) Composition: NaCl 5.0 g/l Trypticase soy broth 3.0 g/l KH2PO4 1.0 g/l Distilled water
37445MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119491CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6913positivegrowth28mesophilic
30085positivegrowth20-35
30085positiveoptimum25mesophilic
37445positivegrowth25mesophilic
58367positivegrowth20-30
67772positiveoptimum28mesophilic
119491positivegrowth5-30
119491nogrowth37mesophilic
119491nogrowth41thermophilic

culture pH

  • @ref: 30085
  • ability: positive
  • type: optimum
  • pH: 6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30085aerobe
58367aerobe
119491obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
119491NaClpositivegrowth0 %
119491NaClnogrowth2 %
119491NaClnogrowth4 %
119491NaClnogrowth6 %
119491NaClnogrowth8 %
119491NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3008517596inosine+carbon source
3008525017leucine+carbon source
3008527082trehalose+carbon source
3008516704uridine+carbon source
1194914853esculin-hydrolysis
11949117632nitrate-reduction
11949116301nitrite-reduction
11949117632nitrate-respiration

antibiotic resistance

  • @ref: 119491
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119491
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
30085cytochrome oxidase+1.9.3.1
119491oxidase+
119491beta-galactosidase+3.2.1.23
119491alcohol dehydrogenase-1.1.1.1
119491gelatinase+
119491amylase-
119491DNase+
119491caseinase-3.4.21.50
119491catalase-1.11.1.6
119491tween esterase-
119491lecithinase-
119491lipase-
119491lysine decarboxylase-4.1.1.18
119491ornithine decarboxylase-4.1.1.17
119491protease+
119491tryptophan deaminase-
119491urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119491-+++-+----++-+------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119491+++++--------------+++--+-+-+--+++--+--+---++----+++-+++---+--+++------+-+-+--+++-+---+-++++-+---++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitude
6913dune soil with Marram grass tussocksTerschellingNetherlandsNLDEurope
58367Soil,slightly acidic dune soilWadden Island TerschellingNetherlandsNLDEurope1994
67772Dune soilWadden IslandsNetherlandsNLDEurope199453.45.31667
119491Environment, Soil, duneNetherlandsNLDEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1512.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_1012;98_1195;99_1512&stattab=map
  • Last taxonomy: Collimonas
  • 16S sequence: AJ310394
  • Sequence Identity:
  • Total samples: 1345
  • soil counts: 741
  • aquatic counts: 386
  • animal counts: 129
  • plant counts: 89

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69131Risk group (German classification)
677721
1194911Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6913
  • description: Collimonas fungivorans partial 16S rRNA gene, isolate Ter6
  • accession: AJ310394
  • length: 1453
  • database: ena
  • NCBI tax ID: 158899

Genome sequences

  • @ref: 67772
  • description: Collimonas fungivorans Ter6
  • accession: GCA_001584145
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 158899

GC content

  • @ref: 30085
  • GC-content: 57.8

External links

@ref: 6913

culture collection no.: CCUG 48868, DSM 17622, LMG 21973, NCCB 100033, TER Ter6, TER 6, UCCCB6, CIP 108645

straininfo link

  • @ref: 80541
  • straininfo: 100062

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143036Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae.de Boer W, Leveau JHJ, Kowalchuk GA, Gunnewiek PJAK, Abeln ECA, Figge MJ, Sjollema K, Janse JD, van Veen JAInt J Syst Evol Microbiol10.1099/ijs.0.02920-02004Base Composition, Chitin/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Fungi, Microscopy, Electron, Molecular Sequence Data, Netherlands, Oxalobacteraceae/*classification/genetics/growth & development/*metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyMetabolism
Phylogeny20935085Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite.Zhang DC, Redzic M, Schinner F, Margesin RInt J Syst Evol Microbiol10.1099/ijs.0.028001-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6913Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17622)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17622
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
30085Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2644228776041
37445Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6297
58367Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48868)https://www.ccug.se/strain?id=48868
67772Curators of the UCCCBhttps://ucccb.uc.pt/
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
80541Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100062.1StrainInfo: A central database for resolving microbial strain identifiers
119491Curators of the CIPCollection of Institut Pasteur (CIP 108645)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108645