Strain identifier

BacDive ID: 7643

Type strain: Yes

Species: Kocuria palustris

Strain Designation: TAGA27

Strain history: CIP <- 1999, DSMZ <- E. Stackebrandt <- G. Kovacs: strain TAGA27

NCBI tax ID(s): 71999 (species)

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General

@ref: 4540

BacDive-ID: 7643

DSM-Number: 11925

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

description: Kocuria palustris TAGA27 is an aerobe, Gram-positive bacterium that was isolated from rhizosphere of Typha angustiflora.

NCBI tax id

  • NCBI tax id: 71999
  • Matching level: species

strain history

@refhistory
4540<- E. Stackebrandt <- G. Kovács; TAGA27
67770IFO 16318 <-- DSM 11925 <-- E. Stackebrandt <-- G. Kovács TAGA27.
121518CIP <- 1999, DSMZ <- E. Stackebrandt <- G. Kovacs: strain TAGA27

doi: 10.13145/bacdive7643.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Kocuria
  • species: Kocuria palustris
  • full scientific name: Kocuria palustris Kovács et al. 1999

@ref: 4540

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Kocuria

species: Kocuria palustris

full scientific name: Kocuria palustris Kovács et al. 1999

strain designation: TAGA27

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121518positivecoccus-shapedno
69480positive91.894
69480no93.5

colony morphology

@refcolony colorincubation periodmedium used
18437Beige (1001)10-14 daysISP 2
18437Colorless10-14 daysISP 3
18437Beige (1001)10-14 daysISP 4
18437Sulfur yellow (1016)10-14 daysISP 5
18437Sulfur yellow (1016)10-14 daysISP 6
18437Sulfur yellow (1016)10-14 daysISP 7
121518

multicellular morphology

@refforms multicellular complexmedium name
18437noISP 2
18437noISP 3
18437noISP 4
18437noISP 5
18437noISP 6
18437noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4540TRYPTICASE 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
18437ISP 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
18437ISP 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:
18437ISP 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
18437ISP 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
18437ISP 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
18437ISP 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
38595MEDIUM 307 - for Kocuria rhizophilayesDistilled water make up to (1000.000 ml);Yeast extract (3.000 g);Tryptocasein soy agar (40.000 g)
121518CIP Medium 307yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=307

culture temp

@refgrowthtypetemperature
18437positiveoptimum28
4540positivegrowth30
38595positivegrowth30
59536positivegrowth30
67770positivegrowth30
121518positivegrowth25-37
121518nogrowth10
121518nogrowth41
121518nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59536aerobe
121518obligate aerobe

halophily

  • @ref: 121518
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 4540
  • murein short key: A11.06
  • type: A3alpha L-Lys-L-Ala3

observation

  • @ref: 67770
  • observation: quinones: MK-7(H2), MK-6(H2)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371melibiose-builds acid from28053
68371lactose+builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea+hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
121518hippurate+hydrolysis606565
121518nitrate+reduction17632
121518nitrite-reduction16301
68379nitrate+reduction17632
68379esculin-hydrolysis4853
68379urea+hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose+fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose+fermentation17306
68379lactose+fermentation17716
68379sucrose+fermentation17992
68379glycogen-fermentation28087

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12151835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-
12151815688acetoin-

enzymes

@refvalueactivityec
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
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
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
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
121518oxidase-
121518beta-galactosidase+3.2.1.23
121518alcohol dehydrogenase-1.1.1.1
121518gelatinase-
121518amylase-
121518DNase-
121518caseinase-3.4.21.50
121518catalase+1.11.1.6
121518coagulase-
121518tween esterase-
121518gamma-glutamyltransferase+2.3.2.2
121518lecithinase-
121518lipase-
121518lysine decarboxylase-4.1.1.18
121518ornithine decarboxylase-4.1.1.17
121518protease-
121518urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18437++-+-++--+-+---+++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18437+---+--+-+--+-+----
121518+--------+--+-+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18437------+--+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121518-----+/----+++----------------+-+/---------+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121518++++---+-+++++------------+----+-+-+------------++-------------++--------------++---------+-+++-+-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
4540rhizosphere of Typha angustifloraTypha angustifoliaSoroksar river (tributary of Danube river)HungaryHUNEurope
59536Rhizosphere of Typha angustifloraHungaryHUNEurope
67770Rhizosphere of narrow-leaved cattail (Typha angustifolia) from a floating mat in the Soroksár tributary of the River DanubeTypha angustifoliaHungaryHUNEurope
121518Environment, Rhizosphere of Typha angustifloraSoroksar riverHungaryHUNEurope1995

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
45401Risk group (German classification)
184371Hazard group
1215181Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Kocuria palustris 16S rRNA gene
  • accession: Y16263
  • length: 1467
  • database: nuccore
  • NCBI tax ID: 71999

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kocuria palustris TAGA27GCA_016907795contigncbi71999
66792Kocuria palustris strain TAGA2771999.21wgspatric71999
66792Kocuria palustris DSM 119252893684298draftimg71999
66792Kocuria palustris TAGA272562617128draftimg71999

GC content

  • @ref: 4540
  • GC-content: 69.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes91.894no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.762yes
69480spore-formingspore-formingAbility to form endo- or exosporesno82.792no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.663no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno93.5no

External links

@ref: 4540

culture collection no.: DSM 11925, CCM 4949, IFO 16318, NBRC 16318, CCUG 52395, CIP 105971, JCM 11652, IAM 15064, LMG 19167

straininfo link

  • @ref: 77087
  • straininfo: 12992

literature

  • topic: Phylogeny
  • Pubmed-ID: 10028258
  • title: Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia).
  • authors: Kovacs G, Burghardt J, Pradella S, Schumann P, Stackebrandt E, Marialigeti K
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-49-1-167
  • year: 1999
  • mesh: Actinobacteria/*classification, Base Sequence, DNA, Bacterial/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plants/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
4540Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11925)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11925
18437Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM11925.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
38595Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18049
59536Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52395)https://www.ccug.se/strain?id=52395
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
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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)
77087Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12992.1StrainInfo: A central database for resolving microbial strain identifiers
121518Curators of the CIPCollection of Institut Pasteur (CIP 105971)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105971