Massilia armeniaca (DSM 104676, CGMCC 1.16209, ZMN-3)

Name: Massilia armeniaca (DSM 104676, CGMCC 1.16209, ZMN-3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159643

Type strain

Strain Designation ZMN-3

Culture col. no. DSM 104676 CGMCC 1.16209 ZMN-3

NCBI tax ID(s) 2072590

Special Collections DSMZ Literature strains

History <- H. Huang; Tianjin Agricultural University, Tianjin, CHINA; ZMN-3<-H. Huang<-Y. Zhang;

Links

Massilia armeniaca ZMN-3 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from sandy desert soil.

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

Name and taxonomic classification

SI-ID 404091

DSM 104676

@ref 20215

Last LPSN update 2026-02-09 11:38:41

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Massilia

Species Massilia armeniaca

Full scientific name Massilia armeniaca Ren et al. 2018

Synonyms (1)

Pseudoduganella armeniaca

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
66589	negative	1.7-2.6 µm	0.4-0.7 µm	rod-shaped	peritrichous
125439	negative					99.2
125438	negative					97.375

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
66589	3-4 mm	apricot	circular	3 days	Reasoner's 2A agar (R2A)

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
66493	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
66589	Nutrient agar (NA)
66589	Reasoner's 2A agar (R2A)
66589	tryptic soy agar (TSA)
66589	LB (Luria-Bertani) agar

Culture temp

@ref	Growth	Type	Temperature (°C)
66493	positive	growth	30
66589	positive	optimum	30
66589	positive	growth	10-45

Culture pH

@ref	Ability	Type	PH	PH range
66589	positive	optimum	7
66589	positive	growth	5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
66589	aerobe
125439	obligate aerobe	99.1

