Strain identifier

BacDive ID: 6229

Type strain: Yes

Species: Idiomarina loihiensis

Strain Designation: L2-TR

Strain history: CIP <- 2004, S.P. Donachie, Hawaii Univ., Honolulu, Hawaii, USA: strain L2-TR

NCBI tax ID(s): 135577 (species)

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General

@ref: 5958

BacDive-ID: 6229

DSM-Number: 15497

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

description: Idiomarina loihiensis L2-TR is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from hydrothermal vent fluids mixed with ambient seawater.

NCBI tax id

  • NCBI tax id: 135577
  • Matching level: species

strain history

@refhistory
5958<- S. P. Donachie; L2-TR
120644CIP <- 2004, S.P. Donachie, Hawaii Univ., Honolulu, Hawaii, USA: strain L2-TR

doi: 10.13145/bacdive6229.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Idiomarinaceae
  • genus: Idiomarina
  • species: Idiomarina loihiensis
  • full scientific name: Idiomarina loihiensis Donachie et al. 2003

@ref: 5958

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Idiomarinaceae

genus: Idiomarina

species: Idiomarina loihiensis

full scientific name: Idiomarina loihiensis Donachie et al. 2003

strain designation: L2-TR

type strain: yes

Morphology

cell morphology

  • @ref: 120644
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5958BACTO 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
37428Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120644CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5958positivegrowth30mesophilic
37428positivegrowth30mesophilic
120644positivegrowth15-41
120644nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120644
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120644NaClpositivegrowth2-10 %
120644NaClnogrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12064416947citrate-carbon source
1206444853esculin-hydrolysis
12064417632nitrate-reduction
12064416301nitrite-reduction
12064417632nitrate-respiration

metabolite production

  • @ref: 120644
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12064415688acetoin-
12064417234glucose-

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
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
120644oxidase+
120644beta-galactosidase+3.2.1.23
120644alcohol dehydrogenase-1.1.1.1
120644gelatinase-
120644amylase-
120644DNase+
120644caseinase-3.4.21.50
120644catalase+1.11.1.6
120644tween esterase+
120644gamma-glutamyltransferase+2.3.2.2
120644lecithinase-
120644lipase-
120644lysine decarboxylase-4.1.1.18
120644ornithine decarboxylase-4.1.1.17
120644phenylalanine ammonia-lyase-4.3.1.24
120644tryptophan deaminase-
120644urease-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
120644-+++-+--+-++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5958hydrothermal vent fluids mixed with ambient seawaterHawaii, Loihi submarine volcanoUSAUSANorth America
120644Lo'ihi hydrothermal ventHawaiiUnited States of AmericaUSANorth America1999

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Hydrothermal vent
#Environmental#Aquatic#Marine
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5707.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_197;96_1775;97_3370;98_4251;99_5707&stattab=map
  • Last taxonomy: Idiomarina
  • 16S sequence: AF288370
  • Sequence Identity:
  • Total samples: 4304
  • soil counts: 591
  • aquatic counts: 2509
  • animal counts: 1041
  • plant counts: 163

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59581Risk group (German classification)
1206441Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5958
  • description: Idiomarina loihiensis 16S ribosomal RNA gene, partial sequence
  • accession: AF288370
  • length: 1415
  • database: ena
  • NCBI tax ID: 135577

GC content

  • @ref: 5958
  • GC-content: 47.4

External links

@ref: 5958

culture collection no.: DSM 15497, CIP 108396, ATCC BAA 735

straininfo link

  • @ref: 75708
  • straininfo: 127994

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14657116Idiomarina loihiensis sp. nov., a halophilic gamma-Proteobacterium from the Lo'ihi submarine volcano, Hawai'i.Donachie SP, Hou S, Gregory TS, Malahoff A, Alam MInt J Syst Evol Microbiol10.1099/ijs.0.02701-02003Alteromonadaceae/*classification/isolation & purification/physiology/ultrastructure, DNA, Bacterial/genetics/isolation & purification, DNA, Ribosomal/genetics/isolation & purification, Hawaii, Microscopy, Electron, Scanning, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics/isolation & purification, Seawater/*microbiology, *Volcanic EruptionsEnzymology
Metabolism18355891Ca-Mg kutnahorite and struvite production by Idiomarina strains at modern seawater salinities.Gonzalez-Munoz MT, De Linares C, Martinez-Ruiz F, Morcillo F, Martin-Ramos D, Arias JMChemosphere10.1016/j.chemosphere.2008.02.0102008Alteromonadaceae/classification/*metabolism/ultrastructure, Ammonia/metabolism, Carbon Dioxide/metabolism, Magnesium Compounds/chemistry/*metabolism, Microscopy, Electron, Scanning, Microscopy, Electron, Transmission, Phosphates/chemistry/*metabolism, Phylogeny, Protons, RNA, Ribosomal, 16S/genetics, Salinity, Seawater/chemistry/*microbiology, StruvitePhylogeny
Enzymology29688454Gene expression of terminal oxidases in two marine bacterial strains exposed to nanomolar oxygen concentrations.Gong X, Garcia-Robledo E, Lund MB, Lehner P, Borisov SM, Klimant I, Revsbech NP, Schramm AFEMS Microbiol Ecol10.1093/femsec/fiy0722018Alteromonadaceae/enzymology/genetics/*metabolism, Electron Transport/genetics, Electron Transport Complex IV/*biosynthesis/genetics, Gene Expression/genetics, Gene Expression Regulation, Bacterial/genetics, Marinobacter/enzymology/genetics/*metabolism, Oxidoreductases/*biosynthesis/genetics, Oxygen/metabolism, PhylogenyMetabolism
Phylogeny36385389Idiomarina rhizosphaerae sp. nov. isolated from rhizosphere soil of Kalidium cuspidatum, and reclassification of Idiomarina andamanensis as Pseudidiomarina andamanensis comb. nov., and Idiomarina mangrovi as Pseudidiomarina mangrovi comb. nov.Li LF, Xu L, Wei HM, Sun JQArch Microbiol10.1007/s00203-022-03335-52022Rhizosphere, RNA, Ribosomal, 16S/genetics, Phylogeny, Soil, DNA, Bacterial/genetics, Bacterial Typing Techniques, Sequence Analysis, DNA, *Alteromonadaceae, *Gammaproteobacteria/genetics, *Chenopodiaceae, Phospholipids/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
5958Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15497)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15497
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
37428Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6013
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
75708Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID127994.1StrainInfo: A central database for resolving microbial strain identifiers
120644Curators of the CIPCollection of Institut Pasteur (CIP 108396)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108396