Cite this strain

Pseudophaeobacter arcticus (DSM 23566, CGMCC 1.6500, JCM 14644)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13733

Type strain

Strain Designation 20188

Culture col. no. DSM 23566 CGMCC 1.6500 JCM 14644 20188

NCBI tax ID(s) 999550 385492

Special Collections DSMZ JCM Literature strains

Links

Name and taxonomic classification

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

Gram-negative motile rod-shaped aerobe psychrophilic genome sequence 16S sequence Bacteria

SI-ID 408279

DSM 23566

Last LPSN update 2024-12-09 10:44:37

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Pseudophaeobacter

Species Pseudophaeobacter arcticus

Full scientific name Pseudophaeobacter arcticus (Zhang et al. 2008) Breider et al. 2014

Synonyms (1)

Phaeobacter arcticus

BacDive ID	Other strains from **Pseudophaeobacter arcticus** (3)	Type strain
175280	P. arcticus TrK17, DSM 110510
175281	P. arcticus pe03_e4, DSM 110729
175282	P. arcticus RW5_PP_4, DSM 110730

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
32569	negative	1.8 µm	0.4 µm	rod-shaped
125438	negative
125439	negative

Colony morphology

17288

Incubation period1-2 days

Multimedia

@ref:	66793
manual_annotation:	1
multimedia content:	EM_DSM_23566_1.jpg
multimedia.multimedia content:	EM_DSM_23566_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde

Pigmentation

32569

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17288	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17288	positive	growth	20	psychrophilic
32569	positive	growth	0-25
32569	positive	optimum	19.5	psychrophilic
67770	positive	growth	20	psychrophilic

Culture pH

@ref	Ability	Type	PH
32569	positive	optimum	7.5
32569	positive	growth	05-10

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32569	NaCl	positive	growth	02-09 %

Observation

67770

Observationquinones: Q-10

Spore formation

@ref	Spore formation	Confidence
125438		90.796
125439		94.9

Enzymes

@ref	Value	Activity	Ec
32569	alkaline phosphatase	+	3.1.3.1
17288	catalase	+	1.11.1.6
32569	catalase	+	1.11.1.6
32569	cytochrome oxidase	+	1.9.3.1
17288	cytochrome-c oxidase	+	1.9.3.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32569	22599 ChEBI	arabinose	+	carbon source
32569	28757 ChEBI	fructose	+	carbon source
32569	24265 ChEBI	gluconate	+	carbon source
32569	17234 ChEBI	glucose	+	carbon source
32569	17754 ChEBI	glycerol	+	carbon source
32569	25115 ChEBI	malate	+	carbon source
32569	17306 ChEBI	maltose	+	carbon source
32569	29864 ChEBI	mannitol	+	carbon source
32569	37684 ChEBI	mannose	+	carbon source
32569	506227 ChEBI	N-acetylglucosamine	+	carbon source

Oxygen tolerance

@ref	Oxygen tolerance
32569	aerobe
125439	obligate aerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Latitude	Longitude
17288	marine sediment	(75° 00' 24" N 169° 59' 37" W) at a depth of 167 m	75.0067	-169.994 75.0067/-169.994
67770	Marine sediment of the Arctic Ocean (75° 00' 24" N 169° 59' 37" W) at a depth of 167 m		75.0067	-169.994 75.0067/-169.994

Taxonmaps

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

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
17288	1	Risk group (German classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)	Method
17288	59.6	thermal denaturation, midpoint method (Tm)
32569	59.6
67770	59.27	genome sequence analysis

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17288	Phaeobacter arcticus strain 20188 16S ribosomal RNA gene, partial sequence	DQ514304	1425		999550

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Pseudophaeobacter arcticus DSM 23566	GCA_000473205	scaffold		999550
66792	Phaeobacter arcticus DSM 23566	999550.5	wgs	PATRIC	999550
66792	Pseudophaeobacter arcticus DSM 23566	2521172622	draft	JGI IMG/M	999550

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Pseudophaeobacter arcticus DSM 23566
NCBI: GCA_000473205

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.90	no
125439	motility	BacteriaNetⓘ	yes	72.40	no
125439	gram_stain	BacteriaNetⓘ	negative	97.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	91.20	no

Predictions from Diaspora project based on:
Pseudophaeobacter arcticus DSM 23566 DSM 23566
NCBI: GCA_000473205.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.32	yes
125438	anaerobic	anaerobicⓘ	no	92.42	no
125438	aerobic	aerobicⓘ	yes	80.73	no
125438	spore-forming	spore-formingⓘ	no	90.80	no
125438	thermophilic	thermophileⓘ	no	96.11	no
125438	flagellated	motile2+ⓘ	yes	51.04	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
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	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
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

Straininfo Link

@ref	Straininfo	Culture collections
82915	408279	DSM 23566

Culture collection no.

Culture collection no.
DSM 23566
CGMCC 1.6500
JCM 14644
20188

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 .
#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 )
#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 .

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