Name: Sandarakinorhabdus limnophila so42
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14167

Type strain:

Species: Sandarakinorhabdus limnophila

Strain Designation: so42

Culture col. no.: DSM 17366, CECT 7086, CIP 109260

Strain history: CIP <- 2006, CECT <- 2005, F. Gich: strain so42

NCBI tax ID(s): 1123240 (strain), 210512 (species)

SI-ID 291010

CECT 7086, DSM 17366, CIP 109260

Section

Sandarakinorhabdus limnophila so42 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from mesotrophic freshwater lake Starnberger See.

Gram-negative
rod-shaped
aerobe
psychrophilic
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	*Sphingosinicellaceae*
	Genus	*Sandarakinorhabdus*
	Species	**Sandarakinorhabdus limnophila**
	Full Scientific Name (LPSN)	Sandarakinorhabdus limnophila Gich and Overmann 2006

Information on morphological and physiological properties Morphology

[Ref.: #31653]	Gram stain	negative
[Ref.: #120603]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.987

[Ref.: #31653]	Cell length	0.8 µm

[Ref.: #31653]	Cell width	0.31 µm

[Ref.: #31653]	Cell shape	rod-shaped
[Ref.: #120603]	Cell shape	rod-shaped

[Ref.: #31653]	Motility	no
[Ref.: #120603]	Motility	no

[Ref.: #31653]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6836]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #6836]

Culture medium growth

[Ref.: #6836]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6836]

Culture medium composition

expand / minimize

[Ref.: #37493]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

[Ref.: #37493]

Culture medium growth

[Ref.: #37493]

Culture medium composition

expand / minimize

[Ref.: #120603]

Culture medium

CIP Medium 566

[Ref.: #120603]

Culture medium growth

[Ref.: #120603]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #6836]			growth	15 °C
[Ref.: #37493]			growth	15 °C

[Ref.: #6836]	Temperature range	psychrophilic
[Ref.: #37493]	Temperature range	psychrophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31653]

Oxygen tolerance

aerobe

[Ref.: #31653]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

[Ref.: #31653]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31653]	acetate ChEBI	+	carbon source
[Ref.: #31653]	lactate ChEBI	+	carbon source
[Ref.: #120603]	nitrate ChEBI	-	reduction
[Ref.: #120603]	nitrite ChEBI	-	reduction
[Ref.: #31653]	succinate ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #120603]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31653]	catalase	+	1.11.1.6
[Ref.: #120603]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120603]	oxidase	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #120603]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #120603]	11748	-	+	+	+	-	+	+	-	+	-	+	+	+	+	-	-	-	-	-	-

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

[Ref.: #6836]	Sample type/isolated from	mesotrophic freshwater lake Starnberger See
[Ref.: #6836]	Geographic location (country and/or sea, region)	Bavaria, Starnberg
[Ref.: #6836]	Country	Germany
[Ref.: #6836]	Country ISO 3 Code	DEU
[Ref.: #6836]	Continent	Europe

[Ref.: #120603]	Sample type/isolated from	Environment, Mesotrophic freshwater lake Starnberger See
[Ref.: #120603]	Geographic location (country and/or sea, region)	Bavaria
[Ref.: #120603]	Country	Germany
[Ref.: #120603]	Country ISO 3 Code	DEU
[Ref.: #120603]	Continent	Europe
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY902680 (>99% sequence identity) for Sandarakinorhabdus limnophila subclade from Microbeatlas

Aquatic Samples	4615
Soil Samples	361
Animal Samples	424
Plant Samples	146
Total Samples	5546

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

[Ref.: #6836]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120603]	Biosafety level	1	Risk group (French classification)

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.: #6836]	Sandarakinorhabdus limnophila strain so42 16S ribosomal RNA gene, partial sequence	AY902680	1346	ENA	210512 tax ID

Genome sequence information:

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

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sandarakinorhabdus limnophila DSM 17366 strain AE-03may19-188	1123240.18	wgs	PATRIC	1123240 tax ID	*
[Ref.: #66792]	Sandarakinorhabdus limnophila DSM 17366	1123240.4	wgs	PATRIC	1123240 tax ID	*
[Ref.: #66792]	Sandarakinorhabdus limnophila DSM 17366	2523231034	draft	JGI IMG/M	1123240 tax ID	*
[Ref.: #66792]	Sandarakinorhabdus limnophila DSM 17366 AE-03may19-188	GCA_945860695	contig	GenBank	1123240 tax ID	*
[Ref.: #66792]	Sandarakinorhabdus limnophila DSM 17366 TrE-25oct19-257	GCA_945866105	scaffold	GenBank	1123240 tax ID	*
[Ref.: #66792]	Sandarakinorhabdus limnophila DSM 17366 MaE-04nov19-252	GCA_945878055	contig	GenBank	1123240 tax ID	*

[Ref.: #6836]	GC-content	64.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31653]	GC-content	64.3 mol%

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: Sandarakinorhabdus limnophila DSM 17366 PATRIC: 1123240.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sandarakinorhabdus limnophila DSM 17366 PATRIC: 1123240.4
[Ref.: #69480]	motile	no	81.863	yes
[Ref.: #69480]	flagellated	no	96.421	no
[Ref.: #69480]	gram-positive	no	97.328	no
[Ref.: #69480]	anaerobic	no	99.651	yes
[Ref.: #69480]	aerobic	yes	94.79	no
[Ref.: #69480]	halophile	no	82.644	no
[Ref.: #69480]	spore-forming	no	96.723	no
[Ref.: #69480]	glucose-util	yes	69.935	no
[Ref.: #69480]	thermophile	no	95.039	yes
[Ref.: #69480]	glucose-ferment	no	90.47	no

Availability in culture collections External links

[Ref.: #6836]

Culture collection no.

DSM 17366, CECT 7086, CIP 109260

[Ref.: #83330]

SI-ID 291010

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Glacieibacterium frigidum gen. nov., sp. nov., a novel member of the family Sphingosinicellaceae isolated from a glacier.	Liu Q, Yang LL, Liu HC, Zhang GQ, Xin YH	Int J Syst Evol Microbiol	10.1099/ijsem.0.004886	2021	*
Phylogeny	Sandarakinorhabdus rubra sp. nov., and Sandarakinorhabdus oryzae sp. nov., isolated from oxidized rice paddy soil.	Cho GY, Whang KS	Int J Syst Evol Microbiol	10.1099/ijsem.0.004722	2021	*
Phylogeny	Sandarakinorhabdus limnophila gen. nov., sp. nov., a novel bacteriochlorophyll a-containing, obligately aerobic bacterium isolated from freshwater lakes.	Gich F, Overmann J	Int J Syst Evol Microbiol	10.1099/ijs.0.63970-0	2006	*

References

#6836

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17366

#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 )

#31653

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 #27935 (see below)

#37493 ; Curators of the CIP;

#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) .

#68382

Automatically annotated from API zym .

#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 )

#83330

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-ID291010.1 )

#120603 Collection of Institut Pasteur ; Curators of the CIP; CIP 109260

#27935

IJSEM 847 2006 ( DOI 10.1099/ijs.0.63970-0 , PubMed 16585705 )

* These data were automatically processed and therefore are not curated

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Sandarakinorhabdus limnophila DSM 17366

Sandarakinorhabdus limnophila DSM 17366

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