Name: Afipia sp. 1NLS2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1783

Type strain:

Species: Afipia sp.

Strain Designation: 1NLS2

Culture col. no.: DSM 23597

Strain history: <- S. Green, Oceanography Dept., Florida State Univ., Tallahassee, USA; 1NLS2 <- O. Prakash

NCBI tax ID(s): 1871052 (species)

SI-ID 397021

DSM 23597

Special Collections

DSMZ

Other strains from Afipia sp.

Section

Afipia sp. 1NLS2 is a Gram-negative bacterium that was isolated from contaminated surface sediment.

Gram-negative
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Nitrobacteraceae*
	Genus	*Afipia*
	Full Scientific Name (LPSN)	Afipia Brenner et al. 1992

Synonym

Oligotropha

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.479

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17295]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #17295]

Culture medium growth

[Ref.: #17295]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17295]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #17295]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68377]	D-fructose ChEBI	-	builds acid from	* from API NH
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68377]	D-glucose ChEBI	-	builds acid from	* from API NH
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68377]	maltose ChEBI	-	builds acid from	* from API NH
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68377]	alkaline phosphatase	-	3.1.3.1	* from API NH
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68377]	beta-galactosidase	-	3.2.1.23	* from API NH
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #68377]	gamma-glutamyltransferase	-	2.3.2.2	* from API NH
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68377]	proline-arylamidase	-	3.4.11.5	* from API NH
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #17295]	23871	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	not determinedn.d.

API® NH:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Penicillinase productionPEN	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from maltoseMAL	Acid from sucroseSAC	Ornithine decarboxylaseODC	Urease/urea hydrolysisURE	LipaseLIP	Alkaline phosphatasePAL	beta-Galactosidasebeta GAL	Proline arylamidaseProA	gamma-Glutamyl transferaseGGT	Indole productionIND
[Ref.: #17295]	6209	-	-	-	-	+	-	+	-	-	-	-	-	+
[Ref.: #17295]	5663	+	-	-	-	-	+	-	+	-	-	-	-	-

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

[Ref.: #17295]	Sample type/isolated from	contaminated surface sediment
[Ref.: #17295]	Geographic location (country and/or sea, region)	Oak Ridge, TN
[Ref.: #17295]	Country	USA
[Ref.: #17295]	Country ISO 3 Code	USA
[Ref.: #17295]	Continent	North America
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ851425 (>99% sequence identity) for Afipia from Microbeatlas

Aquatic Samples	275
Soil Samples	269
Animal Samples	203
Plant Samples	60
Total Samples	807

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.: #17295]	Afipia sp. 1NLS2 16S ribosomal RNA gene, partial sequence	FJ851425	1217	GenBank ENA	666684 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Afipia sp. 1NLS2	GCA_000178995	contig	GenBank ENA	666684 tax ID	*
[Ref.: #66792]	Afipia sp. 1NLS2	666684.3	wgs	PATRIC	666684 tax ID	*
[Ref.: #66792]	Afipia sp. 1NLS2	648276616	draft	JGI IMG/M	666684 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Afipia sp. 1NLS2 PATRIC: 666684.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99.479	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	88.484	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.752	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	74.348	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.859	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	69.389	no

Availability in culture collections External links

[Ref.: #17295]

Culture collection no.

DSM 23597

[Ref.: #71430]

SI-ID 397021

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome sequences for three denitrifying bacterial strains isolated from a uranium- and nitrate-contaminated subsurface environment.	Venkatramanan R, Prakash O, Woyke T, Chain P, Goodwin LA, Watson D, Brooks S, Kostka JE, Green SJ	Genome Announc	10.1128/genomeA.00449-13	2013	*

References

#17295

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23597

#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 )

#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) .

#68369

Automatically annotated from API 20NE .

#68377

Automatically annotated from API NH .

#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) .

#71430

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-ID397021.1 )

* These data were automatically processed and therefore are not curated

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