Oryzomicrobium terrae (TPP412, BCRC 80905, JCM 30814)

Name: Oryzomicrobium terrae (TPP412, BCRC 80905, JCM 30814)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133342

Type strain

Strain Designation TPP412

Culture col. no. TPP412 BCRC 80905 JCM 30814

NCBI tax ID(s) 1735038

Special Collections JCM Literature strains

Links

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

Gram-negative motile rod-shaped colony-forming facultative anaerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 27314

BCRC 80905,JCM 30814

@ref 20215

Last LPSN update 2025-12-16 10:01:45

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Rhodocyclales

Family Rhodocyclaceae

Genus Oryzomicrobium

Species Oryzomicrobium terrae

Full scientific name Oryzomicrobium terrae Liu et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Flagellum arrangement
25199	negative	1.3-1.6 µm	0.5-0.6 µm	rod-shaped		monotrichous, polar
125438	negative

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25199	1.0-2.0 mm	pale yellow	circular	2 days	Van Niel’s yeast agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
25199	Van Niel’s yeast agar/broth
25199	Van Niel’s yeast agar

Culture temp

@ref	Growth	Type	Temperature (°C)
25199	positive	growth	24.0-45.0
25199	positive	optimum	25
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH
25199	positive	optimum	7
25199	positive	growth	5.0-10.0

Physiology and metabolism

Oxygen tolerance

25199

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125438		93.655

Halophily

@ref	Salt	Tested relation	Concentration
25199	NaCl	maximum	0.75 %(w/v)

Observation

67770

Observationquinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25199	30916 ChEBI	2-oxoglutarate	+	oxidation
25199	37054 ChEBI	3-hydroxybutyrate	+	oxidation
25199	18101 ChEBI	4-hydroxyphenylacetic acid	+	oxidation
25199	355715 ChEBI	4-nitrophenyl beta-D-galactopyranoside	-	hydrolysis
25199	17128 ChEBI	adipate	-	assimilation
25199	73706 ChEBI	bromosuccinate	+	oxidation
25199	16383 ChEBI	cis-aconitate	+	oxidation
25199	16947 ChEBI	citrate	+	oxidation
25199	17634 ChEBI	D-glucose	-	assimilation
25199	16899 ChEBI	D-mannitol	-	assimilation
25199	16024 ChEBI	D-mannose	-	assimilation
25199	27689 ChEBI	decanoate	-	assimilation
25199	4853 ChEBI	esculin	-	hydrolysis
25199	5291 ChEBI	gelatin	-	hydrolysis
25199	17234 ChEBI	glucose	-	fermentation
25199	17240 ChEBI	itaconate	+	oxidation
25199	30849 ChEBI	L-arabinose	-	assimilation
25199	17196 ChEBI	L-asparagine	+	oxidation
25199	29991 ChEBI	L-aspartate	+	oxidation
25199	29985 ChEBI	L-glutamate	+	oxidation
25199	18183 ChEBI	L-pyroglutamic acid	+	oxidation
25199	24996 ChEBI	lactate	+	oxidation
25199	25115 ChEBI	malate	+	assimilation
25199	17306 ChEBI	maltose	-	assimilation
25199	51850 ChEBI	methyl pyruvate	+	oxidation
25199	75146 ChEBI	monomethyl succinate	+	oxidation
25199	506227 ChEBI	N-acetylglucosamine	-	assimilation
25199	17632 ChEBI	nitrate	-	reduction
25199	18401 ChEBI	phenylacetate	+	assimilation
25199	32032 ChEBI	potassium gluconate	-	assimilation
25199	17272 ChEBI	propionate	+	oxidation
25199		skimmed milk	-	hydrolysis
25199	53258 ChEBI	sodium citrate	+	assimilation
25199	28017 ChEBI	starch	-	hydrolysis
25199	143136 ChEBI	succinamate	+	oxidation
25199	30031 ChEBI	succinate	+	oxidation
25199	27897 ChEBI	tryptophan	-	energy source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25199	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
25199	35581 ChEBI	indole	-

Enzymes

@ref	Value	Activity	Ec
25199	acid phosphatase	+	3.1.3.2
25199	alkaline phosphatase	+	3.1.3.1
25199	arginine dihydrolase	-	3.5.3.6
25199	catalase	+	1.11.1.6
25199	cytochrome oxidase	+	1.9.3.1
25199	DNase	-
25199	esterase (C 4)	+
25199	esterase Lipase (C 8)	+
25199	leucine arylamidase	+	3.4.11.1
25199	tryptophan deaminase	-	4.1.99.1
25199	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

@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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Condition	#Anoxic (anaerobic)	-
#Condition	#Humid	-

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
25199	paddy soil	Agricultural Experimental Station, National Taiwan University, Taipei	Taiwan, Province of China	TWN	Asia	25	121 25/121	Van Niel’s yeast agar	containing per litre: K2HPO4 , 1.0 g; MgSO4 , 0.5 g;yeast extract, 10.0 g, pH adjusted to 7.0–7.2	2 days	30	standard serial dilution-plating technique
67770	Paddy soil		Taiwan, Province of China	TWN	Asia

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM827480v1 assembly for Oryzomicrobium terrae TPP412	complete	GCA_008274805	1735038.8	2883351634	1735038	97.74

Genome browser: GCA_008274805

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
25199	Oryzomicrobium terrae strain TPP412 16S ribosomal RNA gene, partial sequence	KR296798	1496		1735038

GC content

@ref	GC-content (mol%)	Method
67770	58.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Oryzomicrobium terrae TPP412
IMG: 2883351634

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	89.90	no
125439	motility	BacteriaNetⓘ	yes	66.60	no
125439	gram_stain	BacteriaNetⓘ	negative	81.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	89.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Oryzomicrobium terrae TPP412
NCBI: GCA_008274805.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	yes
125438	anaerobic	anaerobicⓘ	no	89.48	yes
125438	aerobic	aerobicⓘ	yes	55.85	yes
125438	spore-forming	spore-formingⓘ	no	93.66	no
125438	thermophilic	thermophileⓘ	no	95.23	no
125438	flagellated	motile2+ⓘ	yes	81.85	no

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 .
#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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Oryzomicrobium terrae (TPP412, BCRC 80905, JCM 30814)

Name and taxonomic classification