Name: Pleomorphomonas diazotrophica R5-392
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23098

Type strain:

Species: Pleomorphomonas diazotrophica

Strain Designation: R5-392

Culture col. no.: DSM 25022, KACC 16233

Strain history: <- M. Munusamy, National University of Singapore, Temasek Life Scs. Lab.; R5-392

NCBI tax ID(s): 1166257 (species)

SI-ID 399306

DSM 25022

Section

Pleomorphomonas diazotrophica R5-392 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface-sterilized root tissue of Jatropha curcas cv B1-2.

Gram-negative
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Pleomorphomonadaceae*
	Genus	*Pleomorphomonas*
	Species	**Pleomorphomonas diazotrophica**
	Full Scientific Name (LPSN)	Pleomorphomonas diazotrophica Madhaiyan et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30794]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.977

[Ref.: #30794]	Cell length	2 µm

[Ref.: #30794]	Cell width	0.45 µm

[Ref.: #30794]	Cell shape	rod-shaped

[Ref.: #30794]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %97.651

Multimedia content

[Ref.: #19368]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19368]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #19368]

Culture medium growth

[Ref.: #19368]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19368]

Culture medium composition

expand / minimize

[Ref.: #19368]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #19368]

Culture medium growth

[Ref.: #19368]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19368]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19368]	growth	28 °C
[Ref.: #30794]	growth	20-37 °C
[Ref.: #30794]	optimum	30 °C

[Ref.: #19368]	Temperature range	mesophilic
[Ref.: #30794]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30794]			optimum	7
[Ref.: #30794]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30794]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.965

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30794]		NaCl		growth	0-1	%
[Ref.: #30794]		NaCl		optimum	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30794]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30794]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30794]	glucose ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30794]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #30794]	mannitol ChEBI	+	carbon source
[Ref.: #30794]	mannose ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	+	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #30794]		indole ChEBI	yes
[Ref.: #68369]		indole ChEBI	yes	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #30794]		indole ChEBI	+
[Ref.: #68369]		indole ChEBI	+	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #30794]	acid phosphatase	+	3.1.3.2
[Ref.: #30794]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30794]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #30794]	catalase	+	1.11.1.6
[Ref.: #30794]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #30794]	urease	+	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
	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.: #19368]	24311	-	+	-	-	-	+	-	+	+	+	+	-	+	+	+	-	-	+	-	-	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	pyrimidine metabolism	86.67	39 of 45
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	arachidonate biosynthesis	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	purine metabolism	79.79	75 of 94
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	lipid A biosynthesis	66.67	6 of 9
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	methanofuran biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #19368]	Sample type/isolated from	surface-sterilized root tissue of Jatropha curcas cv B1-2
[Ref.: #19368]	Host species	Jatropha curcas
[Ref.: #19368]	Geographic location (country and/or sea, region)	Lim Chu Kang, Agrotechnology experimental station, Jatropha farm
[Ref.: #19368]	Country	Singapore
[Ref.: #19368]	Country ISO 3 Code	SGP
[Ref.: #19368]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Shrub (Scrub)
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ346801 (>99% sequence identity) for Pleomorphomonas from Microbeatlas

Aquatic Samples	2
Soil Samples	3
Animal Samples	5
Plant Samples	5
Total Samples	15

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

[Ref.: #19368]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #19368]	Pleomorphomonas diazotrophica strain R5-392 16S ribosomal RNA gene, partial sequence	JQ346801	1443	ENA	1166257 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pleomorphomonas diazotrophica R5-392	GCA_900114935	scaffold	GenBank	1166257 tax ID	*
[Ref.: #66792]	Pleomorphomonas diazotrophica R5-392	GCA_002844595	contig	GenBank	1166257 tax ID	*
[Ref.: #66792]	Pleomorphomonas diazotrophica R5-392	2651870105	draft	JGI IMG/M	1166257 tax ID	*
[Ref.: #66792]	Pleomorphomonas diazotrophica R5-392	2839387131	draft	JGI IMG/M	1166257 tax ID	*

[Ref.: #19368]	GC-content	63.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30794]	GC-content	63.2 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: Pleomorphomonas diazotrophica R5-392 NCBI: GCA_900114935.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pleomorphomonas diazotrophica R5-392 NCBI: GCA_900114935.1
[Ref.: #69480]	motile	yes	88.525	no
[Ref.: #69480]	flagellated	no	84.269	yes
[Ref.: #69480]	gram-positive	no	98.164	yes
[Ref.: #69480]	anaerobic	no	94.87	yes
[Ref.: #69480]	aerobic	no	73.144	no
[Ref.: #69480]	halophile	no	96.259	yes
[Ref.: #69480]	spore-forming	no	93.26	no
[Ref.: #69480]	glucose-ferment	no	84.063	yes
[Ref.: #69480]	thermophile	no	98.289	yes
[Ref.: #69480]	glucose-util	yes	93.421	no

Availability in culture collections External links

[Ref.: #19368]

Culture collection no.

DSM 25022, KACC 16233

[Ref.: #87336]

SI-ID 399306

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pleomorphomonas diazotrophica sp. nov., an endophytic N-fixing bacterium isolated from root tissue of Jatropha curcas L.	Madhaiyan M, Jin TY, Roy JJ, Kim SJ, Weon HY, Kwon SW, Ji L	Int J Syst Evol Microbiol	10.1099/ijs.0.044461-0	2012	*

References

#19368

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25022

#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 )

#30794

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 #27125 (see below)

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#68369

Automatically annotated from API 20NE .

#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 )

#87336

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-ID399306.1 )

#27125

IJSEM 2477 2013 ( DOI 10.1099/ijs.0.044461-0 , PubMed 23223815 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Pleomorphomonas diazotrophica in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF