Methanocella paludicola (DSM 17711, JCM 13418, NBRC 101707)

Name: Methanocella paludicola (DSM 17711, JCM 13418, NBRC 101707)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17667

Type strain

Strain Designation SANAE

Culture col. no. DSM 17711 JCM 13418 NBRC 101707 SANAE

NCBI tax ID(s) 570267

Special Collections DSMZ JCM Literature strains

History <- S. Sakai, Nagaoka University of Technology, Japan; SANAE <- S. Sakai; {2005} S. Sakai strain SANAE.

Links

Methanocella paludicola SANAE is an anaerobe, Gram-negative, rod-shaped archaeon that was isolated from rice paddy soil.

Gram-negative rod-shaped anaerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 343805

DSM 17711,JCM 13418,NBRC 101707

@ref 20215

Last LPSN update 2026-02-09 11:22:16

Domain Archaea

Phylum Methanobacteriota

Class Methanosarcinia

Order Methanocellales

Family Methanocellaceae

Genus Methanocella

Species Methanocella paludicola

Full scientific name Methanocella paludicola Sakai et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
32488	negative	rod-shaped
125438				90.5

Colony morphology

7153

Incubation period8-14 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7153	PELOTOMACULUM MEDIUM (DSMZ Medium 960)		Medium recipe at MediaDive	Name: PELOTOMACULUM MEDIUM (DSMZ Medium 960; with strain-specific modifications) Composition: Na2CO3 1.49701 g/l NH4Cl 0.538922 g/l L-Cysteine HCl x H2O 0.299401 g/l Na2S x 9 H2O 0.299401 g/l MgCl2 x 6 H2O 0.199601 g/l KH2PO4 0.139721 g/l Na acetate 0.0998004 g/l Yeast extract 0.0998004 g/l Nitrilotriacetic acid 0.0127745 g/l NaCl 0.000998004 g/l FeCl2 x 4 H2O 0.000998004 g/l Sodium resazurin 0.000499002 g/l Pyridoxine hydrochloride 9.98004e-05 g/l ZnCl2 9.98004e-05 g/l CaCl2 x 2 H2O 9.98004e-05 g/l NiCl2 x 6 H2O 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Na2WO4 x 2 H2O 3.99202e-05 g/l CoCl2 x 6 H2O 2.99401e-05 g/l Na2SeO3 x 5 H2O 2.99401e-05 g/l Na2MoO4 x 2 H2O 2.99401e-05 g/l CuCl2 1.99601e-05 g/l Biotin 1.99601e-05 g/l Folic acid 1.99601e-05 g/l H3BO3 9.98004e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7153	positive	growth	37
32488	positive	growth	25-40
32488	positive	optimum	36
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
32488	positive	optimum	7
32488	positive	growth	6.5-7.8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7153	anaerobe
125439	anaerobe	99.9

Spore formation

@ref	Spore formation	Confidence
125439		93.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32488	30089 ChEBI	acetate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
32488	16183 ChEBI	methane

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7153	rice paddy soil	Niigata, Nakanoshima	Japan	JPN	Asia
67770	Rice paddy soil in Nagaoka	Niigata	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB196288 (>99% sequence identity) for Methanocella paludicola subclade from Microbeatlas

Aquatic Samples	70
Soil Samples	165
Animal Samples	4
Plant Samples	54
Total Samples	293

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7153	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1100v1 assembly for Methanocella paludicola SANAE	complete	GCA_000011005	304371.9	2505679075	304371	98.93

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7153	Methanocella paludicola SANAE gene for 16S rRNA, partial sequence	AB196288	1437		304371

GC content

@ref	GC-content (mol%)	Method
7153	56.6
67770	56.6	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: Methanocella paludicola SANAE
IMG: 2505679075

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.10	no
125439	motility	BacteriaNetⓘ	no	76.70	no
125439	gram_stain	BacteriaNetⓘ	negative	75.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanocella paludicola SANAE SANAE
NCBI: GCA_000011005.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	64.07	no
125438	anaerobic	anaerobicⓘ	yes	79.47	no
125438	aerobic	aerobicⓘ	no	87.90	yes
125438	spore-forming	spore-formingⓘ	no	85.22	no
125438	thermophilic	thermophileⓘ	no	71.03	yes
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales.	Sakai S, Takaki Y, Shimamura S, Sekine M, Tajima T, Kosugi H, Ichikawa N, Tasumi E, Hiraki AT, Shimizu A, Kato Y, Nishiko R, Mori K, Fujita N, Imachi H, Takai K.	PLoS One	10.1371/journal.pone.0022898	2011
Metabolism	Robust Mercury Methylation across Diverse Methanogenic Archaea.	Gilmour CC, Bullock AL, McBurney A, Podar M, Elias DA	mBio	10.1128/mBio.02403-17	2018
Phylogeny	Methanocella conradii sp. nov., a thermophilic, obligate hydrogenotrophic methanogen, isolated from Chinese rice field soil.	Lu Z, Lu Y	PLoS One	10.1371/journal.pone.0035279	2012
Phylogeny	Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil.	Sakai S, Conrad R, Liesack W, Imachi H	Int J Syst Evol Microbiol	10.1099/ijs.0.020883-0	2010
Phylogeny	Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord. nov.	Sakai S, Imachi H, Hanada S, Ohashi A, Harada H, Kamagata Y	Int J Syst Evol Microbiol	10.1099/ijs.0.65571-0	2008

References

#7153	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17711
#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 )
#28708	IJSEM 929 2008 ( DOI 10.1099/ijs.0.65571-0 , PubMed 18398197 )
#32488	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 #28708
#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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Methanocella paludicola (DSM 17711, JCM 13418, NBRC 101707)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000011005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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