Name: Oryzomicrobium terrae TPP412
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133342

Type strain:

Species: Oryzomicrobium terrae

Strain Designation: TPP412

Culture col. no.: BCRC 80905, JCM 30814

Strain history: C.-C. Young; Natl. Chung Hsing Univ., Taiwan; TPP412.

NCBI tax ID(s): 1735038 (species)

Section

Oryzomicrobium terrae TPP412 is a facultative anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from paddy soil.

colony-forming
Gram-negative
motile
rod-shaped
facultative 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	*Betaproteobacteria*
	Order	*Rhodocyclales*
	Family	*Rhodocyclaceae*
	Genus	*Oryzomicrobium*
	Species	**Oryzomicrobium terrae**
	Full Scientific Name (LPSN)	Oryzomicrobium terrae Liu et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25199]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #25199]	Cell length	1.3-1.6 µm

[Ref.: #25199]	Cell width	0.5-0.6 µm

[Ref.: #25199]	Cell shape	rod-shaped

[Ref.: #25199]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.583

[Ref.: #25199]	Flagellum arrangement	monotrichous, polar

[Ref.: #25199]	Colony size	1.0-2.0 mm
[Ref.: #25199]	Colony color	pale yellow
[Ref.: #25199]	Colony shape	circular
[Ref.: #25199]	Incubation period	2 days
[Ref.: #25199]	Cultivation medium used	Van Niel’s yeast agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25199]

Culture medium

Van Niel’s yeast agar/broth

[Ref.: #25199]

Culture medium growth

[Ref.: #25199]

Culture medium

Van Niel’s yeast agar

[Ref.: #25199]

Culture medium growth

[Ref.: #25199]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #25199]	growth	24.0-45.0 °C
[Ref.: #25199]	optimum	25 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #25199]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25199]			optimum	7
[Ref.: #25199]			growth	5.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25199]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.994

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25199]		NaCl	maximum	0.75	%(w/v)

[Ref.: #67770]

Observation

quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25199]	2-oxoglutarate ChEBI	+	oxidation
[Ref.: #25199]	3-hydroxybutyrate ChEBI	+	oxidation
[Ref.: #25199]	4-hydroxyphenylacetic acid ChEBI	+	oxidation
[Ref.: #25199]	4-nitrophenyl beta-D-galactopyranoside ChEBI	-	hydrolysis
[Ref.: #25199]	adipate ChEBI	-	assimilation
[Ref.: #25199]	bromosuccinate ChEBI	+	oxidation
[Ref.: #25199]	cis-aconitate ChEBI	+	oxidation
[Ref.: #25199]	citrate ChEBI	+	oxidation
[Ref.: #25199]	D-glucose ChEBI	-	assimilation
[Ref.: #25199]	D-mannitol ChEBI	-	assimilation
[Ref.: #25199]	D-mannose ChEBI	-	assimilation
[Ref.: #25199]	decanoate ChEBI	-	assimilation
[Ref.: #25199]	esculin ChEBI	-	hydrolysis
[Ref.: #25199]	gelatin ChEBI	-	hydrolysis
[Ref.: #25199]	glucose ChEBI	-	fermentation
[Ref.: #25199]	itaconate ChEBI	+	oxidation
[Ref.: #25199]	L-arabinose ChEBI	-	assimilation
[Ref.: #25199]	L-asparagine ChEBI	+	oxidation
[Ref.: #25199]	L-aspartate ChEBI	+	oxidation
[Ref.: #25199]	L-glutamate ChEBI	+	oxidation
[Ref.: #25199]	L-pyroglutamic acid ChEBI	+	oxidation
[Ref.: #25199]	lactate ChEBI	+	oxidation
[Ref.: #25199]	malate ChEBI	+	assimilation
[Ref.: #25199]	maltose ChEBI	-	assimilation
[Ref.: #25199]	methyl pyruvate ChEBI	+	oxidation
[Ref.: #25199]	monomethyl succinate ChEBI	+	oxidation
[Ref.: #25199]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #25199]	nitrate ChEBI	-	reduction
[Ref.: #25199]	phenylacetate ChEBI	+	assimilation
[Ref.: #25199]	potassium gluconate ChEBI	-	assimilation
[Ref.: #25199]	propionate ChEBI	+	oxidation
[Ref.: #25199]	skimmed milk	-	hydrolysis
[Ref.: #25199]	sodium citrate ChEBI	+	assimilation
[Ref.: #25199]	starch ChEBI	-	hydrolysis
[Ref.: #25199]	succinamate ChEBI	+	oxidation
[Ref.: #25199]	succinate ChEBI	+	oxidation
[Ref.: #25199]	tryptophan ChEBI	-	energy source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25199]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test
[Ref.: #25199]		indole ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25199]	acid phosphatase	+	3.1.3.2
[Ref.: #25199]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25199]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25199]	catalase	+	1.11.1.6
[Ref.: #25199]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25199]	DNase	-
[Ref.: #25199]	esterase (C 4)	+
[Ref.: #25199]	esterase Lipase (C 8)	+
[Ref.: #25199]	leucine arylamidase	+	3.4.11.1
[Ref.: #25199]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25199]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25199]

