Strain identifier

BacDive ID: 5482

Type strain: Yes

Species: Arenibacter palladensis

Strain Designation: PIBOC FEBRAS

Strain history: CIP <- 2005, KMM <- L.S. Shevchenko: strain PIBOC FEBRAS

NCBI tax ID(s): 237373 (species)

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General

@ref: 7052

BacDive-ID: 5482

DSM-Number: 17539

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

description: Arenibacter palladensis PIBOC FEBRAS is an aerobe, mesophilic, Gram-negative bacterium that was isolated from green alga Ulva fenestrata.

NCBI tax id

  • NCBI tax id: 237373
  • Matching level: species

strain history

@refhistory
7052<- O. I. Nedashkovskaya, RAS, Pacific Inst. Bioorg. Chem.; KMM 3961 <- L. S. Shevchenko
67770KMM 3961 <-- O. I. Nedashkovskaya <-- L. S. Shevchenko.
121506CIP <- 2005, KMM <- L.S. Shevchenko: strain PIBOC FEBRAS

doi: 10.13145/bacdive5482.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Arenibacter
  • species: Arenibacter palladensis
  • full scientific name: Arenibacter palladensis Nedashkovskaya et al. 2006

@ref: 7052

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Arenibacter

species: Arenibacter palladensis

full scientific name: Arenibacter palladensis Nedashkovskaya et al. 2006

strain designation: PIBOC FEBRAS

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
31609negative1.6-2.3 µm0.4-0.5 µmrod-shapedyesgliding
69480negative99.983
121506negativerod-shapedno

colony morphology

@refincubation period
579502 days
121506

pigmentation

@refproductionname
31609yes
121506noFlexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7052BACTO 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
38336Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121506CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7052positivegrowth28mesophilic
31609positivegrowth04-38
31609positiveoptimum23-25
38336positivegrowth25mesophilic
57950positivegrowth30mesophilic
67770positivegrowth25mesophilic
121506positivegrowth5-37
121506nogrowth41thermophilic
121506nogrowth45thermophilic

culture pH

@refabilitytypepH
31609positivegrowth7
31609positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31609aerobe
57950aerobe

spore formation

@refspore formationconfidence
31609no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
31609NaClpositivegrowth0-10 %
31609NaClpositiveoptimum0-10 %
121506NaClpositivegrowth0-10 %

observation

@refobservation
31609aggregates in chains
67770quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3160922599arabinose+carbon source
3160917057cellobiose+carbon source
3160923652dextrin+carbon source
3160928757fructose+carbon source
3160933984fucose+carbon source
3160928260galactose+carbon source
3160917234glucose+carbon source
3160929987glutamate+carbon source
3160924996lactate+carbon source
3160917716lactose+carbon source
3160917306maltose+carbon source
3160937684mannose+carbon source
3160928053melibiose+carbon source
31609506227N-acetylglucosamine+carbon source
3160916634raffinose+carbon source
3160917992sucrose+carbon source
3160926986threonine+carbon source
3160927082trehalose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside+builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837115963ribitol-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
1215064853esculin+hydrolysis
121506606565hippurate-hydrolysis
12150617632nitrate-reduction
12150616301nitrite-reduction
12150615792malonate+assimilation

metabolite production

  • @ref: 121506
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12150615688acetoin+
12150617234glucose-

enzymes

@refvalueactivityec
31609alkaline phosphatase+3.1.3.1
31609catalase+1.11.1.6
31609cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
121506oxidase-
121506beta-galactosidase-3.2.1.23
121506alcohol dehydrogenase-1.1.1.1
121506gelatinase-
121506amylase-
121506caseinase-3.4.21.50
121506catalase+1.11.1.6
121506tween esterase+
121506gamma-glutamyltransferase+2.3.2.2
121506lecithinase+
121506lipase-
121506lysine decarboxylase-4.1.1.18
121506ornithine decarboxylase-4.1.1.17
121506phenylalanine ammonia-lyase-4.3.1.24
121506protease-
121506tryptophan deaminase-
121506urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121506-+---++---++-+-++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121506--++/--++/--+/-++++-+/-----+++++++++++++/-+/--+---++---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121506+++++-+++++++++++++--+++++------++++-----+------------++---+------------------+-------+--++--------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcontinentsampling datecountryisolation date
7052green alga Ulva fenestrataUlva fenestrataSea of Japan, Pallada BayAsia
57950Green alga (Ulva fenestrata)Pallada BayAsia2000-06-01Sea of Japan
67770Green alga, Ulva fenestrataUlva fenestrataPallada Bay
121506Green alga, Ulva fenestrataPallada baySea of Japan1999

