Name: Novosphingobium acidiphilum FSW 06-204d
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14164

Type strain:

Species: Novosphingobium acidiphilum

Strain Designation: FSW 06-204d

Culture col. no.: DSM 19966, CCM 7496, CCUG 55538

Strain history: <- J. Glaeser, Univ. Giessen

NCBI tax ID(s): 1122612 (strain), 505248 (species)

SI-ID 402442

DSM 19966, CCUG 55538

Section

Novosphingobium acidiphilum FSW 06-204d is an aerobe, mesophilic, Gram-negative bacterium that was isolated from subsurface water of the humic acid-rich bog lake Grosse Fuchskuhle.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
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	*Sphingomonadales*
	Family	*Erythrobacteraceae*
	Genus	*Novosphingobium*
	Species	**Novosphingobium acidiphilum**
	Full Scientific Name (LPSN)	Novosphingobium acidiphilum Glaeser et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #32654]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.807

[Ref.: #32654]	Cell length	1.4 µm

[Ref.: #32654]	Cell width	0.58 µm

[Ref.: #32654]	Cell shape	rod-shaped

[Ref.: #32654]	Motility	yes

[Ref.: #32654]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8411]

Culture medium

K7 MEDIUM (DSMZ Medium 1199)

[Ref.: #8411]

Culture medium growth

[Ref.: #8411]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8411]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8411]	growth	28 °C
[Ref.: #32654]	growth	04-32 °C
[Ref.: #32654]	optimum	25 °C

[Ref.: #8411]	Temperature range	mesophilic
[Ref.: #32654]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32654]			optimum	5.75
[Ref.: #32654]			growth	4.5-7.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32654]

Oxygen tolerance

aerobe

[Ref.: #32654]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32654]		NaCl		growth	<0.75	%

[Ref.: #32654]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32654]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32654]	cellobiose ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[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.: #32654]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32654]	fructose ChEBI	+	carbon source
[Ref.: #32654]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32654]	glucose ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #32654]	leucine ChEBI	+	carbon source
[Ref.: #32654]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #32654]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #32654]	mannose ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #32654]	proline ChEBI	+	carbon source
[Ref.: #32654]	rhamnose ChEBI	+	carbon source
[Ref.: #32654]	sucrose ChEBI	+	carbon source
[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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #32654]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[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.: #8411]	23247	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	+

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

[Ref.: #8411]	Sample type/isolated from	subsurface water of the humic acid-rich bog lake Grosse Fuchskuhle
[Ref.: #8411]	Geographic location (country and/or sea, region)	north-eastern Germany
[Ref.: #8411]	Country	Germany
[Ref.: #8411]	Country ISO 3 Code	DEU
[Ref.: #8411]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Environmental	#Terrestrial	#Wetland (Swamp)
#Condition	#Acidic	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU336977 (>99% sequence identity) for Novosphingobium from Microbeatlas

Aquatic Samples	808
Soil Samples	635
Animal Samples	1036
Plant Samples	175
Total Samples	2654

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

[Ref.: #8411]

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.: #8411]	Novosphingobium acidiphilum strain FSW06-204d 16S ribosomal RNA gene, partial sequence	EU336977	1376	ENA	505248 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Novosphingobium acidiphilum DSM 19966	GCA_000429005	scaffold	GenBank	1122612 tax ID	*
[Ref.: #66792]	Novosphingobium acidiphilum DSM 19966	1122612.4	wgs	PATRIC	1122612 tax ID	*
[Ref.: #66792]	Novosphingobium acidiphilum DSM 19966	2523533537	draft	JGI IMG/M	1122612 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Novosphingobium acidiphilum DSM 19966 DSM 19966 NCBI: GCA_000429005.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Novosphingobium acidiphilum DSM 19966 DSM 19966 NCBI: GCA_000429005.1
[Ref.: #69480]	motile	yes	74.978	yes
[Ref.: #69480]	flagellated	no	87.391	no
[Ref.: #69480]	gram-positive	no	96.447	yes
[Ref.: #69480]	anaerobic	no	98.849	yes
[Ref.: #69480]	aerobic	yes	86.724	yes
[Ref.: #69480]	halophile	no	93.321	yes
[Ref.: #69480]	spore-forming	no	94.051	yes
[Ref.: #69480]	glucose-util	yes	90.056	no
[Ref.: #69480]	glucose-ferment	no	90.281	yes
[Ref.: #69480]	thermophile	no	89.278	no

Availability in culture collections External links

[Ref.: #8411]

Culture collection no.

DSM 19966, CCM 7496, CCUG 55538

[Ref.: #83327]

SI-ID 402442

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novosphingobium acidiphilum sp. nov., an acidophilic salt-sensitive bacterium isolated from the humic acid-rich Lake Grosse Fuchskuhle.	Glaeser SP, Kampfer P, Busse HJ, Langer S, Glaeser J	Int J Syst Evol Microbiol	10.1099/ijs.0.65852-0	2009	*

References

#8411

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19966

#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 )

#32654

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 #28865 (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) .

#68369

Automatically annotated from API 20NE .

#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 )

#83327

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-ID402442.1 )

#28865

IJSEM 323 2009 ( DOI 10.1099/ijs.0.65852-0 , PubMed 19196772 )

* These data were automatically processed and therefore are not curated

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Novosphingobium acidiphilum DSM 19966 DSM 19966

Novosphingobium acidiphilum DSM 19966 DSM 19966

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