Pseudooceanicola nanhaiensis SS011B1-20 | Type strain | DSM 18065, CGMCC 1.6293, LMG 23508, CIP 109530 | BacDiveID:13688

Strain identifier

BacDive ID: 13688

Type strain:

Species: Pseudooceanicola nanhaiensis

Strain Designation: SS011B1-20

Culture col. no.: DSM 18065, CGMCC 1.6293, LMG 23508, CIP 109530

Strain history: CIP <- 2007, X.L. Wu, Tsinghua Univ., Beijing, China: strain SS011B1-20

NCBI tax ID(s): 1122614 (strain), 375761 (species)

SI-ID 290411

LMG 23508, CGMCC 1.6293, DSM 18065, KCTC 22754, CECT 7831, CIP 109530

Section

Pseudooceanicola nanhaiensis SS011B1-20 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediments at a depth of around 1500 m.

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	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Pseudooceanicola*
	Species	**Pseudooceanicola nanhaiensis**
	Full Scientific Name (LPSN)	Pseudooceanicola nanhaiensis (Gu et al. 2007) Lai et al. 2015

Synonym

Oceanicola nanhaiensis

Information on morphological and physiological properties Morphology

[Ref.: #31853]	Gram stain	negative
[Ref.: #121232]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.989

[Ref.: #31853]	Cell length	0.8 µm

[Ref.: #31853]	Cell width	0.5 µm

[Ref.: #31853]	Cell shape	rod-shaped
[Ref.: #121232]	Cell shape	rod-shaped

[Ref.: #31853]	Motility	no
[Ref.: #121232]	Motility	no

Pigment production

yes

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

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

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

Marine agar (MA)

Culture medium growth

Culture medium composition

expand / minimize

[Ref.: #121232]

Culture medium

CIP Medium 13

[Ref.: #121232]

Culture medium growth

[Ref.: #121232]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #7358]			growth	30 °C
[Ref.: #31853]			growth	10-37 °C
[Ref.: #31853]			optimum	28 °C
[Ref.: #41993]			growth	30 °C

[Ref.: #7358]	Temperature range	mesophilic
[Ref.: #31853]	Temperature range	mesophilic
[Ref.: #41993]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31853]			optimum	7.5-8
[Ref.: #31853]			growth	6-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31853]	Oxygen tolerance	aerobe
[Ref.: #121232]	Oxygen tolerance	obligate aerobe

[Ref.: #31853]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31853]		NaCl		growth	0-10	%
[Ref.: #31853]		NaCl		optimum	02-03	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31853]		acetate ChEBI	+	carbon source
[Ref.: #31853]		cellobiose ChEBI	+	carbon source
[Ref.: #31853]		citrate ChEBI	+	carbon source
[Ref.: #31853]		dextrin ChEBI	+	carbon source
[Ref.: #31853]		ethanol ChEBI	+	carbon source
[Ref.: #31853]		fructose ChEBI	+	carbon source
[Ref.: #31853]		galactose ChEBI	+	carbon source
[Ref.: #31853]		gluconate ChEBI	+	carbon source
[Ref.: #31853]		glucose ChEBI	+	carbon source
[Ref.: #31853]		lactose ChEBI	+	carbon source
[Ref.: #31853]		malonate ChEBI	+	carbon source
[Ref.: #31853]		mannitol ChEBI	+	carbon source
[Ref.: #31853]		nitrate ChEBI	+	reduction
[Ref.: #121232]		nitrate ChEBI	-	reduction
[Ref.: #121232]		nitrite ChEBI	-	reduction
[Ref.: #31853]		pyruvate ChEBI	+	carbon source
[Ref.: #31853]		ribose ChEBI	+	carbon source
[Ref.: #31853]		sorbitol ChEBI	+	carbon source
[Ref.: #31853]		succinate ChEBI	+	carbon source
[Ref.: #31853]		sucrose ChEBI	+	carbon source
		Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #121232]		indole ChEBI	no

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #68382]		acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]		alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]		alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]		alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]		alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]		alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]		alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]		beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]		beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]		beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31853]		catalase	+	1.11.1.6
[Ref.: #121232]		catalase	+	1.11.1.6
[Ref.: #68382]		cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #31853]		cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]		esterase (C 4)	+		* from API zym
[Ref.: #68382]		esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]		leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]		lipase (C 14)	-		* from API zym
[Ref.: #68382]		N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]		naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121232]		oxidase	+
[Ref.: #68382]		trypsin	-	3.4.21.4	* from API zym
[Ref.: #121232]		urease	+	3.5.1.5
[Ref.: #68382]		valine arylamidase	+		* from API zym
		Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #121232]	11933	-	+	+	+	-	+	+	+	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #7358]	Sample type/isolated from	sediments at a depth of around 1500 m
[Ref.: #7358]	Geographic location (country and/or sea, region)	South China Sea
[Ref.: #7358]	Country	China
[Ref.: #7358]	Country ISO 3 Code	CHN
[Ref.: #7358]	Continent	Asia

