Strain identifier

BacDive ID: 17653

Type strain: Yes

Species: Thermolithobacter carboxydivorans

Strain Designation: Z-R1

Culture col. no.: DSM 7242, R1 , VKM B-2359

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General

@ref: 3071

BacDive-ID: 17653

DSM-Number: 7242

keywords: coccus-shaped, gram-positive, thermophilic, anaerobe, Bacteria, 16S sequence, colony-forming

description: Thermolithobacter carboxydivorans Z-R1 is an anaerobe, thermophilic, gram-positive bacterium that forms circular colonies and was isolated from litoral hydrothermal sample.

strain history: <- V.A. Svetlichny, Z-R1

doi: 10.13145/bacdive17653.20201210.5

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/firmicutes
  • domain: Bacteria
  • phylum: Firmicutes
  • class: Thermolithobacteria
  • order: Thermolithobacterales
  • family: Thermolithobacteraceae
  • genus: Thermolithobacter
  • species: Thermolithobacter carboxydivorans
  • full scientific name: Thermolithobacter carboxydivorans corrig. Sokolova et al. 2007
  • synonyms

    • @ref: 20215
    • synonym: Thermolithobacter carboxidivorans

@ref: 3071

domain: Bacteria

phylum: Firmicutes

class: Thermolithobacteria

order: Thermolithobacterales

family: Thermolithobacteraceae

genus: Thermolithobacter

species: Thermolithobacter carboxydivorans

full scientific name: Thermolithobacter carboxydivorans Sokolova et al. 2007

strain designation: Z-R1

type strain: yes

Morphology

cell morphology

  • @ref: 25184
  • gram stain: positive
  • cell length: 0.5-0.6 µm
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 25184
  • colony color: creamy white
  • colony shape: circular
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowthlink
3071CARBOXYDOTHERMUS MEDIUM (DSMZ Medium 507), anaerobicyeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium507.pdf
25184Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperaturerange
3071positivegrowth65thermophilic
25184positivegrowth10.0-37.0
25184positiveoptimum30mesophilic

culture pH

@refabilitytypepH
25184positivegrowth5.0-9.0
25184positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
3071anaerobe
25184obligate aerobe

spore formation

  • @ref: 25184
  • spore formation: no

compound production

  • @ref: 3071
  • compound: H2

halophily

@refsaltgrowthtested relationconcentration
25184NaClpositivegrowth0.0-3.0 %(w/v)
25184NaCloptimum0 %(w/v)

murein

  • @ref: 25184
  • murein short key: A11.39
  • type: A4alpha L-Lys-L-Ser2-D-Glu

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25184168082-dehydro-D-gluconate-builds acid from
2518417128adipate-assimilation
2518427613amygdalin-builds acid from
2518415963ribitol-builds acid from
2518418333D-arabitol-builds acid from
2518428847D-fucose-builds acid from
2518417716lactose-builds acid from
2518416899D-mannitol-builds acid from
251846731melezitose-builds acid from
2518428053melibiose-builds acid from
2518416634raffinose-builds acid from
2518416988D-ribose-builds acid from
2518417992sucrose-builds acid from
2518417924D-sorbitol-builds acid from
2518416443D-tagatose-builds acid from
2518427689decanoate-assimilation
2518417113erythritol-builds acid from
2518416813galactitol-builds acid from
251845291gelatin-hydrolysis
2518428066gentiobiose-builds acid from
2518424265gluconate-builds acid from
2518417754glycerol-builds acid from
2518415443inulin-builds acid from
2518430849L-arabinose-assimilation
2518430849L-arabinose-builds acid from
2518418403L-arabitol-builds acid from
2518462345L-rhamnose-builds acid from
2518417266L-sorbose-builds acid from
2518465328L-xylose-builds acid from
2518474863methyl beta-D-xylopyranoside-builds acid from
25184506227N-acetylglucosamine-assimilation
25184506227N-acetylglucosamine-builds acid from
2518432032potassium gluconate-assimilation
2518453258sodium citrate-assimilation
2518428017starch-builds acid from
2518427897tryptophan-energy source
2518453424tween 20-hydrolysis
2518453426tween 80-hydrolysis
2518418186tyrosine-hydrolysis
2518416199urea-hydrolysis
2518417151xylitol-builds acid from
25184581435-dehydro-D-gluconate+builds acid from
2518418305arbutin+builds acid from
25184casein+hydrolysis
2518417057cellobiose+builds acid from
2518417108D-arabinose+builds acid from
2518415824D-fructose+builds acid from
2518412936D-galactose+builds acid from
2518417634D-glucose+assimilation
2518417634D-glucose+builds acid from
2518462318D-lyxose+builds acid from
2518416899D-mannitol+assimilation
2518416024D-mannose+assimilation
2518416024D-mannose+builds acid from
2518465327D-xylose+builds acid from
251844853esculin+hydrolysis
251844853esculin+builds acid from
2518417754glycerol+builds acid from
2518428087glycogen+builds acid from
2518417268myo-inositol+builds acid from
2518418287L-fucose+builds acid from
2518425115malate+assimilation
2518417306maltose+assimilation
2518417306maltose+builds acid from
25184320061methyl alpha-D-glucopyranoside+builds acid from
2518443943methyl alpha-D-mannoside+builds acid from
2518417632nitrate+reduction
2518418401phenylacetate+assimilation
2518417814salicin+builds acid from
2518428017starch+hydrolysis
2518417992sucrose+builds acid from
2518427082trehalose+builds acid from
2518432528turanose+builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
2518435581indoleno
2518472813exopolysaccharideyes

