Strain identifier

BacDive ID: 6239

Type strain: Yes

Species: Arsenicicoccus bolidensis

Strain history: CIP <- 2004, CCUG <- 2003, J. Routh, Dept. of Geol & Geochem., Stockholm, Sweden

NCBI tax ID(s): 1121017 (strain), 229480 (species)

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General

@ref: 6095

BacDive-ID: 6239

DSM-Number: 15745

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, coccus-shaped

description: Arsenicicoccus bolidensis DSM 15745 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from lake sediment.

NCBI tax id

NCBI tax idMatching level
1121017strain
229480species

strain history

@refhistory
6095<- M. D. Collins <- E. Falsen, CCUG <- J. Routh
67770CCUG 47306 <-- J. Routh.
116834CIP <- 2004, CCUG <- 2003, J. Routh, Dept. of Geol & Geochem., Stockholm, Sweden

doi: 10.13145/bacdive6239.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermatophilaceae
  • genus: Arsenicicoccus
  • species: Arsenicicoccus bolidensis
  • full scientific name: Arsenicicoccus bolidensis Collins et al. 2004

@ref: 6095

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermatophilaceae

genus: Arsenicicoccus

species: Arsenicicoccus bolidensis

full scientific name: Arsenicicoccus bolidensis Collins et al. 2004

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30082positivecoccus-shaped
69480no91.22
69480positive100
116834positivecoccus-shapedno

colony morphology

@refincubation periodmedium usedhemolysis ability
1839410-14 daysISP 2
1168341

multicellular morphology

  • @ref: 18394
  • forms multicellular complex: no
  • medium name: ISP 2

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_15745_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15745_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15745_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15745_4.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6095TRYPTICASE 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
6095TRYPTICASE 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
18394ISP 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
33229MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
116834CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116834CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
18394positiveoptimum28mesophilic
6095positivegrowth28mesophilic
33229positivegrowth37
57632positivegrowth30-37
67770positivegrowth30mesophilic
116834positivegrowth10-37
116834nogrowth41thermophilic
116834nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30082facultative anaerobe
57632aerobe
57632anaerobe
116834facultative anaerobe

spore formation

@refspore formationconfidence
30082no
69481no99
69480no99.936

halophily

@refsaltgrowthtested relationconcentration
116834NaClpositivegrowth0-4 %
116834NaClnogrowth6 %
116834NaClnogrowth8 %
116834NaClnogrowth10 %

murein

  • @ref: 6095
  • murein short key: A41.02
  • type: A3gamma LL-Dpm-Gly3; alpha-carboxyl group of D-Glu substituted by Gly

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1839417234glucose-
1839422599arabinose-
1839417992sucrose-
1839418222xylose-
1839417268myo-inositol-
1839429864mannitol-
1839428757fructose-
1839426546rhamnose-
1839416634raffinose-
1839462968cellulose-
3008217057cellobiose+carbon source
3008228757fructose+carbon source
300825291gelatin+carbon source
3008217234glucose+carbon source
3008228087glycogen+carbon source
3008217716lactose+carbon source
3008217306maltose+carbon source
3008229864mannitol+carbon source
3008237684mannose+carbon source
3008233942ribose+carbon source
3008217992sucrose+carbon source
3008218222xylose+carbon source
300824853esculin+hydrolysis
3008217632nitrate+reduction
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
6837116634raffinose+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
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+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
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+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
11683416947citrate-carbon source
1168344853esculin+hydrolysis
116834606565hippurate-hydrolysis
11683417632nitrate+reduction
11683416301nitrite-reduction
11683417632nitrate+respiration

antibiotic resistance

  • @ref: 116834
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116834
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11683415688acetoin-
11683417234glucose-

enzymes

@refvalueactivityec
30082acid phosphatase+3.1.3.2
30082alkaline phosphatase+3.1.3.1
30082alpha-galactosidase+3.2.1.22
30082catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
116834oxidase-
116834beta-galactosidase+3.2.1.23
116834alcohol dehydrogenase-1.1.1.1
116834gelatinase+
116834amylase+
116834DNase+
116834caseinase+3.4.21.50
116834catalase+1.11.1.6
116834tween esterase+
116834gamma-glutamyltransferase+2.3.2.2
116834lecithinase-
116834lipase-
116834lysine decarboxylase-4.1.1.18
116834ornithine decarboxylase-4.1.1.17
116834phenylalanine ammonia-lyase-4.3.1.24
116834protease+
116834tryptophan deaminase-
116834urease-3.5.1.5

