Strain identifier

BacDive ID: 133579

Type strain: Yes

Species: Gemmobacter aquaticus

Strain Designation: A1-9

Strain history: <- Y. Muramatsu, NBRC; NBRC 104254 <- Z.-P. Liu, Inst. Microbiol., Chinese Acad. Sci., Beijing, China; A1-9

NCBI tax ID(s): 490185 (species)

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General

@ref: 64732

BacDive-ID: 133579

DSM-Number: 108272

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

description: Gemmobacter aquaticus A1-9 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater .

NCBI tax id

  • NCBI tax id: 490185
  • Matching level: species

strain history

  • @ref: 64732
  • history: <- Y. Muramatsu, NBRC; NBRC 104254 <- Z.-P. Liu, Inst. Microbiol., Chinese Acad. Sci., Beijing, China; A1-9

doi: 10.13145/bacdive133579.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Gemmobacter
  • species: Gemmobacter aquaticus
  • full scientific name: Gemmobacter aquaticus Chen et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Catellibacterium aquatile

@ref: 64732

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Gemmobacter

species: Gemmobacter aquaticus

full scientific name: Gemmobacter aquaticus Chen et al. 2013

strain designation: A1-9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29638negative1-1.6 µm0.5-0.6 µmrod-shapedyes
69480negative99.999

pigmentation

  • @ref: 29638
  • production: no

Culture and growth conditions

culture medium

  • @ref: 64732
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
64732positivegrowth30mesophilic
29638positivegrowth10-40
30689positivegrowth15-40
29638positiveoptimum25-30mesophilic
30689positiveoptimum32.5mesophilic

culture pH

@refabilitytypepHPH range
30689positivegrowth04-08acidophile
29638positivegrowth5.5-9alkaliphile
29638positiveoptimum6-6.5
30689positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29638
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29638no
69481no98
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
29638NaClpositivegrowth0-1 %
30689NaClpositivegrowth1.5 %
30689NaClpositiveoptimum0-5 %

observation

  • @ref: 29638
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2963822599arabinose+carbon source
2963824996lactate+carbon source
3068953424tween 20+carbon source
296384853esculin+hydrolysis
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

@refChebi-IDmetaboliteproduction
2963816136hydrogen sulfideyes
6836935581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29638acid phosphatase+3.1.3.2
29638catalase+1.11.1.6
29638cytochrome oxidase+1.9.3.1
30689alkaline phosphatase+3.1.3.1
30689alpha-galactosidase+3.2.1.22
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase-3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
64732--+/-+/-----------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
64732+---++-+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
29638freshwater (river, lake, pond)
64732Reservoir waterDaqing, Helongjiang (46° 47' 40.9'' N, 125° 06' 46.9'' E)ChinaCHNAsia46.7947125.113

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Pond (small)
#Environmental#Aquatic#River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_47037.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_926;97_3623;98_33949;99_47037&stattab=map
  • Last taxonomy: Gemmobacter aquaticus
  • 16S sequence: EU313813
  • Sequence Identity:
  • Total samples: 2685
  • soil counts: 61
  • aquatic counts: 2284
  • animal counts: 282
  • plant counts: 58

Sequence information

16S sequences

  • @ref: 29638
  • description: Catellibacterium aquatile strain A1-9 16S ribosomal RNA gene, partial sequence
  • accession: EU313813
  • length: 1333
  • database: nuccore
  • NCBI tax ID: 490185

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gemmobacter aquaticus A1-9GCA_007859075contigncbi490185
66792Gemmobacter aquaticus CGMCC 1.7029GCA_014645295scaffoldncbi490185
66792Gemmobacter aquaticus strain CGMCC 1.7029490185.6wgspatric490185

GC content

  • @ref: 29638
  • GC-content: 64.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
flagellatedno87.22no
gram-positiveno98.761yes
anaerobicno96.563yes
aerobicyes80.803no
halophileno90.434no
spore-formingno96.666yes
thermophileno96.498yes
glucose-utilyes86.605no
motileno63.969yes
glucose-fermentno88.733yes

External links

@ref: 64732

culture collection no.: CGMCC 1.7029, NBRC 104254, DSM 108272

straininfo link

  • @ref: 91515
  • straininfo: 404494

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19820000Catellibacterium aquatile sp. nov., isolated from fresh water, and emended description of the genus Catellibacterium Tanaka et al. 2004.Liu Y, Xu CJ, Jiang JT, Liu YH, Song XF, Li H, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.017632-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/metabolism, Sodium Chloride/metabolismGenetics
Phylogeny22493172Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis.Chen WM, Cho NT, Huang WC, Young CC, Sheu SYInt J Syst Evol Microbiol10.1099/ijs.0.042051-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Natural Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, TaiwanGenetics
Phylogeny30938664Gemmobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat.Yoo Y, Lee DW, Lee H, Kwon BO, Khim JS, Yim UH, Park H, Park B, Choi IG, Kim BS, Jeon SW, Kim GH, Kim JJInt J Syst Evol Microbiol10.1099/ijsem.0.0033752019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny31999238Gemmobacter caeruleus sp. nov., a novel species originating from lake sediment.Qu JH, Ma WW, Zhou J, Wang XF, Lu WL, Qu LB, Wang LFInt J Syst Evol Microbiol10.1099/ijsem.0.0040072020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Lakes/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny32553048Gemmobacter serpentinus sp. nov., isolated from conserved forages.Lim K, Kannan AD, Shobnam N, Mahmood M, Lee J, Im JInt J Syst Evol Microbiol10.1099/ijsem.0.0042762020Animal Feed/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Kansas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
29638Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172602728776041
30689Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172702028776041
64732Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-108272Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108272)
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
68369Automatically annotated from API 20NE
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91515Reimer, 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-ID404494.1