Lonsdalea populi (DSM 25466, NCAIM B 02483, CFCC 13125)

Name: Lonsdalea populi (DSM 25466, NCAIM B 02483, CFCC 13125)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23013

Type strain

Strain Designation NY060

Culture col. no. DSM 25466 NCAIM B 02483 CFCC 13125 LMG 27349 NY060

NCBI tax ID(s) 1172565

Special Collections DSMZ Literature strains

History DSMZ <- T. Lakatos, Nemaform Ltd., Nagykálló, Hungary; NY060 <- T. Tóth and T. Lakatos, Research and Extension Centre for Fruit Growing, Hungary

Links

Lonsdalea populi NY060 is a Gram-negative, motile, rod-shaped plant pathogen that forms circular colonies and was isolated from bark canker of poplar Populus x euramericana.

Gram-negative motile rod-shaped colony-forming plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 382488

NCAIM B.02483,LMG 27349,DSM 25466

@ref 20215

Last LPSN update 2026-05-29 08:30:21

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Pectobacteriaceae

Genus Lonsdalea

Species Lonsdalea populi

Full scientific name Lonsdalea populi (Tóth et al. 2013) Li et al. 2017

Synonyms (1)

Lonsdalea quercina subsp. populi

BacDive ID	Other strains from **Lonsdalea populi** (2)	Type strain
23014	L. populi NY041, DSM 25467
23015	L. populi NY011, DSM 25468

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
30717	negative	1.5 µm	0.5 µm	rod-shaped
65502	negative	1.0-2.0 µm	0.5-1.0 µm	rod-shaped	peritrichous
125439	negative					98.72

Colony morphology

@ref	Colony color	Colony shape	Medium used
65502	light cream	circular	TSA

Pigmentation

30717

Productionyes

Multimedia

@ref:	19344
multimedia content:	DSM_25466.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_25466.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19344	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
65502	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)
19344	positive	growth	28
30717	positive	growth	08-44
30717	positive	optimum	32
65502	positive	growth	8-44
65502	positive	optimum	30-34

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.618

Spore formation

@ref	Spore formation	Confidence
125439		99.705

Observation

30717

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65502	30916 ChEBI	2-oxoglutarate	+/-	carbon source
65502	18305 ChEBI	arbutin	+	builds acid from
30717	35391 ChEBI	aspartate	+	carbon source
30717	17057 ChEBI	cellobiose	+	carbon source
65502	17057 ChEBI	cellobiose	+/-	carbon source
65502	16947 ChEBI	citrate	-	carbon source
65502	15824 ChEBI	D-fructose	+	builds acid from
65502	15824 ChEBI	D-fructose	+	carbon source
65502	12936 ChEBI	D-galactose	+	builds acid from
65502	12936 ChEBI	D-galactose	+	carbon source
65502	8391 ChEBI	D-gluconate	+	carbon source
65502	17634 ChEBI	D-glucose	+	builds acid from
65502	17634 ChEBI	D-glucose	+	carbon source
65502	14314 ChEBI	D-glucose 6-phosphate	+	carbon source
65502	16899 ChEBI	D-mannitol	+	builds acid from
65502	16899 ChEBI	D-mannitol	+	carbon source
65502	16024 ChEBI	D-mannose	+	builds acid from
65502	16024 ChEBI	D-mannose	+	carbon source
65502	27605 ChEBI	D-psicose	+	carbon source
65502	16988 ChEBI	D-ribose	+	builds acid from
65502		esculin ferric citrate	+	builds acid from
65502	15740 ChEBI	formate	-	carbon source
30717	28757 ChEBI	fructose	+	carbon source
30717	28260 ChEBI	galactose	+	carbon source
65502	28066 ChEBI	gentiobiose	+/-	carbon source
30717	24265 ChEBI	gluconate	+	carbon source
30717	17234 ChEBI	glucose	+	carbon source
30717	29987 ChEBI	glutamate	+	carbon source
30717	17754 ChEBI	glycerol	+	carbon source
65502	17754 ChEBI	glycerol	+	builds acid from
65502	17754 ChEBI	glycerol	+	carbon source
65502	29985 ChEBI	L-glutamate	+/-	carbon source
65502	15971 ChEBI	L-histidine	-	carbon source
65502	15603 ChEBI	L-leucine	-	carbon source
65502	17295 ChEBI	L-phenylalanine	-	carbon source
65502	16857 ChEBI	L-threonine	-	carbon source
65502	24996 ChEBI	lactate	-	carbon source
30717	29864 ChEBI	mannitol	+	carbon source
30717	37684 ChEBI	mannose	+	carbon source
65502	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
65502	320055 ChEBI	methyl beta-D-glucopyranoside	+	carbon source
30717	37657 ChEBI	methyl D-glucoside	+	carbon source
30717	51850 ChEBI	methyl pyruvate	+	carbon source
65502	51850 ChEBI	methyl pyruvate	+	carbon source
30717	506227 ChEBI	N-acetylglucosamine	+	carbon source
65502	506227 ChEBI	N-acetylglucosamine	+	builds acid from
65502	506227 ChEBI	N-acetylglucosamine	+	carbon source
65502	17632 ChEBI	nitrate	-	reduction
65502	32032 ChEBI	potassium gluconate	+	builds acid from
65502	16634 ChEBI	raffinose	-	builds acid from
65502	16634 ChEBI	raffinose	-	carbon source
65502	17814 ChEBI	salicin	+	builds acid from
30717	30031 ChEBI	succinate	+	carbon source
30717	17992 ChEBI	sucrose	+	carbon source
65502	17992 ChEBI	sucrose	+	builds acid from
65502	17992 ChEBI	sucrose	+	carbon source
30717	27082 ChEBI	trehalose	+	carbon source
65502	27082 ChEBI	trehalose	+	builds acid from
65502	27082 ChEBI	trehalose	+	carbon source
65502	32528 ChEBI	turanose	-	builds acid from
65502	32528 ChEBI	turanose	-	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite
65502	15688 ChEBI	acetoin
65502	16136 ChEBI	hydrogen sulfide
65502	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
65502	arginine dihydrolase	-	3.5.3.6
65502	beta-galactosidase	-	3.2.1.23
30717	catalase	+	1.11.1.6
65502	catalase	+	1.11.1.6
65502	cytochrome oxidase	-	1.9.3.1
65502	gelatinase	-
65502	lysine decarboxylase	-	4.1.1.18
65502	ornithine decarboxylase	-	4.1.1.17
65502	tryptophan deaminase	-	4.1.99.1
65502	urease	-	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Bark