Spore formation

@ref	Spore formation	Confidence
125439		95.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66589	NaCl	positive	growth	0-0.2 %(w/v)
66589	NaCl	positive	optimum	0.05 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66589	30796 ChEBI	(R)-malic acid	-	carbon source
66589	16651 ChEBI	(S)-lactate	-	carbon source
66589	30797 ChEBI	(S)-malic acid	-	assimilation
66589	30797 ChEBI	(S)-malic acid	-	carbon source
66589		1 % sodium lactate	-	carbon source
66589	64552 ChEBI	2-hydroxybutyrate	-	carbon source
66589	16763 ChEBI	2-oxobutanoate	-	carbon source
66589	16810 ChEBI	2-oxoglutarate	-	carbon source
66589	37054 ChEBI	3-hydroxybutyrate	-	carbon source
66589	73918 ChEBI	3-O-methyl-D-glucose	-	carbon source
66589	18101 ChEBI	4-hydroxyphenylacetic acid	-	carbon source
66589	16411 ChEBI	acetic acid	-	carbon source
66589	13705 ChEBI	acetoacetate	-	carbon source
66589	17128 ChEBI	adipate	-	assimilation
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
66589	17925 ChEBI	alpha-D-glucose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
66589	161680 ChEBI	aztreonam	-	carbon source
66589	73706 ChEBI	bromosuccinate	-	carbon source
66589		casein	+	degradation
66589	17057 ChEBI	cellobiose	-	carbon source
66589	62968 ChEBI	cellulose	-	degradation
66589	53258 ChEBI	citric acid	-	carbon source
66589	18333 ChEBI	D-arabitol	-	carbon source
66589	29990 ChEBI	D-aspartate	-	carbon source
66589	15824 ChEBI	D-fructose	+	carbon source
66589	78697 ChEBI	D-fructose 6-phosphate	+	carbon source
66589	28847 ChEBI	D-fucose	+	carbon source
66589	12936 ChEBI	D-galactose	+	carbon source
66589	18024 ChEBI	D-galacturonic acid	+	carbon source
66589	30612 ChEBI	D-glucarate	-	carbon source
66589	17634 ChEBI	D-glucose	+	assimilation
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
66589	14314 ChEBI	D-glucose 6-phosphate	+	carbon source
66589	15748 ChEBI	D-glucuronate	-	carbon source
66589	15748 ChEBI	D-glucuronate	+	carbon source
66589	16899 ChEBI	D-mannitol	+	assimilation
66589	16899 ChEBI	D-mannitol	+	carbon source
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
66589	16024 ChEBI	D-mannose	+	assimilation
66589	16024 ChEBI	D-mannose	+	carbon source
66589	16523 ChEBI	D-serine	-	carbon source
66589	17924 ChEBI	D-sorbitol	-	carbon source
66589	16551 ChEBI	D-trehalose	+	carbon source
66589	27689 ChEBI	decanoate	-	assimilation
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
66589	23652 ChEBI	dextrin	+	carbon source
66589	4853 ChEBI	esculin	+	degradation
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
66589	15740 ChEBI	formate	-	carbon source
66589	71321 ChEBI	fusidate	-	carbon source
66589	16537 ChEBI	galactarate	+	carbon source
66589	16865 ChEBI	gamma-aminobutyric acid	-	carbon source
66589	5291 ChEBI	gelatin	+	carbon source
66589	5291 ChEBI	gelatin	+	degradation
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
66589	28066 ChEBI	gentiobiose	-	carbon source
66589	17234 ChEBI	glucose	+	fermentation
66589	32323 ChEBI	glucuronamide	+	carbon source
66589	17754 ChEBI	glycerol	-	carbon source
66589	70744 ChEBI	glycine-proline	-	carbon source
66589	17596 ChEBI	inosine	-	carbon source
66589	16977 ChEBI	L-alanine	-	carbon source
66589	30849 ChEBI	L-arabinose	+	assimilation
66589	16467 ChEBI	L-arginine	-	carbon source
66589	29991 ChEBI	L-aspartate	-	carbon source
66589	18287 ChEBI	L-fucose	-	carbon source
66589	17464 ChEBI	L-galactonic acid gamma-lactone	-	carbon source
66589	29985 ChEBI	L-glutamate	-	carbon source
66589	15971 ChEBI	L-histidine	+	carbon source
66589	18183 ChEBI	L-pyroglutamic acid	-	carbon source
66589	62345 ChEBI	L-rhamnose	-	carbon source
66589	17115 ChEBI	L-serine	-	carbon source
66589	17716 ChEBI	lactose	-	carbon source
66589	48607 ChEBI	lithium chloride	-	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
66589	17306 ChEBI	maltose	+	assimilation
66589	17306 ChEBI	maltose	+	carbon source
66589	28053 ChEBI	melibiose	-	carbon source
66589	74611 ChEBI	methyl (R)-lactate	-	carbon source
66589	320055 ChEBI	methyl beta-D-glucopyranoside	+	carbon source
66589	51850 ChEBI	methyl pyruvate	-	carbon source
66589	17268 ChEBI	myo-inositol	-	carbon source
66589	63153 ChEBI	N-acetyl-D-mannosamine	-	carbon source
66589	28800 ChEBI	N-acetylgalactosamine	+	carbon source
66589	59640 ChEBI	N-acetylglucosamine	-	assimilation
66589	59640 ChEBI	N-acetylglucosamine	-	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
66589	35418 ChEBI	n-acetylneuraminate	-	carbon source
66589	100147 ChEBI	nalidixic acid	-	carbon source
66589	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
66589	17309 ChEBI	pectin	-	carbon source
66589	18401 ChEBI	phenylacetate	-	assimilation
66589	32032 ChEBI	potassium gluconate	-	assimilation
66589	75248 ChEBI	potassium tellurite	-	carbon source
66589	17272 ChEBI	propionate	-	carbon source
66589	26490 ChEBI	quinate	-	carbon source
66589	16634 ChEBI	raffinose	-	carbon source
66589	17814 ChEBI	salicin	-	carbon source
66589	75229 ChEBI	sodium bromate	-	carbon source
66589	64103 ChEBI	sodium butyrate	-	carbon source
66589	53258 ChEBI	sodium citrate	-	assimilation
66589	17164 ChEBI	stachyose	-	carbon source
66589	28017 ChEBI	starch	-	degradation
66589	17992 ChEBI	sucrose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
66589	32528 ChEBI	turanose	-	carbon source
66589	53423 ChEBI	tween 40	-	carbon source
66589	53426 ChEBI	tween 80	+	degradation
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite
66589	15688 ChEBI	acetoin
66589	16136 ChEBI	hydrogen sulfide
66589	35581 ChEBI	indole
68369	35581 ChEBI	indole	from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Methylred-test
66589	15688 ChEBI	acetoin		-
66589	17234 ChEBI	glucose			+
68369	35581 ChEBI	indole	-			from API 20NE

