Archive BacDiveID:10.13145/bacdive13733.20250331.9.3

Strain identifier

BacDive ID: 13733

Type strain:

Species: Pseudophaeobacter arcticus

Strain Designation: 20188

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

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

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 17288

BacDive-ID: 13733

DSM-Number: 23566

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

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

NCBI tax id

NCBI tax id	Matching level
999550	strain
385492	species

strain history

@ref	history
17288	<- JCM <- D.-C. Zhang, Ocean Univ. China, Qingdao, P. R. China; strain 20188
67770	D.-C. Zhang et al. 20188.

doi: 10.13145/bacdive13733.20250331.9.3

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
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
- @ref: 20215
- synonym: Phaeobacter arcticus

@ref: 17288

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Pseudophaeobacter

species: Pseudophaeobacter arcticus

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

strain designation: 20188

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
32569	negative	1.8 µm	0.4 µm	rod-shaped	yes
125438	negative					97.315
125439	negative					97.1

colony morphology

@ref: 17288
incubation period: 1-2 days

pigmentation

@ref: 32569
production: yes

multimedia

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

Culture and growth conditions

culture medium

@ref: 17288
name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
growth: yes
link: https://mediadive.dsmz.de/medium/514
composition: 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
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	growth	05-10	alkaliphile
32569	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
32569	aerobe
125439	obligate aerobe	91.2

spore formation

@ref	spore formation	confidence
125438	no	90.796
125439	no	94.9

halophily

@ref: 32569
salt: NaCl
growth: positive
tested relation: growth
concentration: 02-09 %

observation

@ref: 67770
observation: quinones: Q-10

metabolite utilization

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

enzymes

@ref	value	activity	ec
17288	catalase	+	1.11.1.6
17288	cytochrome-c oxidase	+	1.9.3.1
32569	alkaline phosphatase	+	3.1.3.1
32569	catalase	+	1.11.1.6
32569	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

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
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

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_3375.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_97;97_104;98_113;99_3375&stattab=map
Last taxonomy: Pseudophaeobacter arcticus
16S sequence: DQ514304
Sequence Identity:
Total samples: 559
soil counts: 31
aquatic counts: 483
animal counts: 41
plant counts: 4

Safety information

risk assessment

@ref: 17288
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 17288
description: Phaeobacter arcticus strain 20188 16S ribosomal RNA gene, partial sequence
accession: DQ514304
length: 1425
database: nuccore
NCBI tax ID: 999550

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Pseudophaeobacter arcticus DSM 23566	GCA_000473205	scaffold	ncbi	999550
66792	Phaeobacter arcticus DSM 23566	999550.5	wgs	patric	999550
66792	Pseudophaeobacter arcticus DSM 23566	2521172622	draft	img	999550

GC content

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

Genome-based predictions

predictions

@ref	model	trait	description	prediction	confidence	training_data
125438	gram-positive	gram-positive	Positive reaction to Gram-staining	no	97.315	yes
125438	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	no	92.42	no
125438	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	yes	80.733	no
125438	spore-forming	spore-forming	Ability to form endo- or exospores	no	90.796	no
125438	thermophile	thermophilic	Ability to grow at temperatures above or equal to 45°C	no	96.111	no
125438	motile2+	flagellated	Ability to perform flagellated movement	yes	51.035	no
125439	BacteriaNet	spore_formation	Ability to form endo- or exospores	no	94.9
125439	BacteriaNet	motility	Ability to perform movement	yes	72.4
125439	BacteriaNet	gram_stain	Reaction to gram-staining	negative	97.1
125439	BacteriaNet	oxygen_tolerance	Oxygenic conditions needed for growth	obligate aerobe	91.2

External links

@ref: 17288

culture collection no.: DSM 23566, CGMCC 1.6500, JCM 14644

straininfo link

@ref: 82915
straininfo: 408279

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	18523182	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	Arctic Regions, Bacterial Typing Techniques, Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Species Specificity	Genetics
Genetics	24501630	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	25355001	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	Aerobiosis, Animals, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Intestines/microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Stichopus/*microbiology, Temperature	Genetics
Phylogeny	35639600	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	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
17288	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23566)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-23566
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32569	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	28784	28776041
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life		28604660	35: 676-683 2017
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
82915	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID408279.1	StrainInfo: A central database for resolving microbial strain identifiers
125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann		10.1101/2024.08.12.607695	Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy		https://github.com/GenomeNet/deepG	deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

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

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference