Name: Pseudophaeobacter arcticus 20188
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13733

Type strain:

Species: Pseudophaeobacter arcticus

Strain Designation: 20188

Culture col. no.: DSM 23566, CGMCC 1.6500, JCM 14644

Strain history: D.-C. Zhang et al. 20188.

NCBI tax ID(s): 999550 (strain), 385492 (species)

SI-ID 408279

DSM 23566

Section

Pseudophaeobacter arcticus 20188 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from marine sediment.

Gram-negative
motile
rod-shaped
aerobe
psychrophilic
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	*Pseudophaeobacter*
	Species	**Pseudophaeobacter arcticus**
	Full Scientific Name (LPSN)	Pseudophaeobacter arcticus (Zhang et al. 2008) Breider et al. 2014

Synonym

Phaeobacter arcticus

Information on morphological and physiological properties Morphology

[Ref.: #32569]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #32569]	Cell length	1.8 µm

[Ref.: #32569]	Cell width	0.4 µm

[Ref.: #32569]	Cell shape	rod-shaped

[Ref.: #32569]	Motility	yes

[Ref.: #17288]

Incubation period

1-2 days

[Ref.: #32569]

Pigment production

yes

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17288]

Culture medium

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

[Ref.: #17288]

Culture medium growth

[Ref.: #17288]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17288]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17288]	growth	20 °C
[Ref.: #32569]	growth	0-25 °C
[Ref.: #32569]	optimum	19.5 °C
[Ref.: #67770]	growth	20 °C

[Ref.: #17288]	Temperature range	psychrophilic
[Ref.: #32569]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #32569]			optimum	7.5
[Ref.: #32569]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32569]

Oxygen tolerance

aerobe

[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.: #32569]		NaCl		growth	02-09	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32569]	arabinose ChEBI	+	carbon source
[Ref.: #32569]	fructose ChEBI	+	carbon source
[Ref.: #32569]	gluconate ChEBI	+	carbon source
[Ref.: #32569]	glucose ChEBI	+	carbon source
[Ref.: #32569]	glycerol ChEBI	+	carbon source
[Ref.: #32569]	malate ChEBI	+	carbon source
[Ref.: #32569]	maltose ChEBI	+	carbon source
[Ref.: #32569]	mannitol ChEBI	+	carbon source
[Ref.: #32569]	mannose ChEBI	+	carbon source
[Ref.: #32569]	N-acetylglucosamine ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32569]	alkaline phosphatase	+	3.1.3.1
[Ref.: #17288]	catalase	+	1.11.1.6
[Ref.: #32569]	catalase	+	1.11.1.6
[Ref.: #32569]	cytochrome oxidase	+	1.9.3.1
[Ref.: #17288]	cytochrome-c oxidase	+	1.9.3.1

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

[Ref.: #17288]	Sample type/isolated from	marine sediment
[Ref.: #17288]	Geographic location (country and/or sea, region)	(75° 00' 24" N 169° 59' 37" W) at a depth of 167 m
[Ref.: #17288]	Geographic location	75.0067°/-169.9940°

[Ref.: #67770]	Sample type/isolated from	Marine sediment of the Arctic Ocean (75° 00' 24" N 169° 59' 37" W) at a depth of 167 m
[Ref.: #67770]	Geographic location	75.0067°/-169.9940°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ514304 (>99% sequence identity) for Pseudophaeobacter arcticus from Microbeatlas

Aquatic Samples	483
Soil Samples	31
Animal Samples	41
Plant Samples	4
Total Samples	559

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

[Ref.: #17288]

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.: #17288]	Phaeobacter arcticus strain 20188 16S ribosomal RNA gene, partial sequence	DQ514304	1425	ENA	999550 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudophaeobacter arcticus DSM 23566	GCA_000473205	scaffold	GenBank	999550 tax ID	*
[Ref.: #66792]	Phaeobacter arcticus DSM 23566	999550.5	wgs	PATRIC	999550 tax ID	*
[Ref.: #66792]	Pseudophaeobacter arcticus DSM 23566	2521172622	draft	JGI IMG/M	999550 tax ID	*

[Ref.: #17288]	GC-content	59.6 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #32569]	GC-content	59.6 mol%
[Ref.: #67770]	GC-content	59.27 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: Pseudophaeobacter arcticus DSM 23566 DSM 23566 NCBI: GCA_000473205.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudophaeobacter arcticus DSM 23566 DSM 23566 NCBI: GCA_000473205.1
[Ref.: #69480]	motile	yes	75.434	yes
[Ref.: #69480]	flagellated	no	76.379	no
[Ref.: #69480]	gram-positive	no	98.185	yes
[Ref.: #69480]	anaerobic	no	99.359	yes
[Ref.: #69480]	aerobic	yes	90.181	no
[Ref.: #69480]	halophile	yes	75.333	no
[Ref.: #69480]	spore-forming	no	94.851	no
[Ref.: #69480]	thermophile	no	98.183	yes
[Ref.: #69480]	glucose-util	yes	70.363	yes
[Ref.: #69480]	glucose-ferment	no	90.985	no

Availability in culture collections External links

[Ref.: #17288]

Culture collection no.

DSM 23566, CGMCC 1.6500, JCM 14644

[Ref.: #82915]

SI-ID 408279

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudophaeobacter flagellatus sp. nov., isolated from coastal water.	Guan Y, Jiang Y, Kim YM, Yu SY, Choi SH, Choe H, Li Z, Lee MK	Int J Syst Evol Microbiol	10.1099/ijsem.0.005399	2022	*
Phylogeny	Phaeobacter marinintestinus sp. nov., isolated from the intestine of a sea cucumber (Apostichopus japonicus).	Lee MH, Song EJ, Seo MJ, Hyun DW, Bae JW, Lee SY, Roh SW, Nam YD	Antonie Van Leeuwenhoek	10.1007/s10482-014-0318-x	2014	*
Genetics	Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T.).	Freese HM, Dalingault H, Petersen J, Pradella S, Davenport K, Teshima H, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Brinkhoff T, Goker M, Overmann J, Klenk HP	Stand Genomic Sci	10.4056/sigs.383362	2013	*
Phylogeny	Phaeobacter arcticus sp. nov., a psychrophilic bacterium isolated from the Arctic.	Zhang DC, Li HR, Xin YH, Liu HC, Chi ZM, Zhou PJ, Yu Y	Int J Syst Evol Microbiol	10.1099/ijs.0.65708-0	2008	*

References

#17288

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23566

#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 )

#32569

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 #28784 (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) .

#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 )

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

#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 )

#82915

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-ID408279.1 )

#28784

IJSEM 1384 2008 ( DOI 10.1099/ijs.0.65708-0 , PubMed 18523182 )

* These data were automatically processed and therefore are not curated

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Pseudophaeobacter arcticus DSM 23566 DSM 23566

Pseudophaeobacter arcticus DSM 23566 DSM 23566

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