Name: Chryseomonas luteola BY-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24437

Type strain:

Species: Chryseomonas luteola

Strain Designation: BY-1

Culture col. no.: DSM 27927, ACCC 05688, KACC 15471

Strain history: <- KACC <- Z. Zeng et al., Key Laboratory of Microbiological Engineering of Agricultural Environment, Nanjing Agricultural University

NCBI tax ID(s): 1076620 (species)

Section

Chryseomonas luteola BY-1 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from soil form agricultural field exposed to herbicide fomesafen for many years.

Gram-negative
rod-shaped
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	*Gammaproteobacteria*
	Order	*Pseudomonadales*
	Family	*Pseudomonadaceae*
	Genus	*Chryseomonas*
	Species	**Chryseomonas luteola**
	Full Scientific Name (LPSN)	Chryseomonas luteola (Kodama et al. 1985) Holmes et al. 1987

	Synonym	Pseudomonas luteola
	Synonym	Chryseomonas polytricha
	Synonym	Pseudomonas zeshuii

Information on morphological and physiological properties Morphology

[Ref.: #30513]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #30513]	Cell length	3 µm

[Ref.: #30513]	Cell width	0.7 µm

[Ref.: #30513]	Cell shape	rod-shaped

[Ref.: #30513]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %99.075

[Ref.: #30513]

Pigment production

yes

Multimedia content

[Ref.: #21140]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21140]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #21140]

Culture medium growth

[Ref.: #21140]

Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #21140]

Culture medium

LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)

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Culture medium growth

[Ref.: #21140]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21140]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21140]	growth	28 °C
[Ref.: #30513]	growth	20-40 °C
[Ref.: #30513]	optimum	32.5 °C

[Ref.: #21140]	Temperature range	mesophilic
[Ref.: #30513]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30513]			optimum	7
[Ref.: #30513]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30513]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30513]		NaCl		growth	0-5	%
[Ref.: #30513]		NaCl		optimum	0.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30513]	2-oxopentanoate ChEBI	+	carbon source
[Ref.: #30513]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #30513]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30513]	alanine ChEBI	+	carbon source
[Ref.: #30513]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #30513]	asparagine ChEBI	+	carbon source
[Ref.: #30513]	aspartate ChEBI	+	carbon source
[Ref.: #30513]	citrate 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.: #30513]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #30513]	formate ChEBI	+	carbon source
[Ref.: #30513]	fucose ChEBI	+	carbon source
[Ref.: #30513]	galacturonate ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #30513]	gluconate ChEBI	+	carbon source
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30513]	glucose ChEBI	+	carbon source
[Ref.: #30513]	glutamate ChEBI	+	carbon source
[Ref.: #30513]	glycerol ChEBI	+	carbon source
[Ref.: #30513]	L-alaninamide ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30513]	malonate ChEBI	+	carbon source
[Ref.: #30513]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #30513]	mannitol ChEBI	+	carbon source
[Ref.: #30513]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #30513]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #30513]	proline ChEBI	+	carbon source
[Ref.: #30513]	quinate ChEBI	+	carbon source
[Ref.: #30513]	rhamnose ChEBI	+	carbon source
[Ref.: #30513]	serine ChEBI	+	carbon source
[Ref.: #30513]	succinate ChEBI	+	carbon source
[Ref.: #30513]	trehalose 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.: #30513]	catalase	+	1.11.1.6
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[Ref.: #30513]	gelatinase	+
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #30513]	urease	+	3.5.1.5
[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.: #21140]	23409	+	-	-	+	+	+	+	+	+	+	+	+	-	+	+	+	-	+	+	-	-

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

[Ref.: #21140]	Sample type/isolated from	soil form agricultural field exposed to herbicide fomesafen for many years
[Ref.: #21140]	Geographic location (country and/or sea, region)	Heilongjiang province, Qiqihar city
[Ref.: #21140]	Country	China
[Ref.: #21140]	Country ISO 3 Code	CHN
[Ref.: #21140]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JN411093 (>99% sequence identity) for Pseudomonas from Microbeatlas

Aquatic Samples	6287
Soil Samples	2524
Animal Samples	12446
Plant Samples	2307
Total Samples	23564

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

[Ref.: #21140]

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.: #21140]	Pseudomonas zeshuii strain BY-1 16S ribosomal RNA gene, partial sequence	JN411093	1459	ENA	1076620 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudomonas zeshuii KACC 15471	GCA_900141925	scaffold	GenBank	1076620 tax ID	*
[Ref.: #66792]	Pseudomonas zeshuii strain KACC 15471	1076620.3	wgs	PATRIC	1076620 tax ID	*
[Ref.: #66792]	Pseudomonas zeshuii DSM 27927	2663762797	draft	JGI IMG/M	1076620 tax ID	*

[Ref.: #21140]

GC-content

55.3 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: Pseudomonas zeshuii KACC 15471 NCBI: GCA_900141925.1
[Ref.: #69481]	spore-forming	no	72	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudomonas zeshuii KACC 15471 NCBI: GCA_900141925.1
[Ref.: #69480]	motile	yes	86.59	no
[Ref.: #69480]	flagellated	no	52.765	yes
[Ref.: #69480]	gram-positive	no	98.438	yes
[Ref.: #69480]	anaerobic	no	98.498	no
[Ref.: #69480]	aerobic	yes	92.152	no
[Ref.: #69480]	halophile	no	91.232	yes
[Ref.: #69480]	spore-forming	no	94.438	yes
[Ref.: #69480]	thermophile	no	99.58	yes
[Ref.: #69480]	glucose-util	yes	95.535	yes
[Ref.: #69480]	glucose-ferment	no	87.952	yes

Availability in culture collections External links

[Ref.: #21140]

Culture collection no.

DSM 27927, ACCC 05688, KACC 15471

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudomonas zeshuii sp. nov., isolated from herbicide-contaminated soil.	Feng Z, Zhang J, Huang X, Zhang J, Chen M, Li S	Int J Syst Evol Microbiol	10.1099/ijs.0.037796-0	2011	*
Metabolism	Microbial degradation of fomesafen by a newly isolated strain Pseudomonas zeshuii BY-1 and the biochemical degradation pathway.	Feng ZZ, Li QF, Zhang J, Zhang J, Huang X, Lu P, Li SP	J Agric Food Chem	10.1021/jf3011307	2012	*

References

#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 )

#21140

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27927

#30513

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 #26845 (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 )

#26845

IJSEM 2608 2012 ( DOI 10.1099/ijs.0.037796-0 , PubMed 22199212 )

* These data were automatically processed and therefore are not curated

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Pseudomonas zeshuii KACC 15471

Pseudomonas zeshuii KACC 15471

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