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18394----++----+-+--+---
116834+++-+---+++++-++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116834+----+---++++---+/-+---+-+++++++++-+/-++/-+-+-------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116834++-++--+-+++++---+++-+---------+-+------+------------------++-------------------------+--------+-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6095lake sedimentBoliden regionSwedenSWEEurope
57632Sediment containing mine tailingsBolidenSwedenSWEEurope2002-08-12
67770Lake sediment containing mine wasteBolidenSwedenSWEEurope
116834Environment, Sediment containing mine tailingsSwedenSWEEurope2002

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_26804.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_3635;97_4467;98_5732;99_26804&stattab=map
  • Last taxonomy: Arsenicicoccus bolidensis subclade
  • 16S sequence: AJ558133
  • Sequence Identity:
  • Total samples: 10568
  • soil counts: 2314
  • aquatic counts: 3288
  • animal counts: 4338
  • plant counts: 628

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183941German classification
60951Risk group (German classification)
1168341Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6095
  • description: Arsenicicoccus bolidensis partial 16S rRNA gene, strain CCUG 47306
  • accession: AJ558133
  • length: 1467
  • database: ena
  • NCBI tax ID: 229480

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arsenicicoccus bolidensis DSM 157451121017.3wgspatric1121017
66792Arsenicicoccus bolidensis DSM 157452524614535draftimg1121017
67770Arsenicicoccus bolidensis DSM 15745GCA_000426385contigncbi1121017

GC content

@refGC-contentmethod
609572.2
6777072.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno94.244no
flagellatedno97.917no
gram-positiveyes90.437no
anaerobicno98.725no
aerobicyes76.549no
halophileno95.785no
spore-formingno81.175yes
thermophileno97.854no
glucose-utilyes86.955no
glucose-fermentno82.161no

External links

@ref: 6095

culture collection no.: DSM 15745, CCUG 47306, JCM 13385, IAM 15342, NBRC 105202, CIP 108315

straininfo link

  • @ref: 75718
  • straininfo: 110991

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023982Arsenicicoccus bolidensis gen. nov., sp. nov., a novel actinomycete isolated from contaminated lake sediment.Collins MD, Routh J, Saraswathy A, Lawson PA, Schumann P, Welinder-Olsson C, Falsen EInt J Syst Evol Microbiol10.1099/ijs.0.02918-02004Actinomycetales/classification/genetics/*isolation & purification/physiology, Fresh Water/microbiology, Geologic Sediments/microbiology, Gram-Positive Bacteria/classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Phenotype, Phylogeny, Water PollutionEnzymology
Phylogeny21515710Aquipuribacter hungaricus gen. nov., sp. nov., an actinobacterium isolated from the ultrapure water system of a power plant.Toth EM, Keki Z, Bohus V, Borsodi AK, Marialigeti K, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.032672-02011Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hungary, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Power Plants, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis, *Water MicrobiologyGenetics
Phylogeny22888195Ornithinimicrobium murale sp. nov., isolated from an indoor wall colonized by moulds.Kampfer P, Glaeser SP, Schafer J, Lodders N, Martin K, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.035873-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Environmental Microbiology, Fatty Acids/analysis, Fungi/growth & development, Germany, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny35580017Arsenicicoccus cauae sp. nov., isolated from the blood of a pediatric gastroenteritis patient.Kweon OJ, Kim KH, Kim HM, Khan SA, Jeong JH, Lim YK, Kim HR, Jeon CO, Lee MKInt J Syst Evol Microbiol10.1099/ijsem.0.0053812022*Actinomycetales/isolation & purification, *Actinomycetales Infections/blood/microbiology, Animals, Bacterial Typing Techniques, Base Composition, Catalase/genetics, Child, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gastroenteritis/blood/microbiology, Humans, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, SheepPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6095Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15745)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15745
18394Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM15745.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
30082Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2643928776041
33229Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5924
57632Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47306)https://www.ccug.se/strain?id=47306
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
75718Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID110991.1StrainInfo: A central database for resolving microbial strain identifiers
116834Curators of the CIPCollection of Institut Pasteur (CIP 108315)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108315