isolation source categories

  • Cat1: #Host
  • Cat2: #Algae
  • Cat3: #Green algae

taxonmaps

  • @ref: 69479
  • File name: preview.99_2346.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_102;96_1267;97_1502;98_1829;99_2346&stattab=map
  • Last taxonomy: Arenibacter
  • 16S sequence: AJ575643
  • Sequence Identity:
  • Total samples: 9391
  • soil counts: 1235
  • aquatic counts: 7063
  • animal counts: 925
  • plant counts: 168

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70521Risk group (German classification)
1215061Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7052
  • description: Arenibacter palladensis 16S rRNA gene, type strain LMG 21972T
  • accession: AJ575643
  • length: 1476
  • database: ena
  • NCBI tax ID: 237373

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arenibacter palladensis strain DSM 17539237373.5wgspatric237373
66792Arenibacter palladensis DSM 175392634166303draftimg237373
67770Arenibacter palladensis DSM 17539GCA_900129275scaffoldncbi237373

GC content

  • @ref: 67770
  • GC-content: 39-40

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno87.767no
gram-positiveno98.126yes
anaerobicno99.733yes
aerobicyes93.648no
halophileno84.422no
spore-formingno97.003yes
glucose-utilyes90.887yes
flagellatedno95.136yes
thermophileno99.4no
glucose-fermentno90.208no

External links

@ref: 7052

culture collection no.: CCUG 48011, DSM 17539, CIP 108849, JCM 13509, KMM 3961, LMG 21972, NCIMB 14299

straininfo link

  • @ref: 74969
  • straininfo: 93607

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16403881Arenibacter palladensis sp. nov., a novel marine bacterium isolated from the green alga Ulva fenestrata, and emended description of the genus Arenibacter.Nedashkovskaya OI, Vancanneyt M, Cleenwerck I, Snauwaert C, Kim SB, Lysenko AM, Shevchenko LS, Lee KH, Park MS, Frolova GM, Mikhailov VV, Bae KS, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.63893-02006Aerobiosis, Bacteroidetes/*classification/genetics/isolation & purification, Japan, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Homology, Nucleic Acid, Species Specificity, Ulva/*microbiologyGenetics
Metabolism22339637Structure of the O-specific polysaccharide of the marine bacterium Arenibacter palladensis KMM 3961(T) containing 2-acetamido-2-deoxy-l-galacturonic acid.Tomshich SV, Isakov VV, Komandrova NA, Shevchenko LSBiochemistry (Mosc)10.1134/S00062979120101052012Carbohydrate Sequence, Flavobacteriaceae/*metabolism, Hexuronic Acids/*chemistry, Lipopolysaccharides/metabolism, Magnetic Resonance Spectroscopy, Molecular Sequence Data, O Antigens/*chemistryGenetics
Phylogeny22544794Arenibacter hampyeongensis sp. nov., a marine bacterium isolated from a tidal flat.Jeong SH, Jin HM, Kim JM, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.040683-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny27125652Spongiimicrobium salis gen. nov., sp. nov., a bacterium of the family Flavobacteriaceae isolated from a marine sponge.Yoon J, Adachi K, Kasai HArch Microbiol10.1007/s00203-016-1227-32016Animals, Bacterial Typing Techniques, Base Composition/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, *Flavobacteriaceae/classification/genetics/isolation & purification, Japan, Phosphatidylethanolamines/analysis, Phospholipids/analysis, Phylogeny, Porifera/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7052Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17539)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17539
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
31609Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2789728776041
38336Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6524
57950Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48011)https://www.ccug.se/strain?id=48011
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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)
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
74969Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93607.1StrainInfo: A central database for resolving microbial strain identifiers
121506Curators of the CIPCollection of Institut Pasteur (CIP 108849)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108849