Name: Massilia plicata 76
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11327

Type strain:

Species: Massilia plicata

Strain Designation: 76

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

Strain history: CIP <- 2006, KCTC

NCBI tax ID(s): 321984 (species)

SI-ID 232831

KCTC 12344, DSM 17505, CCUG 52215, CIP 109191

Section

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

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	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Massilia*
	Species	**Massilia plicata**
	Full Scientific Name (LPSN)	Massilia plicata Zhang et al. 2006

Synonym

Pseudoduganella plicata

Information on morphological and physiological properties Morphology

[Ref.: #31701]	Gram stain	negative
[Ref.: #121871]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #31701]	Cell length	2-2.5 µm

[Ref.: #31701]	Cell width	0.6-0.7 µm

[Ref.: #31701]	Cell shape	rod-shaped
[Ref.: #121871]	Cell shape	rod-shaped

[Ref.: #31701]	Motility	yes
[Ref.: #121871]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %95.978

[Ref.: #7027]

Incubation period

1-2 days

[Ref.: #31701]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7027]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7027]

Culture medium growth

[Ref.: #7027]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7027]

Culture medium composition

expand / minimize

[Ref.: #33281]

Culture medium

MEDIUM 328- for nutrient agar

[Ref.: #33281]

Culture medium growth

[Ref.: #33281]

Culture medium composition

expand / minimize

[Ref.: #121871]

Culture medium

CIP Medium 328

[Ref.: #121871]

Culture medium growth

[Ref.: #121871]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7027]	growth	30 °C
[Ref.: #31701]	growth	10-45 °C
[Ref.: #31701]	optimum	28-30 °C
[Ref.: #33281]	growth	30 °C

[Ref.: #7027]	Temperature range	mesophilic
[Ref.: #31701]	Temperature range	mesophilic
[Ref.: #33281]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31701]			optimum	7-7.5
[Ref.: #31701]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31701]	Oxygen tolerance	aerobe
[Ref.: #121871]	Oxygen tolerance	facultative anaerobe

[Ref.: #31701]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31701]		NaCl		growth	0-1	%
[Ref.: #31701]		NaCl		optimum	0-1	%

[Ref.: #31701]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #31701]	glucose ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31701]	malonate ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31701]	nitrate ChEBI	+	reduction
[Ref.: #121871]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #121871]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31701]	sucrose ChEBI	+	carbon source
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #121871]		indole ChEBI	no
[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.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #121871]	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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #7027]	catalase	+	1.11.1.6
[Ref.: #31701]	catalase	+	1.11.1.6
[Ref.: #121871]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #7027]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #121871]	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.: #121871]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121871]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #31701]	urease	+	3.5.1.5
[Ref.: #121871]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #7027]	23789	-	-	-	-	-	+	+	+/-	+	+	+	-	-	+	+/-	-	-	+/-	-	-	+

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #7027]	14191	-	-	-	-	+	-	+	-	-	-	+	+	-	+	-	+/-	-	-	-	-	-	-	-	-	+/-	+	-	+	+	-	-	-	+	-	-	-	+	+	-	+	-	-	-	-	-	-	-	+/-	-	-
[Ref.: #121871]	11491	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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.: #121871]	11708	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #7027]	Sample type/isolated from	heavy-metal-polluted farm soil
[Ref.: #7027]	Geographic location (country and/or sea, region)	Nanjing, Jiangsu province
[Ref.: #7027]	Country	China
[Ref.: #7027]	Country ISO 3 Code	CHN
[Ref.: #7027]	Continent	Asia

[Ref.: #121871]	Sample type/isolated from	Environment, Heavy metal, polluted farm soil
[Ref.: #121871]	Geographic location (country and/or sea, region)	Nanjing, Jiangsu
[Ref.: #121871]	Country	China
[Ref.: #121871]	Country ISO 3 Code	CHN
[Ref.: #121871]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	-
#Engineered	#Contamination	#Heavy metal
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

[Ref.: #7027]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121871]	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.: #7027]	Massilia plicata strain 76 16S ribosomal RNA gene, partial sequence	AY966000	1471	ENA	321984 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoduganella plicata KCTC 12344	GCA_014651435	scaffold	GenBank	321984 tax ID	*
[Ref.: #66792]	Pseudoduganella plicata DSM 17505	GCA_004421005	complete	GenBank	321984 tax ID	*
[Ref.: #66792]	Massilia plicata strain DSM 17505	321984.3	complete	PATRIC	321984 tax ID	*
[Ref.: #66792]	Massilia plicata strain KCTC 12344	321984.4	wgs	PATRIC	321984 tax ID	*
[Ref.: #66792]	Massilia plicata DSM 17505	2847005498	complete	JGI IMG/M	321984 tax ID	*

[Ref.: #7027]	GC-content	65 mol%
[Ref.: #31701]	GC-content	65.1 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: Massilia plicata strain DSM 17505 PATRIC: 321984.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Massilia plicata DSM 17505 NCBI: GCA_004421005.1
[Ref.: #69480]	motile	yes	89.599	yes
[Ref.: #69480]	flagellated	yes	79.752	no
[Ref.: #69480]	gram-positive	no	98.683	no
[Ref.: #69480]	anaerobic	no	98.987	yes
[Ref.: #69480]	aerobic	yes	94.617	yes
[Ref.: #69480]	halophile	no	94.711	yes
[Ref.: #69480]	spore-forming	no	93.19	yes
[Ref.: #69480]	glucose-util	yes	90.559	no
[Ref.: #69480]	thermophile	no	99.101	yes
[Ref.: #69480]	glucose-ferment	no	89.449	yes

Availability in culture collections External links

[Ref.: #7027]

Culture collection no.

DSM 17505, CCTCC AB 204072, KCTC 12344, CIP 109191

[Ref.: #80560]

SI-ID 232831

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (see below)

#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 .

#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 )

#80560

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-ID232831.1 )

#121871 Collection of Institut Pasteur ; Curators of the CIP; CIP 109191

#27978

IJSEM 459 2006 ( DOI 10.1099/ijs.0.64083-0 , PubMed 16449458 )

* These data were automatically processed and therefore are not curated

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Massilia plicata strain DSM 17505

Massilia plicata DSM 17505

Change proposal

Change proposal