Strain identifier

BacDive ID: 7623

Type strain: Yes

Species: Arthrobacter psychrochitiniphilus

Strain Designation: GP3

Strain history: F. Wang GP3.

NCBI tax ID(s): 291045 (species)

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General

@ref: 16728

BacDive-ID: 7623

DSM-Number: 23143

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-positive, motile, rod-shaped

description: Arthrobacter psychrochitiniphilus GP3 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from guano of Adélie penguins.

NCBI tax id

  • NCBI tax id: 291045
  • Matching level: species

strain history

@refhistory
16728<- JCM/RIKEN <- F. Wang, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China; GP3
67770F. Wang GP3.

doi: 10.13145/bacdive7623.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Arthrobacter
  • species: Arthrobacter psychrochitiniphilus
  • full scientific name: Arthrobacter psychrochitiniphilus Wang et al. 2009

@ref: 16728

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter psychrochitiniphilus

full scientific name: Arthrobacter psychrochitiniphilus Wang et al. 2009

strain designation: GP3

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29225positiverod-shapedyes
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
18351Sulfur yellow (1016)10-14 daysISP 3
18351Sulfur yellow (1016)10-14 daysISP 4
18351Green beige (1000)/ Sulfur yellow (1016)10-14 daysISP 5
18351Sulfur yellow (1016)10-14 daysISP 6
18351Green beige (1000)/ Sulfur yellow (1016)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18351noISP 3
18351noISP 4
18351noISP 5
18351noISP 6
18351noISP 7

pigmentation

  • @ref: 29225
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16728TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18351ISP 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:
18351ISP 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
18351ISP 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
18351ISP 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
18351ISP 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

culture temp

@refgrowthtypetemperaturerange
16728positivegrowth20psychrophilic
18351positiveoptimum20psychrophilic
29225positivegrowth0-25
29225positiveoptimum20psychrophilic
67770positivegrowth20psychrophilic

culture pH

@refabilitytypepH
29225positivegrowth06-08
29225positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29225
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29225no
69481no100
69480no99.827

halophily

@refsaltgrowthtested relationconcentration
29225NaClpositivegrowth0-3 %
29225NaClpositiveoptimum1.5 %

murein

  • @ref: 16728
  • murein short key: A11.25
  • type: A3alpha L-Lys-L-Thr-L-Ala

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1835117234glucose+
1835122599arabinose+/-
1835117992sucrose+
1835118222xylose-
1835117268myo-inositol+/-
1835129864mannitol+
1835128757fructose+
1835126546rhamnose+/-
1835116634raffinose+/-
1835162968cellulose+/-
29225620642,3-butanediol+carbon source
2922530089acetate+carbon source
2922516449alanine+carbon source
2922522599arabinose+carbon source
2922518403L-arabitol+carbon source
2922522653asparagine+carbon source
2922517057cellobiose+carbon source
2922523652dextrin+carbon source
2922528757fructose+carbon source
2922528260galactose+carbon source
2922529987glutamate+carbon source
2922517754glycerol+carbon source
2922517596inosine+carbon source
2922517716lactose+carbon source
2922525115malate+carbon source
2922517306maltose+carbon source
2922529864mannitol+carbon source
2922537684mannose+carbon source
2922528053melibiose+carbon source
29225506227N-acetylglucosamine+carbon source
2922517272propionate+carbon source
2922517148putrescine+carbon source
2922515361pyruvate+carbon source
2922551850methyl pyruvate+carbon source
2922533942ribose+carbon source
2922517822serine+carbon source
2922530911sorbitol+carbon source
2922530031succinate+carbon source
2922517992sucrose+carbon source
2922517748thymidine+carbon source
2922527082trehalose+carbon source
2922553423tween 40+carbon source
2922553426tween 80+carbon source
2922516704uridine+carbon source
2922517151xylitol+carbon source
2922518222xylose+carbon source
2922517632nitrate+reduction
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29225catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18351-+---++-+-++/--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18351-++-++-+-++-++++-+-

Isolation, sampling and environmental information

isolation

@refsample typecontinentcountryorigin.country
16728guano of Adélie penguinsAustralia and Oceania
67770Guano of Adélie penguinsAntarcticaAntarcticaATA

isolation source categories

Cat1Cat2Cat3
#Host#Birds
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_16200.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_773;97_901;98_1057;99_16200&stattab=map
  • Last taxonomy: Arthrobacter
  • 16S sequence: AJ810896
  • Sequence Identity:
  • Total samples: 2628
  • soil counts: 738
  • aquatic counts: 471
  • animal counts: 1302
  • plant counts: 117

Safety information

risk assessment

  • @ref: 16728
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Arthrobacter psychrochitiniphilus gene for 16S rRNA, partial sequence, strain: JCM 13874AB5886331446ena291045
16728Arthrobacter psychrochitiniphilus partial 16S rRNA gene, type strain GP3TAJ8108961276ena291045

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter psychrochitiniphilus strain DSM 23143291045.5wgspatric291045
66792Arthrobacter psychrochitiniphilus strain GP3291045.4wgspatric291045
66792Arthrobacter psychrochitiniphilus GP32866268577draftimg291045
66792Arthrobacter psychrochitiniphilus DSM 231432844608859draftimg291045
67770Arthrobacter psychrochitiniphilus DSM 23143GCA_013408645contigncbi291045
67770Arthrobacter psychrochitiniphilus GP3GCA_003185915scaffoldncbi291045

GC content

@refGC-contentmethod
1672858.5high performance liquid chromatography (HPLC)
2922558.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes95.168yes
anaerobicno99.712yes
halophileno85.666no
spore-formingno90.256yes
glucose-utilyes89.704yes
motileno90.464yes
flagellatedno97.433no
aerobicyes93.802yes
thermophileno99.282yes
glucose-fermentno80.099no

External links

@ref: 16728

culture collection no.: DSM 23143, CGMCC 1.6355, JCM 13874

straininfo link

  • @ref: 77067
  • straininfo: 312284

literature

  • topic: Phylogeny
  • Pubmed-ID: 19625417
  • title: Arthrobacter psychrochitiniphilus sp. nov., a psychrotrophic bacterium isolated from Antarctica.
  • authors: Wang F, Gai Y, Chen M, Xiao X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.008912-0
  • year: 2009
  • mesh: Antarctic Regions, Arthrobacter/*chemistry/classification/genetics/*isolation & purification, Cold Temperature, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16728Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23143)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23143
18351Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM23143.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
29225Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125646
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
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
77067Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312284.1StrainInfo: A central database for resolving microbial strain identifiers