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
19344	bark canker of poplar Populus x euramericana	Populus x euramericana	Mikebuda (19° 40' 17.2'' N, 47° 09' 43.6'' E)	Hungary	HUN	Europe	47.1621	19.6714 47.1621/19.6714
65502	Populus x euramericana		Mikebuda	Hungary	HUN	Europe

Taxonmaps

69479

Global distribution of 16S sequence JQ291575 (>99% sequence identity) for Lonsdalea from Microbeatlas

Aquatic Samples	154
Soil Samples	95
Animal Samples	1104
Plant Samples	208
Total Samples	1561

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
19344		1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
65502	ASM211155v1 assembly for Lonsdalea populi CFCC 11748	contig	GCA_002111555	1172565.4	2849716479	1172565	38.78

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19344	Lonsdalea quercina subsp. populi strain NY060 16S ribosomal RNA gene, partial sequence	JQ291575	1503		1172565
124043	Lonsdalea quercina subsp. populi strain DSM 25466 16S ribosomal RNA gene, partial sequence.	KU531470	670		1172565

GC content

@ref	GC-content (mol%)	Method
19344	55.4	sequence analysis
65502	55.4	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM211155v1 assembly for Lonsdalea populi CFCC 11748
NCBI: GCA_002111555

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	98.72	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.62	no
125439	motility	BacteriaNetⓘ	yes	84.41	no
125439	spore_formation	BacteriaNetⓘ	no	99.71	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Elevation of three subspecies of Lonsdalea quercina to species level: Lonsdalea britannica sp. nov., Lonsdalea iberica sp. nov. and Lonsdalea populi sp. nov.	Li Y, Xue H, Guo LM, Koltay A, Palacio-Bielsa A, Chang J, Xie S, Yang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.002353	2017

References

#19344	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25466
#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 )
#27048	IJSEM 2309 2013 ( DOI 10.1099/ijs.0.042911-0 , PubMed 23159756 )
#30717	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 #27048
#65502	Yong Li, Han Xue, Li-min Guo, Andr as Koltay, Ana Palacio-Bielsa, Jupu Chang, Shoujiang Xie and Xuqi Yang: Elevation of three subspecies of Lonsdalea quercina to species level: Lonsdalea britannica sp. nov., Lonsdalea iberica sp. nov. and Lonsdalea populi sp. nov.. IJSEM 67: 4680 - 4684 2017 ( DOI 10.1099/ijsem.0.002353 , PubMed 28954646 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Lonsdalea populi (DSM 25466, NCAIM B 02483, CFCC 13125)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002111555

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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