Strain identifier

BacDive ID: 159090

Type strain: Yes

Species: Pseudogemmobacter bohemicus

Strain Designation: cd10, Cd-10

Strain history: <- O. Uhlik, VSCHT; Cd10 <- J. Suman

NCBI tax ID(s): 2250708 (species)

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General

@ref: 65913

BacDive-ID: 159090

DSM-Number: 103618

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, mesophilic, Gram-negative, rod-shaped

description: Pseudogemmobacter bohemicus cd10 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from Heavy metal-contaminated sludge from decantation basin.

NCBI tax id

  • NCBI tax id: 2250708
  • Matching level: species

strain history

  • @ref: 65913
  • history: <- O. Uhlik, VSCHT; Cd10 <- J. Suman

doi: 10.13145/bacdive159090.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Pseudogemmobacter
  • species: Pseudogemmobacter bohemicus
  • full scientific name: Pseudogemmobacter bohemicus Suman et al. 2019

@ref: 65913

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Pseudogemmobacter

species: Pseudogemmobacter bohemicus

full scientific name: Pseudogemmobacter bohemicus Suman et al. 2019

strain designation: cd10, Cd-10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
68144negative1-2 µm0.8 µmrod-shapedno
69480negative99.996

colony morphology

  • @ref: 68144
  • colony color: creamy white to beige
  • incubation period: 3 days
  • medium used: half-strength LB medium

Culture and growth conditions

culture medium

  • @ref: 65913
  • name: HALF-CONCENTRATED LB (LURIA BERTANI) MEDIUM (DSMZ Medium 1623)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1623
  • composition: Name: HALF-CONCENTRATED LB (Luria-Bertani) MEDIUM (DSMZ Medium 1623; with strain-specific modifications) Composition: NaCl 5.0 g/l Tryptone 5.0 g/l Yeast extract 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
65913positivegrowth28mesophilic
68144positiveoptimum28mesophilic

culture pH

  • @ref: 68144
  • ability: positive
  • type: optimum
  • pH: 7-8

Physiology and metabolism

tolerance

@refcompoundconcentration
68144Cd1.0 g/kg dry matter
68144Zn1.0 g/kg dry matter
68144Pb1.0 g/kg dry matter

oxygen tolerance

  • @ref: 68144
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 68144
  • type: chemoorganotroph

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.998

halophily

@refsaltgrowthtested relationconcentration
68144NaClpositiveoptimum0 %(w/v)
68144NaClpositivegrowth0-1 %(w/v)

observation

  • @ref: 68144
  • observation: tolerate CdCl 2 in the cultivation medium

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68144skimmed milk-hydrolysis
68144esculin-hydrolysis4853
68144gelatin-hydrolysis5291
68144starch-hydrolysis28017
68144glycerol+carbon source17754
68144erythritol+carbon source17113
68144D-xylose+carbon source65327
68144ribitol+carbon source15963
68144D-galactose+carbon source12936
68144D-glucose+carbon source17634
68144D-fructose+carbon source15824
68144D-mannose+carbon source16024
68144D-mannitol+carbon source16899
68144D-sorbitol+carbon source17924
68144methyl D-glucoside+carbon source37657
68144amygdalin+carbon source27613
68144arbutin+carbon source18305
68144salicin+carbon source17814
68144cellobiose+carbon source17057
68144maltose+carbon source17306
68144sucrose+carbon source17992
68144trehalose+carbon source27082
68144inulin+carbon source15443
68144raffinose+carbon source16634
68144turanose+carbon source32528
68144D-lyxose+carbon source62318
68144D-arabitol+carbon source18333
68144L-arabitol+carbon source18403
68144L-arabinose-carbon source30849
68144D-arabinose-carbon source17108
68144D-ribose-carbon source16988
68144L-xylose-carbon source65328
68144methyl beta-D-xylopyranoside-carbon source74863
68144sorbose-carbon source27922
68144L-rhamnose-carbon source62345
68144galactitol-carbon source16813
68144myo-inositol-carbon source17268
68144methyl alpha-D-mannoside-carbon source43943
68144N-acetyl-D-glucosamine-carbon source506227
68144esculin-carbon source4853
68144lactose-carbon source17716
68144melibiose-carbon source28053
68144glycogen-carbon source28087
68144xylitol-carbon source17151
68144D-tagatose-carbon source16443
68144D-fucose-carbon source28847
68144L-fucose-carbon source18287
68144gluconate-carbon source24265
681442-dehydro-D-gluconate-carbon source16808
681445-dehydro-D-gluconate-carbon source58143

