Strain identifier

BacDive ID: 133213

Type strain: Yes

Species: Silicimonas algicola

Strain Designation: KC90B

Strain history: <- C. Jeanthon, CNRS & Sorbonne Universités, Station Biologique Roscoff <- K. Crenn, CNRS & Sorbonne Universités, Station Biologique Roscoff; KC90B

NCBI tax ID(s): 1826607 (species)

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General

@ref: 64139

BacDive-ID: 133213

DSM-Number: 103371

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, pleomorphic-shaped, colony-forming

description: Silicimonas algicola KC90B is an aerobe, Gram-negative, pleomorphic-shaped bacterium that forms circular colonies and was isolated from silica cell wall of Thalassiosira delicatula RCC 2565, a marine diatom originating from Roscoff; offshore seawater.

NCBI tax id

  • NCBI tax id: 1826607
  • Matching level: species

strain history

  • @ref: 64139
  • history: <- C. Jeanthon, CNRS & Sorbonne Universités, Station Biologique Roscoff <- K. Crenn, CNRS & Sorbonne Universités, Station Biologique Roscoff; KC90B

doi: 10.13145/bacdive133213.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Silicimonas
  • species: Silicimonas algicola
  • full scientific name: Silicimonas algicola Crenn et al. 2016

@ref: 64139

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Silicimonas

species: Silicimonas algicola

full scientific name: Silicimonas algicola Crenn et al. 2016

strain designation: KC90B

type strain: yes

Morphology

cell morphology

  • @ref: 25009
  • gram stain: negative
  • cell length: 0.2-17.0 µm
  • cell width: 0.2-0.5 µm
  • cell shape: pleomorphic-shaped
  • motility: no

colony morphology

  • @ref: 25009
  • colony size: 0.3-1.0 mm
  • colony color: beige
  • colony shape: circular
  • incubation period: 14 days
  • medium used: MA agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25009MA agaryes
64139BACTO 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

culture temp

@refgrowthtypetemperaturerange
25009positivegrowth10-40
25009positiveoptimum25mesophilic
25009nogrowth4psychrophilic
25009nogrowth45thermophilic
64139positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
25009positivegrowth6.0-9.0alkaliphile
25009positiveoptimum6.5-7.5
25009nogrowth5.5
25009nogrowth9.5

Physiology and metabolism

oxygen tolerance

  • @ref: 25009
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
25009NaClnogrowth0 %
25009NaClpositivegrowth0.5-4.0 %(w/v)
25009NaCloptimum1.5-2.0 %(w/v)
25009NaClnogrowth4.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25009174265-dehydro-D-gluconate-carbon source
2500927613amygdalin-carbon source
2500917057cellobiose-carbon source
2500917057cellobiose-assimilation
2500915963ribitol-carbon source
2500917108D-arabinose-carbon source
2500918333D-arabitol-carbon source
2500915824D-fructose-carbon source
2500915824D-fructose-assimilation
2500928847D-fucose-carbon source
2500912936D-galactose-carbon source
2500912936D-galactose-assimilation
2500917634D-glucose-carbon source
2500917634D-glucose-assimilation
2500916899D-mannitol-carbon source
2500916899D-mannitol-assimilation
2500916024D-mannose-carbon source
2500916024D-mannose-assimilation
2500916988D-ribose-carbon source
2500916988D-ribose-assimilation
2500917924D-sorbitol-carbon source
2500917924D-sorbitol-assimilation
2500916443D-tagatose-carbon source
2500965327D-xylose-carbon source
2500965327D-xylose-assimilation
2500917113erythritol-carbon source
2500916813galactitol-carbon source
250095291gelatin-assimilation
2500928066gentiobiose-carbon source
2500917754glycerol-carbon source
2500917754glycerol-assimilation
2500928087glycogen-carbon source
2500917268myo-inositol-carbon source
2500917268myo-inositol-assimilation
2500915443inulin-carbon source
2500930849L-arabinose-carbon source
2500930849L-arabinose-assimilation
2500918403L-arabitol-carbon source
2500916467L-arginine-assimilation
2500918287L-fucose-carbon source
2500962320L-lyxose-carbon source
2500962345L-rhamnose-carbon source
2500962345L-rhamnose-assimilation
2500917266L-sorbose-carbon source
2500965328L-xylose-carbon source
2500917716lactose-carbon source
2500917716lactose-assimilation
2500917306maltose-carbon source
2500917306maltose-assimilation
250096731melezitose-carbon source
2500928053melibiose-carbon source
25009320061methyl alpha-D-glucopyranoside-carbon source
2500943943methyl alpha-D-mannoside-carbon source
2500974863methyl beta-D-xylopyranoside-carbon source
25009506227N-acetylglucosamine-carbon source
25009506227N-acetylglucosamine-assimilation
2500917632nitrate-reduction
2500932032potassium gluconate-carbon source
2500916634raffinose-carbon source
2500916634raffinose-assimilation
2500917814salicin-carbon source
2500953258sodium citrate-assimilation
2500928017starch-carbon source
2500917992sucrose-carbon source
2500927082trehalose-carbon source
2500927082trehalose-assimilation
2500932528turanose-carbon source
2500916199urea-assimilation
2500917151xylitol-carbon source
25009168082-dehydro-D-gluconate+carbon source
2500918305arbutin+carbon source
2500916024D-mannose+carbon source
2500916024D-mannose+assimilation
25009esculin ferric citrate+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitive
2500928971ampicillinyesyes
2500917698chloramphenicolyesyes
2500918208penicillin gyesyes
2500917833gentamicinyesyes
250096104kanamycinyesyes
2500917076streptomycinyesyes
2500927902tetracyclineyesyes
25009100147nalidixic acidyesno
2500948923erythromycinyesyes
250097507neomycinyesyes

