Archive BacDiveID:10.13145/bacdive7121.20230509.8.1

Strain identifier

BacDive ID: 7121

Type strain:

Species: Methanosarcina thermophila

Strain Designation: TM-1

Strain history: <- P. Scherer <- S.H. Zinder, TM-1

NCBI tax ID(s): 523844 (strain), 2210 (species)

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

General

@ref: 668

BacDive-ID: 7121

DSM-Number: 1825

keywords: genome sequence, 16S sequence, Archaea, anaerobe, thermophilic, methane production

description: Methanosarcina thermophila TM-1 is an anaerobe, thermophilic archaeon that produces methane and was isolated from thermophilic digester sludge.

NCBI tax id

NCBI tax id	Matching level
2210	species
523844	strain

strain history

@ref: 668
history: <- P. Scherer <- S.H. Zinder, TM-1

doi: 10.13145/bacdive7121.20230509.8.1

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 thermophila
full scientific name: Methanosarcina thermophila Zinder et al. 1985

@ref: 668

domain: Archaea

phylum: Euryarchaeota

class: Methanomicrobia

order: Methanosarcinales

family: Methanosarcinaceae

genus: Methanosarcina

species: Methanosarcina thermophila

full scientific name: Methanosarcina thermophila Zinder et al. 1985

strain designation: TM-1

type strain: yes

Culture and growth conditions

culture medium

@ref: 668
name: METHANOSARCINA MEDIUM (DSMZ Medium 120)
growth: yes
link: https://mediadive.dsmz.de/medium/120
composition: Name: METHANOSARCINA MEDIUM (DSMZ Medium 120; with strain-specific modifications) Composition: Methanol 7.92 g/l Na-acetate 2.5 g/l NaCl 2.25 g/l Casitone 2.0 g/l NaHCO3 2.0 g/l Yeast extract 2.0 g/l NH4Cl 0.5 g/l MgSO4 x 7 H2O 0.5 g/l K2HPO4 0.35 g/l Na2S x 9 H2O 0.3 g/l L-Cysteine HCl x H2O 0.3 g/l CaCl2 x 2 H2O 0.25 g/l KH2PO4 0.23 g/l HCl 0.0025 g/l FeSO4 x 7 H2O 0.002 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l ZnCl2 7e-05 g/l (DL)-alpha-Lipoic acid 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Thiamine HCl 5e-05 g/l Riboflavin 5e-05 g/l Nicotinic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Vitamin B12 1e-06 g/l Rumen fluid Distilled water

culture temp

@ref: 668
growth: positive
type: growth
temperature: 50
range: thermophilic

Physiology and metabolism

oxygen tolerance

@ref: 668
oxygen tolerance: anaerobe

compound production

@ref: 668
compound: methane

Isolation, sampling and environmental information

isolation

@ref: 668
sample type: thermophilic digester sludge
geographic location: California, El Segundo
country: USA
origin.country: USA
continent: North America

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Thermophilic (>45°C)

Safety information

risk assessment

@ref: 668
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Enterococcus faecalis clone OCM012 16S ribosomal RNA gene, partial sequence	GU417214	455	ena	1351
20218	Methanosarcina thermophila TM-1 16S ribosomal RNA gene, partial sequence	JQ346758	1268	ena	523844
668	Methanosarcina thermophila TM-1 strain DSM 1825 16S ribosomal RNA gene, partial sequence	M59140	1427	ena	523844

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Methanosarcina thermophila TM-1	GCA_000969885	complete	ncbi	523844
66792	Methanosarcina thermophila TM-1	2636415612	complete	img	523844
66792	Methanosarcina thermophila TM-1	523844.20	complete	patric	523844

GC content

@ref: 668
GC-content: 42.0

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	no	88.757	no
flagellated	no	97.568	no
gram-positive	no	95.533	no
anaerobic	yes	96.598	yes
aerobic	no	93.554	yes
halophile	no	87.958	no
spore-forming	no	95.183	no
thermophile	no	70.186	no
glucose-util	yes	68.483	no
glucose-ferment	no	71.66	no

