Strain identifier

BacDive ID: 7632

Type strain: Yes

Species: Citricoccus alkalitolerans

Strain history: CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 70010

NCBI tax ID(s): 246603 (species)

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General

@ref: 6020

BacDive-ID: 7632

DSM-Number: 15665

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped

description: Citricoccus alkalitolerans CCUG 51943 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 246603
  • Matching level: species

strain history

@refhistory
6020<- W.-J. Li, YIM
407352003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 70010
67770KCTC 19012 <-- W.-J. Li YIM 70010.
67771<- W. J. Li
116251CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 70010

doi: 10.13145/bacdive7632.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Citricoccus
  • species: Citricoccus alkalitolerans
  • full scientific name: Citricoccus alkalitolerans Li et al. 2005

@ref: 6020

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Citricoccus

species: Citricoccus alkalitolerans

full scientific name: Citricoccus alkalitolerans Li et al. 2005 emend. Schäfer et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31296positive0.65 µm0.65 µmcoccus-shapedno
67771positive
116251positivecoccus-shapedno

colony morphology

  • @ref: 116251

pigmentation

  • @ref: 31296
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6020ISP2 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
40735MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116251CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6020positivegrowth28mesophilic
31296positivegrowth10-37
31296positiveoptimum28mesophilic
40735positivegrowth30mesophilic
59381positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
116251positivegrowth10-30
116251nogrowth37mesophilic
116251nogrowth41thermophilic
116251nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
31296positivegrowth5.5-12alkaliphile
31296positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31296aerobe
59381aerobe
67771aerobe
116251facultative anaerobe

spore formation

  • @ref: 31296
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31296NaClpositivegrowth0-15 %
31296NaClpositiveoptimum2.5 %

murein

  • @ref: 6020
  • murein short key: A11.40
  • type: A4alpha L-Lys-Gly-D-Glu

observation

@refobservation
67770quinones: MK-9(H2)
67771quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3129622599arabinose+carbon source
3129617057cellobiose+carbon source
3129623652dextrin+carbon source
3129628260galactose+carbon source
3129617234glucose+carbon source
3129615428glycine+carbon source
3129617716lactose+carbon source
3129617306maltose+carbon source
3129629864mannitol+carbon source
3129637684mannose+carbon source
3129633942ribose+carbon source
3129617814salicin+carbon source
3129630911sorbitol+carbon source
3129617992sucrose+carbon source
3129618222xylose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
116251606565hippurate+hydrolysis
11625117632nitrate-reduction
11625116301nitrite-reduction

metabolite production

  • @ref: 116251
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 116251
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
31296catalase+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
116251oxidase-
116251beta-galactosidase-3.2.1.23
116251alcohol dehydrogenase-1.1.1.1
116251gelatinase+/-
116251amylase+
116251DNase+
116251caseinase-3.4.21.50
116251catalase+1.11.1.6
116251tween esterase-
116251gamma-glutamyltransferase-2.3.2.2
116251lecithinase-
116251lipase-
116251lysine decarboxylase-4.1.1.18
116251ornithine decarboxylase-4.1.1.17
116251phenylalanine ammonia-lyase-4.3.1.24
116251urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116251--+--+--+--+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116251------------------------------+/-------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116251--------------------------------------------------------------+------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6020soilThe eastern desertEgyptEGYAfrica
67770Desert soilEgyptEGYAfrica
67771Desert soilEgyptEGYAfrica
116251Environment, SoilEastern desertEgyptEGYAfrica2002

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_8847.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_453;97_3040;98_6467;99_8847&stattab=map
  • Last taxonomy: Micrococcus
  • 16S sequence: AY376164
  • Sequence Identity:
  • Total samples: 949
  • soil counts: 425
  • aquatic counts: 94
  • animal counts: 352
  • plant counts: 78

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
60201Risk group (German classification)
1162511Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6020
  • description: Citricoccus alkalitolerans strain YIM 70010 16S ribosomal RNA gene, partial sequence
  • accession: AY376164
  • length: 1480
  • database: ena
  • NCBI tax ID: 246603

GC content

@refGC-contentmethod
602067.8high performance liquid chromatography (HPLC)
3129663.8
6777067.8
6777163.8thermal denaturation, midpoint method (Tm)

External links

@ref: 6020

culture collection no.: CCUG 51943, CCTCC AA 203008, DSM 15665, CCTCC AA 20308, KCTC 19012, YIM 70010, JCM 13012, CIP 107968

straininfo link

  • @ref: 77076
  • straininfo: 134253

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653858Citricoccus alkalitolerans sp. nov., a novel actinobacterium isolated from a desert soil in Egypt.Li WJ, Chen HH, Zhang YQ, Kim CJ, Park DJ, Lee JC, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63237-02005Bacterial Typing Techniques, Benzoquinones/analysis, DNA, Ribosomal/analysis, *Desert Climate, Egypt, Fatty Acids/analysis, Hydrogen-Ion Concentration, Lipids/analysis, Micrococcaceae/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Peptidoglycan/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny19651738Citricoccus parietis sp. nov., isolated from a mould-colonized wall and emended description of Citricoccus alkalitolerans Li et al. 2005.Schafer J, Martin K, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.012567-02009Base Sequence, DNA, Bacterial/genetics, *Environmental Microbiology, Genes, Bacterial/genetics, Micrococcaceae/*classification/genetics/physiology, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species SpecificityGenetics
Phylogeny19654363Citricoccus zhacaiensis sp. nov., isolated from a bioreactor for saline wastewater treatment.Meng FX, Yang XC, Yu PS, Pan JM, Wang CS, Xu XW, Wu MInt J Syst Evol Microbiol10.1099/ijs.0.011635-02009Bioreactors/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Micrococcaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, Sodium Chloride/metabolismMetabolism
Phylogeny27502023Citricoccus lacusdiani sp. nov., an actinobacterium promoting Microcystis growth with limited soluble phosphorus.Zhang BH, Salam N, Cheng J, Xiao M, Li HQ, Yang JY, Zha DM, Li WJAntonie Van Leeuwenhoek10.1007/s10482-016-0745-y2016Base Composition, DNA, Bacterial, Micrococcaceae/classification/*isolation & purification/metabolism, *Microcystis/metabolism, Molecular Typing, Phosphorus/*metabolism, RNA, Bacterial, RNA, Ribosomal, 16SMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6020Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15665)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15665
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
31296Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2761528776041
40735Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5537
59381Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51943)https://www.ccug.se/strain?id=51943
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
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
77076Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134253.1StrainInfo: A central database for resolving microbial strain identifiers
116251Curators of the CIPCollection of Institut Pasteur (CIP 107968)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107968