Archive BacDiveID:10.13145/bacdive293.20230509.8.1

Strain identifier

BacDive ID: 293

Type strain:

Species: Oceanisphaera sediminis

Strain Designation: TW92

Strain history: J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; TW92.

NCBI tax ID(s): 981381 (species)

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

General

@ref: 18082

BacDive-ID: 293

DSM-Number: 25666

keywords: 16S sequence, Bacteria, facultative aerobe, mesophilic, Gram-negative, motile, coccus-shaped

description: Oceanisphaera sediminis TW92 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment from a cage-cultured ark clam farm.

NCBI tax id

NCBI tax id: 981381
Matching level: species

strain history

@ref	history
18082	<- KACC
67770	J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; TW92.

doi: 10.13145/bacdive293.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Aeromonadales
family: Aeromonadaceae
genus: Oceanisphaera
species: Oceanisphaera sediminis
full scientific name: Oceanisphaera sediminis Shin et al. 2012

@ref: 18082

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Aeromonadales

family: Aeromonadaceae

genus: Oceanisphaera

species: Oceanisphaera sediminis

full scientific name: Oceanisphaera sediminis Shin et al. 2012

strain designation: TW92

type strain: yes

Morphology

cell morphology

@ref: 30377
gram stain: negative
cell width: 1.25 µm
cell shape: coccus-shaped
motility: yes

colony morphology

@ref: 18082
incubation period: 1-2 days

pigmentation

@ref: 30377
production: yes

Culture and growth conditions

culture medium

@ref: 18082
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
18082	positive	growth	28	mesophilic
30377	positive	growth	04-42
30377	positive	optimum	30	mesophilic
67770	positive	growth	30	mesophilic

culture pH

@ref	ability	type	pH	PH range
30377	positive	growth	06-09	alkaliphile
30377	positive	optimum	7

Physiology and metabolism

oxygen tolerance

@ref: 30377
oxygen tolerance: facultative aerobe

halophily

@ref: 30377
salt: NaCl
growth: positive
tested relation: growth
concentration: 1-5 %

observation

@ref: 67770
observation: quinones: Q-8

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
30377	30089	acetate	+	carbon source
30377	21217	L-alaninamide	+	carbon source
30377	28644	2-oxopentanoate	+	carbon source
30377	23652	dextrin	+	carbon source
30377	29987	glutamate	+	carbon source
30377	17754	glycerol	+	carbon source
30377	25115	malate	+	carbon source
30377	37657	methyl D-glucoside	+	carbon source
30377	17272	propionate	+	carbon source
30377	17148	putrescine	+	carbon source
30377	51850	methyl pyruvate	+	carbon source
30377	17151	xylitol	+	carbon source
30377	17632	nitrate	+	reduction

enzymes

@ref	value	activity	ec
30377	acid phosphatase	+	3.1.3.2
30377	alkaline phosphatase	+	3.1.3.1
30377	catalase	+	1.11.1.6
30377	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
18082	marine sediment from a cage-cultured ark clam farm	south coast, Gang-jin bay	Republic of Korea	KOR	Asia
67770	Marine sediment from a cage-cultured ark clam farm in the Gang-jin bay of Korea

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Aquaculture
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Host	#Invertebrates (Other)	#Mollusca

taxonmaps

@ref: 69479
File name: preview.99_130122.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_11;96_6771;97_8105;98_42659;99_130122&stattab=map
Last taxonomy: Oceanisphaera sediminis
16S sequence: HQ171441
Sequence Identity:
Total samples: 32
soil counts: 1
aquatic counts: 18
animal counts: 13

Safety information

risk assessment

@ref: 18082
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 18082
description: Oceanisphaera sediminis strain TW92 16S ribosomal RNA gene, partial sequence
accession: HQ171441
length: 1464
database: ena
NCBI tax ID: 981381

GC content

@ref	GC-content	method
18082	58.5	fluorimetric
30377	58.5
67770	58.5	thermal denaturation, midpoint method (Tm)

External links

@ref: 18082

culture collection no.: DSM 25666, JCM 17329, KACC 15117

straininfo link

@ref: 69975
straininfo: 399142

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	21856983	Oceanisphaera sediminis sp. nov., isolated from marine sediment.	Shin NR, Whon TW, Roh SW, Kim MS, Kim YO, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.034645-0	2011	Aerobiosis, Aeromonadaceae/classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature	Metabolism
Phylogeny	25991663	Oceanisphaera psychrotolerans sp. nov., isolated from coastal sediment samples.	Zhou S, Wang H, Wang Y, Ma K, He M, Chen X, Kong D, Guo X, Ruan Z, Zhao B	Int J Syst Evol Microbiol	10.1099/ijs.0.000331	2015	Aeromonadaceae/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Temperature, Ubiquinone/chemistry	Genetics
Phylogeny	34665377	Production of extracellular lipase from psychrotrophic bacterium Oceanisphaera sp. RSAP17 isolated from arctic soil.	Uddin MR, Roy P, Mandal S	Antonie Van Leeuwenhoek	10.1007/s10482-021-01671-y	2021	Aeromonadaceae, Hydrogen-Ion Concentration, Lipase/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil, Temperature	Biotechnology

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
18082	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25666)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-25666
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
30377	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	26716	28776041
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
69975	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID399142.1	StrainInfo: A central database for resolving microbial strain identifiers