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25009acid phosphatase+3.1.3.2
25009alkaline phosphatase+3.1.3.1
25009alpha-chymotrypsin-3.4.21.1
25009alpha-fucosidase-3.2.1.51
25009alpha-galactosidase-3.2.1.22
25009alpha-glucosidase+3.2.1.20
25009alpha-mannosidase-3.2.1.24
25009beta-galactosidase+3.2.1.23
25009beta-glucosidase+3.2.1.21
25009beta-glucuronidase-3.2.1.31
25009catalase+1.11.1.6
25009cystine arylamidase-3.4.11.3
25009cytochrome oxidase+1.9.3.1
25009esterase (C 4)+
25009esterase lipase (C 8)+
25009leucine arylamidase+3.4.11.1
25009lipase (C 14)+
25009N-acetyl-beta-glucosaminidase-3.2.1.52
25009naphthol-AS-BI-phosphohydrolase+
25009trypsin-3.4.21.4
25009valine arylamidase+
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
64139-----+-+------------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
25009silica cell wall of Thalassiosira delicatula RCC 2565, a marine diatom originating from Roscoff offshore seawaternorth off Roscoff, western English ChannelFranceFRAEurope48-32011-01
64139silica cell wall of the marine diatom Thalassiosira delicatula collected from coastal surface waterwestern English Channel, north off Roscoff, station SOMLIT-Astan (48° 45' N 3° 57' W)FranceFRAEurope48.75-3.95

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Microbial#Zooplankton

taxonmaps

  • @ref: 69479
  • File name: preview.99_75447.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_14749;97_20077;98_52753;99_75447&stattab=map
  • Last taxonomy: Silicimonas algicola subclade
  • 16S sequence: KU926270
  • Sequence Identity:
  • Total samples: 3138
  • soil counts: 27
  • aquatic counts: 3091
  • animal counts: 17
  • plant counts: 3

Safety information

risk assessment

  • @ref: 64139
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64139
  • description: Silicimonas algicola strain KC90BT 16S ribosomal RNA gene, partial sequence
  • accession: KU926270
  • length: 1395
  • database: ena
  • NCBI tax ID: 1826607

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Silicimonas algicola DSM 103371GCA_003148765scaffoldncbi1826607
66792Silicimonas algicola strain DSM 1033711826607.3wgspatric1826607
66792Silicimonas algicola strain KC901826607.5completepatric1826607
66792Silicimonas algicola DSM 1033712756170270draftimg1826607

GC content

@refGC-contentmethod
2500965.2genome sequence analysis
6413965.2sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno87.819yes
gram-positiveno97.766yes
anaerobicno96.991yes
aerobicyes89.082yes
halophileno51.661no
spore-formingno95.878no
glucose-utilyes79.815yes
flagellatedno95.901yes
thermophileno98.469no
glucose-fermentno90.138no

External links

@ref: 64139

culture collection no.: DSM 103371, RCC 4681

straininfo link

  • @ref: 91393
  • straininfo: 399564

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27498967Silicimonas algicola gen. nov., sp. nov., a member of the Roseobacter clade isolated from the cell surface of the marine diatom Thalassiosira delicatula.Crenn K, Serpin D, Lepleux C, Overmann J, Jeanthon CInt J Syst Evol Microbiol10.1099/ijsem.0.0013942016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diatoms/*microbiology, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Genetics30834382Complete Genome Sequence of the Silicimonas algicola Type Strain, a Representative of the Marine Roseobacter Group Isolated from the Cell Surface of the Marine Diatom Thalassiosira delicatula.Crenn K, Bunk B, Sproer C, Overmann J, Jeanthon CMicrobiol Resour Announc10.1128/MRA.00108-192019Phylogeny

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
25009K. S. Crenn, D.,Lepleux, C.,Overmann, J.,Jeanthon, C.Silicimonas algicola gen. nov., sp. nov., a member of the Roseobacter clade isolated from the cell surface of the marine diatom Thalassiosira delicatula10.1099/ijsem.0.001394IJSEM 66: 4580-4588 201627498967
64139Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103371Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103371)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91393Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399564.1