Strain identifier

BacDive ID: 14024

Type strain: Yes

Species: Fodinicurvata sediminis

Strain history: <- X-L Cui, Yunnan Inst., China

NCBI tax ID(s): 570952 (strain), 1121832 (species)

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General

@ref: 15571

BacDive-ID: 14024

DSM-Number: 21159

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Fodinicurvata sediminis DSM 21159 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from sediment from a salt mine.

NCBI tax id

NCBI tax idMatching level
570952strain
1121832species

strain history

@refhistory
15571<- X.-L. Cui, The Key Laboratory for Microbial Resources of Ministry of Education; Yunnan Insitute of Microbiology
67771<- X-L Cui, Yunnan Inst., China

doi: 10.13145/bacdive14024.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Rhodovibrionaceae
  • genus: Fodinicurvata
  • species: Fodinicurvata sediminis
  • full scientific name: Fodinicurvata sediminis Wang et al. 2009

@ref: 15571

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodospirillales

family: Rhodovibrionaceae

genus: Fodinicurvata

species: Fodinicurvata sediminis

full scientific name: Fodinicurvata sediminis Wang et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29243negative1.1 µm0.4 µmrod-shapedno
67771negative
69480negative99.986

pigmentation

  • @ref: 29243
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_21159_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21159_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21159_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21159_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21159_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 15571
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15571positivegrowth28mesophilic
29243positivegrowth15-42
29243positiveoptimum28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29243positivegrowth6.5-8.5alkaliphile
29243positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29243facultative anaerobe
67771aerobe

spore formation

@refspore formationconfidence
29243no
69481no100
69480no99.999

compound production

  • @ref: 15571
  • compound: poly-ß-hydroxybutyrate

halophily

  • @ref: 29243
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 1.5-20 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2924330089acetate+carbon source
2924322599arabinose+carbon source
2924322653asparagine+carbon source
2924335391aspartate+carbon source
2924316947citrate+carbon source
2924316236ethanol+carbon source
2924317234glucose+carbon source
2924329987glutamate+carbon source
2924317754glycerol+carbon source
2924329864mannitol+carbon source
2924326271proline+carbon source
2924330911sorbitol+carbon source
2924317992sucrose+carbon source
2924318222xylose+carbon source
292434853esculin+hydrolysis
2924317632nitrate+reduction

metabolite production

  • @ref: 29243
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 29243
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29243alkaline phosphatase+3.1.3.1
29243catalase+1.11.1.6
29243gelatinase+
29243cytochrome oxidase+1.9.3.1
29243urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15571sediment from a salt mineYunnan province, FenggangChinaCHNAsia
67771From sediment from a salt mineYunnan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Condition#Saline
#Environmental#Terrestrial#Sediment
#Environmental#Terrestrial#Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_5953.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_175;96_1930;97_2321;98_2864;99_5953&stattab=map
  • Last taxonomy: Fodinicurvata sediminis
  • 16S sequence: FJ357426
  • Sequence Identity:
  • Total samples: 69
  • soil counts: 19
  • aquatic counts: 40
  • animal counts: 9
  • plant counts: 1

Safety information

risk assessment

  • @ref: 15571
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15571
  • description: Rhodospirillaceae bacterium YIM D82 16S ribosomal RNA gene, partial sequence
  • accession: FJ357426
  • length: 1407
  • database: ena
  • NCBI tax ID: 1121832

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Fodinicurvata sediminis DSM 21159GCA_000420625contigncbi570952
66792Fodinicurvata sediminis DSM 21159570952.8wgspatric570952
66792Fodinicurvata sediminis DSM 211592523533601draftimg570952

GC content

  • @ref: 15571
  • GC-content: 61.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.38yes
anaerobicno97.231yes
halophileyes66.899no
spore-formingno91.734no
glucose-utilyes79.046yes
thermophileno86.995yes
flagellatedno81.537no
aerobicyes84.094no
motileyes52.899yes
glucose-fermentno91.054no

External links

@ref: 15571

culture collection no.: DSM 21159, KCTC 22351, YIM D82

straininfo link

  • @ref: 83192
  • straininfo: 404763

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19622654Fodinicurvata sediminis gen. nov., sp. nov. and Fodinicurvata fenggangensis sp. nov., poly-beta-hydroxybutyrate-producing bacteria in the family Rhodospirillaceae.Wang YX, Liu JH, Zhang XX, Chen YG, Wang ZG, Chen Y, Li QY, Peng Q, Cui XLInt J Syst Evol Microbiol10.1099/ijs.0.009340-02009China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Hydroxybutyrates/*metabolism, Molecular Sequence Data, Phylogeny, Polyesters/*metabolism, RNA, Ribosomal, 16S/genetics, Rhodospirillaceae/classification/genetics/*isolation & purification/*metabolism, *Soil MicrobiologyMetabolism
Phylogeny22904212Limimonas halophila gen. nov., sp. nov., an extremely halophilic bacterium in the family Rhodospirillaceae.Amoozegar MA, Makhdoumi-Kakhki A, Ramezani M, Nikou MM, Fazeli SAS, Schumann P, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.041236-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, Iran, Lakes/*microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodospirillaceae/*classification/genetics/isolation & purification, Salinity, Sequence Analysis, DNA, Ubiquinone/analysis, *Water MicrobiologyGenetics
Phylogeny25479951Fodinicurvata halophila sp. nov., a moderately halophilic bacterium from a marine saltern.Infante-Dominguez C, Lawson PA, Johnson CN, Sanchez-Porro C, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.0000102014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodospirillaceae/*classification/genetics/isolation & purification, Salinity, Seawater/*microbiology, Sequence Analysis, DNA, SpainGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15571Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21159)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21159
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
29243Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2566328776041
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
83192Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404763.1StrainInfo: A central database for resolving microbial strain identifiers