Name: Sulfuricella denitrificans skB26
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6152

Type strain:

Species: Sulfuricella denitrificans

Strain Designation: skB26

Culture col. no.: DSM 22764, NBRC 105220

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

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

SI-ID 374145

NBRC 105220, DSM 22764

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Nitrosomonadales*
	Family	*Sulfuricellaceae*
	Genus	*Sulfuricella*
	Species	**Sulfuricella denitrificans**
	Full Scientific Name (LPSN)	Sulfuricella denitrificans Kojima and Fukui 2010

Information on morphological and physiological properties Morphology

[Ref.: #29613]	Gram stain	negative

[Ref.: #29613]	Cell length	0.8-2 µm

[Ref.: #29613]	Cell width	0.4-0.6 µm

[Ref.: #29613]	Cell shape	rod-shaped

[Ref.: #29613]	Motility	yes

[Ref.: #16503]

Incubation period

8-14 days

[Ref.: #29613]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16503]

Culture medium

SULFURICELLA MEDIUM (DSMZ Medium 1277)

[Ref.: #16503]

Culture medium growth

[Ref.: #16503]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16503]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16503]	growth	22 °C
[Ref.: #29613]	growth	0-28 °C
[Ref.: #29613]	optimum	22 °C

[Ref.: #16503]	Temperature range	psychrophilic
[Ref.: #29613]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #29613]			optimum	7.5-8
[Ref.: #29613]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #16503]	Oxygen tolerance	microaerophile
[Ref.: #29613]	Oxygen tolerance	facultative anaerobe

[Ref.: #29613]

Observation

aggregates in chains

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29613]		nitrate ChEBI	+	reduction

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29613]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	oxidative phosphorylation	40.66	37 of 91
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	vitamin B12 metabolism	32.35	11 of 34
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #16503]	Sample type/isolated from	anoxic lake water of a stratified freshwater lake
[Ref.: #16503]	Geographic location (country and/or sea, region)	Yamanashi, Lake Mizugaki
[Ref.: #16503]	Country	Japan
[Ref.: #16503]	Country ISO 3 Code	JPN
[Ref.: #16503]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB506456 (>99% sequence identity) for Sulfuricella denitrificans subclade from Microbeatlas

Aquatic Samples	9794
Soil Samples	4027
Animal Samples	595
Plant Samples	322
Total Samples	14738

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #16503]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16503]	Sulfuricella denitrificans gene for 16S rRNA, partial sequence	AB506456	1464	ENA	1163617 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sulfuricella denitrificans skB26	GCA_000297055	contig	GenBank	1163617 tax ID	*
[Ref.: #66792]	Sulfuricella denitrificans skB26	1163617.8	plasmid	PATRIC	1163617 tax ID	*
[Ref.: #66792]	Sulfuricella denitrificans skB26	2531839478	complete	JGI IMG/M	1163617 tax ID	*

[Ref.: #16503]	GC-content	59 mol%	fluorimetric
[Ref.: #29613]	GC-content	59 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sulfuricella denitrificans skB26 skB26 NCBI: GCA_000297055.2
[Ref.: #69480]	motile	yes	88.678	yes
[Ref.: #69480]	flagellated	yes	64.876	no
[Ref.: #69480]	gram-positive	no	99.224	yes
[Ref.: #69480]	anaerobic	no	87.107	yes
[Ref.: #69480]	aerobic	no	96.304	yes
[Ref.: #69480]	halophile	no	92.795	no
[Ref.: #69480]	spore-forming	no	95.978	no
[Ref.: #69480]	glucose-util	no	66.742	no
[Ref.: #69480]	thermophile	no	90.904	yes
[Ref.: #69480]	glucose-ferment	no	86.997	no

Availability in culture collections External links

[Ref.: #16503]

Culture collection no.

DSM 22764, NBRC 105220

[Ref.: #75639]

SI-ID 374145

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	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	*
Phylogeny	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	*
Genetics	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	*
Genetics	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	*
Phylogeny	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	*

References

#16503

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22764

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#29613

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26003 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#75639

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID374145.1 )

#26003

IJSEM 2862 2010 ( DOI 10.1099/ijs.0.016980-0 , PubMed 20081014 )

* These data were automatically processed and therefore are not curated

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Sulfuricella denitrificans skB26 skB26

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