Strain identifier

BacDive ID: 482

Type strain: Yes

Species: Marinobacter algicola

Strain Designation: DG893

Strain history: CIP <- 2007, DSMZ <- D.H. Green, Scottish Assoc. Marine Sci., Argyll, UK: strain DG893

NCBI tax ID(s): 236100 (species)

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General

@ref: 6426

BacDive-ID: 482

DSM-Number: 16394

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

description: Marinobacter algicola DG893 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from lab culture of dinoflagellate Gymnodinium catenatum YC499B15.

NCBI tax id

  • NCBI tax id: 236100
  • Matching level: species

strain history

@refhistory
6426<- D. H. Green; DG893
116225CIP <- 2007, DSMZ <- D.H. Green, Scottish Assoc. Marine Sci., Argyll, UK: strain DG893

doi: 10.13145/bacdive482.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Marinobacter
  • species: Marinobacter algicola
  • full scientific name: Marinobacter algicola Green et al. 2006

@ref: 6426

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Marinobacter

species: Marinobacter algicola

full scientific name: Marinobacter algicola Green et al. 2006

strain designation: DG893

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31386negative1.6-2.5 µm0.45-0.55 µmrod-shapedyes
116225negativerod-shapedyes

pigmentation

  • @ref: 31386
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6426BACTO 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
37838Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116225CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6426positivegrowth28mesophilic
31386positivegrowth05-40
31386positiveoptimum25-30mesophilic
37838positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31386positivegrowth05-10alkaliphile
31386positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31386aerobe
116225obligate aerobe

spore formation

  • @ref: 31386
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31386NaClpositivegrowth01-12 %
31386NaClpositiveoptimum03-06 %

observation

  • @ref: 31386
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3138616449alanine+carbon source
3138616947citrate+carbon source
3138628757fructose+carbon source
3138624265gluconate+carbon source
3138617234glucose+carbon source
3138617754glycerol+carbon source
3138624996lactate+carbon source
3138625017leucine+carbon source
3138617306maltose+carbon source
3138629864mannitol+carbon source
3138628044phenylalanine+carbon source
3138626271proline+carbon source
11622517632nitrate+reduction
11622516301nitrite-reduction

metabolite production

  • @ref: 116225
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31386catalase+1.11.1.6
31386cytochrome oxidase+1.9.3.1
31386urease+3.5.1.5
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
116225oxidase+
116225catalase+1.11.1.6
116225urease-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
116225-++++++---++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciescontinentgeographic locationcountryorigin.country
6426lab culture of dinoflagellate Gymnodinium catenatum YC499B15Gymnodinium catenatumEurope
116225Lab culture of dinoflagellate, Gymnodinium catenatumEuropeScotlandUnited KingdomGBR

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Host#Protozoa#Dinoflagellate

taxonmaps

  • @ref: 69479
  • File name: preview.99_4771.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_89;96_1317;97_1564;98_3576;99_4771&stattab=map
  • Last taxonomy: Marinobacter
  • 16S sequence: AY258110
  • Sequence Identity:
  • Total samples: 424
  • soil counts: 8
  • aquatic counts: 358
  • animal counts: 54
  • plant counts: 4

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64261Risk group (German classification)
1162251Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6426
  • description: Marinobacter algicola DG893 small subunit ribosomal RNA gene, partial sequence
  • accession: AY258110
  • length: 1485
  • database: ena
  • NCBI tax ID: 443152

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinobacter algicola DG893GCA_000170835contigncbi443152
66792Marinobacter algicola DG893443152.3wgspatric443152
66792Marinobacter algicola DG893640963027draftimg443152

GC content

  • @ref: 31386
  • GC-content: 54-55

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno99.002yes
anaerobicno98.306no
halophileyes92.316no
spore-formingno96.256yes
glucose-utilyes67.877no
aerobicyes91.913yes
flagellatedyes87.278no
motileyes88.892yes
thermophileno99.097yes
glucose-fermentno87.827no

