Name: Pararhodospirillum oryzae JA318
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133978

Type strain:

Species: Pararhodospirillum oryzae

Strain Designation: JA318

Culture col. no.: KCTC 5960, NBRC 107573

Strain history: <- Ch Sasikala, Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, JNT Univ. Hyderabad, India

NCBI tax ID(s): 478448 (species)

Section

Pararhodospirillum oryzae JA318 is an anaerobe, Gram-negative, motile bacterium that was isolated from soil.

Gram-negative
motile
spiral-shaped
anaerobe
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	*Rhodospirillales*
	Family	*Rhodospirillaceae*
	Genus	*Pararhodospirillum*
	Species	**Pararhodospirillum oryzae**
	Full Scientific Name (LPSN)	Pararhodospirillum oryzae (Lakshmi et al. 2013) Lakshmi et al. 2014

Synonym

Rhodospirillum oryzae

Information on morphological and physiological properties Morphology

[Ref.: #30987]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #30987]	Cell length	10 µm

[Ref.: #30987]	Cell width	2 µm

[Ref.: #30987]	Cell shape	spiral-shaped
[Ref.: #67771]	Cell shape	spiral-shaped
[Ref.: #67771]	Cell shape	spiral-shaped

[Ref.: #30987]	Motility	yes
[Ref.: #67771]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %95.521

[Ref.: #67771]	Flagellum arrangement	amphitrichous

[Ref.: #30987]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30987]	growth	25-40 °C
[Ref.: #30987]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #30987]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30987]			optimum	7
[Ref.: #30987]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %98
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.986

[Ref.: #30987]	Observation	aggregates in chains
[Ref.: #67771]	Observation	quinones: Q-8, RQ-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30987]	acetate ChEBI	+	carbon source
[Ref.: #30987]	ethanol ChEBI	+	carbon source
[Ref.: #30987]	formate ChEBI	+	carbon source
[Ref.: #30987]	lactate ChEBI	+	carbon source
[Ref.: #30987]	malate ChEBI	+	carbon source
[Ref.: #30987]	mannitol ChEBI	+	carbon source
[Ref.: #30987]	pyruvate ChEBI	+	carbon source
[Ref.: #30987]	succinate ChEBI	+	carbon source
[Ref.: #30987]	valerate ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	propionate fermentation	100	10 of 10
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	oxidative phosphorylation	58.24	53 of 91
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[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.: #30987]	Sample type/isolated from	soil

[Ref.: #67771]	Sample type/isolated from	From rhizosphere soil of a paddy field
[Ref.: #67771]	Geographic location (country and/or sea, region)	Nadergul, Andhra Pradesh
[Ref.: #67771]	Country	India
[Ref.: #67771]	Country ISO 3 Code	IND
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	17.2667°/78.5333°
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM901295 (>99% sequence identity) for Pararhodospirillum from Microbeatlas

Aquatic Samples	132
Soil Samples	14
Animal Samples	8
Plant Samples	8
Total Samples	162

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.: #30987]	Rhodospirillum oryzae partial 16S rRNA gene, type strain JA318T	AM901295	1383	GenBank	478448 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pararhodospirillum oryzae NBRC 107573	GCA_007992075	contig	GenBank	478448 tax ID	*
[Ref.: #66792]	Pararhodospirillum oryzae strain NBRC 107573	478448.3	wgs	PATRIC	478448 tax ID	*
[Ref.: #66792]	Pararhodospirillum oryzae NBRC 107573	2887752426	draft	JGI IMG/M	478448 tax ID	*

[Ref.: #30987]	GC-content	60.2 mol%
[Ref.: #67771]	GC-content	60.2 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: Pararhodospirillum oryzae strain NBRC 107573 PATRIC: 478448.3
[Ref.: #69481]	spore-forming	no	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pararhodospirillum oryzae strain NBRC 107573 PATRIC: 478448.3
[Ref.: #69480]	gram-positive	no	99.475	no
[Ref.: #69480]	anaerobic	yes	97.514	yes
[Ref.: #69480]	halophile	no	87.861	no
[Ref.: #69480]	spore-forming	no	90.361	no
[Ref.: #69480]	glucose-util	yes	58.657	no
[Ref.: #69480]	aerobic	no	96.992	yes
[Ref.: #69480]	motile	yes	90.894	yes
[Ref.: #69480]	thermophile	no	92.828	yes
[Ref.: #69480]	flagellated	yes	79.063	yes
[Ref.: #69480]	glucose-ferment	no	85.896	no

Availability in culture collections External links

[Ref.: #30987]

Culture collection no.

KCTC 5960, NBRC 107573

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodospirillum oryzae sp. nov., a phototrophic bacterium isolated from rhizosphere soil of paddy.	Lakshmi KVNS, Sasikala C, Ramaprasad EVV, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.049023-0	2013	*

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 )

#30987

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 #27317 (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 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#27317

IJSEM 3050 2013 ( DOI 10.1099/ijs.0.049023-0 , PubMed 23416569 )

* These data were automatically processed and therefore are not curated

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Pararhodospirillum oryzae strain NBRC 107573

Pararhodospirillum oryzae strain NBRC 107573

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