Strain identifier

BacDive ID: 10596

Type strain: Yes

Species: Gordonia rhizosphera

Strain Designation: 141

Strain history: CIP <- 1998, IFO <- K. Hatano: strain 141

NCBI tax ID(s): 1108045 (strain), 83341 (species)

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General

@ref: 11504

BacDive-ID: 10596

DSM-Number: 44383

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

description: Gordonia rhizosphera 141 is an obligate aerobe, mesophilic bacterium that was isolated from soil of the Mangrove rhizosphere.

NCBI tax id

NCBI tax idMatching level
1108045strain
83341species

strain history

@refhistory
11504<- IFO; 141
67770IFO 16068 <-- M. Takeuchi 141.
122213CIP <- 1998, IFO <- K. Hatano: strain 141

doi: 10.13145/bacdive10596.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Gordoniaceae
  • genus: Gordonia
  • species: Gordonia rhizosphera
  • full scientific name: Gordonia rhizosphera Takeuchi and Hatano 1998

@ref: 11504

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia rhizosphera

full scientific name: Gordonia rhizosphera Takeuchi and Hatano 1998

strain designation: 141

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.024
69480100positive
122213nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20052Salmon orange (2012)10-14 daysISP 2
20052Salmon orange (2012)10-14 daysISP 3
20052Salmon orange (2012)10-14 daysISP 4
20052Salmon orange (2012)10-14 daysISP 5
20052Salmon orange (2012)10-14 daysISP 6
20052Salmon orange (2012)10-14 daysISP 7
122213

multicellular morphology

@refforms multicellular complexmedium name
20052noISP 2
20052noISP 3
20052noISP 4
20052noISP 5
20052noISP 6
20052noISP 7

multimedia

  • @ref: 11504
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44383.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11504TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
20052ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20052ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20052ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20052ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20052ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20052ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
39324MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122213CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
20052positiveoptimum28mesophilic
11504positivegrowth28mesophilic
39324positivegrowth30mesophilic
67770positivegrowth28mesophilic
122213positivegrowth25-37mesophilic
122213nogrowth10psychrophilic
122213nogrowth41thermophilic
122213nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122213
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no90
69480no99.848

halophily

@refsaltgrowthtested relationconcentration
122213NaClpositivegrowth0-6 %
122213NaClnogrowth8 %
122213NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2005217234glucose+
2005222599arabinose-
2005217992sucrose+
2005218222xylose-
2005217268myo-inositol+
2005229864mannitol+
2005228757fructose+
2005226546rhamnose+
2005216634raffinose-
2005262968cellulose-
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose+builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol+builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12221316947citrate+carbon source
1222134853esculin+hydrolysis
122213606565hippurate-hydrolysis
12221317632nitrate-reduction
12221316301nitrite-reduction
12221317632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 122213
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12221335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12221315688acetoin-
12221317234glucose-

enzymes

@refvalueactivityec
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
122213oxidase-
122213beta-galactosidase-3.2.1.23
122213alcohol dehydrogenase-1.1.1.1
122213gelatinase-
122213amylase-
122213DNase-
122213caseinase-3.4.21.50
122213catalase+1.11.1.6
122213tween esterase-
122213gamma-glutamyltransferase-2.3.2.2
122213lecithinase-
122213lipase-
122213lysine decarboxylase-4.1.1.18
122213ornithine decarboxylase-4.1.1.17
122213phenylalanine ammonia-lyase-4.3.1.24
122213protease-
122213tryptophan deaminase-
122213urease+3.5.1.5
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20052---------+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20052----+---------+----
122213+++-+-+--+----+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20052-++++-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122213--+-------+++/--+-++---+/---+/--++--+--+-----+---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122213++-+---+-++----+------++++------++-+-------------++--+-----++-+++-+++--+--++---++---+-+-+----+--+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinenthost speciesgeographic locationisolation date
11504soil of the Mangrove rhizosphereJapanJPNAsia
67770Soil and the surface of fine roots in rhizosphere of Bruguiera gymnorrhiza (mangrove)JapanJPNAsiaBruguiera gymnorrhizaShiira River estuary, Iriomote Island
122213Environment, Mangrove rhizosphere, rootJapanJPNAsiaIriomote Island1995

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Mangrove
#Environmental#Terrestrial#Soil
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_5411.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_90;98_4036;99_5411&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: AB004729
  • Sequence Identity:
  • Total samples: 211
  • soil counts: 6
  • aquatic counts: 31
  • animal counts: 164
  • plant counts: 10

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115041Risk group (German classification)
200521German classification
1222131Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11504
  • description: Gordonia rhizosphera gene for 16S rRNA, partial sequence
  • accession: AB004729
  • length: 1475
  • database: ena
  • NCBI tax ID: 1108045

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia rhizosphera NBRC 160681108045.3wgspatric1108045
66792Gordonia rhizosphera NBRC 160682523231044draftimg1108045
67770Gordonia rhizosphera NBRC 16068GCA_000298195contigncbi1108045

GC content

@refGC-contentmethod
1150466.8
6777066.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
motileno93.841no
flagellatedno98.204no
gram-positiveyes83.076no
anaerobicno98.896no
aerobicyes83.311no
halophileno84.602no
spore-formingno84.285no
thermophileno98.588yes
glucose-utilyes90.807yes
glucose-fermentno85.841no

External links

@ref: 11504

culture collection no.: DSM 44383, IFO 16068, NBRC 16068, JCM 10426, BCRC 16393, CIP 105727, IFM 10357, KCTC 9824, NCIMB 13848, VKM Ac-2072

straininfo link

  • @ref: 79871
  • straininfo: 50603

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734045Gordonia rhizosphera sp. nov. isolated from the mangrove rhizosphere.Takeuchi M, Hatano KInt J Syst Bacteriol10.1099/00207713-48-3-9071998Actinomycetales/classification/*isolation & purification, Base Sequence, DNA, Ribosomal/chemistry, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny30932808Gordonia oryzae sp. nov., isolated from rice plant stems (Oryza sativa L.).Muangham S, Lipun K, Thamchaipenet A, Matsumoto A, Duangmal KInt J Syst Evol Microbiol10.1099/ijsem.0.0033682019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gordonia Bacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/chemistryTranscriptome
Phylogeny30994431Gordonia sediminis sp. nov., an actinomycete isolated from mangrove sediment.Sangkanu S, Suriyachadkun C, Phongpaichit SInt J Syst Evol Microbiol10.1099/ijsem.0.0033992019Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Gordonia Bacterium/*classification/isolation & purification, Mycolic Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32667871Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan.Xie Y, Zhou S, Xu Y, Wu W, Xia W, Zhang R, Huang D, Huang XInt J Syst Evol Microbiol10.1099/ijsem.0.0043102020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gordonia Bacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11504Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44383)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44383
20052Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44383.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
39324Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17779
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
79871Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50603.1StrainInfo: A central database for resolving microbial strain identifiers
122213Curators of the CIPCollection of Institut Pasteur (CIP 105727)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105727