Archive BacDiveID:10.13145/bacdive13866.20230509.8.1

Strain identifier

BacDive ID: 13866

Type strain:

Species: Oceanicella actignis

Strain Designation: PRQ-67

Strain history: <- M. da Costa, Univ. Coimbra, Portugal <- L. Albuquerque; PRQ-67

NCBI tax ID(s): 1189325 (species)

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

General

@ref: 16457

BacDive-ID: 13866

DSM-Number: 22673

keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative

description: Oceanicella actignis PRQ-67 is a thermophilic, Gram-negative bacterium that was isolated from water of shallow marine hot spring on a beach.

NCBI tax id

NCBI tax id: 1189325
Matching level: species

strain history

@ref: 16457
history: <- M. da Costa, Univ. Coimbra, Portugal <- L. Albuquerque; PRQ-67

doi: 10.13145/bacdive13866.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Rhodobacterales
family: Paracoccaceae
genus: Oceanicella
species: Oceanicella actignis
full scientific name: Oceanicella actignis Albuquerque et al. 2012
synonyms
- @ref: 20215
- synonym: Pleomorphobacterium xiamenense

@ref: 16457

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Oceanicella

species: Oceanicella actignis

full scientific name: Oceanicella actignis Albuquerque et al. 2012

strain designation: PRQ-67

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.997

Culture and growth conditions

culture medium

@ref: 16457
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: 16457
growth: positive
type: growth
temperature: 50
range: thermophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	99
69480	no	99.993

Isolation, sampling and environmental information

isolation

@ref: 16457
sample type: water of shallow marine hot spring on a beach
geographic location: Azores, Island of São Miguel, Praia do Fogo, at Ribeira Quente
country: Portugal
origin.country: PRT
continent: Europe

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)

taxonmaps

@ref: 69479
File name: preview.99_92721.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1892;96_38208;97_48616;98_63812;99_92721&stattab=map
Last taxonomy: Oceanicella actignis subclade
16S sequence: JQ864435
Sequence Identity:
Total samples: 331
soil counts: 91
aquatic counts: 191
animal counts: 37
plant counts: 12

Safety information

risk assessment

@ref: 16457
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 16457
description: Oceanicella actignis strain PRQ-67 16S ribosomal RNA gene, partial sequence
accession: JQ864435
length: 1431
database: ena
NCBI tax ID: 1189325

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Oceanicella actignis DSM 22673	GCA_008124525	scaffold	ncbi	1189325
66792	Oceanicella actignis strain DSM 22673	1189325.5	wgs	patric	1189325
66792	Oceanicella actignis DSM 22673	2593339287	draft	img	1189325

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	99	no
motile	yes	70.942	no
flagellated	no	76.145	no
gram-positive	no	98.522	no
anaerobic	no	95.665	no
aerobic	yes	84.923	no
halophile	yes	59.623	no
spore-forming	no	96.522	no
glucose-util	no	50	no
thermophile	yes	79.806	yes
glucose-ferment	no	90.484	no

External links

@ref: 16457

culture collection no.: DSM 22673, LMG 25334

straininfo link

@ref: 83042
straininfo: 362876

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	22898658	Oceanicella actignis gen. nov., sp. nov., a halophilic slightly thermophilic member of the Alphaproteobacteria.	Albuquerque L, Rainey FA, Nobre MF, da Costa MS	Syst Appl Microbiol	10.1016/j.syapm.2012.07.001	2012	Azores, Chromatography, Thin Layer, Genes, Bacterial/genetics, Hot Springs/microbiology, Lipids/analysis/chemistry, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/chemistry/classification/genetics/isolation & purification, Seawater/microbiology	Genetics
Phylogeny	28869003	Pleomorphobacterium xiamenense Yin et al. 2013 is a later heterotypic synonym of Oceanicella actignis Albuquerque et al. 2012.	Huang Z, Lai Q, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.002160	2017	Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hot Springs/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA	Transcriptome
Phylogeny	31743595	Physiological and genomic features of Paraoceanicella profunda gen. nov., sp. nov., a novel piezophile isolated from deep seawater of the Mariana Trench.	Liu P, Ding W, Lai Q, Liu R, Wei Y, Wang L, Xie Z, Cao J, Fang J	Microbiologyopen	10.1002/mbo3.966	2019	Alphaproteobacteria/classification/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial, Fatty Acids/metabolism, Genome, Bacterial, Genomics/methods, Geologic Sediments/microbiology, Lipid Metabolism, Phenotype, Phylogeny, Seawater/*microbiology	Genetics

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
16457	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22673)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-22673
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
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	Nucleic Acids Res. 49: D498-D508 2020	33211880
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
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
83042	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID362876.1	StrainInfo: A central database for resolving microbial strain identifiers

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

spore formation

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

Genome-based predictions

predictions

External links

straininfo link

literature

Reference