Strain identifier

BacDive ID: 10435

Type strain: Yes

Species: Aquaspirillum serpens

Strain history: CIP <- 1963, NCIB <- M.A. Williams: strain Giesberger, Spirillum serpens subsp. serpens

NCBI tax ID(s): 1121004 (strain), 190 (species)

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General

@ref: 2049

BacDive-ID: 10435

DSM-Number: 68

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative

description: Aquaspirillum serpens DSM 68 is an aerobe, Gram-negative bacterium that was isolated from Fresh water.

NCBI tax id

NCBI tax idMatching level
190species
1121004strain

strain history

@refhistory
2049<- N.R. Krieg <- ATCC <- M.A. Williams (Spirillum serpens). Growth of this strain is better when grown on agar slopes that have a wet surface ie. there is a liquid medium film on the surface of the agar and a small amount of liquid medium collects at the bottom of the slope
67770IAM 13944 <-- DSM 68 <-- N. R. Krieg <-- ATCC 12638 <-- M. A. Williams strain Giesberger.
122572CIP <- 1963, NCIB <- M.A. Williams: strain Giesberger, Spirillum serpens subsp. serpens

doi: 10.13145/bacdive10435.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Chromobacteriaceae
  • genus: Aquaspirillum
  • species: Aquaspirillum serpens
  • full scientific name: Aquaspirillum serpens (Müller 1786) Hylemon et al. 1973 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Vibrio serpens

@ref: 2049

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Chromobacteriaceae

genus: Aquaspirillum

species: Aquaspirillum serpens

full scientific name: Aquaspirillum serpens (Müller 1786) Hylemon et al. 1973 emend. Boivin et al. 1985

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
122572negativerod-shapedyes
69480negative99.212

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_68_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_68_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_68_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_68_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_68_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37610MEDIUM 14 - Williams and Rittenberg medium for Aquaspirillum genusyesDistilled water make up to (1000.000 ml);Agar (13.000 g);Yeast extract (3.000 g);Peptone (5.000 g);Beef extract (3.000 g)
2049ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7)yesName: ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7) Composition: Agar 15.0 g/l Yeast extract 1.0 g/l Peptone 1.0 g/l Glucose 1.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/7
2049SPIRILLUM MEDIUM (DSMZ Medium 37)yesName: SPIRILLUM MEDIUM (DSMZ Medium 37) Composition: Peptone 10.0 g/l (NH4)2SO4 1.0 g/l Succinic acid 1.0 g/l MgSO4 x 7 H2O 1.0 g/l FeCl3 x 6 H2O 0.002 g/l MnSO4 x H2O 0.002 g/l Distilled waterhttps://mediadive.dsmz.de/medium/37
122572CIP Medium 14yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=14

culture temp

@refgrowthtypetemperature
37610positivegrowth25
44485positivegrowth25-33
2049positivegrowth30
67770positivegrowth30
122572positivegrowth15-41
122572nogrowth5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44485aerobe
44485microaerophile

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 91.462

halophily

@refsaltgrowthtested relationconcentration
122572NaClpositivegrowth0 %
122572NaClnogrowth2 %
122572NaClnogrowth4 %
122572NaClnogrowth6 %
122572NaClnogrowth8 %
122572NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68369malate+assimilation25115
68369adipate-assimilation17128
68369decanoate+assimilation27689
68369gluconate-assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin-hydrolysis5291
68369esculin-hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
122572citrate-carbon source16947
122572esculin-hydrolysis4853
122572glucose-fermentation17234
122572lactose-fermentation17716
122572nitrate-reduction17632
122572nitrite-reduction16301
122572sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 122572
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12257235581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12257215688acetoin-
12257217234glucose-

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
122572oxidase+
122572beta-galactosidase-3.2.1.23
122572alcohol dehydrogenase-1.1.1.1
122572gelatinase-
122572amylase-
122572DNase-
122572caseinase-3.4.21.50
122572catalase+1.11.1.6
122572tween esterase-
122572gamma-glutamyltransferase-2.3.2.2
122572lecithinase-
122572lipase-
122572lysine decarboxylase-4.1.1.18
122572ornithine decarboxylase-4.1.1.17
122572phenylalanine ammonia-lyase-4.3.1.24
122572protease-
122572tryptophan deaminase-
122572urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    44485C12:04.412
    44485C16:019.116
    44485C17:02.417
    44485C18:07.518
    44485C12:0 3OH6.513.455
    44485C16:1 ω7c38.315.819
    44485C18:1 ω7c /12t/9t21.917.824
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122572-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
44485---------------+-+--+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122572------------------------------------------------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122572-------------------------------------------------------------------------------------------------+-

Isolation, sampling and environmental information

isolation

@refsample type
44485Fresh water
67770Freshwater
122572Environment, Fresh water

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_77397.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_23870;97_29864;98_38181;99_77397&stattab=map
  • Last taxonomy: Aquaspirillum serpens subclade
  • 16S sequence: AB074518
  • Sequence Identity:
  • Total samples: 11827
  • soil counts: 408
  • aquatic counts: 9687
  • animal counts: 1624
  • plant counts: 108

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20491Risk group (German classification)
1225721Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
2049Aquaspirillum serpens gene for 16S rRNA, partial sequenceAB0745181491nuccore190
124043Aquaspirillum serpens gene for 16S rRNA, partial sequence, strain: NBRC 14924.AB6807101461nuccore190

Genome sequences

  • @ref: 67770
  • description: Aquaspirillum serpens DSM 68
  • accession: GCA_000420525
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1121004

GC content

  • @ref: 67770
  • GC-content: 50
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno99.212no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no87.503no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes67.206no
69480spore-formingspore-formingAbility to form endo- or exosporesno91.462no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno90.278no
69480flagellatedmotile2+Ability to perform flagellated movementyes74.589no

External links

@ref: 2049

culture collection no.: DSM 68, ATCC 12638, CCUG 2092, NCTC 10593, LMG 3734, NRRL B-2045, CIP 63.19, JCM 20995, IAM 13944, IFO 14924, NBRC 14924, NCIMB 8658, NRRL: B-2045

straininfo link

  • @ref: 79716
  • straininfo: 13575

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18048733Reclassification of Aquaspirillum itersonii and Aquaspirillum peregrinum as Novispirillum itersonii gen. nov., comb. nov. and Insolitispirillum peregrinum gen. nov., comb. nov.Yoon JH, Kang SJ, Park S, Lee SY, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.65340-02007Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Neisseriaceae/chemistry/*classification/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Ubiquinone/analysisGenetics
Phylogeny18175708Paludibacterium yongneupense gen. nov., sp. nov., isolated from a wetland, Yongneup, in Korea.Kwon SW, Kim BY, Kim WG, Yoo KH, Yoo SH, Son JA, Weon HYInt J Syst Evol Microbiol10.1099/ijs.0.64831-02008Bacterial Typing Techniques, Base Composition, Betaproteobacteria/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, *WetlandsGenetics
Phylogeny28109204Aquaspirillum soli sp. nov., isolated from a soil sample.Moya G, Trinh H, Yan ZF, Won KH, Yang JE, Wang QJ, Kook MC, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0018022017Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2049Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 68)https://www.dsmz.de/collection/catalogue/details/culture/DSM-68
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
37610Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10025
44485Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 2092)https://www.ccug.se/strain?id=2092
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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)
79716Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13575.1StrainInfo: A central database for resolving microbial strain identifiers
122572Curators of the CIPCollection of Institut Pasteur (CIP 63.19)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2063.19
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy