Name: Ferriphaselus amnicola OYT1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24052

Type strain:

Species: Ferriphaselus amnicola

Strain Designation: OYT1

Culture col. no.: DSM 26810, JCM 18545

Strain history: S. Kato OYT1.

NCBI tax ID(s): 1188319 (species)

SI-ID 403122

DSM 26810

Special Collections

DSMZ
JCM

Section

Ferriphaselus amnicola OYT1 is a microaerophile, Gram-negative bacterium that was isolated from iron-rich floc from a groundwater seep.

Gram-negative
microaerophile
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	*Gallionellaceae*
	Genus	*Ferriphaselus*
	Species	**Ferriphaselus amnicola**
	Full Scientific Name (LPSN)	Ferriphaselus amnicola Kato et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %98.333

[Ref.: #21315]

Incubation period

3-7 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21315]

Culture medium

FERRIPHASELUS (ES) MEDIUM (DSMZ Medium 1267)

[Ref.: #21315]

Culture medium growth

[Ref.: #21315]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21315]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21315]			growth	25 °C
[Ref.: #67770]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #21315]

Oxygen tolerance

microaerophile

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	glutamate and glutamine metabolism	53.57	15 of 28
[Ref.: #66794]	glycolysis	52.94	9 of 17
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	oxidative phosphorylation	47.25	43 of 91
[Ref.: #66794]	vitamin B12 metabolism	47.06	16 of 34
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	lysine metabolism	42.86	18 of 42
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	arginine metabolism	37.5	9 of 24
[Ref.: #66794]	acetoin degradation	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	25	3 of 12
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	carotenoid biosynthesis	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.: #21315]	Sample type/isolated from	iron-rich floc from a groundwater seep
[Ref.: #21315]	Geographic location (country and/or sea, region)	Tokyo, Ohyato Park
[Ref.: #21315]	Country	Japan
[Ref.: #21315]	Country ISO 3 Code	JPN
[Ref.: #21315]	Continent	Asia
[Ref.: #21315]	Geographic location	35.6394°/139.4580°

[Ref.: #67770]	Sample type/isolated from	Iron-rich floc in a groundwater seep in Ohyato Park
[Ref.: #67770]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Groundwater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB720115 (>99% sequence identity) for Ferriphaselus amnicola subclade from Microbeatlas

Aquatic Samples	704
Soil Samples	107
Animal Samples	70
Plant Samples	29
Total Samples	910

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

[Ref.: #21315]

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.: #21315]	Ferriphaselus amnicola gene for 16S rRNA, partial sequence	AB720115	1385	GenBank ENA	1188319 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ferriphaselus amnicola OYT1	GCA_000974685	complete	GenBank ENA	1188319 tax ID	*
[Ref.: #66792]	Ferriphaselus amnicola OYT1	2834899978	complete	JGI IMG/M	1188319 tax ID	*

[Ref.: #21315]

GC-content

57.6 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Ferriphaselus amnicola OYT1 NCBI: GCA_000974685.2
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ferriphaselus amnicola OYT1 NCBI: GCA_000974685.2
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.333	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	76.652	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	53.651	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.157	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	89.284	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	68.049	no

Availability in culture collections External links

[Ref.: #21315]

Culture collection no.

DSM 26810, JCM 18545

[Ref.: #88023]

SI-ID 403122

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ferriphaselus amnicola gen. nov., sp. nov., a neutrophilic, stalk-forming, iron-oxidizing bacterium isolated from an iron-rich groundwater seep.	Kato S, Krepski S, Chan C, Itoh T, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijs.0.058487-0	2013	*

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 )

#21315

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26810

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88023

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-ID403122.1 )

* 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 Ferriphaselus amnicola in external resources:
SILVA
BRENDA
PANGAEA
GBIF