Name: Limnohabitans parvus II-B4
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3034

Type strain:

Species: Limnohabitans parvus

Strain Designation: II-B4

Culture col. no.: DSM 21592, CIP 109845, CCUG 56787

Strain history: CIP <- 2008, V. Kasalicky, CAS Center, Ceske Budejovice, Czech Republic: strain II-B4

NCBI tax ID(s): 540061 (species)

SI-ID 371486

CIP 109845, DSM 21592, CCUG 56787

Special Collections

Section

Limnohabitans parvus II-B4 is an aerobe, chemoorganotroph, Gram-negative bacterium that was isolated from meso-eutrophic freshwater reservoir.

Gram-negative
rod-shaped
aerobe
chemoorganotroph
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	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Limnohabitans*
	Species	**Limnohabitans parvus**
	Full Scientific Name (LPSN)	Limnohabitans parvus Kasalický et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #23094]	Gram stain	negative
[Ref.: #121613]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.462

[Ref.: #23094]	Cell length	0.46-0.74 µm

[Ref.: #23094]	Cell width	0.25-0.35 µm

[Ref.: #23094]	Cell shape	rod-shaped
[Ref.: #121613]	Cell shape	rod-shaped

[Ref.: #23094]	Motility	no
[Ref.: #121613]	Motility	no

[Ref.: #23094]	Colony size	1.0-2.0 mm
[Ref.: #23094]	Incubation period	2-5 days

[Ref.: #61090]	Incubation period	2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15832]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15832]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #15832]

Culture medium composition

expand / minimize

[Ref.: #23094]

Culture medium

Brain Heart Infusion agar

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Culture medium growth

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Culture medium

Casitone agar

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Culture medium growth

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Culture medium

lysogeny broth agar

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Culture medium growth

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Culture medium

nutrient broth soyotone yeast extract medium

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Culture medium growth

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Culture medium

peptone agar

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

standards method agar

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Culture medium growth

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Culture medium

tryptic soy broth agar

[Ref.: #23094]

Culture medium growth

[Ref.: #40072]

Culture medium

MEDIUM 701 - for -Limnicola

[Ref.: #40072]

Culture medium growth

[Ref.: #121613]

Culture medium

CIP Medium 701

[Ref.: #121613]

Culture medium growth

[Ref.: #121613]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15832]	growth	28 °C
[Ref.: #23094]	growth	4.0-34.0 °C
[Ref.: #40072]	growth	21 °C
[Ref.: #61090]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23094]	Oxygen tolerance	aerobe
[Ref.: #23094]	Oxygen tolerance	facultative anaerobe
[Ref.: #61090]	Oxygen tolerance	aerobe
[Ref.: #121613]	Oxygen tolerance	obligate aerobe

[Ref.: #23094]

