Cite this strain

Devosia submarina (NRIC 0884, JCM 18935, KMM 9415)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133922

Type strain

Culture col. no. NRIC 0884 JCM 18935 KMM 9415

NCBI tax ID(s) 1173082

Special Collections JCM Literature strains

Links

Name and taxonomic classification

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

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

Culture Collection Numbers

NRIC 0884 JCM 18935 KMM 9415

Last LPSN update 2024-12-09 10:49:19

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Devosiaceae

Genus Devosia

Species Devosia submarina

Full scientific name Devosia submarina Romanenko et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
30880	negative	1.6 µm	1 µm	rod-shaped
125438	negative
125439	negative

Pigmentation

30880

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
30880	positive	growth	05-38
30880	positive	optimum	29
67770	positive	growth	25

Culture pH

@ref	Ability	Type	PH
30880	positive	optimum	7.5
30880	positive	growth	6.0-9.0

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30880	NaCl	positive	growth	0-5 %
30880	NaCl	positive	optimum	1.5 %

Observation

67770

Observationquinones: Q-10

Spore formation

@ref	Spore formation	Confidence
125438		90.29
125439		93.9

Enzymes

@ref	Value	Activity	Ec
30880	acid phosphatase	+	3.1.3.2
30880	alkaline phosphatase	+	3.1.3.1
30880	catalase	+	1.11.1.6
30880	cytochrome oxidase	+	1.9.3.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30880	16808 ChEBI	2-dehydro-D-gluconate	+	carbon source
30880	4853 ChEBI	esculin	+	hydrolysis
30880	26271 ChEBI	proline	+	carbon source

Oxygen tolerance

@ref	Oxygen tolerance
30880	aerobe
125439	obligate aerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type
30880	marine sediment
67770	Deep surface-sediment sample collected from the Sea of Japan

Safety information

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30880	Devosia submarina gene for 16S ribosomal RNA, partial sequence, strain: Sl74	AB712348	1442		1173082

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Devosia submarina JCM 18935	GCA_003056345	contig		1173082
66792	Devosia submarina strain JCM 18935	1173082.4	wgs	PATRIC	1173082
66792	Devosia submarina JCM 18935	2848589509	draft	JGI IMG/M	1173082

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Devosia submarina JCM 18935
NCBI: GCA_003056345

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.20	no
125439	gram_stain	BacteriaNetⓘ	negative	95.70	no
125439	motility	BacteriaNetⓘ	yes	60.80	no
125439	spore_formation	BacteriaNetⓘ	no	93.90	no

Predictions from Diaspora project based on:
Devosia submarina strain JCM 18935
PATRIC: 1173082.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.97	yes
125438	anaerobic	anaerobicⓘ	no	97.02	yes
125438	spore-forming	spore-formingⓘ	no	90.29	no
125438	aerobic	aerobicⓘ	yes	83.12	no
125438	thermophilic	thermophileⓘ	no	95.56	yes
125438	flagellated	motile2+ⓘ	yes	64.13	no

External links

Literature

Title	Authors	Journal	DOI	Year
Structure of the Cell-Wall-Associated Polysaccharides from the Deep-Sea Marine Bacterium Devosia submarina KMM 9415(T).	Kokoulin MS, Romanenko LA, Kuzmich AS, Chernikov O	Mar Drugs	10.3390/md19120665	2021
Devosia beringensis sp. nov., isolated from surface sediment of the Bering Sea.	Zhang YX, Yu Y, Luo W, Zeng YX, Du ZJ, Li HR	Int J Syst Evol Microbiol	10.1099/ijsem.0.004995	2021
Devosia 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 CO	Curr Microbiol	10.1007/s00284-021-02515-8	2021
Devosia submarina sp. nov., isolated from deep-sea surface sediments.	Romanenko LA, Tanaka N, Svetashev VI	Int J Syst Evol Microbiol	10.1099/ijs.0.046607-0	2013
Devosia naphthalenivorans sp. nov., isolated from East Pacific Ocean sediment.	Chen Y, Zhu S, Lin D, Wang X, Yang J, Chen J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003410	2019

Culture collection no.

Culture collection no.
NRIC 0884
JCM 18935
KMM 9415

References

#20215	Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#30880	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27210 (see below)
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

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