Strain identifier

BacDive ID: 132051

Type strain: Yes

Species: Loktanella agnita

Strain Designation: R10SW5

Strain history: CIP <- 2003, E. Ivanova, Swinburne Inst., Victoria, Australia: strain R10SW5, Ruegeria sp

NCBI tax ID(s): 287097 (species)

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General

@ref: 23842

BacDive-ID: 132051

DSM-Number: 104149

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

description: Loktanella agnita R10SW5 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea water.

NCBI tax id

  • NCBI tax id: 287097
  • Matching level: species

strain history

@refhistory
23842<- CIP <- E. P. Ivanova; R10SW5
116162CIP <- 2003, E. Ivanova, Swinburne Inst., Victoria, Australia: strain R10SW5, Ruegeria sp

doi: 10.13145/bacdive132051.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Loktanella
  • species: Loktanella agnita
  • full scientific name: Loktanella agnita Ivanova et al. 2005

@ref: 23842

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Loktanella

species: Loktanella agnita

full scientific name: Loktanella agnita Ivanova et al. 2005

strain designation: R10SW5

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
31393negative0.8 µmrod-shapedno
116162negativerod-shapedno

pigmentation

  • @ref: 31393
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
23842BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
116162CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
23842positivegrowth25mesophilic
31393positivegrowth08-35
31393positiveoptimum25mesophilic
116162positivegrowth15-30
116162nogrowth5psychrophilic
116162nogrowth37mesophilic
116162nogrowth41thermophilic
116162nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
31393positivegrowth6.0-10.0alkaliphile
31393positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

  • @ref: 31393
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31393
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
116162NaClpositivegrowth4-6 %
116162NaClnogrowth0 %
116162NaClnogrowth2 %
116162NaClnogrowth8 %
116162NaClnogrowth10 %

observation

  • @ref: 31393
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3139321217L-alaninamide+carbon source
3139335391aspartate+carbon source
3139329987glutamate+carbon source
3139317632nitrate+reduction
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11616216947citrate-carbon source
1161624853esculin-hydrolysis
116162606565hippurate+hydrolysis
11616217632nitrate-builds gas from
11616217632nitrate-reduction
11616216301nitrite-builds gas from
11616216301nitrite-reduction
11616215792malonate-assimilation
11616217234glucose-degradation

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11616235581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
11616215688acetoin-
11616217234glucose-

enzymes

@refvalueactivityec
31393catalase+1.11.1.6
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
116162oxidase+
116162beta-galactosidase+3.2.1.23
116162alcohol dehydrogenase-1.1.1.1
116162gelatinase+/-
116162amylase-
116162caseinase-3.4.21.50
116162catalase+1.11.1.6
116162tween esterase-
116162gamma-glutamyltransferase+2.3.2.2
116162lecithinase-
116162lipase-
116162lysine decarboxylase-4.1.1.18
116162ornithine decarboxylase-4.1.1.17
116162phenylalanine ammonia-lyase-4.3.1.24
116162protease+
116162tryptophan deaminase-
116162urease-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
116162-+++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
23842-----+-+---+-+---+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
23842sea waterChazma Bay, Sea of Japan, Pacific OceanJapanJPNAsia
116162Environment, Sea, water sampleJapanJPNAsia2000

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
238421Risk group (German classification)
1161621Risk group (French classification)

Sequence information

16S sequences

  • @ref: 23842
  • description: Loktanella agnita 16S ribosomal RNA gene, partial sequence
  • accession: AY682198
  • length: 1396
  • database: ena
  • NCBI tax ID: 287097

GC content

  • @ref: 23842
  • GC-content: 59.1

External links

@ref: 23842

culture collection no.: DSM 104149, CIP 107883, KMM 3788, LMG 22534

straininfo link

  • @ref: 90412
  • straininfo: 362276

literature

  • topic: Phylogeny
  • Pubmed-ID: 16166733
  • title: Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean.
  • authors: Ivanova EP, Zhukova NV, Lysenko AM, Gorshkova NM, Sergeev AF, Mikhailov VV, Bowman JP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63461-0
  • year: 2005
  • mesh: DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/chemistry/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
23842Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104149Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104149)
31393Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172770428776041
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
90412Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID362276.1
116162Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107883Collection of Institut Pasteur (CIP 107883)