Archive BacDiveID:10.13145/bacdive6152.20230509.8.1

Strain identifier

BacDive ID: 6152

Type strain:

Species: Sulfuricella denitrificans

Strain Designation: skB26

Strain history: <- Y. Uchino, NBRC <- H. Kojima; skB26 {2008}

NCBI tax ID(s): 1163617 (strain), 649841 (species)

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

General

@ref: 16503

BacDive-ID: 6152

DSM-Number: 22764

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

description: Sulfuricella denitrificans skB26 is a microaerophile, psychrophilic, Gram-negative bacterium that was isolated from anoxic lake water of a stratified freshwater lake.

NCBI tax id

NCBI tax id	Matching level
649841	species
1163617	strain

strain history

@ref: 16503
history: <- Y. Uchino, NBRC <- H. Kojima; skB26 {2008}

doi: 10.13145/bacdive6152.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Betaproteobacteria
order: Nitrosomonadales
family: Sulfuricellaceae
genus: Sulfuricella
species: Sulfuricella denitrificans
full scientific name: Sulfuricella denitrificans Kojima and Fukui 2010

@ref: 16503

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Hydrogenophilales

family: Sulfuricellaceae

genus: Sulfuricella

species: Sulfuricella denitrificans

full scientific name: Sulfuricella denitrificans Kojima and Fukui 2010

strain designation: skB26

type strain: yes

Morphology

cell morphology

@ref: 29613
gram stain: negative
cell length: 0.8-2 µm
cell width: 0.4-0.6 µm
cell shape: rod-shaped
motility: yes

colony morphology

@ref: 16503
incubation period: 8-14 days

pigmentation

@ref: 29613
production: yes

Culture and growth conditions

culture medium

@ref: 16503
name: SULFURICELLA MEDIUM (DSMZ Medium 1277)
growth: yes
link: https://mediadive.dsmz.de/medium/1277
composition: Name: SULFURICELLA MEDIUM (DSMZ Medium 1277) Composition: Na2S2O3 x 5 H2O 2.49252 g/l NaNO3 1.69492 g/l Na2CO3 1.49551 g/l NaCl 0.249252 g/l MgCl2 x 6 H2O 0.199402 g/l KCl 0.0997009 g/l CaCl2 x 2 H2O 0.0997009 g/l (NH4)2SO4 0.0997009 g/l KH2PO4 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
16503	positive	growth	22	psychrophilic
29613	positive	growth	0-28
29613	positive	optimum	22	psychrophilic

culture pH

@ref	ability	type	pH	PH range
29613	positive	growth	06-09	alkaliphile
29613	positive	optimum	7.5-8

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
16503	microaerophile
29613	facultative anaerobe

observation

@ref: 29613
observation: aggregates in chains

metabolite utilization

@ref: 29613
Chebi-ID: 17632
metabolite: nitrate
utilization activity: +
kind of utilization tested: reduction

enzymes

@ref: 29613
value: cytochrome oxidase
activity: +
ec: 1.9.3.1

Isolation, sampling and environmental information

isolation

@ref: 16503
sample type: anoxic lake water of a stratified freshwater lake
geographic location: Yamanashi, Lake Mizugaki
country: Japan
origin.country: JPN
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Condition	#Anoxic (anaerobic)

taxonmaps

@ref: 69479
File name: preview.99_5227.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_2539;97_3103;98_3898;99_5227&stattab=map
Last taxonomy: Sulfuricella denitrificans subclade
16S sequence: AB506456
Sequence Identity:
Total samples: 14738
soil counts: 4027
aquatic counts: 9794
animal counts: 595
plant counts: 322

Safety information

risk assessment

@ref: 16503
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 16503
description: Sulfuricella denitrificans gene for 16S rRNA, partial sequence
accession: AB506456
length: 1464
database: ena
NCBI tax ID: 1163617

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Sulfuricella denitrificans skB26	GCA_000297055	contig	ncbi	1163617
66792	Sulfuricella denitrificans skB26	1163617.8	plasmid	patric	1163617
66792	Sulfuricella denitrificans skB26	2531839478	complete	img	1163617

GC content

@ref	GC-content	method
16503	59	fluorimetric
29613	59

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	88.678	yes
flagellated	yes	64.876	no
gram-positive	no	99.224	yes
anaerobic	no	87.107	yes
aerobic	no	96.304	yes
halophile	no	92.795	no
spore-forming	no	95.978	no
glucose-util	no	66.742	no
thermophile	no	90.904	yes
glucose-ferment	no	86.997	no

External links

@ref: 16503

culture collection no.: DSM 22764, NBRC 105220

straininfo link

@ref: 75639
straininfo: 374145

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	20081014	Sulfuricella denitrificans gen. nov., sp. nov., a sulfur-oxidizing autotroph isolated from a freshwater lake.	Kojima H, Fukui M	Int J Syst Evol Microbiol	10.1099/ijs.0.016980-0	2010	Bacterial Typing Techniques, Base Composition, Betaproteobacteria/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fresh Water/microbiology, Japan, Lakes/microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfates/metabolism, Sulfur/metabolism, Thiosulfates/metabolism	Metabolism
Genetics	22773644	Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium, Sulfuricella denitrificans skB26, and proteomic insights into cold adaptation.	Watanabe T, Kojima H, Fukui M	Appl Environ Microbiol	10.1128/AEM.01349-12	2012	Bacterial Proteins/analysis, Carbon Cycle, Cold Temperature, DNA, Bacterial/chemistry/genetics, Denitrification, Fresh Water/microbiology, Genome, Bacterial, Hydrogenophilaceae/genetics/isolation & purification/physiology/radiation effects, Lakes, Metabolic Networks and Pathways/genetics, Molecular Sequence Data, Oxidation-Reduction, Proteome/analysis, RNA, Transfer/genetics, *Sequence Analysis, DNA, Stress, Physiological, Sulfur Compounds/metabolism, rRNA Operon	Transcriptome
Genetics	25017294	Complete genomes of freshwater sulfur oxidizers Sulfuricella denitrificans skB26 and Sulfuritalea hydrogenivorans sk43H: genetic insights into the sulfur oxidation pathway of betaproteobacteria.	Watanabe T, Kojima H, Fukui M	Syst Appl Microbiol	10.1016/j.syapm.2014.05.010	2014	Betaproteobacteria/genetics/metabolism, Fatty Acids/metabolism, Fresh Water/chemistry/microbiology, Genes, Bacterial, Genome, Bacterial, Genomics, Metabolic Networks and Pathways, Molecular Sequence Data, Operon, Oxidation-Reduction, Phylogeny, Plasmids/genetics, Sulfur/metabolism, Thiosulfates/metabolism	Metabolism
Phylogeny	26475581	Sulfurirhabdus autotrophica gen. nov., sp. nov., isolated from a freshwater lake.	Watanabe T, Kojima H, Shinohara A, Fukui M	Int J Syst Evol Microbiol	10.1099/ijsem.0.000679	2015	Bacterial Typing Techniques, Base Composition, Betaproteobacteria/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Japan, Lakes/microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA	Genetics
Enzymology	29275285	A 3DBER-S-EC process for simultaneous nitrogen and phosphorus removal from wastewater with low organic carbon content.	Hao R, Zhou Y, Li J, Wang J	J Environ Manage	10.1016/j.jenvman.2017.12.018	2017	Bioreactors, Carbon, Denitrification, Nitrogen, Phosphorus/isolation & purification, Waste Water	Phylogeny

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
16503	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22764)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-22764
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
29613	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	26003	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)
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
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
75639	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID374145.1	StrainInfo: A central database for resolving microbial strain identifiers