Strain identifier

BacDive ID: 6199

Type strain: Yes

Species: Hirschia baltica

Strain history: <- H. Schlesner

NCBI tax ID(s): 582402 (strain), 2724 (species)

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General

@ref: 2335

BacDive-ID: 6199

DSM-Number: 5838

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

description: Hirschia baltica DSM 5838 is an aerobe, chemoheterotroph, mesophilic bacterium that was isolated from brackish water.

NCBI tax id

NCBI tax idMatching level
582402strain
2724species

strain history

  • @ref: 2335
  • history: <- H. Schlesner

doi: 10.13145/bacdive6199.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Caulobacterales
  • family: Hyphomonadaceae
  • genus: Hirschia
  • species: Hirschia baltica
  • full scientific name: Hirschia baltica Schlesner et al. 1990

@ref: 2335

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Caulobacterales

family: Hyphomonadaceae

genus: Hirschia

species: Hirschia baltica

full scientific name: Hirschia baltica Schlesner et al. 1990

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43364negative0.5-6 µm0.5-1 µmrod-shapedyesmonotrichous, polar
69480yes95.056
69480negative99.998

colony morphology

  • @ref: 43364
  • colony color: yellow

Culture and growth conditions

culture medium

  • @ref: 2335
  • 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
2335positivegrowth28mesophilic
43364positiveoptimum22-28

Physiology and metabolism

oxygen tolerance

  • @ref: 43364
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 43364
  • type: chemoheterotroph

spore formation

@refspore formationconfidence
43364no
69481no100
69480no99.997

observation

  • @ref: 43364
  • observation: expert on budding and hyphal bacteria (1 or 2 polarly inserted hyphae)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4336427856acetamide-assimilation
4336430089acetate+assimilation
4336417128adipate-growth
4336415963ribitol-growth
4336416449alanine+assimilation
4336458187alginate+hydrolysis
4336416134ammonia+nitrogen source
4336427613amygdalin-assimilation
4336429016arginine+assimilation
4336422653asparagine+assimilation
4336435391aspartate+assimilation
4336417968butyrate+assimilation
4336427689decanoate+assimilation
43364casein-hydrolysis
4336417057cellobiose+assimilation
4336462968cellulose-hydrolysis
4336416947citrate-growth
4336424996lactate+assimilation
4336425115malate-growth
4336416236ethanol-growth
4336416397formamide-growth
4336416397formamide-assimilation
4336415740formate-growth
4336428757fructose-assimilation
4336429806fumarate-growth
433645291gelatin+hydrolysis
4336424265gluconate+assimilation
4336417234glucose+assimilation
4336424297glucuronate-assimilation
4336429987glutamate+assimilation
4336429987glutamate+nitrogen source
4336428300glutamine+assimilation
4336417754glycerol-growth
4336417754glycerol-assimilation
4336415428glycine-growth
4336427570histidine-growth
4336424898isoleucine+assimilation
4336417716lactose-growth
4336417716lactose-assimilation
4336461995lecithin-hydrolysis
4336425017leucine-assimilation
4336425094lysine-growth
4336417306maltose+assimilation
4336429864mannitol-growth
4336417790methanol-growth
4336432544nicotinate-assimilation
4336417632nitrate+nitrogen source
4336426271proline+assimilation
4336417272propionate+assimilation
4336415361pyruvate+assimilation
4336416634raffinose-growth
4336426546rhamnose+assimilation
4336433942ribose-growth
4336417822serine-assimilation
4336430031succinate-assimilation
4336427082trehalose-growth
4336453426tween 80+hydrolysis
4336416199urea+nitrogen source
4336427266valine-growth
4336418222xylose-growth

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
4336428971ampicillinyesyes
4336427701oxytetracyclineyesyes
433648309polymyxin byesyes
4336417076streptomycinyesyes
4336427902tetracyclineyesyes
4336428669bacitracinyesyes
43364100147nalidixic acidyesyes
433647809oxacillinyesyes

