Strain identifier

BacDive ID: 130633

Type strain: Yes

Species: Tropicimonas sediminicola

Strain Designation: M97

Strain history: J.-W. Bae M97.

NCBI tax ID(s): 1031541 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 22056

BacDive-ID: 130633

DSM-Number: 29339

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

description: Tropicimonas sediminicola M97 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment of a cage-cultured ark clam farm.

NCBI tax id

  • NCBI tax id: 1031541
  • Matching level: species

strain history

doi: 10.13145/bacdive130633.20220920.7

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Rhodobacteraceae
  • genus: Tropicimonas
  • species: Tropicimonas sediminicola
  • full scientific name: Tropicimonas sediminicola Shin et al. 2012

@ref: 22056

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Tropicimonas

species: Tropicimonas sediminicola

full scientific name: Tropicimonas sediminicola Shin et al. 2012

strain designation: M97

type strain: yes

Morphology

cell morphology

  • @ref: 30520
  • gram stain: negative
  • cell length: 1.25 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 22056
  • incubation period: 2-3 days

pigmentation

  • @ref: 30520
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 22056
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://bacmedia.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
22056positivegrowth37mesophilic
30520positivegrowth15-42
30520positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
30520positivegrowth06-10
30520positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30520
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
30520NaClpositivegrowth0-8 %
30520NaClpositiveoptimum1.5 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3052030089acetate+carbon source
30520286442-oxopentanoate+carbon source
3052018403L-arabitol+carbon source
3052033984fucose+carbon source
3052024265gluconate+carbon source
3052017234glucose+carbon source
3052029987glutamate+carbon source
3052017596inosine+carbon source
3052025115malate+carbon source
3052028053melibiose+carbon source
3052017268myo-inositol+carbon source
3052017272propionate+carbon source
3052051850methyl pyruvate+carbon source
3052017822serine+carbon source
3052030911sorbitol+carbon source
3052017748thymidine+carbon source
3052018222xylose+carbon source
305204853esculin+hydrolysis
3052017632nitrate+reduction
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-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

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
22056catalase+1.11.1.6
22056cytochrome-c oxidase+1.9.3.1
30520acid phosphatase+3.1.3.2
30520alkaline phosphatase+3.1.3.1
30520catalase+1.11.1.6
30520cytochrome oxidase+1.9.3.1
30520urease+3.5.1.5
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
22056+/----++-++-+++++/---++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
22056marine sediment of a cage-cultured ark clam farmsouth coastRepublic of KoreaKORAsia
67770Marine sediment of a cage-cultured ark clam farm on the south coast of Korea

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Aquaculture
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Host#Invertebrates (Other)#Mollusca

Safety information

risk assessment

  • @ref: 22056
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22056
  • description: Tropicimonas sediminicola strain M97 16S ribosomal RNA gene, partial sequence
  • accession: JF748735
  • length: 1390
  • database: ena
  • NCBI tax ID: 1031541

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tropicimonas sediminicola DSM 29339GCA_900188335contigncbi1031541
66792Tropicimonas sediminicola strain DSM 293391031541.3wgspatric1031541
66792Tropicimonas sediminicola DSM 293392681813518draftimg1031541

GC content

@refGC-contentmethod
2205668.5
6777068.5thermal denaturation, midpoint method (Tm)

External links

@ref: 22056

culture collection no.: DSM 29339, JCM 17731, KACC 15544

straininfo link

@refpassport
20218http://www.straininfo.net/strains/873477
20218http://www.straininfo.net/strains/873478

literature

  • topic: Phylogeny
  • Pubmed-ID: 22140172
  • title: Tropicimonas sediminicola sp. nov., isolated from marine sediment.
  • authors: Shin NR, Roh SW, Kim MS, Yun B, Whon TW, Kim YO, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.037929-0
  • year: 2011
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urljournalpubmedcatalogueID_cross_reference
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
22056Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29339Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29339)
2685210.1099/ijs.0.037929-022140172
30520Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604126852
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE