Name: Oceanicella actignis CLW
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24525

Type strain:

Species: Oceanicella actignis

Strain Designation: CLW

Culture col. no.: DSM 24423, CGMCC 1.10808, LMG 26245, MCCC 1A06272

Strain history: <- D. Yin and X. Chen, Third Inst. Oceanography, State Oceanic Admin., China; CLW <- D. Yin

NCBI tax ID(s): 1189325 (species)

SI-ID 405591

DSM 24423

Special Collections

Other strains from Oceanicella actignis

Section

Oceanicella actignis CLW is an aerobe, Gram-negative, motile bacterium that was isolated from water from terrestrial hot spring.

Gram-negative
motile
rod-shaped
aerobe
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	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Oceanicella*
	Species	**Oceanicella actignis**
	Full Scientific Name (LPSN)	Oceanicella actignis Albuquerque et al. 2012

Synonym

Pleomorphobacterium xiamenense

Information on morphological and physiological properties Morphology

[Ref.: #30709]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98

[Ref.: #30709]	Cell length	1.75 µm

[Ref.: #30709]	Cell width	0.5 µm

[Ref.: #30709]	Cell shape	rod-shaped

[Ref.: #30709]	Motility	yes

[Ref.: #21254]

Incubation period

3-7 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21254]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #21254]

Culture medium growth

[Ref.: #21254]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21254]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21254]	growth	55 °C
[Ref.: #30709]	growth	28-65 °C
[Ref.: #30709]	optimum	54 °C

	pH	Kind of pH		pH
[Ref.: #30709]			optimum	7
[Ref.: #30709]			growth	5.5-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30709]

Oxygen tolerance

aerobe

[Ref.: #30709]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %94.119
[Ref.: #69481]	Ability of spore formation	no Confidence in %97

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30709]		NaCl		optimum	3.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30709]	acetate ChEBI	+	carbon source
[Ref.: #30709]	alanine ChEBI	+	carbon source
[Ref.: #30709]	leucine ChEBI	+	carbon source
[Ref.: #30709]	malonate ChEBI	+	carbon source
[Ref.: #30709]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #30709]	nitrate ChEBI	+	reduction
[Ref.: #30709]	serine ChEBI	+	carbon source
[Ref.: #30709]	sorbitol ChEBI	+	carbon source
[Ref.: #30709]	succinate ChEBI	+	carbon source
[Ref.: #30709]	tween 40 ChEBI	+	carbon source
[Ref.: #30709]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30709]	acid phosphatase	+	3.1.3.2
[Ref.: #30709]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30709]	catalase	+	1.11.1.6
[Ref.: #30709]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30709]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	purine metabolism	78.72	74 of 94
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
		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.: #21254]	Sample type/isolated from	water from terrestrial hot spring
[Ref.: #21254]	Geographic location (country and/or sea, region)	Fujian Province, Xiamen city (24° 34' N 118° 04' E)
[Ref.: #21254]	Country	China
[Ref.: #21254]	Country ISO 3 Code	CHN
[Ref.: #21254]	Continent	Asia
[Ref.: #21254]	Geographic location	24.5667°/118.0670°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Thermal spring
#Environmental	#Terrestrial	-
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ709062 (>99% sequence identity) for Oceanicella actignis subclade from Microbeatlas

Aquatic Samples	191
Soil Samples	91
Animal Samples	37
Plant Samples	12
Total Samples	331

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #21254]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #21254]	Pleomorphobacterium xiamenense strain CLW 16S ribosomal RNA gene, partial sequence	HQ709062	1432	GenBank ENA	1189325 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Oceanicella actignis DSM 24423	GCA_900111545	scaffold	GenBank ENA	1189325 tax ID	*
[Ref.: #66792]	Oceanicella actignis CGMCC 1.10808	GCA_900143155	scaffold	GenBank ENA	1189325 tax ID	*
[Ref.: #66792]	Pleomorphobacterium xiamenense strain CGMCC 1.10808	1234555.4	wgs	PATRIC	1189325 tax ID	*
[Ref.: #66792]	Pleomorphobacterium xiamenense strain DSM 24423	1234555.3	wgs	PATRIC	1189325 tax ID	*
[Ref.: #66792]	Oceanicella actignis DSM 24423	2615840710	draft	JGI IMG/M	1189325 tax ID	*
[Ref.: #66792]	Oceanicella actignis CGMCC 1.10808	2663762749	draft	JGI IMG/M	1189325 tax ID	*

[Ref.: #21254]	GC-content	72.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30709]	GC-content	72.2 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Oceanicella actignis DSM 24423 NCBI: GCA_900111545.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	97	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Oceanicella actignis DSM 24423 NCBI: GCA_900111545.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	91.954	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	78.752	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	94.119	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	65.863	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	67.163	no

Availability in culture collections External links

[Ref.: #21254]

Culture collection no.

DSM 24423, CGMCC 1.10808, LMG 26245, MCCC 1A06272

[Ref.: #88380]

SI-ID 405591

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pleomorphobacterium xiamenense gen. nov., sp. nov., a moderate thermophile isolated from a terrestrial hot spring.	Yin D, Chen L, Ao J, Ai C, Chen X	Int J Syst Evol Microbiol	10.1099/ijs.0.042713-0	2012	*

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 )

#21254

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24423

#30709

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 #27040 (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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#69479

João 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 beta .

#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 )

#88380

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID405591.1 )

#27040

IJSEM 1868 2013 ( DOI 10.1099/ijs.0.042713-0 , PubMed 23041633 )

* These data were automatically processed and therefore are not curated

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Oceanicella actignis DSM 24423

Oceanicella actignis DSM 24423

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