Name: Massilia putida 6NM-7
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 141141

Type strain:

Species: Massilia putida

Strain Designation: 6NM-7

Culture col. no.: DSM 27523, KCTC 42761

NCBI tax ID(s): 1141883 (species)

Section

Massilia putida 6NM-7 is an aerobe, non-halophilic, mesophilic bacterium that forms circular colonies and was isolated from wolfram mine tailing sample.

colony-forming
Gram-negative
motile
rod-shaped
aerobe
mesophilic
non-halophilic
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 putida**
	Full Scientific Name (LPSN)	Massilia putida Feng et al. 2016

Synonym

Telluria putida

Information on morphological and physiological properties Morphology

[Ref.: #44058]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.996

[Ref.: #44058]	Cell length	2.0-2.5 µm

[Ref.: #44058]	Cell width	0.8-1.2 µm

[Ref.: #44058]	Cell shape	rod-shaped

[Ref.: #44058]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.516

[Ref.: #44058]	Flagellum arrangement	polar

[Ref.: #44058]	Colony size	2-3 mm
[Ref.: #44058]	Colony color	grey-white
[Ref.: #44058]	Colony shape	circular
[Ref.: #44058]	Incubation period	3 days
[Ref.: #44058]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

PYE agar

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #44058]			growth	25-37 °C
[Ref.: #44058]			optimum	30 °C

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Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #44058]			optimum	7
[Ref.: #44058]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

[Ref.: #44058]	Type of spore	spore
[Ref.: #44058]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.964

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Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #44058]		NaCl		growth	0-0.5	%(w/v)
[Ref.: #44058]		NaCl		optimum	0	%(w/v)

[Ref.: #44058]	Name of tolerated compound	Cadmium
[Ref.: #44058]	Tolerated concentration	1
[Ref.: #44058]	Name of tolerated compound	Zinc
[Ref.: #44058]	Tolerated concentration	0.5
[Ref.: #44058]	Name of tolerated compound	Lead
[Ref.: #44058]	Tolerated concentration	1.5

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #44058]	2-oxoglutarate ChEBI	+	assimilation
[Ref.: #44058]	4-hydroxyphenylacetic acid ChEBI	-	assimilation
[Ref.: #44058]	acetate ChEBI	-	assimilation
[Ref.: #44058]	adipate ChEBI	-	assimilation
[Ref.: #44058]	bromosuccinate ChEBI	+	assimilation
[Ref.: #44058]	D-galactose ChEBI	+	assimilation
[Ref.: #44058]	D-gluconate ChEBI	+	assimilation
[Ref.: #44058]	D-glucuronate ChEBI	+	assimilation
[Ref.: #44058]	D-mannitol ChEBI	-	assimilation
[Ref.: #44058]	D-mannose ChEBI	+	assimilation
[Ref.: #44058]	D-serine ChEBI	-	assimilation
[Ref.: #44058]	D-sorbitol ChEBI	-	assimilation
[Ref.: #44058]	decanoate ChEBI	-	assimilation
[Ref.: #44058]	esculin ChEBI	-	hydrolysis
[Ref.: #44058]	formate ChEBI	-	assimilation
[Ref.: #44058]	gamma-aminobutyric acid ChEBI	-	assimilation
[Ref.: #44058]	gelatin ChEBI	+	hydrolysis
[Ref.: #44058]	glucose ChEBI	-	builds acid from
[Ref.: #44058]	glucose ChEBI	+	assimilation
[Ref.: #44058]	glucuronamide ChEBI	+	assimilation
[Ref.: #44058]	glycine-proline ChEBI	+	assimilation
[Ref.: #44058]	inosine ChEBI	-	assimilation
[Ref.: #44058]	L-arabinose ChEBI	+	assimilation
[Ref.: #44058]	L-arginine ChEBI	-	assimilation
[Ref.: #44058]	L-histidine ChEBI	-	assimilation
[Ref.: #44058]	L-pyroglutamic acid ChEBI	-	assimilation
[Ref.: #44058]	L-serine ChEBI	-	assimilation
[Ref.: #44058]	lactose ChEBI	-	assimilation
[Ref.: #44058]	malate ChEBI	-	assimilation
[Ref.: #44058]	malate ChEBI	+	assimilation
[Ref.: #44058]	maltose ChEBI	+	assimilation
[Ref.: #44058]	methyl pyruvate ChEBI	+	assimilation
[Ref.: #44058]	nitrate ChEBI	-	reduction
[Ref.: #44058]	pectin ChEBI	-	assimilation
[Ref.: #44058]	phenylacetate ChEBI	-	assimilation
[Ref.: #44058]	potassium gluconate ChEBI	+	assimilation
[Ref.: #44058]	propionate ChEBI	-	assimilation
[Ref.: #44058]	raffinose ChEBI	-	assimilation
[Ref.: #44058]	salicin ChEBI	-	assimilation
[Ref.: #44058]	sodium citrate ChEBI	-	assimilation
[Ref.: #44058]	stachyose ChEBI	-	assimilation
[Ref.: #44058]	starch ChEBI	+	hydrolysis
[Ref.: #44058]	sucrose ChEBI	+	assimilation
[Ref.: #44058]	trehalose ChEBI	+	assimilation
[Ref.: #44058]	tween 40 ChEBI	+	hydrolysis
[Ref.: #44058]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #44058]		dimethyl disulfide ChEBI	yes
[Ref.: #44058]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #44058]	arginine dihydrolase	-	3.5.3.6
[Ref.: #44058]	beta-galactosidase	-	3.2.1.23
[Ref.: #44058]	catalase	+	1.11.1.6
[Ref.: #44058]	cytochrome oxidase	-	1.9.3.1
[Ref.: #44058]	urease	-	3.5.1.5