Fatty acid	Percentage
C16:1ω7c / C16:1ω6c	40.5
C16:0	21.8
C18:1ω7c / C18:1ω6c	13.9
C12:0 3OH	8.2
C12:0	6.6
C15:0 iso 3OH	4.7

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

[Ref.: #25199]	Sample type/isolated from	paddy soil
[Ref.: #25199]	Geographic location (country and/or sea, region)	Agricultural Experimental Station, National Taiwan University, Taipei
[Ref.: #25199]	Country	Taiwan
[Ref.: #25199]	Country ISO 3 Code	TWN
[Ref.: #25199]	Continent	Asia
[Ref.: #25199]	Geographic location	25.0000°/121.0000°
[Ref.: #25199]	Enrichment culture	Van Niel’s yeast agar
[Ref.: #25199]	Enrichment culture composition	containing per litre: K2HPO4 , 1.0 g; MgSO4 , 0.5 g;yeast extract, 10.0 g, pH adjusted to 7.0–7.2
[Ref.: #25199]	Enrichment culture duration	2 days
[Ref.: #25199]	Enrichment culture temperature	30 ̊C
[Ref.: #25199]	Isolation/enrichment procedure	standard serial dilution-plating technique

[Ref.: #67770]	Sample type/isolated from	Paddy soil
[Ref.: #67770]	Country	Taiwan
[Ref.: #67770]	Country ISO 3 Code	TWN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Condition	#Anoxic (anaerobic)	-
#Condition	#Humid	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KR296798 (>99% sequence identity) for Oryzomicrobium terrae subclade from Microbeatlas

Aquatic Samples	2702
Soil Samples	528
Animal Samples	398
Plant Samples	122
Total Samples	3750

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.: #25199]	Propionivibrio sp. TPP412 16S ribosomal RNA gene, partial sequence	KR296798	1496	GenBank	1735038 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Oryzomicrobium terrae TPP412	GCA_008274805	complete	GenBank	1735038 tax ID	*
[Ref.: #66792]	Oryzomicrobium terrae TPP412	2883351634	complete	JGI IMG/M	1735038 tax ID	*

[Ref.: #67770]

GC-content

58.4 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: Oryzomicrobium terrae TPP412 NCBI: GCA_008274805.1
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Oryzomicrobium terrae TPP412 NCBI: GCA_008274805.1
[Ref.: #69480]	motile	yes	90.919	yes
[Ref.: #69480]	flagellated	yes	84.321	no
[Ref.: #69480]	gram-positive	no	99.361	yes
[Ref.: #69480]	anaerobic	no	89.923	no
[Ref.: #69480]	aerobic	no	72.045	yes
[Ref.: #69480]	halophile	no	94.964	no
[Ref.: #69480]	spore-forming	no	95.799	no
[Ref.: #69480]	glucose-util	no	89.127	yes
[Ref.: #69480]	thermophile	no	95.2	yes
[Ref.: #69480]	glucose-ferment	no	90.718	yes

Availability in culture collections External links

[Ref.: #25199]

Culture collection no.

BCRC 80905, JCM 30814

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Oryzomicrobium terrae gen. nov., sp. nov., of the family Rhodocyclaceae isolated from paddy soil.	Liu CT, Lin SY, Hameed A, Liu YC, Hsu YH, Wong WT, Tseng CH, Lur HS, Young CC	Int J Syst Evol Microbiol	10.1099/ijsem.0.001565	2017	*

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 )

#25199

C. T. L. Liu, S. Y.,Hameed, A.,Liu, Y. C.,Hsu, Y. H.,Wong, W. T.,Tseng, C. H.,Lur, H. S.,Young, C. C.: Oryzomicrobium terrae gen. nov., sp. nov., of the family Rhodocyclaceae isolated from paddy soil. IJSEM 67: 183 - 189 2017 ( DOI 10.1099/ijsem.0.001565 , PubMed 27902185 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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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