Name: Rhodoferax saidenbachensis ED16
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23872

Type strain:

Species: Rhodoferax saidenbachensis

Strain Designation: ED16, ED16I

Culture col. no.: DSM 22694, ATCC BAA 1852, CCUG 57711

Strain history: <- R. Kaden, Forschungszentrum Karlsruhe, Institute Functional Interfaces (IFG), Germany; ED16I (the accession form gives the strain designation as ED16I, but at the time of valid publication the strain designation is given as ED16)

NCBI tax ID(s): 1484693 (species)

Section

Rhodoferax saidenbachensis ED16 is an aerobe, psychrophilic bacterium that was isolated from sediment of a drinking water reservoir.

aerobe
psychrophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Rhodoferax*
	Species	**Rhodoferax saidenbachensis**
	Full Scientific Name (PNU)	Rhodoferax saidenbachensis Kaden et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #61428]

Incubation period

3 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20765]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #20765]

Culture medium growth

[Ref.: #20765]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #20765]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #20765]			growth	20 °C
[Ref.: #61428]			growth	30 °C

[Ref.: #20765]	Temperature range	psychrophilic
[Ref.: #61428]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #61428]

Oxygen tolerance

aerobe

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	tryptophan metabolism	76.32	29 of 38
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	degradation of pentoses	75	21 of 28
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	oxidative phosphorylation	73.63	67 of 91
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	chlorophyll metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
		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.: #20765]	Sample type/isolated from	sediment of a drinking water reservoir
[Ref.: #20765]	Geographic location (country and/or sea, region)	Saxony, Saidenbach reservoir (50° 44' 9'' N 13° 14' 3'' E)
[Ref.: #20765]	Country	Germany
[Ref.: #20765]	Country ISO 3 Code	DEU
[Ref.: #20765]	Continent	Europe
[Ref.: #20765]	Geographic location	50.7358°/13.2342°

[Ref.: #61428]	Sample type/isolated from	Water,drinking reservoir
[Ref.: #61428]	Sampling date	2006-06-01
[Ref.: #61428]	Geographic location (country and/or sea, region)	Saxony,Saidenbach reservoir
[Ref.: #61428]	Country	Germany
[Ref.: #61428]	Country ISO 3 Code	DEU
[Ref.: #61428]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Built environment	#Water reservoir (Aquarium/pool)
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ755906 (>99% sequence identity) for Rhodoferax saidenbachensis from Microbeatlas

Aquatic Samples	3
Soil Samples	1
Animal Samples
Plant Samples
Total Samples	4

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

[Ref.: #20765]

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.: #20765]	Rhodoferax saidenbachensis ED16 16S ribosomal RNA gene, partial sequence	FJ755906	1499	ENA	614083 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodoferax saidenbachensis ED16 ED16	GCA_000498435	contig	GenBank	614083 tax ID	*
[Ref.: #66792]	Rhodoferax saidenbachensis DSM 22694	GCA_001955715	complete	GenBank	1484693 tax ID	*
[Ref.: #66792]	Rhodoferax saidenbachensis strain DSM 22694	1484693.3	complete	PATRIC	1484693 tax ID	*
[Ref.: #66792]	Rhodoferax saidenbachensis ED16	2582581024	draft	JGI IMG/M	614083 tax ID	*
[Ref.: #66792]	Rhodoferax saidenbachensis DSM 22694	2773857796	complete	JGI IMG/M	1484693 tax ID	*
[Ref.: #66792]	Klebsiella pneumoniae k2330	GCA_900085585	scaffold	PATRIC	573 tax ID	*

[Ref.: #20765]

GC-content

60.3 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #20765]

Culture collection no.

DSM 22694, ATCC BAA 1852, CCUG 57711

[Ref.: #20218]

Associated Passport(s) in StrainInfo

894874, 894873, 894872

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodoferax saidenbachensis sp. nov., a psychrotolerant, very slowly growing bacterium within the family Comamonadaceae, proposal of appropriate taxonomic position of Albidiferax ferrireducens strain T118T in the genus Rhodoferax and emended description of the genus Rhodoferax.	Kaden R, Sproer C, Beyer D, Krolla-Sidenstein P	Int J Syst Evol Microbiol	10.1099/ijs.0.054031-0	2014	*
Phylogeny	Rhodoferax koreense sp. nov, an obligately aerobic bacterium within the family Comamonadaceae, and emended description of the genus Rhodoferax.	Farh ME, Kim YJ, Singh P, Jung SY, Kang JP, Yang DC	J Microbiol	10.1007/s12275-017-7033-z	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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#20765

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22694

#61428 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57711

#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) .

* These data were automatically processed and therefore are not curated

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