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

[Ref.: #44058]	Sample type/isolated from	wolfram mine tailing sample
[Ref.: #44058]	Geographic location (country and/or sea, region)	Dayu County, Jiangxi Province
[Ref.: #44058]	Country	China
[Ref.: #44058]	Country ISO 3 Code	CHN
[Ref.: #44058]	Continent	Asia
[Ref.: #44058]	Geographic location	25.4603°/114.3350°
[Ref.: #44058]	Enrichment culture	R2A agar
[Ref.: #44058]	Enrichment culture duration	7 days
[Ref.: #44058]	Enrichment culture temperature	30 ̊C
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	#Heavy metal
#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Geologic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ608336 (>99% sequence identity) for Massilia putida from Microbeatlas

Aquatic Samples	28
Soil Samples	53
Animal Samples	14
Plant Samples	43
Total Samples	138

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.: #44058]	16S rRNA gene sequence	JQ608336		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Massilia putida 6NM-7	GCA_001941825	complete	GenBank	1141883 tax ID	*
[Ref.: #66792]	Massilia putida strain 6NM-7T	1141883.4	complete	PATRIC	1141883 tax ID	*
[Ref.: #66792]	Massilia putida strain 6NM-7T	1141883.6	plasmid	PATRIC	1141883 tax ID	*
[Ref.: #66792]	Massilia putida strain 6NM-7T	1141883.5	plasmid	PATRIC	1141883 tax ID	*

[Ref.: #44058]

GC-content

66.8 mol%

high performance liquid chromatography (HPLC)

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 putida 6NM-7 NCBI: GCA_001941825.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Massilia putida 6NM-7 NCBI: GCA_001941825.1
[Ref.: #69480]	flagellated	yes	73.221	no
[Ref.: #69480]	gram-positive	no	98.282	yes
[Ref.: #69480]	anaerobic	no	99.179	yes
[Ref.: #69480]	halophile	no	94.391	yes
[Ref.: #69480]	spore-forming	no	92.024	yes
[Ref.: #69480]	glucose-util	yes	92.053	yes
[Ref.: #69480]	aerobic	yes	93.142	no
[Ref.: #69480]	thermophile	no	99.607	no
[Ref.: #69480]	motile	yes	90.405	yes
[Ref.: #69480]	glucose-ferment	no	90.894	no

Availability in culture collections External links

[Ref.: #44058]

Culture collection no.

DSM 27523, KCTC 42761

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Massilia putida sp. nov., a dimethyl disulfide-producing bacterium isolated from wolfram mine tailing.	Feng GD, Yang SZ, Li HP, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.000670	2015	*
Phylogeny	Massilia cellulosiltytica sp. nov., a novel cellulose-degrading bacterium isolated from rhizosphere soil of rice (Oryza sativa L.) and its whole genome analysis.	Du C, Li C, Cao P, Li T, Du D, Wang X, Zhao J, Xiang W	Antonie Van Leeuwenhoek	10.1007/s10482-021-01618-3	2021	*

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 )

#44058

Guang-Da Feng, Song-Zhen Yang, Hua-Ping Li and Hong-Hui Zhu: Massilia putida sp. nov., a dimethyl disulfide-producing bacterium isolated from wolfram mine tailing. IJSEM 66: 50 - 55 2016 ( DOI 10.1099/ijsem.0.000670 , PubMed 26449383 )

#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) .

#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 )

* These data were automatically processed and therefore are not curated

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