Name: Silvanigrella aquatica MWH-Nonnen-W8red
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140357

Type strain:

Species: Silvanigrella aquatica

Strain Designation: MWH-Nonnen-W8red

Culture col. no.: DSM 23856, CCUG 58639

Strain history: <- M. W. Hahn, Austrian Academy of Sci., Inst. Limnology; Nonnen-W8red

NCBI tax ID(s): 1915309 (species)

SI-ID 396520

DSM 23856, CCUG 58639

Section

Silvanigrella aquatica MWH-Nonnen-W8red is an aerobe, chemoorganoheterotroph, Gram-negative bacterium that forms circular colonies and was isolated from freshwater.

colony-forming
Gram-negative
motile
pleomorphic-shaped
aerobe
chemoorganoheterotroph
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	*Oligoflexia*
	Order	*Silvanigrellales*
	Family	*Silvanigrellaceae*
	Genus	*Silvanigrella*
	Species	**Silvanigrella aquatica**
	Full Scientific Name (LPSN)	Silvanigrella aquatica Hahn et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43466]	Gram stain	negative

[Ref.: #43466]	Cell length	3.6 µm

[Ref.: #43466]	Cell width	0.6 µm

[Ref.: #43466]	Cell shape	pleomorphic-shaped

[Ref.: #43466]	Motility	yes

[Ref.: #43466]	Colony size	5 mm
[Ref.: #43466]	Colony color	red
[Ref.: #43466]	Colony shape	circular
[Ref.: #43466]	Incubation period	18 days
[Ref.: #43466]	Cultivation medium used	NSY agar plates (1.5% agar)

[Ref.: #61730]	Incubation period	4-6 days

Multimedia content

[Ref.: #42964]

Caption:

DSM 23856 on medium 830 at 28 °C

[Ref.: #42964]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43466]

Culture medium

NSY

[Ref.: #43466]

Culture medium growth

[Ref.: #43466]

Culture medium

NSY agar plates (1.5% agar)

[Ref.: #43466]

Culture medium growth

[Ref.: #43466]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #43466]

Culture medium growth

[Ref.: #42964]

Culture medium

NSY-MEDIUM FOR POLYNUCLEOBACTER (DSMZ Medium 1167)

[Ref.: #42964]

Culture medium growth

[Ref.: #42964]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42964]

Culture medium composition

expand / minimize

[Ref.: #42964]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #42964]

Culture medium growth

[Ref.: #42964]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42964]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #42964]	growth	28 °C
[Ref.: #43466]	growth	10-32 °C
[Ref.: #61730]	growth	20 °C

[Ref.: #42964]	Temperature range	mesophilic
[Ref.: #61730]	Temperature range	psychrophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43466]	Oxygen tolerance	aerobe
[Ref.: #61730]	Oxygen tolerance	aerobe

[Ref.: #43466]

Nutrition type

chemoorganoheterotroph

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43466]		NaCl		growth	0-1	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43466]	acetate ChEBI	+/-	assimilation
[Ref.: #43466]	betaine ChEBI	-	assimilation
[Ref.: #43466]	citrate ChEBI	-	assimilation
[Ref.: #43466]	D-fucose ChEBI	-	assimilation
[Ref.: #43466]	D-glucose ChEBI	+	assimilation
[Ref.: #43466]	D-mannose ChEBI	+	assimilation
[Ref.: #43466]	D-sorbitol ChEBI	-	assimilation
[Ref.: #43466]	D-xylose ChEBI	-	assimilation
[Ref.: #43466]	fumarate ChEBI	+/-	assimilation
[Ref.: #43466]	glycine ChEBI	+/-	assimilation
[Ref.: #43466]	glycolate ChEBI	-	assimilation
[Ref.: #43466]	glyoxylate ChEBI	-	assimilation
[Ref.: #43466]	L-alanine ChEBI	+	assimilation
[Ref.: #43466]	L-glutamate ChEBI	+	assimilation
[Ref.: #43466]	L-methionine ChEBI	-	assimilation
[Ref.: #43466]	L-proline ChEBI	+	assimilation
[Ref.: #43466]	lactate ChEBI	-	assimilation
[Ref.: #43466]	malonate ChEBI	-	assimilation
[Ref.: #43466]	oxaloacetate ChEBI	-	assimilation
[Ref.: #43466]	propionate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43466]		catalase	+/-	1.11.1.6
[Ref.: #43466]		cytochrome oxidase	-	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	coenzyme A metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	histidine metabolism	44.83	13 of 29
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	heme metabolism	42.86	6 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	arginine metabolism	37.5	9 of 24
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	isoprenoid biosynthesis	34.62	9 of 26
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[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]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	molybdenum cofactor biosynthesis	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		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.: #42964]	Sample type/isolated from	freshwater
[Ref.: #42964]	Geographic location (country and/or sea, region)	Black Forest, Lake Nonnenmattweiher
[Ref.: #42964]	Country	Germany
[Ref.: #42964]	Country ISO 3 Code	DEU
[Ref.: #42964]	Continent	Europe

[Ref.: #43466]	Sample type/isolated from	freshwater lake located in the Black Forest Mountains (Schwarzwald)
[Ref.: #43466]	Geographic location (country and/or sea, region)	Black Forest Mountains (Schwarzwald)
[Ref.: #43466]	Country	Germany
[Ref.: #43466]	Country ISO 3 Code	DEU
[Ref.: #43466]	Continent	Europe

[Ref.: #61730]	Sample type/isolated from	Freshwater,lake
[Ref.: #61730]	Sampling date	2008-08-01
[Ref.: #61730]	Geographic location (country and/or sea, region)	Black Forest,Nonnenmattweiher
[Ref.: #61730]	Country	Germany
[Ref.: #61730]	Country ISO 3 Code	DEU
[Ref.: #61730]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)

What are isolation sources categories?

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

[Ref.: #42964]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Silvanigrella aquatica MWH-Nonnen-W8red	GCA_001907975	chromosome	GenBank	1915309 tax ID	*
[Ref.: #66792]	Silvanigrella aquatica MWH-Nonnen-W8red	2767802763	complete	JGI IMG/M	1915309 tax ID	*

[Ref.: #43466]	GC-content	32.63 mol%
[Ref.: #42964]	GC-content	32.6 mol%	sequence analysis

Availability in culture collections External links

[Ref.: #42964]

Culture collection no.

DSM 23856, CCUG 58639

[Ref.: #96655]

SI-ID 396520

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales.	Hahn MW, Schmidt J, Koll U, Rohde M, Verbarg S, Pitt A, Nakai R, Naganuma T, Lang E	Int J Syst Evol Microbiol	10.1099/ijsem.0.001965	2017	*

References

#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 )

#42964

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23856

#43466

Martin W. Hahn, Johanna Schmidt, Ulrike Koll, Manfred Rohde, Susanne Verbarg, Alexandra Pitt, Ryosuke Nakai, Takeshi Naganuma, Elke Lang: Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales. IJSEM 67: 2555 - 2568 2017 ( DOI 10.1099/ijsem.0.001965 , PubMed 28771119 )

#61730 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 58639

#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 )

#96655

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-ID396520.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Silvanigrella aquatica in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF