Archive BacDiveID:10.13145/bacdive6236.20230509.8.1

Strain identifier

BacDive ID: 6236

Type strain:

Species: Pseudidiomarina salinarum

Strain Designation: ISL-52

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 435908 (species)

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

General

@ref: 16028

BacDive-ID: 6236

DSM-Number: 21900

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

description: Pseudidiomarina salinarum ISL-52 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine solar saltern.

NCBI tax id

NCBI tax id: 435908
Matching level: species

strain history

@ref	history
16028	<- CCUG <- J. H. Yoon, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea
67771	<- JH Yoon, KRIBB

doi: 10.13145/bacdive6236.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Alteromonadales
family: Idiomarinaceae
genus: Pseudidiomarina
species: Pseudidiomarina salinarum
full scientific name: Pseudidiomarina salinarum (Yoon et al. 2007) Jean et al. 2009
synonyms
- @ref: 20215
- synonym: Idiomarina salinarum

@ref: 16028

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Idiomarinaceae

genus: Pseudidiomarina

species: Pseudidiomarina salinarum

full scientific name: Pseudidiomarina salinarum (Yoon et al. 2007) Jean et al. 2009 emend. Liu et al. 2018

strain designation: ISL-52

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility
32249	negative	2.25 µm	0.45 µm	rod-shaped	yes
67771	negative

colony morphology

@ref: 60150
incubation period: 3 days

pigmentation

@ref: 32249
production: no

Culture and growth conditions

culture medium

@ref: 16028
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	range
16028	positive	growth	37	mesophilic
32249	positive	growth	04-42
32249	positive	optimum	33.5	mesophilic
60150	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

culture pH

@ref	ability	type	pH
32249	positive	growth	06-08
32249	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
32249	aerobe
67771	aerobe

halophily

@ref	salt	growth	tested relation	concentration
32249	NaCl	positive	growth	0.5-14 %
32249	NaCl	positive	optimum	2.5 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
32249	53423	tween 40	+	carbon source
32249	53425	tween 60	+	carbon source
32249	53426	tween 80	+	carbon source
32249	17632	nitrate	+	reduction

enzymes

@ref	value	activity	ec
32249	alkaline phosphatase	+	3.1.3.1
32249	catalase	+	1.11.1.6
32249	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	sampling date
16028	marine solar saltern	Yellow Sea	Republic of Korea	KOR	Asia
60150	Marine solar saltern		Republic of Korea	KOR	Asia	2005
67771	From saltern field	the Yellow Sea	Republic of Korea	KOR	Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Condition	#Saline
#Engineered	#Industrial	#Industrial production
#Environmental	#Terrestrial	#Coast

Safety information

risk assessment

@ref: 16028
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 16028
description: Idiomarina salinarum strain ISL-52 16S ribosomal RNA gene, partial sequence
accession: EF486355
length: 1497
database: ena
NCBI tax ID: 435908

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Pseudidiomarina salinarum ISL-52	GCA_003987105	contig	ncbi	435908
66792	Pseudidiomarina salinarum ISL-52	GCA_000753715	contig	ncbi	435908

GC content

@ref: 16028
GC-content: 53.9

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	88.032	yes
flagellated	no	79.795	no
gram-positive	no	98.893	no
anaerobic	no	98.442	yes
aerobic	yes	86.15	yes
halophile	yes	57.964	no
spore-forming	no	97.071	no
thermophile	no	98.695	no
glucose-util	yes	81.273	no
glucose-ferment	no	82.609	no

External links

@ref: 16028

culture collection no.: DSM 21900, CCUG 54359, KCTC 12971

straininfo link

@ref: 75715
straininfo: 398644

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	17978209	Idiomarina salinarum sp. nov., isolated from a marine solar saltern in Korea.	Yoon JH, Jung SY, Jung YT, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.65189-0	2007	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Gammaproteobacteria/classification/genetics/isolation & purification/physiology, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA	Genetics
Phylogeny	20511464	Idiomarina xiamenensis sp. nov., isolated from surface seawater, and proposal to transfer Pseudidiomarina aestuarii to the genus Idiomarina as Idiomarina aestuarii comb. nov.	Wang L, Lai Q, Fu Y, Chen H, Wang W, Wang J, Sun F, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.022970-0	2010	Alteromonadaceae/classification/genetics/isolation & purification/physiology, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Temperature	Genetics
Phylogeny	21441375	Idiomarina maris sp. nov., a marine bacterium isolated from sediment.	Zhang YJ, Zhang XY, Zhao HL, Zhou MY, Li HJ, Gao ZM, Chen XL, Dang HY, Zhang YZ	Int J Syst Evol Microbiol	10.1099/ijs.0.027896-0	2011	Alteromonadaceae/chemistry/classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/microbiology, Lipids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Species Specificity	Genetics
Phylogeny	25015677	Idiomarina planktonica sp. nov., isolated from a saline lake.	Zhong ZP, Liu Y, Liu HC, Wang F, Song L, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.065938-0	2014	Alteromonadaceae/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/microbiology, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Water Microbiology	Genetics
Phylogeny	25417054	Idiomarina atlantica sp. nov., a marine bacterium isolated from the deep sea sediment of the North Atlantic Ocean.	Du J, Lai Q, Liu Y, Du Y, Liu X, Sun F, Shao Z	Antonie Van Leeuwenhoek	10.1007/s10482-014-0337-7	2014	Aerobiosis, Alteromonadaceae/classification/genetics/isolation & purification, Atlantic Ocean, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature	Genetics
Phylogeny	25634943	Idiomarina halophila sp. nov., isolated from a solar saltern sediment.	Lee JC, Kim YS, Yun BS, Whang KS	Int J Syst Evol Microbiol	10.1099/ijs.0.000094	2015	Alteromonadaceae/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Salinity, Sequence Analysis, DNA, Ubiquinone/chemistry, Water Microbiology	Genetics

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
16028	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21900)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-21900
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
32249	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	28490	28776041
60150	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 54359)	https://www.ccug.se/strain?id=54359
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)
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates		33211880	Nucleic Acids Res. 49: D498-D508 2020
67771	Curators of the KCTC		https://kctc.kribb.re.kr/En/Kctc
75715	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID398644.1	StrainInfo: A central database for resolving microbial strain identifiers

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

colony morphology

pigmentation

Culture and growth conditions

culture medium

culture temp

culture pH

Physiology and metabolism

oxygen tolerance

halophily

metabolite utilization

enzymes

Isolation, sampling and environmental information

isolation

isolation source categories

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference