Strain identifier

BacDive ID: 13735

Type strain: Yes

Species: Pseudorhodobacter ferrugineus

Strain Designation: A7

Strain history: CIP <- 1999, ATCC <- R. Ahrens: strain A7

NCBI tax ID(s): 1123027 (strain), 77008 (species)

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General

@ref: 2346

BacDive-ID: 13735

DSM-Number: 5888

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

description: Pseudorhodobacter ferrugineus A7 is a mesophilic, Gram-negative bacterium that was isolated from brackish water.

NCBI tax id

NCBI tax idMatching level
1123027strain
77008species

strain history

@refhistory
2346<- ATCC <- R. Ahrens, A7
67770IAM 12616 <-- ATCC 25652 <-- R. Ahrens A7.
119335CIP <- 1999, ATCC <- R. Ahrens: strain A7

doi: 10.13145/bacdive13735.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Pseudorhodobacter
  • species: Pseudorhodobacter ferrugineus
  • full scientific name: Pseudorhodobacter ferrugineus (Rüger and Höfle 1992 ex Ahrens and Rheinheimer 1967) Uchino et al. 2003

  • synonyms

    • @ref: 20215
    • synonym: Agrobacterium ferrugineum

@ref: 2346

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Pseudorhodobacter

species: Pseudorhodobacter ferrugineus

full scientific name: Pseudorhodobacter ferrugineus (Rüger and Höfle 1992) Uchino et al. 2003

strain designation: A7

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.996
119335negativerod-shapedyes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_5888_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_5888_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_5888_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_5888_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_5888_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2346MARINE AGAR (DSMZ Medium 123)yeshttps://mediadive.dsmz.de/medium/123Name: MARINE AGAR (DSMZ Medium 123) Composition: NaCl 24.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 11.0 g/l Bacto peptone 5.0 g/l Na2SO4 4.0 g/l CaCl2 x 6 H2O 2.0 g/l Yeast extract 1.0 g/l KCl 0.7 g/l KBr 0.1 g/l SrCl2 x 6 H2O 0.04 g/l H3BO3 0.03 g/l NaSiO3 x 9 H2O 0.005 g/l NaF 0.003 g/l NH4NO3 0.002 g/l Fe(III)PO4 x 4 H2O 0.001 g/l Distilled water
40273Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119335CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
2346positivegrowth26mesophilic
40273positivegrowth25mesophilic
67770positivegrowth25mesophilic
119335positivegrowth5-30
119335nogrowth37mesophilic
119335nogrowth41thermophilic
119335nogrowth45thermophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.997

halophily

@refsaltgrowthtested relationconcentration
119335NaClpositivegrowth2 %
119335NaClnogrowth0 %
119335NaClnogrowth4 %
119335NaClnogrowth6 %
119335NaClnogrowth8 %
119335NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1193354853esculin-hydrolysis
119335606565hippurate-hydrolysis
11933517632nitrate-builds gas from
11933517632nitrate-reduction
11933516301nitrite-reduction
11933515792malonate-assimilation

metabolite production

  • @ref: 119335
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11933515688acetoin-
11933517234glucose-

enzymes

@refvalueactivityec
119335oxidase+
119335beta-galactosidase-3.2.1.23
119335alcohol dehydrogenase-1.1.1.1
119335gelatinase-
119335amylase-
119335caseinase-3.4.21.50
119335catalase+1.11.1.6
119335tween esterase-
119335gamma-glutamyltransferase-2.3.2.2
119335lecithinase-
119335lipase-
119335lysine decarboxylase-4.1.1.18
119335ornithine decarboxylase-4.1.1.17
119335phenylalanine ammonia-lyase-4.3.1.24
119335protease-
119335tryptophan deaminase-
119335urease-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
119335-+++-+----+++--+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119335---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountry
2346brackish waterBaltic Sea
67770Brackish waterBaltic Sea
119335Environment, Brackish water from the Baltic SeaBaltic Sea

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5769.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_979;97_1139;98_4297;99_5769&stattab=map
  • Last taxonomy: Pseudorhodobacter ferrugineus subclade
  • 16S sequence: AB680963
  • Sequence Identity:
  • Total samples: 1335
  • soil counts: 22
  • aquatic counts: 1245
  • animal counts: 65
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
23461Risk group (German classification)
1193351Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agrobacterium ferrugineum gene for 16S rRNA, partial sequenceD885221400ena77008
20218Pseudorhodobacter ferrugineus gene for 16S rRNA, partial sequence, strain: NBRC 15767AB6809631405ena77008

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudorhodobacter ferrugineus DSM 58881123027.3wgspatric1123027
66792Pseudorhodobacter ferrugineus strain LMG 2204777008.4wgspatric77008
66792Pseudorhodobacter ferrugineus LMG 220472772190752draftimg77008
66792Pseudorhodobacter ferrugineus DSM 58882524023154draftimg1123027
67770Pseudorhodobacter ferrugineus DSM 5888GCA_000420745contigncbi1123027
67770Pseudorhodobacter ferrugineus LMG 22047GCA_001202045contigncbi77008

