Name: Devosia naphthalenivorans CM5-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 164276

Type strain:

Species: Devosia naphthalenivorans

Strain Designation: CM5-1

Culture col. no.: JCM 32509, CGMCC 1.13553

Strain history: J. Chen; Zhejiang Wanli Univ., China; CM5-1.

NCBI tax ID(s): 2082392 (species)

Section

Devosia naphthalenivorans CM5-1 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Sediment sample from the East Pacific Ocean.

colony-forming
Gram-negative
rod-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Devosiaceae*
	Genus	*Devosia*
	Species	**Devosia naphthalenivorans**
	Full Scientific Name (LPSN)	Devosia naphthalenivorans Chen et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #67950]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.988

[Ref.: #67950]	Cell length	0.6-0.7 µm

[Ref.: #67950]	Cell width	0.2-0.3 µm

[Ref.: #67950]	Cell shape	rod-shaped

[Ref.: #67950]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %94.125

[Ref.: #67950]	Colony color	white
[Ref.: #67950]	Colony shape	circular
[Ref.: #67950]	Cultivation medium used	Marine agar (MA)

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #67770]	growth	30 °C
[Ref.: #67950]	growth	5-30 °C
[Ref.: #67950]	optimum	25 °C

[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67950]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #67950]			optimum	7
[Ref.: #67950]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67950]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.96
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #67950]		NaCl		growth	0-5	%(w/v)
[Ref.: #67950]		NaCl		optimum	3-4	%(w/v)

[Ref.: #67770]	Observation	quinones: Q-10
[Ref.: #67950]	Observation	The major isoprenoid quinone is Q-10
[Ref.: #67950]	Observation	polar lipids include diphosphatidylglycerol, phosphatidylglycerol, three glycolipids and four unidentified lipids

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #67950]	4-nitrophenyl beta-D-galactopyranoside ChEBI	+	degradation
[Ref.: #67950]	arginine ChEBI	+	reduction
[Ref.: #67950]	casein	-	hydrolysis
[Ref.: #67950]	esculin ChEBI	+	hydrolysis
[Ref.: #67950]	gelatin ChEBI	+	degradation
[Ref.: #67950]	nitrate ChEBI	+	reduction
[Ref.: #67950]	starch ChEBI	-	hydrolysis
[Ref.: #67950]	tween 20 ChEBI	-	hydrolysis
[Ref.: #67950]	tween 40 ChEBI	-	hydrolysis
[Ref.: #67950]	tween 60 ChEBI	-	hydrolysis
[Ref.: #67950]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #67950]	acid phosphatase	+	3.1.3.2
[Ref.: #67950]	alkaline phosphatase	+	3.1.3.1
[Ref.: #67950]	alpha-glucosidase	+	3.2.1.20
[Ref.: #67950]	alpha-mannosidase	+	3.2.1.24
[Ref.: #67950]	beta-galactosidase	+	3.2.1.23
[Ref.: #67950]	beta-glucosidase	+	3.2.1.21
[Ref.: #67950]	catalase	+	1.11.1.6
[Ref.: #67950]	cytochrome oxidase	+	1.9.3.1
[Ref.: #67950]	esterase (C 4)	+
[Ref.: #67950]	esterase Lipase (C 8)	+
[Ref.: #67950]	leucine arylamidase	+	3.4.11.1
[Ref.: #67950]	lipase (C 14)	+
[Ref.: #67950]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #67950]	trypsin	+	3.4.21.4
[Ref.: #67950]	urease	+	3.5.1.5
[Ref.: #67950]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #67770]	Sample type/isolated from	Sediment sample from the East Pacific Ocean

[Ref.: #67950]	Sample type/isolated from	sediment sample collected at a water depth of 5160 m
[Ref.: #67950]	Sampling date	2011-10
[Ref.: #67950]	Geographic location (country and/or sea, region)	Eastern Pacific Ocean
[Ref.: #67950]	Country	Pacific Ocean
[Ref.: #67950]	Geographic location	10.0490°/-154.2980°
* marker position based on {}

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67950]	Devosia naphthalenivorans 16S ribosomal RNA gene, partial sequence	MG230310	1404	ENA	2082392 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Devosia naphthalenivorans CM5-1	GCA_003056355	scaffold	GenBank	2082392 tax ID

[Ref.: #67770]

GC-content

61.4 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Devosia naphthalenivorans CM5-1 NCBI: GCA_003056355.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Devosia naphthalenivorans CM5-1 NCBI: GCA_003056355.1
[Ref.: #69480]	flagellated	no	83.392	no
[Ref.: #69480]	gram-positive	no	96.428	yes
[Ref.: #69480]	anaerobic	no	98.698	yes
[Ref.: #69480]	halophile	no	93.39	no
[Ref.: #69480]	spore-forming	no	95.139	no
[Ref.: #69480]	glucose-util	yes	90.023	no
[Ref.: #69480]	aerobic	yes	92.929	no
[Ref.: #69480]	thermophile	no	97.888	yes
[Ref.: #69480]	motile	yes	75.037	yes
[Ref.: #69480]	glucose-ferment	no	88.531	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 32509, CGMCC 1.13553

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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	*
Phylogeny	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	*

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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#67950

Yong Chen, Sidong Zhu, Danqiu Lin, Xing Wang, Jifang Yang, Jigang Chen: Devosia naphthalenivorans sp. nov., isolated from East Pacific Ocean sediment. IJSEM 69: 1974 - 1979 2019 ( DOI 10.1099/ijsem.0.003410 )

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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