External links

@ref: 668

culture collection no.: DSM 1825, ATCC 43570, OCM 12, VKM B-1830

straininfo link

@ref: 76576
straininfo: 41920

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Metabolism	1575487	Effect of magnesium on methanogenic subpopulations in a thermophilic acetate-degrading granular consortium.	Schmidt JE, Macario AJ, Ahring BK, Conway de Macario E	Appl Environ Microbiol	10.1128/aem.58.3.862-868.1992	1992	Acetates/metabolism, Euryarchaeota/drug effects/metabolism, Immunohistochemistry, Magnesium/*pharmacology, Temperature, Waste Disposal, Fluid	Pathogenicity
Enzymology	2013570	Purification and properties of methyl coenzyme M methylreductase from acetate-grown Methanosarcina thermophila.	Jablonski PE, Ferry JG	J Bacteriol	10.1128/jb.173.8.2481-2487.1991	1991	Adenosine Triphosphate/pharmacology, Aldehyde Oxidoreductases/pharmacology, Amino Acid Sequence, Centrifugation, Density Gradient, Citrates/pharmacology, Citric Acid, Electrophoresis, Polyacrylamide Gel, Euryarchaeota/metabolism, Ferredoxins/pharmacology, Hydrogen-Ion Concentration, Molecular Sequence Data, Multienzyme Complexes, Oxidoreductases/*chemistry/genetics, Phosphothreonine/analogs & derivatives/pharmacology, Sequence Homology, Nucleic Acid, Temperature	Genetics
Enzymology	2307649	Protein content and enzyme activities in methanol- and acetate-grown Methanosarcina thermophila.	Jablonski PE, DiMarco AA, Bobik TA, Cabell MC, Ferry JG	J Bacteriol	10.1128/jb.172.3.1271-1275.1990	1990	Acetates/metabolism, Bacterial Proteins/isolation & purification, Electrophoresis, Gel, Two-Dimensional, Euryarchaeota/enzymology/growth & development/metabolism, Methanol/metabolism, Species Specificity	Metabolism
Cultivation	3338976	Adaptation for growth at various saline concentrations by the archaebacterium Methanosarcina thermophila.	Sowers KR, Gunsalus RP	J Bacteriol	10.1128/jb.170.2.998-1002.1988	1988	Adaptation, Physiological, Cell Membrane/ultrastructure, Culture Media, Euryarchaeota/drug effects/growth & development/ultrastructure, Microscopy, Electron, Phenotype, Polysaccharides, Bacterial/biosynthesis, Sodium Chloride/pharmacology	Phenotype
Enzymology	8226623	Cloning, sequence analysis, and hyperexpression of the genes encoding phosphotransacetylase and acetate kinase from Methanosarcina thermophila.	Latimer MT, Ferry JG	J Bacteriol	10.1128/jb.175.21.6822-6829.1993	1993	Acetate Kinase/biosynthesis/genetics/isolation & purification, Amino Acid Sequence, Base Sequence, Blotting, Southern, Chromatography, Ion Exchange, Cloning, Molecular, DNA Primers, DNA Probes, Electrophoresis, Polyacrylamide Gel, Escherichia coli/enzymology/genetics, Gene Expression, Genes, Bacterial, Kinetics, Methanosarcina/enzymology/genetics, Molecular Sequence Data, Molecular Weight, Phosphate Acetyltransferase/biosynthesis/*genetics/isolation & purification, Polymerase Chain Reaction, Recombinant Proteins/biosynthesis/isolation & purification/metabolism, Restriction Mapping, Sequence Homology, Amino Acid, Thermodynamics	Phylogeny
Metabolism	8368841	Effect of medium composition and sludge removal on the production, composition, and architecture of thermophilic (55 degrees C) acetate-utilizing granules from an upflow anaerobic sludge blanket reactor.	Ahring BK, Schmidt JE, Winther-Nielsen M, Macario AJ, Conway de Macario E	Appl Environ Microbiol	10.1128/aem.59.8.2538-2545.1993	1993	Acetates/metabolism, Acetic Acid, Anaerobiosis, Biodegradation, Environmental, Culture Media, Euryarchaeota/growth & development/metabolism/ultrastructure, Hot Temperature, Methanosarcina/growth & development/metabolism/ultrastructure, *Waste Disposal, Fluid	Cultivation