Nutrition type

chemoorganotroph

[Ref.: #69480]	Ability of spore formation	no Confidence in %93.532
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23094]		NaCl	no	growth	>0.5	%
[Ref.: #23094]		NaCl		growth	0.0-0.5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23094]	2-oxoglutarate ChEBI	+	assimilation
[Ref.: #23094]	acetate ChEBI	-	assimilation
[Ref.: #23094]	betaine ChEBI	-	assimilation
[Ref.: #23094]	butyrate ChEBI	+	assimilation
[Ref.: #23094]	citrate ChEBI	+	assimilation
[Ref.: #23094]	D-galactose ChEBI	-	assimilation
[Ref.: #23094]	D-gluconate ChEBI	-	assimilation
[Ref.: #23094]	D-glucose ChEBI	+	assimilation
[Ref.: #23094]	D-mannose ChEBI	+	assimilation
[Ref.: #23094]	D-ribose ChEBI	-	assimilation
[Ref.: #23094]	ethanol ChEBI	-	assimilation
[Ref.: #23094]	fumarate ChEBI	+	assimilation
[Ref.: #23094]	glutamine ChEBI	+	assimilation
[Ref.: #23094]	glycerate ChEBI	+	assimilation
[Ref.: #23094]	glycerol ChEBI	+	assimilation
[Ref.: #23094]	glycolate ChEBI	-	assimilation
[Ref.: #23094]	glyoxylate ChEBI	-	assimilation
[Ref.: #23094]	L-arginine ChEBI	-	assimilation
[Ref.: #23094]	L-carnitine ChEBI	-	assimilation
[Ref.: #23094]	L-glutamate ChEBI	+	assimilation
[Ref.: #23094]	L-histidine ChEBI	-	assimilation
[Ref.: #23094]	L-phenylalanine ChEBI	-	assimilation
[Ref.: #23094]	L-proline ChEBI	+	assimilation
[Ref.: #23094]	L-serine ChEBI	-	assimilation
[Ref.: #23094]	L-sorbose ChEBI	-	assimilation
[Ref.: #23094]	L-tryptophan ChEBI	+	assimilation
[Ref.: #23094]	lactate ChEBI	-	assimilation
[Ref.: #23094]	malate ChEBI	+	assimilation
[Ref.: #23094]	malonate ChEBI	-	assimilation
[Ref.: #23094]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #121613]	nitrate ChEBI	-	reduction
[Ref.: #121613]	nitrite ChEBI	-	reduction
[Ref.: #23094]	oxalate ChEBI	-	assimilation
[Ref.: #23094]	oxaloacetate ChEBI	-	assimilation
[Ref.: #23094]	propionate ChEBI	-	assimilation
[Ref.: #23094]	pyruvate ChEBI	+	assimilation
[Ref.: #23094]	spermidine ChEBI	-	assimilation
[Ref.: #23094]	succinate ChEBI	+	assimilation
[Ref.: #23094]	sucrose ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #121613]		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.: #23094]	catalase	+	1.11.1.6
[Ref.: #121613]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #23094]	cytochrome oxidase	+	1.9.3.1
[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.: #121613]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121613]	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.: #121613]	12155	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #15832]	Sample type/isolated from	meso-eutrophic freshwater reservoir
[Ref.: #15832]	Geographic location (country and/or sea, region)	Rimov
[Ref.: #15832]	Country	Czech Republic
[Ref.: #15832]	Country ISO 3 Code	CZE
[Ref.: #15832]	Continent	Europe

[Ref.: #61090]	Sample type/isolated from	Freshwater
[Ref.: #61090]	Sampling date	2006-10-09
[Ref.: #61090]	Geographic location (country and/or sea, region)	Rimov reservoir
[Ref.: #61090]	Country	Czech Republic
[Ref.: #61090]	Country ISO 3 Code	CZE
[Ref.: #61090]	Continent	Europe

[Ref.: #121613]	Sample type/isolated from	Environment, Water, pelagial
[Ref.: #121613]	Geographic location (country and/or sea, region)	Rimov
[Ref.: #121613]	Country	Czech Republic
[Ref.: #121613]	Country ISO 3 Code	CZE
[Ref.: #121613]	Continent	Europe

[Ref.: #23094]	Enrichment culture	Nutrient broth soyotone yeast extract (NSY) medium
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

[Ref.: #15832]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121613]	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.: #15832]	Limnohabitans parvus partial 16S rRNA, IGS, tRNA-Ile, tRNA-Ala and 23S rRNA genes, type strain II-B4T	FM165536	2324	GenBank ENA	1293052 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Limnohabitans parvus II-B4	GCA_003063455	contig	GenBank ENA	1293052 tax ID	*
[Ref.: #66792]	Limnohabitans parvus II-B4	1293052.5	wgs	PATRIC	1293052 tax ID	*
[Ref.: #66792]	Limnohabitans parvus II-B4	2834088864	draft	JGI IMG/M	1293052 tax ID	*

[Ref.: #15832]	GC-content	59.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #23094]	GC-content	59.9 mol%

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: Limnohabitans parvus II-B4 PATRIC: 1293052.5
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Limnohabitans parvus II-B4 PATRIC: 1293052.5
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.462	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.314	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	93.532	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	84.774	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.379	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	82.147	yes

Availability in culture collections External links

[Ref.: #15832]

Culture collection no.

DSM 21592, CIP 109845, CCUG 56787

[Ref.: #72554]

SI-ID 371486

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans.	Kasalicky V, Jezbera J, Simek K, Hahn MW	Int J Syst Evol Microbiol	10.1099/ijs.0.018952-0	2010	*

References

#15832

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21592

#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 )

#23094

Vojtech Kasalický,Jan Jezbera,Karel Simek,Martin W. Hahn: Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans. IJSEM 60: 2710 - 2714 2010 ( DOI 10.1099/ijs.0.018952-0 , PubMed 20061501 )

#40072 ; Curators of the CIP;
#61090 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56787

#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 .

#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 )

#72554

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-ID371486.1 )

#121613 Collection of Institut Pasteur ; Curators of the CIP; CIP 109845
* These data were automatically processed and therefore are not curated

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