Strain identifier

BacDive ID: 13682

Type strain: Yes

Species: Nereida ignava

Strain Designation: 2SM4

Strain history: CIP <- 2004, M.J. Pujalte, Burjassot, Spain: strain 2SM4

NCBI tax ID(s): 1122600 (strain), 282199 (species)

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General

@ref: 6356

BacDive-ID: 13682

DSM-Number: 16309

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

description: Nereida ignava 2SM4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Mediterranean sea water.

NCBI tax id

NCBI tax idMatching level
282199species
1122600strain

strain history

@refhistory
6356<- M. J. Pujalte; 2SM4 <- M. Ortigosa et al.
374292004, M.J. Pujalte, Burjassot, Spain: strain 2SM4
120044CIP <- 2004, M.J. Pujalte, Burjassot, Spain: strain 2SM4

doi: 10.13145/bacdive13682.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Nereida
  • species: Nereida ignava
  • full scientific name: Nereida ignava Pujalte et al. 2005

@ref: 6356

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Nereida

species: Nereida ignava

full scientific name: Nereida ignava Pujalte et al. 2005

strain designation: 2SM4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31383negative2 µm0.25 µmrod-shapedno
69480negative99.996
120044negativeoval-shapedno

colony morphology

@refincubation period
585522 days
120044

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6356BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
37429Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120044CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6356positivegrowth25mesophilic
31383positivegrowth13-28
31383positiveoptimum20.5psychrophilic
37429positivegrowth25mesophilic
58552positivegrowth24-26
120044positivegrowth15-25psychrophilic
120044nogrowth5psychrophilic
120044nogrowth37mesophilic
120044nogrowth41thermophilic
120044nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31383aerobe
58552aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
31383NaClpositivegrowth<8 %
31383NaClpositiveoptimum4 %
120044NaClnogrowth0 %
120044NaClnogrowth2 %
120044NaClnogrowth4 %
120044NaClnogrowth6 %
120044NaClnogrowth8 %
120044NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3138330089acetate+carbon source
3138316947citrate+carbon source
3138317234glucose+carbon source
3138324996lactate+carbon source
3138325115malate+carbon source
3138317306maltose+carbon source
3138329864mannitol+carbon source
3138337684mannose+carbon source
3138318257ornithine+carbon source
3138317272propionate+carbon source
3138315361pyruvate+carbon source
3138317822serine+carbon source
3138330031succinate+carbon source
12004416947citrate-carbon source
1200444853esculin-hydrolysis
120044606565hippurate+hydrolysis
12004417632nitrate-builds gas from
12004417632nitrate-reduction
12004416301nitrite-builds gas from
12004416301nitrite-reduction
12004415792malonate-assimilation

metabolite production

  • @ref: 120044
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12004415688acetoin-
12004417234glucose-

enzymes

@refvalueactivityec
31383catalase+1.11.1.6
31383cytochrome oxidase+1.9.3.1
120044oxidase+
120044beta-galactosidase+3.2.1.23
120044alcohol dehydrogenase-1.1.1.1
120044gelatinase-
120044amylase-
120044DNase-
120044caseinase-3.4.21.50
120044catalase+1.11.1.6
120044tween esterase-
120044gamma-glutamyltransferase-2.3.2.2
120044lecithinase-
120044lipase-
120044lysine decarboxylase-4.1.1.18
120044ornithine decarboxylase-4.1.1.17
120044phenylalanine ammonia-lyase-4.3.1.24
120044tryptophan deaminase-
120044urease-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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120044---+-+----++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6356Mediterranean sea waternear ValenciaSpainESPEurope
58552Oyster meatValenciaSpainESPEurope1990-02-01
120044Environment, Sea waterValenciaSpainESPEurope1990

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3111.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1623;97_1941;98_2387;99_3111&stattab=map
  • Last taxonomy: Nereida ignava subclade
  • 16S sequence: AJ748748
  • Sequence Identity:
  • Total samples: 13220
  • soil counts: 272
  • aquatic counts: 12489
  • animal counts: 376
  • plant counts: 83

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63561Risk group (German classification)
1200441Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nereida ignava strain CECT5292 16S ribosomal RNA gene, partial sequenceDQ9156131307ena282199
6356Nereida ignava 16S rRNA gene, type strain 2SM4TAJ7487481455ena282199

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nereida ignava DSM 16309GCA_900114125contigncbi1122600
66792Nereida ignava CECT 5292GCA_001049735contigncbi282199
66792Nereida ignava CECT 5292GCA_001404155contigncbi282199
66792Nereida ignava DSM 163091122600.3wgspatric1122600
66792Nereida ignava strain CECT 5292282199.8wgspatric282199
66792Nereida ignava strain CECT 5292282199.9wgspatric282199
66792Nereida ignava CECT 52922706794653draftimg282199
66792Nereida ignava DSM 163092599185238draftimg1122600

GC content

  • @ref: 6356
  • GC-content: 56

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno56.767yes
flagellatedno83.696no
gram-positiveno98.759yes
anaerobicno98.692yes
halophileyes83.836yes
spore-formingno95.055no
glucose-utilyes53.131no
aerobicyes88.523yes
thermophileno90.304yes
glucose-fermentno91.269no

External links

@ref: 6356

culture collection no.: DSM 16309, CCUG 49433, CECT 5292, CIP 108404

straininfo link

  • @ref: 82865
  • straininfo: 138022

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774635Nereida ignava gen. nov., sp. nov., a novel aerobic marine alpha-proteobacterium that is closely related to uncultured Prionitis (alga) gall symbionts.Pujalte MJ, Macian MC, Arahal DR, Ludwig W, Schleifer KH, Garay EInt J Syst Evol Microbiol10.1099/ijs.0.63442-02005Aerobiosis, Alphaproteobacteria/chemistry/*classification/genetics/growth & development, Culture Media, DNA, Ribosomal/analysis, Fatty Acids/analysis, Mediterranean Sea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodophyta/*microbiology, Roseobacter/*classification/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *SymbiosisCultivation
26929790Draft genomic sequence of Nereida ignava CECT 5292(T), a marine bacterium of the family Rhodobacteraceae.Arahal DR, Pujalte MJ, Rodrigo-Torres LStand Genomic Sci10.1186/s40793-016-0141-22016

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6356Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16309)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16309
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
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
31383Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127695
37429Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6023
58552Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49433)https://www.ccug.se/strain?id=49433
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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)
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
82865Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138022.1StrainInfo: A central database for resolving microbial strain identifiers
120044Curators of the CIPCollection of Institut Pasteur (CIP 108404)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108404