Massilia plicata (DSM 17505, CCTCC AB 204072, KCTC 12344)

Name: Massilia plicata (DSM 17505, CCTCC AB 204072, KCTC 12344)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11327

Type strain

Strain Designation 76

Culture col. no. DSM 17505 CCTCC AB 204072 KCTC 12344 76 CIP 109191

NCBI tax ID(s) 321984

Special Collections DSMZ KCTC Literature strains CIP

History DSMZ <- W.-J- Li, Yunnan University, China CIP <- 2006, KCTC CIP <- 2006, KCTC

Links

Massilia plicata 76 is an aerobe, Gram-negative, motile bacterium that was isolated from heavy-metal-polluted farm soil.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 232831

KCTC 12344,DSM 17505,CCUG 52215,CIP 109191

@ref 20215

Last LPSN update 2026-05-29 08:27:32

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Massilia

Species Massilia plicata

Full scientific name Massilia plicata Zhang et al. 2006

Synonyms (1)

Pseudoduganella plicata

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31701	negative	2-2.5 µm	0.6-0.7 µm	rod-shaped
121871	negative			rod-shaped
125439	negative				98.057
125438	negative				97.875

Colony morphology

@ref	Incubation period	Hemolysis ability
7027	1-2 days
121871		0

Pigmentation

31701

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7027	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
33281	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
121871	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7027	positive	growth	30
31701	positive	growth	10-45
31701	positive	optimum	28-30
33281	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31701	positive	optimum	7-7.5
31701	positive	growth	6.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31701	aerobe
121871	facultative anaerobe
125438	aerobe	91.962
125439	obligate aerobe	97.64

Spore formation

@ref	Spore formation	Confidence
31701
125439		98.859

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31701	NaCl	positive	growth	0-1 %
31701	NaCl	positive	optimum	0-1 %

Observation

31701

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
31701	17234 ChEBI	glucose	+	carbon source
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
31701	15792 ChEBI	malonate	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
31701	17632 ChEBI	nitrate	+	reduction
121871	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121871	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
31701	17992 ChEBI	sucrose	+	carbon source
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
121871	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121871	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
7027	catalase	+	1.11.1.6
31701	catalase	+	1.11.1.6
121871	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
7027	cytochrome-c oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	+		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
121871	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121871	ornithine decarboxylase	-	4.1.1.17
121871	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
31701	urease	+	3.5.1.5
121871	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121871	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
7027	-	-	-	-	-	+	+	+/-	+	+	+	-	-	+	+/-	-	-	+/-	-	-	+

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
7027	-	-	-	-	+	-	+	-	-	-	+	+	-	+	-	+/-	-	-	-	-	-	-	-	-	+/-	+	-	+	+	-	-	-	+	-	-	-	+	+	-	+	-	-	-	-	-	-	-	+/-	-	-
121871	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	-
#Engineered	#Contamination	#Heavy metal
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7027	heavy-metal-polluted farm soil	Nanjing, Jiangsu province	China	CHN	Asia
121871	Environment, Heavy metal, polluted farm soil	Nanjing, Jiangsu	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7027	1	Risk group (German classification) According to TRBA 466
121871	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM442100v1 assembly for Pseudoduganella plicata DSM 17505	complete	GCA_004421005	321984.3	2847005498	321984	98.04
124043	ASM4243016v1 assembly for Pseudoduganella plicata KCTC 12344	contig	GCA_042430165			321984	70.33
66792	ASM1465143v1 assembly for Pseudoduganella plicata KCTC 12344	scaffold	GCA_014651435	321984.4	8068496194	321984	69.11

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
7027	Massilia plicata strain 76 16S ribosomal RNA gene, partial sequence	AY966000	1471	321984
124043	Massilia plicata strain KCTC 12344 16S ribosomal RNA gene, partial sequence.	MT758059	1353	321984
124043	Massilia plicata strain KCTC 12344 16S ribosomal RNA gene, partial sequence.	MT759910	1353	321984

GC content

@ref	GC-content (mol%)
7027	65
31701	65.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM442100v1 assembly for Pseudoduganella plicata DSM 17505
BV-BRC: 321984.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.64	no
125439	motility	BacteriaNetⓘ	yes	66.18	no
125439	gram_stain	BacteriaNetⓘ	negative	98.06	no
125439	spore_formation	BacteriaNetⓘ	no	98.86	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Massilia plicata DSM 17505
NCBI: GCA_004421005.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.88	yes
125438	anaerobic	anaerobicⓘ	no	96.86	no
125438	aerobic	aerobicⓘ	yes	91.96	no
125438	spore-forming	spore-formingⓘ	no	83.72	yes
125438	thermophilic	thermophileⓘ	no	97.50	yes
125438	flagellated	motile2+ⓘ	yes	86.24	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Prevalence and Correlates of Phenazine Resistance in Culturable Bacteria from a Dryland Wheat Field.	Perry EK, Newman DK.	Appl Environ Microbiol	10.1128/aem.02320-21	2022
	Janthinobacterium tructae sp. nov., Isolated from Kidney of Rainbow Trout (Oncorhynchus mykiss).	Jung WJ, Kim SW, Giri SS, Kim HJ, Kim SG, Kang JW, Kwon J, Lee SB, Oh WT, Jun JW, Park SC.	Pathogens	10.3390/pathogens10020229	2021
Phylogeny	Massilia aquatica sp. nov., Isolated from a Subtropical Stream in China.	Lu HB, Deng TC, Xu MY	Curr Microbiol	10.1007/s00284-020-02104-1	2020
Phylogeny	Massilia buxea sp. nov., isolated from a rock surface.	Sun LN, Yang ED, Cui DX, Ni YW, Wang YB, Sun DD, Wang WY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002301	2017
Phylogeny	Massilia humi sp. nov. isolated from soil in Incheon, South Korea.	Du J, Yin CS	Arch Microbiol	10.1007/s00203-016-1195-7	2016
Phylogeny	Massilia lurida sp. nov., isolated from soil.	Luo X, Xie Q, Wang J, Pang H, Fan J, Zhang J	Int J Syst Evol Microbiol	10.1099/ijs.0.047068-0	2012
Phylogeny	Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China.	Zhang YQ, Li WJ, Zhang KY, Tian XP, Jiang Y, Xu LH, Jiang CL, Lai R	Int J Syst Evol Microbiol	10.1099/ijs.0.64083-0	2006

References

#7027	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17505
#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 )
#27978	IJSEM 459 2006 ( DOI 10.1099/ijs.0.64083-0 , PubMed 16449458 )
#31701	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 #27978
#33281	; Curators of the CIP;
#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 .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#121871	Collection of Institut Pasteur ; Curators of the CIP; CIP 109191
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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Massilia plicata (DSM 17505, CCTCC AB 204072, KCTC 12344)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004421005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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