Strain identifier

BacDive ID: 130608

Type strain: Yes

Species: Limimaricola cinnabarinus

Strain Designation: LL-001

Strain history: T. Tsubouchi LL-001.

NCBI tax ID(s): 1125964 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 21635

BacDive-ID: 130608

DSM-Number: 29954

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

description: Limimaricola cinnabarinus LL-001 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from a deep-sea sediment subsample.

NCBI tax id

  • NCBI tax id: 1125964
  • Matching level: species

strain history

@refhistory
21635<- CECT <- T. Tsubouchi, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Extremobiosphere Res. Center, Yokosuka
67770T. Tsubouchi LL-001.

doi: 10.13145/bacdive130608.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Limimaricola
  • species: Limimaricola cinnabarinus
  • full scientific name: Limimaricola cinnabarinus (Tsubouchi et al. 2013) Wirth and Whitman 2018

  • synonyms

    • @ref: 20215
    • synonym: Loktanella cinnabarina

@ref: 21635

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Limimaricola

species: Limimaricola cinnabarinus

full scientific name: Limimaricola cinnabarinus (Tsubouchi et al. 2013) Wirth and Whitman 2018

strain designation: LL-001

type strain: yes

Morphology

cell morphology

  • @ref: 30728
  • gram stain: negative
  • cell length: 3.25 µm
  • cell width: 0.95 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 21635
  • incubation period: 1-2 days

pigmentation

  • @ref: 30728
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21635
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
21635positivegrowth30mesophilic
30728positivegrowth15-35
30728positiveoptimum25mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
30728positivegrowth5.5-7.5
30728positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30728
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
30728NaClpositivegrowth01-08 %
30728NaClpositiveoptimum3 %

observation

@refobservation
30728aggregates in clumps
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
307284853esculin+hydrolysis
6836925115malate+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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
21635catalase+1.11.1.6
21635cytochrome-c oxidase+1.9.3.1
30728alkaline phosphatase+3.1.3.1
30728alpha-galactosidase+3.2.1.22
30728catalase+1.11.1.6
30728cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21635-----+-++-+++++-+/-++/--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21635a deep-sea sediment subsampleShimokita PeninsulaJapanJPNAsia
67770Deep subseafloor sediment (108 m below the seafloor, at a water depth of 1,180 m)Shimokita PeninsulaJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_73.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_59;97_62;98_67;99_73&stattab=map
  • Last taxonomy: Limimaricola cinnabarinus
  • 16S sequence: AB688112
  • Sequence Identity:
  • Total samples: 272
  • soil counts: 11
  • aquatic counts: 229
  • animal counts: 31
  • plant counts: 1

Safety information

risk assessment

  • @ref: 21635
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21635
  • description: Loktanella cinnabarina gene for 16S ribosomal RNA, partial sequence
  • accession: AB688112
  • length: 1385
  • database: ena
  • NCBI tax ID: 1337093

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Limimaricola cinnabarinus LL-001GCA_000466965contigncbi1337093
66792Limimaricola cinnabarinus LL-0012602041674draftimg1337093

GC content

@refGC-contentmethod
2163569.3
6777069.3high performance liquid chromatography (HPLC)

External links

@ref: 21635

culture collection no.: DSM 29954, CECT 8072, JCM 18161

straininfo link

  • @ref: 89122
  • straininfo: 387790

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22843714Loktanella cinnabarina sp. nov., isolated from a deep subseafloor sediment, and emended description of the genus Loktanella.Tsubouchi T, Shimane Y, Mori K, Miyazaki M, Tame A, Uematsu K, Maruyama T, Hatada YInt J Syst Evol Microbiol10.1099/ijs.0.043174-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysis, Water MicrobiologyGenetics
Phylogeny23824249Loktanella soesokkakensis sp. nov., isolated from the junction between the North Pacific Ocean and a freshwater spring.Park S, Lee JS, Lee KC, Yoon JHAntonie Van Leeuwenhoek10.1007/s10482-013-9962-92013Bacteria, Aerobic/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ubiquinone/analysis, *Water MicrobiologyEnzymology
Genetics24233588Draft Genome Sequence of Loktanella cinnabarina LL-001T, Isolated from Deep-Sea Floor Sediment.Nishi S, Tsubouchi T, Takaki Y, Koyanagi R, Satoh N, Maruyama T, Hatada YGenome Announc10.1128/genomeA.00927-132013Phylogeny
Genetics29242219Draft Genome Sequence of Loktanella cinnabarina Strain XM1 Isolated from Coastal Surface Water.Ma R, Wang J, Wang Q, Ma Z, Li J, Chen LGenome Announc10.1128/genomeA.01310-172017Phylogeny
Phylogeny34323677Pseudoroseicyclus tamaricis sp. nov., isolated from seashore sediment of a Tamarix chinensis forest and emended descriptions of the genus Pseudoroseicyclus Park et al. 2016.Gai Y, Yang Y, Liu X, Li G, Wang S, Lai Q, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0049082021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae, Seawater, Sequence Analysis, DNA, *TamaricaceaeTranscriptome

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
21635Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29954Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29954)
30728Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172705928776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
89122Reimer, 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-ID387790.1