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, Gram-positive

description: Agreia bicolorata DL-4 is an obligate aerobe, 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/bacdive7249.20240916.9.1

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

@refgram staincell shapemotilityconfidence
116801positiverod-shapedyes
69480positive91.203
69480no90.5

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

@refgrowthtypetemperature
18385positiveoptimum28
5392positivegrowth24
32884positivegrowth25
67770positivegrowth22
116801positivegrowth15-30
116801nogrowth10
116801nogrowth37
116801nogrowth41
116801nogrowth45

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 14575AM4106721486nuccore110935
5392Agrevia bicolorata 16S ribosomal RNA gene, partial sequenceAF1593631486nuccore110935

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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes91.203no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.054yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.218yes
69480spore-formingspore-formingAbility to form endo- or exosporesno74.719no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.429yes
69480flagellatedmotile2+Ability to perform flagellated movementno90.5no

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
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)
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