metabolite production

  • @ref: 68144
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
68144cytochrome oxidase+1.9.3.1
68144catalase+1.11.1.6
68144alkaline phosphatase+3.1.3.1
68144nitrate reductase+1.7.99.4
68144alpha-glucosidase+3.2.1.20
68144esterase (C 4)+
68144esterase Lipase (C 8)+
68144lipase (C 14)+
68144trypsin+3.4.21.4
68144alpha-chymotrypsin+3.4.21.1
68144arginine arylamidase+
68144proline-arylamidase+3.4.11.5
68144leucine arylamidase+3.4.11.1
68144tyrosine arylamidase+
68144alanine arylamidase+3.4.11.2
68144glycin arylamidase+
68144histidine arylamidase+
68144valine arylamidase+
68144serine arylamidase+
68144cystine arylamidase+3.4.11.3
68144leucyl glycin arylamidase+3.4.11.1
68144urease-3.5.1.5
68144alpha-galactosidase-3.2.1.22
68144beta-galactosidase-3.2.1.23
681446-phospho-beta-galactosidase-3.2.1.85
68144beta-glucosidase-3.2.1.21
68144alpha-arabinosidase-
68144beta-glucuronidase-3.2.1.31
68144alpha-mannosidase-3.2.1.24
68144alpha-fucosidase-3.2.1.51
68144N-acetyl-beta-glucosaminidase-3.2.1.52
68144glutamate decarboxylase-4.1.1.15
68144arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68144C18:1 w7c50.3
    68144C18:026.3
    68144C16:019.9
    68144C16:1 w7c2.9
  • type of FA analysis: whole cell analysis
  • incubation medium: ?LB supplemented with 10 % sea sand
  • incubation temperature: 28
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateenrichment cultureenrichment culture temperature
65913Heavy metal-contaminated sludge from decantation basinCentral Bohemia, PribramCzech RepublicCZEEurope
68144heavy-metal-contaminated sludge from a decantation basin of a heavy metal processing factoryPríbram, BohemiaCzech RepublicCZEEurope03.06.2013solid basic mineral medium28

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Heavy metal
#Engineered#Built environment#Water reservoir (Aquarium/pool)

Sequence information

16S sequences

  • @ref: 68144
  • description: Pseudogemmobacter bohemicus strain Cd-10 16S ribosomal RNA gene, complete sequence
  • accession: MF164150.2
  • length: 1471
  • database: ena
  • NCBI tax ID: 2250708

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudogemmobacter bohemicus Cd-102886545291draftimg2250708
68144Pseudogemmobacter bohemicus Cd-10GCA_003290025scaffoldncbi2250708

GC content

  • @ref: 68144
  • GC-content: 63.2
  • method: genome sequence analysis

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 80
  • training_data: no

External links

@ref: 65913

culture collection no.: DSM 103618, NCCB 100645

straininfo link

  • @ref: 111600
  • straininfo: 406443

literature

  • topic: Phylogeny
  • Pubmed-ID: 31166163
  • title: Pseudogemmobacter bohemicus gen. nov., sp. nov., a novel taxon from the Rhodobacteraceae family isolated from heavy-metal-contaminated sludge.
  • authors: Suman J, Zubrova A, Rojikova K, Pechar R, Svec P, Cajthaml T, Ulbrich P, Ridl J, Strnad H, Uhlik O
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003493
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Metals, Heavy, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
65913Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103618Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103618)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68144Jachym Suman, Andrea Zubrova, Katerina Rojikova, Radko Pechar, Pavel Svec, Tomas Cajthaml, Pavel Ulbrich, Jakub Ridl, Hynek Strnad and Ondrej UhlikPseudogemmobacter bohemicus gen. nov., sp. nov., a novel taxon from the Rhodobacteraceae family isolated from heavy-metal-contaminated sludge10.1099/ijsem.0.003493IJSEM 69: 2401-2407 2019
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
111600Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID406443.1