Oceanicaulis alexandrii C116-18 | Type strain | DSM 11625, NCIMB 13905, CIP 108206 | BacDiveID:6213

Strain identifier

BacDive ID: 6213

Type strain:

Species: Oceanicaulis alexandrii

Strain Designation: C116-18

Culture col. no.: DSM 11625, NCIMB 13905, CIP 108206

Strain history: CIP <- 2003, NCIMB

NCBI tax ID(s): 1122613 (strain), 153233 (species)

SI-ID 128003

DSM 11625, NCIMB 13905, KCTC 12475, CIP 108206

Special Collections

DSMZ
CIP

Other strains from Oceanicaulis alexandrii

Section

When using BacDive for research please cite our paper

Oceanicaulis alexandrii C116-18 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from culture of Alexandrium tamarense.

Gram-negative
rod-shaped
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Caulobacterales*
	Family	*Maricaulaceae*
	Genus	*Oceanicaulis*
	Species	**Oceanicaulis alexandrii**
	Full Scientific Name (LPSN)	Oceanicaulis alexandrii Strömpl et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #116216]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98.328
[Ref.: #125439]	Gram stain	negative Confidence in %99.8

[Ref.: #116216]	Cell shape	rod-shaped

[Ref.: #116216]	Motility	no

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.: #116216]

Culture medium

CIP Medium 13

[Ref.: #116216]

Culture medium growth

[Ref.: #116216]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #4426]			growth	30 °C
[Ref.: #33212]			growth	30 °C
[Ref.: #116216]			growth	10-37 °C
[Ref.: #116216]		negative	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %92

[Ref.: #125438]	Ability of spore formation	no Confidence in %92.757
[Ref.: #125439]	Ability of spore formation	no Confidence in %99.3

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #116216]		NaCl	no	growth	0	%
[Ref.: #116216]		NaCl	no	growth	2	%
[Ref.: #116216]		NaCl	no	growth	4	%
[Ref.: #116216]		NaCl	no	growth	6	%
[Ref.: #116216]		NaCl	no	growth	8	%
[Ref.: #116216]		NaCl	no	growth	10	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #116216]		citrate ChEBI	-	carbon source
[Ref.: #116216]		esculin ChEBI	-	hydrolysis
[Ref.: #116216]		nitrate ChEBI	-	reduction
[Ref.: #116216]		nitrate ChEBI	-	respiration
[Ref.: #116216]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #116216]		indole ChEBI	no

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #68382]		acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #116216]		alcohol dehydrogenase	-	1.1.1.1
[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.: #116216]		amylase	-
[Ref.: #116216]		beta-galactosidase	-	3.2.1.23
[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.: #116216]		caseinase	-	3.4.21.50
[Ref.: #116216]		catalase	+	1.11.1.6
[Ref.: #68382]		cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]		esterase (C 4)	+		* from API zym
[Ref.: #68382]		esterase lipase (C 8)	+		* from API zym
[Ref.: #116216]		gelatinase	+/-
[Ref.: #116216]		lecithinase	-
[Ref.: #68382]		leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #116216]		lipase	-
[Ref.: #68382]		lipase (C 14)	-		* from API zym
[Ref.: #116216]		lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]		N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]		naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116216]		ornithine decarboxylase	-	4.1.1.17
[Ref.: #116216]		oxidase	+
[Ref.: #68382]		trypsin	+	3.4.21.4	* from API zym
[Ref.: #116216]		tryptophan deaminase	-
[Ref.: #116216]		tween esterase	-
[Ref.: #116216]		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.: #116216]	10983	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	-	-	-	-

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

[Ref.: #4426]	Sample type/isolated from	culture of Alexandrium tamarense
[Ref.: #4426]	Host species	Alexandrium tamarense
[Ref.: #4426]	Geographic location (country and/or sea, region)	North Sea
[Ref.: #4426]	Country	United Kingdom
[Ref.: #4426]	Country ISO 3 Code	GBR
[Ref.: #4426]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Laboratory	#Lab enrichment
#Host	#Protozoa	#Dinoflagellate

What are isolation sources categories?

Global distribution of 16S sequence AJ309862 (>99% sequence identity) for Oceanicaulis alexandrii from Microbeatlas

Aquatic Samples	1879
Soil Samples	88
Animal Samples	101
Plant Samples	13
Total Samples	2081

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

[Ref.: #4426]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116216]	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.: #4426]	Oceanicaulis alexandrii 16S rRNA gene, strain C116-18	AJ309862	1424	GenBank ENA	153233 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Oceanicaulis alexandrii DSM 11625	GCA_000420265	contig	GenBank ENA	1122613 tax ID	*
[Ref.: #66792]	Oceanicaulis alexandrii DSM 11625	1122613.3	wgs	PATRIC	1122613 tax ID	*
[Ref.: #66792]	Oceanicaulis alexandrii DSM 11625	2523533582	draft	JGI IMG/M	1122613 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Oceanicaulis alexandrii DSM 11625 PATRIC: 1122613.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.328	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	91.385	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	92.757	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	85.191	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	91.539	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	67.373	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Oceanicaulis alexandrii DSM 11625 NCBI: GCA_000420265
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.3
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	80
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	92

Availability in culture collections External links

Culture collection no.

DSM 11625, NCIMB 13905, CIP 108206

SI-ID 128003

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Euryhalocaulis caribicus gen. nov., sp. nov., a new member [corrected] of the family Hyphomonadaceae isolated from the Caribbean Sea.	Deng W, Zhang Y, Xie X, Zhao Z, Fu Y	Curr Microbiol	10.1007/s00284-013-0314-9	2013	*
Phylogeny	Cauliform bacteria lacking phospholipids from an abyssal hydrothermal vent: proposal of Glycocaulis abyssi gen. nov., sp. nov., belonging to the family Hyphomonadaceae.	Abraham WR, Lunsdorf H, Vancanneyt M, Smit J	Int J Syst Evol Microbiol	10.1099/ijs.0.047894-0	2012	*
Phylogeny	Oceanicaulis stylophorae sp. nov., isolated from the reef-building coral Stylophora pistillata.	Chen MH, Sheu SY, Chen CA, Wang JT, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.036780-0	2011	*
Phylogeny	Oceanicaulis alexandrii gen. nov., sp. nov., a novel stalked bacterium isolated from a culture of the dinoflagellate Alexandrium tamarense (Lebour) Balech.	Strompl C, Hold GL, Lunsdorf H, Graham J, Gallacher S, Abraham WR, Moore ER, Timmis KN	Int J Syst Evol Microbiol	10.1099/ijs.0.02635-0	2003	*

References

#4426

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11625

#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 )

#33212 ; 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 .

#75692

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-ID128003.1 )

#116216 Collection of Institut Pasteur ; Curators of the CIP; CIP 108206

#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 .

* These data were automatically processed and therefore are not curated

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