Strain identifier

BacDive ID: 10892

Type strain: Yes

Species: Rhodococcus marinonascens

Strain Designation: 3438W

Strain history: CIP <- 1994, JCM <- DSM <- H. Weyland: strain 3438W

NCBI tax ID(s): 1219020 (strain), 38311 (species)

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General

@ref: 11249

BacDive-ID: 10892

DSM-Number: 43752

keywords: genome sequence, 16S sequence, obligate aerobe, mesophilic

description: Rhodococcus marinonascens 3438W is an obligate aerobe, mesophilic prokaryote that was isolated from marine sediment.

NCBI tax id

NCBI tax idMatching level
1219020strain
38311species

strain history

@refhistory
11249<- H. Weyland, 3438W
67770DSM 43752 <-- H. Weyland 3438W.
120807CIP <- 1994, JCM <- DSM <- H. Weyland: strain 3438W

doi: 10.13145/bacdive10892.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus marinonascens
  • full scientific name: Rhodococcus marinonascens Helmke and Weyland 1984

@ref: 11249

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus marinonascens

full scientific name: Rhodococcus marinonascens Helmke and Weyland 1984

strain designation: 3438W

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.993
69480100positive
120807nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11249ARTIFICIAL SEA WATER – TRYPTONE SOY BROTH MEDIUM (ASW TSB MEDIUM) (DSMZ Medium 1691)yeshttps://mediadive.dsmz.de/medium/1691Name: Artificial sea water - Tryptone soy broth Medium (ASW TSB Medium) (DSMZ Medium 1691) Composition: NaCl 27.2 g/l Agar 20.0 g/l Trypticase peptone 17.0 g/l MgSO4 x 7 H2O 11.88 g/l MgCl2 x 6 H2O 9.06 g/l Soy peptone 3.0 g/l CaCl2 x 2 H2O 2.6 g/l D-Glucose 2.5 g/l KCl 1.28 g/l Na2HPO4 x 2 H2O 0.02 g/l NH4NO3 0.0042 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Pyridoxine hydrochloride 1e-05 g/l H3BO3 6e-06 g/l Lipoic acid 5e-06 g/l p-Aminobenzoic acid 5e-06 g/l D-Calcium pantothenate 5e-06 g/l Nicotinic acid 5e-06 g/l Riboflavin 5e-06 g/l Thiamine-HCl x 2 H2O 5e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Vitamin B12 1e-07 g/l Double distilled water Distilled water
11249LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381; with strain-specific modifications) Composition: NaCl 30.0 g/l Agar 20.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
11249SEA WATER AGAR (DSMZ Medium 246)yeshttps://mediadive.dsmz.de/medium/246Name: SEA WATER AGAR (DSMZ Medium 246) Composition: Agar 20.0 g/l Peptone 10.0 g/l Beef extract 10.0 g/l Tap water Sea water
34041Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120807CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
11249positivegrowth28mesophilic
11249positivegrowth18psychrophilic
34041positivegrowth18psychrophilic
67770positivegrowth18psychrophilic
120807positivegrowth5-30
120807nogrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120807
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.112

halophily

@refsaltgrowthtested relationconcentration
120807NaClpositivegrowth2-6 %
120807NaClnogrowth0 %
120807NaClnogrowth8 %
120807NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120807citrate-carbon source16947
120807hippurate-hydrolysis606565
120807nitrate-reduction17632
120807nitrite-reduction16301

metabolite production

  • @ref: 120807
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12080715688acetoin-
12080717234glucose-

enzymes

@refvalueactivityec
120807oxidase-
120807beta-galactosidase-3.2.1.23
120807alcohol dehydrogenase-1.1.1.1
120807caseinase-3.4.21.50
120807catalase+1.11.1.6
120807tween esterase+
120807gamma-glutamyltransferase-2.3.2.2
120807lecithinase-
120807lysine decarboxylase-4.1.1.18
120807ornithine decarboxylase-4.1.1.17
120807phenylalanine ammonia-lyase-4.3.1.24
120807urease-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
120807-+++-++---+---------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120807-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120807++--+-------------+-------------+----------++----+-----------------------+++---++--------++--++++++

Isolation, sampling and environmental information

isolation

@refsample typecountry
11249marine sediment
67770Marine sediment
120807Environment, Marine sedimentAtlantic Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_6550.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_181;97_445;98_509;99_6550&stattab=map
  • Last taxonomy: Rhodococcus marinonascens
  • 16S sequence: X80617
  • Sequence Identity:
  • Total samples: 1517
  • soil counts: 1055
  • aquatic counts: 143
  • animal counts: 192
  • plant counts: 127

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112491Risk group (German classification)
195841Risk group (German classification)
1208071Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218R.marinonanscens 16S rRNA gene (ATCC 35653T)X819331315ena38311
20218Rhodococcus marinonascens 16S rRNA gene, strain DSM43752TX806171474ena38311

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus marinonascens NBRC 143631219020.3wgspatric1219020
66792Rhodococcus marinonascens NBRC 143632867152395draftimg1219020
67770Rhodococcus marinonascens NBRC 14363GCA_001894885contigncbi1219020

GC content

@refGC-contentmethod
1124964.9
6777064.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno81no
motileno94.973no
gram-positiveyes88.718no
anaerobicno99.418no
aerobicyes90.195no
halophileno76.395no
spore-formingno71.409no
glucose-utilyes89.575no
flagellatedno98.739no
thermophileno96.589yes
glucose-fermentno89.041no

External links

@ref: 11249

culture collection no.: DSM 43752, ATCC 35653, IFO 14363, JCM 6241, NBRC 14363, NCMB 2246, BCRC 13696, CECT 4621, CGMCC 4.1726, CIP 104177, KCTC 9809, NCIMB 2246, NRRL B-16940, VKM Ac-1182

straininfo link

  • @ref: 80147
  • straininfo: 41211

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11249Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43752)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43752
19584Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43752.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
34041Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16057
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
80147Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41211.1StrainInfo: A central database for resolving microbial strain identifiers
120807Curators of the CIPCollection of Institut Pasteur (CIP 104177)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104177