Archive BacDiveID:10.13145/bacdive7108.20240916.9.1

Strain identifier

BacDive ID: 7108

Type strain:

Species: Methanosarcina sp.

Strain Designation: WH1

Strain history: <- P.E. Rouviere and R.S. Wolfe, WH1

NCBI tax ID(s): 2213 (species)

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

General

@ref: 1670

BacDive-ID: 7108

DSM-Number: 4659

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

description: Methanosarcina sp. WH1 is an anaerobe, Gram-negative archaeon that was isolated from anaerobic sands.

NCBI tax id

NCBI tax id: 2213
Matching level: species

strain history

@ref: 1670
history: <- P.E. Rouviere and R.S. Wolfe, WH1

doi: 10.13145/bacdive7108.20240916.9.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/archaea
keyword: phylum/methanobacteriota
domain: Archaea
phylum: Methanobacteriota
class: Methanomicrobia
order: Methanosarcinales
family: Methanosarcinaceae
genus: Methanosarcina
species: Methanosarcina sp.
full scientific name: Methanosarcina Kluyver and van Niel 1936 (Approved Lists 1980)

@ref: 1670

domain: Archaea

phylum: Euryarchaeota

class: Methanomicrobia

order: Methanosarcinales

family: Methanosarcinaceae

genus: Methanosarcina

species: Methanosarcina sp.

full scientific name: Methanosarcina sp.

strain designation: WH1

type strain: no

Culture and growth conditions

culture medium

@ref: 1670
name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c)
growth: yes
link: https://mediadive.dsmz.de/medium/141c
composition: Name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c; with strain-specific modifications) Composition: NaHCO3 4.89237 g/l MgCl2 x 6 H2O 3.91389 g/l Methanol 3.87476 g/l Yeast extract 1.95695 g/l Trypticase peptone 1.95695 g/l Na-acetate 0.978474 g/l Na2S x 9 H2O 0.489237 g/l L-Cysteine HCl x H2O 0.489237 g/l KCl 0.332681 g/l NH4Cl 0.244618 g/l K2HPO4 0.136986 g/l MgSO4 x 7 H2O 0.0293542 g/l Nitrilotriacetic acid 0.0146771 g/l NaCl 0.00978474 g/l MnSO4 x H2O 0.00489237 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00195695 g/l CoSO4 x 7 H2O 0.00176125 g/l ZnSO4 x 7 H2O 0.00176125 g/l CaCl2 x 2 H2O 0.000978474 g/l FeSO4 x 7 H2O 0.000978474 g/l Sodium resazurin 0.000489237 g/l NiCl2 x 6 H2O 0.000293542 g/l AlK(SO4)2 x 12 H2O 0.000195695 g/l CuSO4 x 5 H2O 9.78474e-05 g/l Pyridoxine hydrochloride 9.78474e-05 g/l Na2MoO4 x 2 H2O 9.78474e-05 g/l H3BO3 9.78474e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l Nicotinic acid 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Biotin 1.95695e-05 g/l Folic acid 1.95695e-05 g/l Na2WO4 x 2 H2O 3.91389e-06 g/l Na2SeO3 x 5 H2O 2.93542e-06 g/l Vitamin B12 9.78474e-07 g/l Distilled water

culture temp

@ref: 1670
growth: positive
type: growth
temperature: 37

Physiology and metabolism

oxygen tolerance

@ref: 1670
oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@ref: 1670
sample type: anaerobic sands
geographic location: Madison, Sippewisset Marsh
country: USA
origin.country: USA
continent: North America

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Sandy
#Condition	#Anoxic (anaerobic)

Sequence information

16S sequences

@ref: 20218
description: Methanosarcina sp. 16S ribosomal RNA gene, partial sequence
accession: M59136
length: 1425
database: nuccore
NCBI tax ID: 2213

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Methanosarcina sp. WH1	GCA_000970005	complete	ncbi	1434102
66792	Methanosarcina sp. WH1	2627853658	complete	img	1434102
66792	Methanosarcina sp. WH1	1434102.4	complete	patric	1434102

GC content

@ref: 1670
GC-content: 43.0

Genome-based predictions

predictions

@ref	trait	model	description	prediction	confidence	training_data
69480	gram-positive	gram-positive	Positive reaction to Gram-staining	no	62.976	no
69480	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	yes	88.854	yes
69480	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	no	91.035	yes
69480	spore-forming	spore-forming	Ability to form endo- or exospores	no	85.985	no
69480	thermophilic	thermophile	Ability to grow at temperatures above or equal to 45°C	no	88.817	yes
69480	flagellated	motile2+	Ability to perform flagellated movement	no	83.083	no

External links

@ref: 1670

culture collection no.: DSM 4659

straininfo link

@ref: 76563
straininfo: 47862

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
1670	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4659)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-4659
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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
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)
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
76563	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID47862.1	StrainInfo: A central database for resolving microbial strain identifiers