Archive BacDiveID:10.13145/bacdive17667.20230509.8.1

Strain identifier

BacDive ID: 17667

Type strain:

Species: Methanocella paludicola

Strain Designation: SANAE

Strain history: S. Sakai strain SANAE.

NCBI tax ID(s): 570267 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 7153

BacDive-ID: 17667

DSM-Number: 17711

keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative, rod-shaped

description: Methanocella paludicola SANAE is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from rice paddy soil.

NCBI tax id

NCBI tax id: 570267
Matching level: species

strain history

@ref	history
7153	<- S. Sakai; SANAE
67770	S. Sakai strain SANAE.

doi: 10.13145/bacdive17667.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/archaea
keyword: phylum/methanobacteriota
domain: Archaea
phylum: Methanobacteriota
class: Methanomicrobia
order: Methanocellales
family: Methanocellaceae
genus: Methanocella
species: Methanocella paludicola
full scientific name: Methanocella paludicola Sakai et al. 2008

@ref: 7153

domain: Archaea

phylum: Euryarchaeota

class: Methanomicrobia

order: Methanocellales

family: Methanocellaceae

genus: Methanocella

species: Methanocella paludicola

full scientific name: Methanocella paludicola Sakai et al. 2008

strain designation: SANAE

type strain: yes

Morphology

cell morphology

@ref: 32488
gram stain: negative
cell shape: rod-shaped
motility: no

colony morphology

@ref: 7153
incubation period: 8-14 days

Culture and growth conditions

culture medium

@ref: 7153
name: PELOTOMACULUM MEDIUM (DSMZ Medium 960)
growth: yes
link: https://mediadive.dsmz.de/medium/960
composition: 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	range
7153	positive	growth	37	mesophilic
32488	positive	growth	25-40
32488	positive	optimum	36	mesophilic
67770	positive	growth	37	mesophilic

culture pH

@ref	ability	type	pH
32488	positive	growth	6.5-7.8
32488	positive	optimum	7

Physiology and metabolism

oxygen tolerance

@ref: 7153
oxygen tolerance: anaerobe

metabolite utilization

@ref: 32488
Chebi-ID: 30089
metabolite: acetate
utilization activity: +
kind of utilization tested: carbon source

metabolite production

@ref: 32488
Chebi-ID: 16183
metabolite: methane
production: yes

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
7153	rice paddy soil	Niigata, Nakanoshima	Japan	JPN	Asia
67770	Rice paddy soil in Nagaoka	Niigata	Japan	JPN	Asia

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_192605.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18017;96_69335;97_90053;98_125525;99_192605&stattab=map
Last taxonomy: Methanocella paludicola subclade
16S sequence: AB196288
Sequence Identity:
Total samples: 293
soil counts: 165
aquatic counts: 70
animal counts: 4
plant counts: 54

Safety information

risk assessment

@ref: 7153
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 7153
description: Methanocella paludicola SANAE gene for 16S rRNA, partial sequence
accession: AB196288
length: 1437
database: ena
NCBI tax ID: 304371

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Methanocella paludicola SANAE	GCA_000011005	complete	ncbi	304371
66792	Methanocella paludicola SANAE	2505679075	complete	img	304371
66792	Methanocella paludicola SANAE	304371.9	complete	patric	304371

GC content

@ref	GC-content	method
7153	56.6
67770	56.6	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	no	91.058	yes
flagellated	no	97.417	yes
gram-positive	no	93.894	no
anaerobic	yes	96.351	yes
halophile	no	88.138	no
spore-forming	no	95.239	no
thermophile	no	51.948	yes
glucose-util	yes	71.527	no
aerobic	no	95.203	yes
glucose-ferment	no	67.004	no

External links

@ref: 7153

culture collection no.: DSM 17711, JCM 13418, NBRC 101707

straininfo link

@ref: 86658
straininfo: 343805

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	18398197	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	Base Composition, DNA, Archaeal/chemistry/genetics, Euryarchaeota/classification/genetics/isolation & purification/metabolism, Genes, Archaeal, Methane/biosynthesis, Microscopy, Electron, Transmission, Molecular Sequence Data, Oryza/microbiology, Oxidoreductases/genetics, Phenotype, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as Topic	Enzymology
Phylogeny	20097796	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	Archaea/classification/genetics/isolation & purification, Base Composition, DNA, Archaeal/genetics, Italy, Methane/metabolism, Molecular Sequence Data, Oryza/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology	Genetics
Phylogeny	22530002	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	Base Composition, DNA Restriction Enzymes/genetics, Methanomicrobiaceae/classification/genetics/growth & development/ultrastructure, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Soil Microbiology	Genetics
Metabolism	29636434	Robust Mercury Methylation across Diverse Methanogenic Archaea.	Gilmour CC, Bullock AL, McBurney A, Podar M, Elias DA	mBio	10.1128/mBio.02403-17	2018	Archaea/genetics/metabolism, Culture Media/chemistry, Cysteine/metabolism, Genes, Archaeal, Mercuric Chloride/metabolism, Methane/metabolism, Methylation, Methylmercury Compounds/metabolism, Sulfides/metabolism	Cultivation

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
7153	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17711)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-17711
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32488	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	28708	28776041
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
86658	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID343805.1	StrainInfo: A central database for resolving microbial strain identifiers