metabolite production

  • @ref: 43364
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
43364alpha-arabinosidase+3.2.1.55
43364alpha-galactosidase-3.2.1.22
43364beta-galactosidase-3.2.1.23
433646-phospho-beta-galactosidase-3.2.1.85
43364lactosidase-
43364alpha-glucosidase+3.2.1.20
43364beta-glucosidase+3.2.1.21
43364alpha-maltosidase+
43364beta-maltosidase+
43364beta-xylosidase+
43364beta-glucuronidase-3.2.1.31
43364N-acetyl-beta-glucosaminidase-3.2.1.52
43364alpha-fucosidase-3.2.1.51
43364beta-D-fucosidase-3.2.1.38
43364alpha-mannosidase-3.2.1.24
43364beta-mannosidase-3.2.1.25
43364alpha-xylosidase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationsampling datecountryorigin.countrycontinent
2335brackish waterBaltic Sea, Kiel Fjord
43364surface brakish water from Kiel Fjord (Baltic Sea)Kiel, Schleswig-Holstein1982-10GermanyDEUEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5105.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_416;96_1904;97_2291;98_3811;99_5105&stattab=map
  • Last taxonomy: Hirschia baltica subclade
  • 16S sequence: AJ421782
  • Sequence Identity:
  • Total samples: 1369
  • soil counts: 210
  • aquatic counts: 1078
  • animal counts: 37
  • plant counts: 44

Safety information

risk assessment

  • @ref: 2335
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessiondatabaselengthNCBI tax ID
4336416S rRNA gene sequenceX52909nuccore
2335Hirschia baltica 16S rRNA gene, strain DSM 5838TAJ421782ena1419582402

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hirschia baltica ATCC 49814GCA_000023785completencbi582402
66792Hirschia baltica ATCC 49814582402.5completepatric582402
66792Hirschia baltica ATCC 49814 strain ATCC 59814582402.11plasmidpatric582402
66792Hirschia baltica ATCC 49814644736375completeimg582402

GC content

  • @ref: 43364
  • GC-content: 45.6
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.19no
flagellatedno50.631no
gram-positiveno99.239no
anaerobicno99.498yes
aerobicyes91.214yes
halophileno73.434no
spore-formingno96.385yes
thermophileno96.21yes
glucose-utilyes84.788yes
glucose-fermentno89.215no

External links

@ref: 2335

culture collection no.: DSM 5838, ATCC 49814, IFAM 1418

straininfo link

  • @ref: 75679
  • straininfo: 42696

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2275859Taxonomic and phylogenetic studies on a new taxon of budding, hyphal Proteobacteria, Hirschia baltica gen. nov., sp. nov.Schlesner H, Bartels C, Sittig M, Dorsch M, Stackebrandt EInt J Syst Bacteriol10.1099/00207713-40-4-4431990Bacteria/classification/*genetics, Base Composition, Base Sequence, DNA, Bacterial/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/chemistryGenetics
Phylogeny19620361Hirschia maritima sp. nov., isolated from seawater.Kang HS, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.008326-02009Aerobiosis, Alphaproteobacteria/*classification/cytology/genetics/*isolation & purification, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella/physiology, Hydrogen-Ion Concentration, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, TemperatureGenetics
Phylogeny19628598Ponticaulis koreensis gen. nov., sp. nov., a new member of the family Hyphomonadaceae isolated from seawater.Kang HS, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.011114-02009Alphaproteobacteria/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/metabolismMetabolism
Genetics22675580Complete genome sequence of Hirschia baltica type strain (IFAM 1418(T)).Chertkov O, Brown PJ, Kysela DT, de Pedro MA, Lucas S, Copeland A, Lapidus A, Del Rio TG, Tice H, Bruce D, Goodwin L, Pitluck S, Detter JC, Han C, Larimer F, Chang YJ, Jeffries CD, Land M, Hauser L, Kyrpides NC, Ivanova N, Ovchinnikova G, Tindall BJ, Goker M, Klenk HP, Brun YVStand Genomic Sci10.4056/sigs.22050042011
Phylogeny22904229Hirschia litorea sp. nov., isolated from seashore sediment, and emended description of the genus Hirschia.Park S, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.044297-02012Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylglycerols/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2335Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5838)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5838
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
43364Heinz Schlesner, Christina Bartels, Manuel Sittig, Matthias Dorsch, Erko Stackebrandt10.1099/00207713-40-4-443Taxonomic and Phylogenetic Studies on a New Taxon of Budding, Hyphal Proteobacteria, Hirschia baltica gen. nov., sp. nov.IJSEM 40: 443-451 19902275859
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
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
75679Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42696.1StrainInfo: A central database for resolving microbial strain identifiers