metabolite tests

  • @ref: 25184
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25184acid phosphatase+3.1.3.2
25184alkaline phosphatase+3.1.3.1
25184alpha-chymotrypsin-3.4.21.1
25184alpha-fucosidase-3.2.1.51
25184alpha-galactosidase-3.2.1.22
25184alpha-glucosidase+3.2.1.20
25184alpha-mannosidase-3.2.1.24
25184arginine dihydrolase-3.5.3.6
25184beta-galactosidase+3.2.1.23
25184beta-glucosidase+3.2.1.21
25184beta-glucuronidase-3.2.1.31
25184catalase+1.11.1.6
25184cystine arylamidase-3.4.11.3
25184cytochrome oxidase-1.9.3.1
25184esterase (C 4)+
25184esterase Lipase (C 8)+
25184leucine arylamidase+3.4.11.1
25184lipase (C 14)-
25184N-acetyl-beta-glucosaminidase-3.2.1.52
25184naphthol-AS-BI-phosphohydrolase+
25184trypsin-3.4.21.4
25184tryptophan deaminase-4.1.99.1
25184valine arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    2518410-Methyl C17:03.8
    2518410-Methyl C18:01.5
    25184C17:0 anteiso10.5
    25184C17:1 anteiso ω9c5
    25184C16:01.2
    25184C16:1 2OH2.9
    25184C16:1ω7c / C16:1ω6c2.8
    25184C17:1ω6c1.9
    25184C18:1ω9c1
    25184C15:0 iso4.5
    25184C16:0 iso28.5
    25184C16:1 iso H3.3
    25184C17:0 iso9.2
    25184C17:1 iso ω9c / C16:0 10-methyl17.4
    25184C18:0 iso1.6
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: liquid
  • incubation temperature: 30
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA 6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
3071litoral hydrothermal sampleRaoul IslandNew ZealandNZLAustralia and Oceania
25184rice paddySacheonRepublic of KoreaKORAsia35128R2A agar (BD)3 days25

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Condition#Thermophilic (>45°C)
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

  • @ref: 3071
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
25184Flexivirga sp. R1 16S ribosomal RNA gene, partial sequenceKR0255221445nuccore1794944
3071Thermolithobacter carboxydivorans strain R1 16S ribosomal RNA gene, partial sequenceDQ0958621546ena335383

GC content

@refGC-contentmethod
307152
307138.8
2518464.5fluorimetric

External links

@ref: 3071

culture collection no.: DSM 7242, R1, VKM B-2359

straininfo link

@refpassport
20218http://www.straininfo.net/strains/160659
20218http://www.straininfo.net/strains/720921

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3071Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7242)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7242
20215D.Gleim, M.Kracht, N.Weiss et. al.http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.htmlProkaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since
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
25184J. W. K. Hyeon, H. R.,Lee, H. J.,Jeong, S. E.,Choi, S. H.,Jeon, C. O.10.1099/ijsem.0.001657Flexivirga oryzae sp. nov., isolated from soil of a rice paddy, and emended description of the genus Flexivirga Anzai et al. 2012IJSEM 67: 479-484 2017