GC content

@refGC-contentmethod
6777058high performance liquid chromatography (HPLC)
6777058thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno72no
motileno72.01no
flagellatedno88.482no
gram-positiveno98.347no
anaerobicno97.835no
aerobicyes81.495no
halophileno59.887no
spore-formingno96.326no
thermophileno96.962no
glucose-utilyes67.088no
glucose-fermentno90.279no

External links

@ref: 2346

culture collection no.: DSM 5888, ATCC 25652, IAM 12616, ICPB 4164, JCM 20687, CIP 105952, IFO 15767, LMG 127, LMG 22047, LMG 8173, NBRC 15767, NCIMB 1537

straininfo link

  • @ref: 82917
  • straininfo: 11529

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1371058Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev.Ruger HJ, Hofle MGInt J Syst Bacteriol10.1099/00207713-42-1-1331992DNA, Bacterial/analysis, Genotype, Phenotype, RNA, Bacterial/analysis, Rhizobium/*classification/genetics/physiology, Seawater, *Water MicrobiologyGenetics
Phylogeny12055311Evolutionary relationship of phototrophic bacteria in the alpha-Proteobacteria based on farnesyl diphosphate synthase.Cantera JJL, Kawasaki H, Seki TMicrobiology (Reading)10.1099/00221287-148-6-19232002Alkyl and Aryl Transferases/*genetics, Alphaproteobacteria/classification/*enzymology/*genetics, *Evolution, Molecular, Geranyltranstransferase, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny12501429Reclassification of marine Agrobacterium species: Proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev.Uchino Y, Hirata A, Yokota A, Sugiyama JJ Gen Appl Microbiol10.2323/jgam.44.2011998
Phylogeny12682869Proposal of Pseudorhodobacter ferrugineus gen nov, comb nov, for a non-photosynthetic marine bacterium, Agrobacterium ferrugineum, related to the genus Rhodobacter.Uchino Y, Hamada T, Yokota AJ Gen Appl Microbiol10.2323/jgam.48.3092002Base Composition, DNA Gyrase/chemistry/genetics, DNA, Ribosomal/analysis, Light-Harvesting Protein Complexes, Photosynthesis/*genetics, Photosynthetic Reaction Center Complex Proteins/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Rhizobium/*classification/*genetics/growth & development, Rhodobacter/*classification/genetics/growth & development, Seawater/*microbiology, Sequence Analysis, DNATranscriptome
Phylogeny15879249Reclassification of Agrobacterium ferrugineum LMG 128 as Hoeflea marina gen. nov., sp. nov.Peix A, Rivas R, Trujillo ME, Vancanneyt M, Velazquez E, Willems AInt J Syst Evol Microbiol10.1099/ijs.0.63291-02005Alphaproteobacteria/*classification/cytology/genetics/physiology, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Base Composition, Carbohydrates, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Esculin/metabolism, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Hydrogen-Ion Concentration, Molecular Sequence Data, Nitrogen/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/cytology/genetics/physiology, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Temperature, Urease/analysis, Water Microbiology, beta-Galactosidase/analysisEnzymology
Phylogeny21335494Pseudorhodobacter aquimaris sp. nov., isolated from seawater, and emended description of the genus Pseudorhodobacter Uchino et al. 2002.Jung YT, Oh KH, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.029769-02011Aerobiosis, Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Base Composition, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny22611201Pseudorhodobacter antarcticus sp. nov., isolated from Antarctic intertidal sandy sediment, and emended description of the genus Pseudorhodobacter Uchino et al. 2002 emend. Jung et al. 2012.Chen CX, Zhang XY, Liu C, Yu Y, Liu A, Li GW, Li H, Chen XL, Chen B, Zhou BC, Zhang YZInt J Syst Evol Microbiol10.1099/ijs.0.042184-02012Antarctic Regions, Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny22843726Pseudorhodobacter wandonensis sp. nov., isolated from wood falls, and emended description of the genus Pseudorhodobacter.Lee MH, Lee SY, Jung YT, Park S, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.042879-02012Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analysis, Wood/*microbiologyGenetics
Phylogeny26476707Pseudorhodobacter collinsensis sp. nov., isolated from a till sample of an icecap front.Zhang Y, Jiang F, Chang X, Qiu X, Ren L, Qu Z, Deng S, Da X, Kan W, Kim M, Fang C, Peng FInt J Syst Evol Microbiol10.1099/ijsem.0.0006932015Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/*microbiology, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryGenetics
Phylogeny27045957Pseudorhodobacter sinensis sp. nov. and Pseudorhodobacter aquaticus sp. nov., isolated from crater lakes.Li AH, Liu HC, Hou WG, Zhou YGInt J Syst Evol Microbiol10.1099/ijsem.0.0010612016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2346Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5888)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5888
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
40273Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18028
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 life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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)
82917Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11529.1StrainInfo: A central database for resolving microbial strain identifiers
119335Curators of the CIPCollection of Institut Pasteur (CIP 105952)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105952