Strain identifier

BacDive ID: 7249

Type strain: Yes

Species: Agreia bicolorata

Strain Designation: DL-4

Strain history: CIP <- 2003, L. Evtushenko, VKM, Moscow, Russia

NCBI tax ID(s): 110935 (species)

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General

@ref: 5392

BacDive-ID: 7249

DSM-Number: 14575

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, motile, rod-shaped

description: Agreia bicolorata DL-4 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from leaf gall; induced by nematode Heteroanguina garaminophila on Calamagrostis neglecta.

NCBI tax id

  • NCBI tax id: 110935
  • Matching level: species

strain history

@refhistory
5392<- L.I. Evtushenko <- T.G. Dobrovolskaya; DL-4
328842003, L. Evtushenko, VKM, Moscow, Russia
67770DSM 14575 <-- L. I. Evtushenko VKM Ac-1804 <-- T. G. Dobrovolskaya DL-4.
116801CIP <- 2003, L. Evtushenko, VKM, Moscow, Russia

doi: 10.13145/bacdive7249.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agreia
  • species: Agreia bicolorata
  • full scientific name: Agreia bicolorata Evtushenko et al. 2001

@ref: 5392

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agreia

species: Agreia bicolorata

full scientific name: Agreia bicolorata Evtushenko et al. 2001 emend. Nouioui et al. 2018

strain designation: DL-4

type strain: yes

Morphology

cell morphology

  • @ref: 116801
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
18385Vermillion (2002)10-14 daysISP 2
18385Yellow orange (2000)10-14 daysISP 3
18385Pastel yellow (1034)10-14 daysISP 4
18385Pastel yellow (1034)10-14 daysISP 5
18385Pastel yellow (1034)10-14 daysISP 6
18385Pastel yellow (1034)10-14 daysISP 7
1168011

multicellular morphology

@refforms multicellular complexmedium name
18385noISP 2
18385noISP 3
18385noISP 4
18385noISP 5
18385noISP 6
18385noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5392TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
5392NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
18385ISP 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
18385ISP 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:
18385ISP 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
18385ISP 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
18385ISP 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
18385ISP 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
32884MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116801CIP Medium 111yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=111
116801CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18385positiveoptimum28mesophilic
5392positivegrowth24psychrophilic
32884positivegrowth25mesophilic
67770positivegrowth22psychrophilic
116801positivegrowth15-30
116801nogrowth10psychrophilic
116801nogrowth37mesophilic
116801nogrowth41thermophilic
116801nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116801
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116801NaClpositivegrowth0-4 %
116801NaClnogrowth6 %
116801NaClnogrowth8 %
116801NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1838517234glucose+
1838522599arabinose+
1838517992sucrose+
1838518222xylose-
1838517268myo-inositol-
1838529864mannitol+
1838528757fructose+
1838526546rhamnose-
1838516634raffinose+
1838562968cellulose+
11680116947citrate-carbon source
1168014853esculin+hydrolysis
116801606565hippurate-hydrolysis
11680117632nitrate-reduction
11680116301nitrite-reduction
11680117632nitrate-respiration
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

antibiotic resistance

  • @ref: 116801
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116801
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11680115688acetoin+
11680117234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase+3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
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
116801oxidase+
116801beta-galactosidase+3.2.1.23
116801alcohol dehydrogenase-1.1.1.1
116801gelatinase+/-
116801amylase-
116801DNase-
116801caseinase-3.4.21.50
116801catalase+1.11.1.6
116801tween esterase-
116801gamma-glutamyltransferase-2.3.2.2
116801lecithinase-
116801lipase-
116801lysine decarboxylase-4.1.1.18
116801ornithine decarboxylase-4.1.1.17
116801phenylalanine ammonia-lyase-4.3.1.24
116801protease-
116801tryptophan deaminase-
116801urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18385----++-++--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18385----++-+-+-+--++-+-
116801+++-++++-++++-++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116801+++++-+++++-----+++-+++--------+-+-+------------------------+-------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrygeographic locationcontinentisolation date
5392leaf gall; induced by nematode Heteroanguina garaminophila on Calamagrostis neglectaHeteroanguina garaminophila;Calamagrostis neglectaRussiaRUS
67770Narrow reed grass (Calamagrostis neglecta) infected by the gall-forming nematode Heteroanguina graminophilaCalamagrostis neglectaRussiaRUSMoscow Region
116801Animal, Leaf galls induced by the nematode heteroanguina graminophilaRussian FederationRUSMoscow regionEurope1991

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Nematoda
#Host#Plants#Herbaceous plants (Grass,Crops)
#Infection#Plant infections#Gall
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2881.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_895;97_1044;98_2229;99_2881&stattab=map
  • Last taxonomy: Agreia
  • 16S sequence: AM410672
  • Sequence Identity:
  • Total samples: 1549
  • soil counts: 290
  • aquatic counts: 204
  • animal counts: 763
  • plant counts: 292

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53921Risk group (German classification)
183851German classification
1168011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agreia bicolorata partial 16S rRNA gene, type strain DSM 14575AM4106721486ena110935
5392Agrevia bicolorata 16S ribosomal RNA gene, partial sequenceAF1593631486ena110935

Genome sequences

  • @ref: 67770
  • description: Agreia bicolorata VKM Ac-1804
  • accession: GCA_000938265
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 110935

GC content

@refGC-contentmethod
539267high performance liquid chromatography (HPLC)
6777067thermal denaturation, midpoint method (Tm)
6777073.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.099no
flagellatedno98.127no
gram-positiveyes93.145no
anaerobicno99.52no
aerobicyes91.26no
halophileno92.258no
spore-formingno91.491no
glucose-utilyes86.54yes
thermophileno99.86yes
glucose-fermentno91.601no

External links

@ref: 5392

culture collection no.: DSM 14575, UCM Ac-620, VKM Ac-1804, JCM 12206, IAM 15124, IAM 15138, NBRC 103053, CIP 108057

straininfo link

  • @ref: 76701
  • straininfo: 49555

literature

  • topic: Phylogeny
  • Pubmed-ID: 11760949
  • title: Agreia bicolorata gen. nov., sp. nov., to accommodate actinobacteria isolated from narrow reed grass infected by the nematode Heteroanguina graminophila.
  • authors: Evtushenko LI, Dorofeeva LV, Dobrovolskaya TG, Streshinskaya GM, Subbotin SA, Tiedje JM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-6-2073
  • year: 2001
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Animals, DNA, Ribosomal/genetics, Molecular Sequence Data, *Nematoda/physiology, Phylogeny, Plant Tumors/*microbiology/parasitology, Poaceae/*microbiology/parasitology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5392Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14575)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14575
18385Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM14575.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
32884Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5637
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
76701Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49555.1StrainInfo: A central database for resolving microbial strain identifiers
116801Curators of the CIPCollection of Institut Pasteur (CIP 108057)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108057