External links

@ref: 6426

culture collection no.: DSM 16394, CIP 109780, NCIMB 14009

straininfo link

  • @ref: 70161
  • straininfo: 237159

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16514021Marinobacter algicola sp. nov., isolated from laboratory cultures of paralytic shellfish toxin-producing dinoflagellates.Green DH, Bowman JP, Smith EA, Gutierrez T, Bolch CJSInt J Syst Evol Microbiol10.1099/ijs.0.63447-02006Alteromonadaceae/*classification/genetics/isolation & purification/physiology, Animals, DNA, Ribosomal/chemistry, Dinoflagellida/*microbiology/pathogenicity, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPhenotype
Metabolism23775459Regulation of iron transport related genes by boron in the marine bacterium Marinobacter algicola DG893.Romano A, Trimble L, Hobusch AR, Schroeder KJ, Amin SA, Hartnett AD, Barker RA, Crumbliss AL, Carrano CJMetallomics10.1039/c3mt00068k2013Bacterial Proteins/metabolism, Boron/*chemistry, Gene Expression Profiling, *Gene Expression Regulation, Bacterial, Hydrogen-Ion Concentration, Iron/*metabolism, Marinobacter/*genetics/*metabolism, Periplasmic Binding Proteins/metabolism, Proteome, Repressor Proteins/metabolism, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationProteome
Metabolism25528647Molecular characterization of a homolog of the ferric-uptake regulator, Fur, from the marine bacterium Marinobacter algicola DG893.Barker RA, Tisnado J, Lambert LA, Gardes A, Carrano MW, Carrano PN, Gillian C, Carrano CJBiometals10.1007/s10534-014-9815-72014Bacterial Proteins/*metabolism, Gene Expression Regulation, Bacterial, Iron/metabolism, Marinobacter/*metabolism, Protein Binding
Phylogeny27902258Marinobacter halotolerans sp. nov., a halophilic bacterium isolated from a saltern crystallizing pond.Kim JO, Lee HJ, Han SI, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0016532017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Marinobacter/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Salinity, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Metabolism29951858Polyhydroxybutyrate (PHB) biodegradation using bacterial strains with demonstrated and predicted PHB depolymerase activity.Martinez-Tobon DI, Gul M, Elias AL, Sauvageau DAppl Microbiol Biotechnol10.1007/s00253-018-9153-82018Bacteria/enzymology/genetics/isolation & purification/*metabolism, Bacterial Proteins/genetics/*metabolism, Biodegradation, Environmental, Carboxylic Ester Hydrolases/genetics/*metabolism, Hydroxybutyrates/*metabolismEnzymology
Phylogeny31592762Marinobacter vulgaris sp. nov., a moderately halophilic bacterium isolated from a marine solar saltern.Zhang Y, Zhong XC, Xu W, Lu DC, Zhao JX, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0037742020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Marinobacter/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water MicrobiologyTranscriptome
Enzymology32087608Streamlined production, purification, and characterization of recombinant extracellular polyhydroxybutyrate depolymerases.Martinez-Tobon DI, Waters B, Elias AL, Sauvageau DMicrobiologyopen10.1002/mbo3.10012020Bacteria/*enzymology/genetics/metabolism, Bioreactors/microbiology, Carboxylic Ester Hydrolases/*genetics, Comamonas testosteroni/enzymology/genetics/metabolism, Cupriavidus/enzymology/genetics/metabolism, Escherichia coli/enzymology/genetics/metabolism, Marinobacter/enzymology/genetics/metabolism, Pseudomonas stutzeri/enzymology/genetics/metabolism, Ralstonia/enzymology/genetics/metabolism, Recombinant Proteins/geneticsMetabolism
Phylogeny32213256Marinobacter denitrificans sp. nov., isolated from marine sediment of southern Scott Coast, Antarctica.Zhang MX, Li AZ, Wu Q, Yao Q, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0041202020Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Marinobacter/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
34512604Characterization and Genomic Analysis of Marinobacter Phage vB_MalS-PS3, Representing a New Lambda-Like Temperate Siphoviral Genus Infecting Algae-Associated Bacteria.Liu Y, Zheng K, Liu B, Liang Y, You S, Zhang W, Zhang X, Jie Y, Shao H, Jiang Y, Guo C, He H, Wang H, Sung YY, Mok WJ, Wong LL, McMinn A, Wang MFront Microbiol10.3389/fmicb.2021.7260742021
Phylogeny35094174Marinobacter arenosus sp. nov., a halotolerant bacterium isolated from a tidal flat.Lee Y, Weerawongwiwat V, Kim JH, Suh MK, Kim HS, Lee JS, Yoon JH, Sukhoom A, Kim WArch Microbiol10.1007/s00203-021-02696-72022Bacterial Typing Techniques, DNA, Bacterial/genetics, *Marinobacter/genetics, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6426Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16394)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16394
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
31386Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2769728776041
37838Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7561
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)
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
70161Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID237159.1StrainInfo: A central database for resolving microbial strain identifiers
116225Curators of the CIPCollection of Institut Pasteur (CIP 109780)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109780