Strain identifier

BacDive ID: 133922

Type strain: Yes

Species: Devosia submarina

Strain history: N. Tanaka Sl74.

NCBI tax ID(s): 1173082 (species)

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General

@ref: 30880

BacDive-ID: 133922

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

description: Devosia submarina NRIC 0884 is an aerobe, Gram-negative, motile bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 1173082
  • Matching level: species

strain history

  • @ref: 67770
  • history: N. Tanaka Sl74.

doi: 10.13145/bacdive133922.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Devosiaceae
  • genus: Devosia
  • species: Devosia submarina
  • full scientific name: Devosia submarina Romanenko et al. 2013

@ref: 30880

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Hyphomicrobiaceae

genus: Devosia

species: Devosia submarina

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30880negative1.6 µm1 µmrod-shapedyes
125438negative94.969
125439negative95.7

pigmentation

  • @ref: 30880
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperature
30880positivegrowth05-38
30880positiveoptimum29
67770positivegrowth25

culture pH

@refabilitytypepHPH range
30880positivegrowth6.0-9.0alkaliphile
30880positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
30880aerobe
125439obligate aerobe93.2

spore formation

@refspore formationconfidence
125438no90.29
125439no93.9

halophily

@refsaltgrowthtested relationconcentration
30880NaClpositivegrowth0-5 %
30880NaClpositiveoptimum1.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30880168082-dehydro-D-gluconate+carbon source
3088026271proline+carbon source
308804853esculin+hydrolysis

enzymes

@refvalueactivityec
30880acid phosphatase+3.1.3.2
30880alkaline phosphatase+3.1.3.1
30880catalase+1.11.1.6
30880cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.country
30880marine sediment
67770Deep surface-sediment sample collected from the Sea of JapanRussiaRUS

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Sequence information

16S sequences

  • @ref: 30880
  • description: Devosia submarina gene for 16S ribosomal RNA, partial sequence, strain: Sl74
  • accession: AB712348
  • length: 1442
  • database: nuccore
  • NCBI tax ID: 1173082

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Devosia submarina JCM 18935GCA_003056345contigncbi1173082
66792Devosia submarina strain JCM 189351173082.4wgspatric1173082
66792Devosia submarina JCM 189352848589509draftimg1173082

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe93.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative95.7
125439BacteriaNetmotilityAbility to perform movementyes60.8
125439BacteriaNetspore_formationAbility to form endo- or exosporesno93.9
125438gram-positivegram-positivePositive reaction to Gram-stainingno94.969yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.017yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90.29no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.122no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.559yes
125438motile2+flagellatedAbility to perform flagellated movementyes64.13no

External links

@ref: 30880

culture collection no.: NRIC 0884, JCM 18935, KMM 9415

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23416574Devosia submarina sp. nov., isolated from deep-sea surface sediments.Romanenko LA, Tanaka N, Svetashev VIInt J Syst Evol Microbiol10.1099/ijs.0.046607-02013DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Japan, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/analysis, Water MicrobiologyGenetics
Phylogeny31046895Devosia naphthalenivorans sp. nov., isolated from East Pacific Ocean sediment.Chen Y, Zhu S, Lin D, Wang X, Yang J, Chen JInt J Syst Evol Microbiol10.1099/ijsem.0.0034102019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Hyphomicrobiaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny33963447Devosia aurantiaca sp. nov., Isolated from Mountain Soil and Proposal of Albitalea gen. nov. to Replace the Illegitimate Prokaryotic Genus Name Geomonas Khan et al. 2020.Khan SA, Kim HM, Chun BH, Jeon COCurr Microbiol10.1007/s00284-021-02515-82021Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Hyphomicrobiaceae, *Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil, UbiquinoneTranscriptome
Phylogeny34435948Devosia beringensis sp. nov., isolated from surface sediment of the Bering Sea.Zhang YX, Yu Y, Luo W, Zeng YX, Du ZJ, Li HRInt J Syst Evol Microbiol10.1099/ijsem.0.0049952021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
34940664Structure of the Cell-Wall-Associated Polysaccharides from the Deep-Sea Marine Bacterium Devosia submarina KMM 9415(T).Kokoulin MS, Romanenko LA, Kuzmich AS, Chernikov OMar Drugs10.3390/md191206652021Animals, Aquatic Organisms, Cell Wall/chemistry, *Hyphomicrobiaceae, Magnetic Resonance Spectroscopy, Polysaccharides, Bacterial/*chemistry, Structure-Activity Relationship

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
30880Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172721028776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG