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

Name: 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

History <- JCM <- D.-C. Zhang, Ocean Univ. China, Qingdao, P. R. China; strain 20188 D.-C. Zhang et al. 20188.

Links

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

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

Name and taxonomic classification

SI-ID 408279

JCM 14644,DSM 23566

@ref 20215

Last LPSN update 2026-02-09 11:21:13

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	Confidence
32569	negative	1.8 µm	0.4 µm	rod-shaped
125438	negative				97.315
125439	negative				97.1

Colony morphology

17288

Incubation period1-2 days

Pigmentation

32569

Productionyes

Multimedia

@ref:	66793
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
manual_annotation:	1

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)
17288	positive	growth	20
32569	positive	growth	0-25
32569	positive	optimum	19.5
67770	positive	growth	20

Culture pH

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

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32569	aerobe
125439	obligate aerobe	91.2

Spore formation

@ref	Spore formation	Confidence
125438		90.796
125439		94.9

Halophily

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

Observation

67770

Observationquinones: Q-10

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

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

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

Interaction and safety

Risk assessment

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

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM47320v1 assembly for Pseudophaeobacter arcticus DSM 23566	scaffold	GCA_000473205	999550.5	2521172622	999550	77.59
124043	ASM4265980v1 assembly for Pseudophaeobacter arcticus CGMCC-1.6500	scaffold	GCA_042659805			385492	67.56
124043	ASM4265136v1 assembly for Pseudophaeobacter arcticus CGMCC 1.6500	contig	GCA_042651365			385492	59.95

16S sequences

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

GC content

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

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 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 bacterial phenotypic traits through improved machine learning using high-quality, curated datasets 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

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Impact of Fertilisation on the Bacterial Core Microbiome of Grassland Soils: Abundance in the Field and Growth In Vitro.	Chamedjeu RR, Jani K, Jetter K, Wilhelm K, Schafer P, Wilfert L, Sommer S, Riedel CU.	Environ Microbiol Rep	10.1111/1758-2229.70235	2025
Metabolism	Ribosomally derived lipopeptides containing distinct fatty acyl moieties.	Hubrich F, Bosch NM, Chepkirui C, Morinaka BI, Rust M, Gugger M, Robinson SL, Vagstad AL, Piel J.	Proc Natl Acad Sci U S A	10.1073/pnas.2113120119	2022
	Engineering lanthipeptides by introducing a large variety of RiPP modifications to obtain new-to-nature bioactive peptides.	Fu Y, Xu Y, Ruijne F, Kuipers OP.	FEMS Microbiol Rev	10.1093/femsre/fuad017	2023
	Genome Sequence and Characterization of a Xanthorhodopsin-Containing, Aerobic Anoxygenic Phototrophic Rhodobacter Species, Isolated from Mesophilic Conditions at Yellowstone National Park.	Kyndt JA, Robertson S, Shoffstall IB, Ramaley RF, Meyer TE.	Microorganisms	10.3390/microorganisms10061169	2022
Metabolism	Biofilm plasmids with a rhamnose operon are widely distributed determinants of the 'swim-or-stick' lifestyle in roseobacters.	Michael V, Frank O, Bartling P, Scheuner C, Goker M, Brinkmann H, Petersen J.	ISME J	10.1038/ismej.2016.30	2016
Enzymology	Characterization of the antagonistic potential of the glyphosate-tolerant Pseudomonas resinovorans SZMC 25872 strain against the plant pathogenic bacterium Agrobacterium tumefaciens.	Zhumakayev AR, Varga M, Voros M, Kocsube S, Ramteke PW, Szekeres A, Vagvolgyi C, Hatvani L, Marik T.	Front Plant Sci	10.3389/fpls.2022.1034237	2022
	Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater.	Liu J, Xue CX, Wang J, Crombie AT, Carrion O, Johnston AWB, Murrell JC, Liu J, Zheng Y, Zhang XH, Todd JD.	Microbiome	10.1186/s40168-022-01304-0	2022
	Plasmids of Psychrotolerant Polaromonas spp. Isolated From Arctic and Antarctic Glaciers - Diversity and Role in Adaptation to Polar Environments.	Ciok A, Budzik K, Zdanowski MK, Gawor J, Grzesiak J, Decewicz P, Gromadka R, Bartosik D, Dziewit L.	Front Microbiol	10.3389/fmicb.2018.01285	2018
Metabolism	Biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms.	Widderich N, Hoppner A, Pittelkow M, Heider J, Smits SH, Bremer E.	PLoS One	10.1371/journal.pone.0093809	2014
Enzymology	Effects of dietary fat source and subtherapeutic levels of antibiotic on the bacterial community in the ileum of broiler chickens at various ages.	Knarreborg A, Simon MA, Engberg RM, Jensen BB, Tannock GW.	Appl Environ Microbiol	10.1128/aem.68.12.5918-5924.2002	2002
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
	Pseudophaeobacter profundi sp. nov., isolated from the Western Pacific Ocean.	Zhu X, Wang L, Lai Q, Wang J, Huang J, Li G, Zeng L, Xia J, Shao Z.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006071	2023
Phylogeny	Belliella kenyensis sp. nov., isolated from an alkaline lake.	Akhwale JK, Goker M, Rohde M, Schumann P, Klenk HP, Boga HI.	Int J Syst Evol Microbiol	10.1099/ijs.0.066951-0	2015
Phylogeny	Octadecabacter jejudonensis sp. nov., isolated from the junction between the ocean and a freshwater spring and emended description of the genus Octadecabacter.	Park S, Yoon JH.	Int J Syst Evol Microbiol	10.1099/ijs.0.057513-0	2014
Phylogeny	Psychrobacter okhotskensis sp. nov., a lipase-producing facultative psychrophile isolated from the coast of the Okhotsk Sea.	Yumoto I, Hirota K, Sogabe Y, Nodasaka Y, Yokota Y, Hoshino T.	Int J Syst Evol Microbiol	10.1099/ijs.0.02686-0	2003
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

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 )
#28784	IJSEM 1384 2008 ( DOI 10.1099/ijs.0.65708-0 , PubMed 18523182 )
#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
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000473205

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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