Name: Lysobacter soli DSM 24712
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17498

Type strain:

Species: Lysobacter soli

Culture col. no.: DSM 24712, KCTC 22011, LMG 24126, DCY 21

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 453783 (species)

SI-ID 307677

LMG 24126, KCTC 22011, DSM 24712

Section

Lysobacter soli DSM 24712 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng field.

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	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Lysobacter*
	Species	**Lysobacter soli**
	Full Scientific Name (LPSN)	Lysobacter soli Srinivasan et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29584]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #29584]	Cell length	0.6-0.9 µm

[Ref.: #29584]	Cell width	0.2-0.5 µm

[Ref.: #29584]	Cell shape	rod-shaped

[Ref.: #29584]	Motility	yes

[Ref.: #29584]	Flagellum arrangement	gliding

[Ref.: #29584]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17735]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #17735]

Culture medium growth

[Ref.: #17735]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17735]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17735]	growth	28 °C
[Ref.: #29584]	growth	04-42 °C
[Ref.: #29584]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #17735]	Temperature range	mesophilic
[Ref.: #29584]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29584]			optimum	7-7.5
[Ref.: #29584]			growth	05-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29584]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29584]	Observation	aggregates in chains
[Ref.: #67771]	Observation	quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29584]	acetate ChEBI	+	carbon source
[Ref.: #29584]	arabinose ChEBI	+	carbon source
[Ref.: #29584]	fucose ChEBI	+	carbon source
[Ref.: #29584]	glucose ChEBI	+	carbon source
[Ref.: #29584]	maltose ChEBI	+	carbon source
[Ref.: #29584]	mannose ChEBI	+	carbon source
[Ref.: #29584]	nitrate ChEBI	+	reduction

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29584]		catalase	+	1.11.1.6
[Ref.: #29584]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	tryptophan metabolism	78.95	30 of 38
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	vitamin B12 metabolism	41.18	14 of 34
[Ref.: #66794]	oxidative phosphorylation	40.66	37 of 91
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #17735]	Sample type/isolated from	soil of ginseng field
[Ref.: #17735]	Geographic location (country and/or sea, region)	Daejeon City
[Ref.: #17735]	Country	Republic of Korea
[Ref.: #17735]	Country ISO 3 Code	KOR
[Ref.: #17735]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil, ginseng field
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF623862 (>99% sequence identity) for Lysobacter from Microbeatlas

Aquatic Samples	78
Soil Samples	1232
Animal Samples	69
Plant Samples	230
Total Samples	1609

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

[Ref.: #17735]

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.: #17735]	Lysobacter sp. DCY21T 16S ribosomal RNA gene, partial sequence	EF623862	1496	ENA	453783 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Lysobacter soli KCTC 22011	GCA_003382285	contig	GenBank	453783 tax ID	*
[Ref.: #66792]	Lysobacter soli strain KCTC 22011	453783.3	wgs	PATRIC	453783 tax ID	*
[Ref.: #66792]	Lysobacter soli KCTC 22011	2838987433	draft	JGI IMG/M	453783 tax ID	*

[Ref.: #17735]

GC-content

65.4 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lysobacter soli strain KCTC 22011 PATRIC: 453783.3
[Ref.: #69480]	gram-positive	no	98.479	yes
[Ref.: #69480]	anaerobic	no	98.344	yes
[Ref.: #69480]	halophile	no	95.762	no
[Ref.: #69480]	spore-forming	no	97.15	no
[Ref.: #69480]	glucose-util	yes	88.631	yes
[Ref.: #69480]	aerobic	yes	94.804	yes
[Ref.: #69480]	flagellated	no	88.085	yes
[Ref.: #69480]	thermophile	no	97.598	yes
[Ref.: #69480]	motile	yes	74.752	no
[Ref.: #69480]	glucose-ferment	no	89.75	no

Availability in culture collections External links

[Ref.: #17735]

Culture collection no.

DSM 24712, KCTC 22011, LMG 24126, DCY 21

[Ref.: #86495]

SI-ID 307677

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lysobacter prati sp. nov., isolated from a plateau meadow sample.	Fang BZ, Xie YG, Zhou XK, Zhang XT, Liu L, Jiao JY, Xiao M, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-020-01386-6	2020	*
Phylogeny	Lysobacter tabacisoli sp. nov., isolated from rhizosphere soil of Nicotiana tabacum L.	Xiao M, Zhou XK, Chen X, Duan YQ, Alkhalifah DHM, Im WT, Hozzein WN, Chen W, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003164	2018	*
Phylogeny	Lysobacter silvisoli sp. nov., isolated from forest soil.	Zhang XJ, Yao Q, Wang YH, Yang SZ, Feng GD, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003105	2018	*
Phylogeny	Lysobacter pedocola sp. nov., a novel species isolated from Korean soil.	Jang JH, Lee D, Seo T	J Microbiol	10.1007/s12275-018-8046-y	2018	*
Phylogeny	Lysobacter cavernae sp. nov., a novel bacterium isolated from a cave sample.	Chen W, Zhao YL, Cheng J, Zhou XK, Salam N, Fang BZ, Li QQ, Hozzein WN, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0704-7	2016	*
Phylogeny	Lysobacter panacisoli sp. nov., isolated from ginseng soil.	Choi JH, Seok JH, Cha JH, Cha CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.062034-0	2014	*
Phylogeny	Lysobacter soli sp. nov., isolated from soil of a ginseng field.	Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.016428-0	2009	*

References

#17735

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24712

#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 )

#29584

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 #25976 (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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

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

#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) .

#86495

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-ID307677.1 )

#25976

IJSEM 1543 2010 ( DOI 10.1099/ijs.0.016428-0 , PubMed 19684312 )

* These data were automatically processed and therefore are not curated

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Lysobacter soli strain KCTC 22011

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