Name: Methylogaea oryzae E10
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7214

Type strain:

Species: Methylogaea oryzae

Strain Designation: E10

Culture col. no.: DSM 23452, JCM 16910

Strain history: S. Tarlera E10.

NCBI tax ID(s): 493385 (strain), 1295382 (species)

SI-ID 405739

DSM 23452

Special Collections

DSMZ
JCM

Section

Methylogaea oryzae E10 is a Gram-negative bacterium that was isolated from soil-water interface from flooded rice fields.

Gram-negative
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	*Gammaproteobacteria*
	Order	*Methylococcales*
	Family	*Methylococcaceae*
	Genus	*Methylogaea*
	Species	**Methylogaea oryzae**
	Full Scientific Name (LPSN)	Methylogaea oryzae Geymonat et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17217]

Culture medium

METHYLOSARCINA QUISQUILLARUM AND M. FIBRATA MEDIUM (DSMZ Medium 921)

[Ref.: #17217]

Culture medium growth

[Ref.: #17217]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17217]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #17217]			growth	30 °C
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

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

[Ref.: #17217]	Sample type/isolated from	soil-water interface from flooded rice fields
[Ref.: #17217]	Geographic location (country and/or sea, region)	Treinta y Tres
[Ref.: #17217]	Country	Uruguay
[Ref.: #17217]	Country ISO 3 Code	URY
[Ref.: #17217]	Continent	Middle and South America

[Ref.: #67770]	Sample type/isolated from	Rice paddy field in Uruguay
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Aquatic	-
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU672873 (>99% sequence identity) for Methylogaea oryzae subclade from Microbeatlas

Aquatic Samples	1564
Soil Samples	1015
Animal Samples	469
Plant Samples	137
Total Samples	3185

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

[Ref.: #17217]

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.: #17217]	Methylogaea oryzae JCM 16910 strain E10 16S ribosomal RNA gene, partial sequence	EU672873	1451	GenBank ENA	493385 tax ID
[Ref.: #124043]	Methylogaea oryzae JCM 16910 strain E10 16S ribosomal RNA gene, partial sequence.	EU672870	628	GenBank ENA	544938 tax ID	*
[Ref.: #124043]	Methylogaea oryzae JCM 16910 strain E10 16S ribosomal RNA gene, partial sequence.	EU672871	759	GenBank ENA	544939 tax ID	*
[Ref.: #124043]	Methylogaea oryzae JCM 16910 strain E10 16S ribosomal RNA gene, partial sequence.	EU672872	729	GenBank ENA	544940 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Methylogaea oryzae JCM 16910	GCA_001312345	contig	GenBank ENA	493385 tax ID
[Ref.: #66792]	Methylogaea oryzae E10	GCA_019669985	complete	GenBank ENA	1295382 tax ID	*
[Ref.: #66792]	Methylogaea oryzae JCM 16910	493385.5	wgs	PATRIC	493385 tax ID	*
[Ref.: #66792]	Methylogaea oryzae strain E10	1295382.3	complete	PATRIC	1295382 tax ID	*
[Ref.: #66792]	Methylogaea oryzae JCM 16910	2675903437	draft	JGI IMG/M	493385 tax ID	*

[Ref.: #17217]

GC-content

63.1 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Methylogaea oryzae E10 NCBI: GCA_019669985.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methylogaea oryzae E10 NCBI: GCA_019669985.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	77.406	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	63.979	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.219	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.711	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	68.425	no

Availability in culture collections External links

[Ref.: #17217]

Culture collection no.

DSM 23452, JCM 16910

[Ref.: #76666]

SI-ID 405739

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field.	Geymonat E, Ferrando L, Tarlera SE	Int J Syst Evol Microbiol	10.1099/ijs.0.028274-0	2010	*

References

#17217

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23452

#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 )

#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 )

#76666

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-ID405739.1 )

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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