Strain identifier

BacDive ID: 7259

Type strain: Yes

Species: Agrococcus carbonis

Strain Designation: G-4T

Strain history: MTCC 10213 <-- S. Dhanjal et al. G4.

NCBI tax ID(s): 684552 (species)

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General

@ref: 16561

BacDive-ID: 7259

DSM-Number: 22965

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

description: Agrococcus carbonis G-4T is a mesophilic bacterium that was isolated from soil from a coal mine.

NCBI tax id

  • NCBI tax id: 684552
  • Matching level: species

strain history

@refhistory
16561<- S. Mayilraj, MTCC; G-4T <- S. Dhanjal
67770MTCC 10213 <-- S. Dhanjal et al. G4.

doi: 10.13145/bacdive7259.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agrococcus
  • species: Agrococcus carbonis
  • full scientific name: Agrococcus carbonis Dhanjal et al. 2011

@ref: 16561

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agrococcus

species: Agrococcus carbonis

full scientific name: Agrococcus carbonis Dhanjal et al. 2011

strain designation: G-4T

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.07
69480100positive

colony morphology

@refcolony colormedium used
69233Lemon yellow (1012)ISP 2
69233Lemon yellow (1012)ISP 3
69233Lemon yellow (1012)ISP 7
69233Lemon yellow (1012)suter with tyrosine
69233Lemon yellow (1012)suter without tyrosine
69233Oyster white (1013)ISP 4

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69233noAerial myceliumISP 2
69233noAerial myceliumISP 3
69233noAerial myceliumISP 4
69233noAerial myceliumISP 7
69233noAerial myceliumsuter with tyrosine
69233noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69233noMelanin
69233nosoluble pigment

Culture and growth conditions

culture temp

  • @ref: 67770
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no100

halophily

  • @ref: 69233
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-9, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6923322599arabinose+growth
6923362968cellulose+growth
6923328757fructose+growth
6923317234glucose+growth
6923317268inositol+growth
6923337684mannose+growth
6923316634raffinose+growth
6923326546rhamnose+growth
6923317992sucrose+growth
6923318222xylose+growth
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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase-3.1.3.2
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69233-++---+--++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69233-+++/-+/-+/-+/-+/-+/--+/----+-+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16561soil from a coal mineWest Bengal, Bonjemehari collieryIndiaINDAsia
67770Soil from a coal mine of West BengalIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 16561
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16561
  • description: Agrococcus carbonis strain G4 16S ribosomal RNA gene, partial sequence
  • accession: GQ504748
  • length: 1470
  • database: ena
  • NCBI tax ID: 684552

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agrococcus carbonis DSM 22965GCA_900104705chromosomencbi684552
66792Agrococcus carbonis strain DSM 22965684552.3completepatric684552
66792Agrococcus carbonis DSM 229652634166154draftimg684552

GC content

  • @ref: 16561
  • GC-content: 73.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveyes91.624no
anaerobicno99.157no
halophileno86.873no
spore-formingno94.349no
glucose-utilyes85.776no
thermophileno99.508no
flagellatedno97.037no
motileno89.748no
aerobicyes94.296no
glucose-fermentno93.897no

External links

@ref: 16561

culture collection no.: DSM 22965, MTCC 10213, JCM 19248

literature

  • topic: Phylogeny
  • Pubmed-ID: 20601492
  • title: Agrococcus carbonis sp. nov., isolated from soil of a coal mine.
  • authors: Dhanjal S, Kaur I, Korpole S, Schumann P, Cameotra SS, Pukall R, Klenk HP, Mayilraj S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.024745-0
  • year: 2010
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Amino Acids/analysis, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Coal, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
16561Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22965)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22965
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
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69233Wink, J.https://cdn.dsmz.de/wink/DSM%2022965.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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