Strain identifier

BacDive ID: 7268

Type strain: Yes

Species: Agromyces rhizosphaerae

Strain Designation: 14

Strain history: CIP <- 2005, JCM <- K. Hatano, IFO

NCBI tax ID(s): 88374 (species)

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General

@ref: 5400

BacDive-ID: 7268

DSM-Number: 14597

keywords: 16S sequence, Bacteria, microaerophile, mesophilic, motile, rod-shaped

description: Agromyces rhizosphaerae 14 is a microaerophile, mesophilic, motile bacterium that was isolated from root of Sonneralia alba.

NCBI tax id

  • NCBI tax id: 88374
  • Matching level: species

strain history

@refhistory
5400<- IFO <- K.Hatano; no. 14
67770IFO 16236 <-- M. Takeuchi 14.
122214CIP <- 2005, JCM <- K. Hatano, IFO

doi: 10.13145/bacdive7268.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agromyces
  • species: Agromyces rhizosphaerae
  • full scientific name: Agromyces rhizosphaerae corrig. Takeuchi and Hatano 2001

  • synonyms

    • @ref: 20215
    • synonym: Agromyces rhizospherae

@ref: 5400

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces rhizosphaerae

full scientific name: Agromyces rhizosphaerae Takeuchi and Hatano 2001

strain designation: 14

type strain: yes

Morphology

cell morphology

  • @ref: 122214
  • cell shape: rod-shaped
  • motility: yes

colony morphology

@refcolony colorincubation periodmedium used
18387Saffron yellow (1017)10-14 daysISP 2
18387Saffron yellow (1017)10-14 daysISP 3
18387Beige (1001)10-14 daysISP 4
18387Beige (1001)10-14 daysISP 5
18387Beige (1001)10-14 daysISP 6
18387Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18387noISP 2
18387noISP 3
18387noISP 4
18387noISP 5
18387noISP 6
18387noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5400PP-MEDIUM (DSMZ Medium 513)yeshttps://mediadive.dsmz.de/medium/513Name: PP-MEDIUM (DSMZ Medium 513) Composition: Agar 15.0 g/l Polypeptone 10.0 g/l Yeast extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Distilled water
18387ISP 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
18387ISP 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:
18387ISP 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
18387ISP 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
18387ISP 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
18387ISP 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
40501MEDIUM 563 - for Novosphingobium roseaeyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (15.000 g);Yeast extract (2.000 g);Polypeptone (10.000 g)
122214CIP Medium 563yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=563

culture temp

@refgrowthtypetemperaturerange
18387positiveoptimum28mesophilic
5400positivegrowth28mesophilic
40501positivegrowth25mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122214
  • oxygen tolerance: microaerophile

murein

  • @ref: 5400
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-11

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
122214nitrate-reduction17632
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose+fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose+fermentation17306
68379lactose-fermentation17716
68379sucrose+fermentation17992
68379glycogen-fermentation28087

metabolite production

  • @ref: 122214
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
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
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
122214oxidase+
122214catalase-1.11.1.6
122214urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18387---+-------+---+-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18387+++------++-+-+----
122214-+++++++-++-++-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122214------------------------+------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
5400root of Sonneralia albaSonneratia albaJapan, Okinawa, Iriomote IslandJapanJPNAsia
67770Soil of the rhizosphere of Sonneratia alba, mangrove in the estuary of the Shiira RiverSonneratia albaIriomote IslandJapanJPNAsia
122214Environment, Soil, rhizosphere of Sonneralia albaShiira river, Iriomote IslandJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Root (Rhizome)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
54001Risk group (German classification)
183871German classification
1222141Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5400
  • description: Agromyces sp. IFO16237 gene for 16S rRNA
  • accession: AB023357
  • length: 1510
  • database: ena
  • NCBI tax ID: 88374

GC content

@refGC-contentmethod
540071.2
6777071.2high performance liquid chromatography (HPLC)

External links

@ref: 5400

culture collection no.: DSM 14597, IFO 16236, NBRC 16236, VKM Ac-2086, JCM 11432, CIP 108986, IAM 15153, KCTC 13908

straininfo link

  • @ref: 76719
  • straininfo: 49558

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11491355Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov. and Agromyces bracchium sp. nov., from the mangrove rhizosphere.Takeuchi M, Hatano KInt J Syst Evol Microbiol10.1099/00207713-51-4-15292001Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Ecosystem, Japan, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Soil Microbiology, Species Specificity, TreesGenetics
Phylogeny29582101Agromyces mangrovi sp. nov., a novel actinobacterium isolated from the rhizosphere of a mangrove.Hamada M, Saitou S, Tamura TArch Microbiol10.1007/s00203-018-1504-42018Actinobacteria/classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Japan, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitle
5400Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14597)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14597
18387Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM14597.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
40501Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6676
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
76719Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49558.1StrainInfo: A central database for resolving microbial strain identifiers
122214Curators of the CIPCollection of Institut Pasteur (CIP 108986)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108986