Name: Chryseobacterium soldanellicola PSD1-4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5683

Type strain:

Species: Chryseobacterium soldanellicola

Strain Designation: PSD1-4

Culture col. no.: DSM 17072, KCTC 12382, NBRC 100864, CCUG 52904, CIP 109194

Strain history: CIP <- 2006, KCTC <- S.B. Kim, Chungnam Natl. Univ.

NCBI tax ID(s): 311333 (species)

SI-ID 232858

KCTC 12382, NBRC 100864, DSM 17072, CCUG 52904, CIP 109194, LMG 24042

Section

Chryseobacterium soldanellicola PSD1-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from roots of Calystegia soldanella growing on a coastal area.

Gram-negative
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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Weeksellaceae*
	Genus	*Chryseobacterium*
	Species	**Chryseobacterium soldanellicola**
	Full Scientific Name (LPSN)	Chryseobacterium soldanellicola Park et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31568]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #122653]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #31568]	Cell shape	rod-shaped
[Ref.: #122653]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #122653]	Motility	no

[Ref.: #31568]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6739]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #6739]

Culture medium growth

[Ref.: #6739]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6739]

Culture medium composition

expand / minimize

[Ref.: #37475]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37475]

Culture medium growth

[Ref.: #37475]

Culture medium composition

expand / minimize

[Ref.: #122653]

Culture medium

CIP Medium 72

[Ref.: #122653]

Culture medium growth

[Ref.: #122653]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6739]	growth	30 °C
[Ref.: #31568]	growth	05-30 °C
[Ref.: #31568]	optimum	25-30 °C
[Ref.: #37475]	growth	25 °C
[Ref.: #59722]	growth	30-37 °C
[Ref.: #67771]	growth	25-30 °C

[Ref.: #6739]	Temperature range	mesophilic
[Ref.: #31568]	Temperature range	mesophilic
[Ref.: #37475]	Temperature range	mesophilic
[Ref.: #59722]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31568]			optimum	5
[Ref.: #31568]			growth	05-07

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31568]	Oxygen tolerance	aerobe
[Ref.: #59722]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #122653]	Oxygen tolerance	obligate aerobe

[Ref.: #31568]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31568]		NaCl		growth	0-4	%
[Ref.: #31568]		NaCl		optimum	0-4	%

[Ref.: #31568]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31568]	acetate ChEBI	+	carbon source
[Ref.: #31568]	alanine ChEBI	+	carbon source
[Ref.: #31568]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #31568]	arabinose ChEBI	+	carbon source
[Ref.: #31568]	asparagine ChEBI	+	carbon source
[Ref.: #31568]	aspartate ChEBI	+	carbon source
[Ref.: #31568]	dextrin ChEBI	+	carbon source
[Ref.: #31568]	esculin ChEBI	+	hydrolysis
[Ref.: #31568]	fructose ChEBI	+	carbon source
[Ref.: #31568]	glucose ChEBI	+	carbon source
[Ref.: #31568]	glutamate ChEBI	+	carbon source
[Ref.: #31568]	glycerol ChEBI	+	carbon source
[Ref.: #31568]	maltose ChEBI	+	carbon source
[Ref.: #31568]	mannose ChEBI	+	carbon source
[Ref.: #122653]	nitrate ChEBI	-	reduction
[Ref.: #122653]	nitrite ChEBI	-	reduction
[Ref.: #31568]	phenylalanine ChEBI	+	carbon source
[Ref.: #31568]	proline ChEBI	+	carbon source
[Ref.: #31568]	propionate ChEBI	+	carbon source
[Ref.: #31568]	rhamnose ChEBI	+	carbon source
[Ref.: #31568]	serine ChEBI	+	carbon source
[Ref.: #31568]	threonine ChEBI	+	carbon source
[Ref.: #31568]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122653]		indole ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #122653]	alcohol dehydrogenase	-	1.1.1.1
[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.: #122653]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31568]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #31568]	gelatinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #122653]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122653]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #122653]	oxidase	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #122653]	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.: #122653]	11710	-	+	+	+	-	+	+	-	+	+	+	+	-	-	-	+	+	+	-	-

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

[Ref.: #6739]	Sample type/isolated from	roots of Calystegia soldanella growing on a coastal area
[Ref.: #6739]	Host species	Calystegia soldanella
[Ref.: #6739]	Geographic location (country and/or sea, region)	Tae-an
[Ref.: #6739]	Country	Republic of Korea
[Ref.: #6739]	Country ISO 3 Code	KOR
[Ref.: #6739]	Continent	Asia

[Ref.: #59722]	Sample type/isolated from	Root of Calystegia soldanella
[Ref.: #59722]	Geographic location (country and/or sea, region)	Taeahn
[Ref.: #59722]	Country	Republic of Korea
[Ref.: #59722]	Country ISO 3 Code	KOR
[Ref.: #59722]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From root of `Calystegia soldanella`
[Ref.: #67771]	Geographic location (country and/or sea, region)	Taeahn
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #122653]	Sample type/isolated from	Plant, Roots of Calystegia soldanella
[Ref.: #122653]	Geographic location (country and/or sea, region)	Taean
[Ref.: #122653]	Country	Republic of Korea
[Ref.: #122653]	Country ISO 3 Code	KOR
[Ref.: #122653]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Coast
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY883415 (>99% sequence identity) for Chryseobacterium soldanellicola from Microbeatlas