[Ref.: #121232]	Sample type/isolated from	Environment, Sea, sediment
[Ref.: #121232]	Geographic location (country and/or sea, region)	China Sea
[Ref.: #121232]	Country	China
[Ref.: #121232]	Country ISO 3 Code	CHN
[Ref.: #121232]	Continent	Asia
[Ref.: #121232]	Isolation date	2004
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Core sample
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

Global distribution of 16S sequence DQ414420 (>99% sequence identity) for Pseudooceanicola nanhaiensis subclade from Microbeatlas

Aquatic Samples	1754
Soil Samples	111
Animal Samples	189
Plant Samples	8
Total Samples	2062

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

[Ref.: #7358]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121232]	Biosafety level	1	Risk group (French classification)

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.: #7358]	Oceanicola nanhaiensis strain SS011B1-20 16S ribosomal RNA gene, partial sequence	DQ414420	1427	ENA	375761 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudooceanicola nanhaiensis DSM 18065	GCA_000688295	contig	GenBank	1122614 tax ID	*
[Ref.: #66792]	Pseudooceanicola nanhaiensis CGMCC 1.6293	GCA_014645095	scaffold	GenBank	375761 tax ID	*
[Ref.: #66792]	Oceanicola nanhaiensis DSM 18065	1122614.3	wgs	PATRIC	1122614 tax ID	*
[Ref.: #66792]	Pseudooceanicola nanhaiensis strain CGMCC 1.6293	375761.4	wgs	PATRIC	375761 tax ID	*
[Ref.: #66792]	Pseudooceanicola nanhaiensis DSM 18065	2558309102	draft	JGI IMG/M	1122614 tax ID	*

GC-content

64.7 mol%

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: Oceanicola nanhaiensis DSM 18065 PATRIC: 1122614.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Oceanicola nanhaiensis DSM 18065 PATRIC: 1122614.3
[Ref.: #69480]	motile	no	84.428	no
[Ref.: #69480]	flagellated	no	93.988	yes
[Ref.: #69480]	gram-positive	no	97.87	yes
[Ref.: #69480]	anaerobic	no	97.844	yes
[Ref.: #69480]	aerobic	yes	87.945	no
[Ref.: #69480]	halophile	yes	67.156	no
[Ref.: #69480]	spore-forming	no	96.431	yes
[Ref.: #69480]	glucose-util	yes	88.539	yes
[Ref.: #69480]	thermophile	no	98.761	yes
[Ref.: #69480]	glucose-ferment	no	90.786	no

Availability in culture collections External links

Culture collection no.

DSM 18065, CGMCC 1.6293, LMG 23508, CIP 109530

SI-ID 290411

*

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudooceanicola pacificus sp. nov., isolated from deep-sea sediment of the Pacific Ocean.	Lyu L, Lai Q, Li J, Shao Z, Yu Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.004298	2020	*
Phylogeny	Pseudooceanicola atlanticus gen. nov. sp. nov., isolated from surface seawater of the Atlantic Ocean and reclassification of Oceanicola batsensis, Oceanicola marinus, Oceanicola nitratireducens, Oceanicola nanhaiensis, Oceanicola antarcticus and Oceanicola flagellatus, as Pseudooceanicola batsensis comb. nov., Pseudooceanicola marinus comb. nov., Pseudooceanicola nitratireducens comb. nov., Pseudooceanicola nanhaiensis comb. nov., Pseudooceanicola antarcticus comb. nov., and Pseudooceanicola flagellatus comb. nov.	Lai Q, Li G, Liu X, Du Y, Sun F, Shao Z	Antonie Van Leeuwenhoek	10.1007/s10482-015-0398-2	2015	*
Phylogeny	Oceanicola nitratireducens sp. nov., a marine alphaproteobacterium isolated from the South China Sea.	Zheng Q, Chen C, Wang YN, Jiao N	Int J Syst Evol Microbiol	10.1099/ijs.0.016311-0	2009	*
Phylogeny	Oceanicola pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium.	Yuan J, Lai Q, Wang B, Sun F, Liu X, Du Y, Li G, Gu L, Zheng T, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.003400-0	2009	*
Phylogeny	Oceanicola marinus sp. nov., a marine alphaproteobacterium isolated from seawater collected off Taiwan.	Lin KY, Sheu SY, Chang PS, Cho JC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.65020-0	2007	*
Phylogeny	Oceanicola nanhaiensis sp. nov., isolated from sediments of the South China Sea.	Gu J, Guo B, Wang YN, Yu SL, Inamori R, Qu R, Ye YG, Wu XL	Int J Syst Evol Microbiol	10.1099/ijs.0.64532-0	2007	*

References

#7358

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18065

#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 )

#31853

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 #28117 (see below)

#41993 ; Curators of the CIP;

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#68382

Automatically annotated from API zym .

#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 )

#82871

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-ID290411.1 )

#121232 Collection of Institut Pasteur ; Curators of the CIP; CIP 109530

#28117

IJSEM 157 2007 ( DOI 10.1099/ijs.0.64532-0 , PubMed 17220459 )

* These data were automatically processed and therefore are not curated

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