Enzymes

@ref	Value	Activity	Ec
66589	acid phosphatase	+	3.1.3.2
66589	alkaline phosphatase	+	3.1.3.1
66589	alpha-galactosidase	-	3.2.1.22
66589	alpha-glucosidase	-	3.2.1.20
66589	alpha-mannosidase	-	3.2.1.24
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
66589	beta-D-fucosidase	-	3.2.1.38
66589	beta-galactosidase	-	3.2.1.23
66589	beta-glucosidase	-	3.2.1.21
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
66589	beta-glucuronidase	-	3.2.1.31
66589	catalase	+	1.11.1.6
66589	chymotrypsin	-	3.4.4.5
66589	cystine arylamidase	-	3.4.11.3
66589	cytochrome oxidase	-	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
66589	esterase (C 4)	-
66589	esterase Lipase (C 8)	-
68369	gelatinase	+		from API 20NE
66589	leucine arylamidase	+	3.4.11.1
66589	lipase (C 14)	-
66589	N-acetyl-beta-glucosaminidase	-	3.2.1.52
66589	naphthol-AS-BI-phosphohydrolase	+
66589	trypsin	-	3.4.21.4
68369	urease	-	3.5.1.5	from API 20NE
66589	valine arylamidase	+

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
66493	+	-	-	-	-	+	+	-	+	+	+	-	-	+	+	-	-	-	-	-	+
66493	+	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Sandy
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
66493	sandy desert soil	Inner Mongolia, Wengniute county, Ongniod Qi	China	CHN	Asia	43.0219	119.021 43.0219/119.021
66589	desert soil sample	Ongniod Qi, Inner Mongolia	China	CHN	Asia	43.0219	119.021 43.0219/119.021	TJA medium	(per litre: 15 g sucrose, 0.5 g peptone, 0.5 g yeast extract, 1.5 g NaNO3, K2HPO4 0.5 g, 0.2 g MgSO4, 0.005 g FeSO4, 15 g agar; pH 7.0)	3 days	30	standard dilution plating method

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM302885v1 assembly for Pseudoduganella armeniaca ZMN-3	complete	GCA_003028855	2072590.3	2788500515	2072590	97.16

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66589	Pseudoduganella armeniaca strain ZMN-3 16S ribosomal RNA gene, partial sequence	KY432691	1406		2072590

GC content

@ref	GC-content (mol%)	Method
66589	66.3	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudoduganella armeniaca ZMN-3
NCBI: GCA_003028855

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.90	no
125439	motility	BacteriaNetⓘ	yes	82.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Massilia armeniaca ZMN-3
NCBI: GCA_003028855.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.38	yes
125438	anaerobic	anaerobicⓘ	no	97.51	no
125438	aerobic	aerobicⓘ	yes	88.12	no
125438	spore-forming	spore-formingⓘ	no	81.52	no
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	yes	87.39	yes

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 armeniaca sp. nov., isolated from desert soil.	Ren M, Li X, Zhang Y, Jin Y, Li S, Huang H	Int J Syst Evol Microbiol	10.1099/ijsem.0.002836	2018

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 )
#66493	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104676
#66589	Mengnan Ren, Xiaoyan Li, Yueqi Zhang, Yu Jin, Siqi Li, Haidong Huang: Massilia armeniaca sp. nov., isolated from desert soil. IJSEM 68: 2319 - 2324 2018 ( DOI 10.1099/ijsem.0.002836 , PubMed 29786497 )
#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 .
#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 armeniaca (DSM 104676, CGMCC 1.16209, ZMN-3)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003028855

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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