Aquatic Samples	14
Soil Samples	3
Animal Samples	11
Plant Samples	2
Total Samples	30

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

[Ref.: #6739]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122653]	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.: #6739]	Chryseobacterium soldanellicola strain PSD1-4 16S ribosomal RNA gene, partial sequence	AY883415	1415	ENA	311333 tax ID
[Ref.: #20218]	Chryseobacterium soldanellicola gene for 16S rRNA, partial sequence, strain: NBRC 100864	AB681270	1442	ENA	311333 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Chryseobacterium soldanellicola DSM 17072	GCA_900100115	contig	GenBank	311333 tax ID	*
[Ref.: #66792]	Chryseobacterium soldanellicola strain DSM 17072	311333.10	wgs	PATRIC	311333 tax ID	*
[Ref.: #66792]	Chryseobacterium soldanellicola DSM 17072	2684622906	draft	JGI IMG/M	311333 tax ID	*

[Ref.: #6739]

GC-content

28.8 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: Chryseobacterium soldanellicola strain DSM 17072 PATRIC: 311333.10
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Chryseobacterium soldanellicola strain DSM 17072 PATRIC: 311333.10
[Ref.: #69480]	gram-positive	no	98.17	yes
[Ref.: #69480]	anaerobic	no	99.501	yes
[Ref.: #69480]	halophile	no	94.025	no
[Ref.: #69480]	spore-forming	no	95.628	no
[Ref.: #69480]	glucose-util	yes	86.977	yes
[Ref.: #69480]	motile	no	90.503	no
[Ref.: #69480]	flagellated	no	96.021	no
[Ref.: #69480]	aerobic	yes	89.323	yes
[Ref.: #69480]	thermophile	no	99.224	yes
[Ref.: #69480]	glucose-ferment	no	91.214	no

Availability in culture collections External links

[Ref.: #6739]

Culture collection no.

DSM 17072, KCTC 12382, NBRC 100864, CCUG 52904, CIP 109194

[Ref.: #75165]

SI-ID 232858

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chryseobacterium subflavum sp. nov., isolated from soil.	Kong D, Wang Y, Li Q, Zhou Y, Jiang X, Xing Z, Wang Z, Ruan Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.005345	2022	*
Phylogeny	Chryseobacterium solani sp. nov., isolated from field-grown eggplant rhizosphere soil.	Du J, Ngo HTT, Won K, Kim KY, Jin FX, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.000266	2015	*
Phylogeny	Chryseobacterium polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Chryseobacterium.	Chen XY, Zhao R, Chen ZL, Liu L, Li XD, Li YH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0338-6	2014	*
Phylogeny	Chryseobacterium piperi sp. nov., isolated from a freshwater creek.	Strahan BL, Failor KC, Batties AM, Hayes PS, Cicconi KM, Mason CT, Newman JD	Int J Syst Evol Microbiol	10.1099/ijs.0.027805-0	2010	*
Phylogeny	Chryseobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a Rhus vernicifera-cultivated field.	Im WT, Yang JE, Kim SY, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.023614-0	2010	*
Phylogeny	Chryseobacterium piscicola sp. nov., isolated from diseased salmonid fish.	Ilardi P, Fernandez J, Avendano-Herrera R	Int J Syst Evol Microbiol	10.1099/ijs.0.007021-0	2009	*
Phylogeny	Chryseobacterium gregarium sp. nov., isolated from decaying plant material.	Behrendt U, Ulrich A, Schumann P	Int J Syst Evol Microbiol	10.1099/ijs.0.65544-0	2008	*
Phylogeny	Chryseobacterium aquaticum sp. nov., isolated from a water reservoir.	Kim KK, Lee KC, Oh HM, Lee JS	Int J Syst Evol Microbiol	10.1099/ijs.0.65491-0	2008	*
Phylogeny	Chryseobacterium soldanellicola sp. nov. and Chryseobacterium taeanense sp. nov., isolated from roots of sand-dune plants.	Park MS, Jung SR, Lee KH, Lee MS, Do JO, Kim SB, Bae KS	Int J Syst Evol Microbiol	10.1099/ijs.0.63825-0	2006	*

References

#6739

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17072

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#31568

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 #27858 (see below)

#37475 ; Curators of the CIP;
#59722 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52904

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#75165

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-ID232858.1 )

#122653 Collection of Institut Pasteur ; Curators of the CIP; CIP 109194

#27858

IJSEM 433 2006 ( DOI 10.1099/ijs.0.63825-0 , PubMed 16449453 )

* These data were automatically processed and therefore are not curated

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Chryseobacterium soldanellicola strain DSM 17072

Chryseobacterium soldanellicola strain DSM 17072

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