Archive BacDiveID:10.13145/bacdive2487.20230509.8.1

Strain identifier

BacDive ID: 2487

Type strain:

Species: Thiocystis violacea

Strain Designation: 2711

Strain history: <- N. Pfennig, 2711

NCBI tax ID(s): 13725 (species)

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

General

@ref: 47

BacDive-ID: 2487

DSM-Number: 207

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile

description: Thiocystis violacea 2711 is an anaerobe, mesophilic, motile bacterium that was isolated from forest pond.

NCBI tax id

NCBI tax id: 13725
Matching level: species

strain history

@ref: 47
history: <- N. Pfennig, 2711

doi: 10.13145/bacdive2487.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Chromatiales
family: Chromatiaceae
genus: Thiocystis
species: Thiocystis violacea
full scientific name: Thiocystis violacea Winogradsky 1888 (Approved Lists 1980)

@ref: 47

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Chromatiales

family: Chromatiaceae

genus: Thiocystis

species: Thiocystis violacea

full scientific name: Thiocystis violacea Winogradsky 1888

strain designation: 2711

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	yes	94.756
69480		99.995	negative

Culture and growth conditions

culture medium

@ref: 47
name: PFENNIG'S MEDIUM I (modified 1988, for purple sulfur bacteria) (DSMZ Medium 28)
growth: yes
link: https://mediadive.dsmz.de/medium/28
composition: Name: PFENNIG'S MEDIUM I (DSMZ Medium 28) Composition: NaHCO3 1.5 g/l Na2S x 9 H2O 0.592592 g/l MgSO4 x 7 H2O 0.500001 g/l KCl 0.349999 g/l KH2PO4 0.349999 g/l Ammonium chloride 0.349999 g/l Pyruvic acid sodium salt 0.25 g/l Dextrose 0.25 g/l CaCl2 x 2 H2O 0.25 g/l Yeast extract 0.25 g/l Ammonium acetate 0.25 g/l Na2-EDTA 0.003 g/l Resazurin 0.00225 g/l FeSO4 x 7 H2O 0.0011 g/l Vitamin B12 0.001 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 2 H2O 5e-05 g/l ZnCl2 4.2e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Na2MoO4 x 2 H2O 1.8e-05 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water

culture temp

@ref: 47
growth: positive
type: growth
temperature: 25
range: mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
47	anaerobe
69480	anaerobe	96.357

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.981

compound production

@ref: 47
compound: carotenoids

Isolation, sampling and environmental information

isolation

@ref: 47
sample type: forest pond

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Terrestrial	#Forest

taxonmaps

@ref: 69479
File name: preview.99_133213.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_169;96_45004;97_66628;98_89047;99_133213&stattab=map
Last taxonomy: Thiocystis violacea subclade
16S sequence: Y11315
Sequence Identity:
Total samples: 40
soil counts: 10
aquatic counts: 20
animal counts: 10

Safety information

risk assessment

@ref: 47
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Thiocystis violacea partial 16S rRNA gene, type strain 4340 = DSM 207T	FN293059	1460	ena	13725
20218	Thiocystis violacea partial 16S rRNA gene, type strain DSMZ 207T	Y11315	1450	ena	13725

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Thiocystis violacea DSM 207	GCA_016583575	contig	ncbi	13725
66792	Thiocystis violacea strain DSM 207	13725.6	wgs	patric	13725

GC content

@ref: 47
GC-content: 63.1

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	89.693	no
gram-positive	no	99.15	no
anaerobic	yes	96.384	yes
halophile	no	92.976	no
spore-forming	no	90.049	no
thermophile	no	96.839	yes
glucose-util	yes	66.292	no
aerobic	no	95.724	yes
flagellated	no	52.223	no
glucose-ferment	no	83.962	no

External links

@ref: 47

culture collection no.: DSM 207, Pfennig 2711

straininfo link

@ref: 72027
straininfo: 47089

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
47	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 207)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-207
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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
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)
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
72027	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID47089.1	StrainInfo: A central database for resolving microbial strain identifiers