Phylogeny	8397116	Inhibition of an archaeal protein phosphatase activity by okadaic acid, microcystin-LR, or calyculin A.	Oxenrider KA, Rasche ME, Thorsteinsson MV, Kennelly PJ	FEBS Lett	10.1016/0014-5793(93)80355-x	1993	Enzyme Activation, Ethers, Cyclic/pharmacology, Marine Toxins, Methanosarcina/enzymology, Microcystins, Okadaic Acid, Oxazoles/pharmacology, Peptides, Cyclic/pharmacology, Phosphoprotein Phosphatases/*antagonists & inhibitors/metabolism, Species Specificity, Substrate Specificity	Pathogenicity
Metabolism	9079930	Protein-tyrosine phosphorylation in the Archaea.	Smith SC, Kennelly PJ, Potts M	J Bacteriol	10.1128/jb.179.7.2418-2420.1997	1997	Archaea/metabolism, Bacterial Proteins/metabolism, Methanosarcina/metabolism, Molecular Weight, Phosphoproteins/metabolism, Phosphotyrosine/metabolism, Sulfolobus/metabolism
Metabolism	9172344	The methanogenic archaeon Methanosarcina thermophila TM-1 possesses a high-affinity glycine betaine transporter involved in osmotic adaptation.	Proctor LM, Lai R, Gunsalus RP	Appl Environ Microbiol	10.1128/aem.63.6.2252-2257.1997	1997	Adaptation, Physiological, Betaine/metabolism, Biological Transport, Active/drug effects, Carrier Proteins/genetics, GABA Plasma Membrane Transport Proteins, Kinetics, Methanosarcina/drug effects/growth & development/*metabolism, Osmotic Pressure, Sodium Chloride/pharmacology, Uncoupling Agents/pharmacology	Pathogenicity
Metabolism	9260948	Gene cloning and expression and characterization of a toxin-sensitive protein phosphatase from the methanogenic archaeon Methanosarcina thermophila TM-1.	Solow B, Young JC, Kennelly PJ	J Bacteriol	10.1128/jb.179.16.5072-5075.1997	1997	Acetates/metabolism, Amino Acid Sequence, Cloning, Molecular, Gene Expression, Genes, Bacterial, Methanosarcina/enzymology/genetics, Molecular Sequence Data, Phosphoprotein Phosphatases/chemistry/genetics/metabolism, Phosphoserine/metabolism, Phosphotyrosine/metabolism, Recombinant Proteins/metabolism, Sequence Homology, Amino Acid, Substrate Specificity	Enzymology
Metabolism	9565696	Methanopterin biosynthesis: methylation of the biosynthetic intermediates.	White RH	Biochim Biophys Acta	10.1016/s0304-4165(97)00148-7	1998	Azo Compounds/chemistry/metabolism, Binding Sites, Glutarates/metabolism, Methanobacterium/chemistry/metabolism, Methylation, Phosphorylation, Pterins/analysis/chemistry/*metabolism, Species Specificity, Subcellular Fractions/chemistry/metabolism, Tritium	Phylogeny
Phylogeny	9689226	Bacterial artificial chromosome (BAC) library as a tool for physical mapping of the archaeon Methanosarcina thermophila TM-1.	Diaz-Perez SV, Alatriste-Mondragon F, Hernandez R, Birren B, Gunsalus RP	Microb Comp Genomics	10.1089/omi.1.1997.2.275	1997	Chromosome Mapping/methods, DNA, Archaeal/genetics, Genomic Library, Methanosarcina/genetics, RNA, Ribosomal, 16S/genetics
Enzymology	10570966	The genes coding for the hsp70 (dnaK) molecular chaperone machine occur in the moderate thermophilic archaeon Methanosarcina thermophila TM-1.	Hofman-Bang J, Lange M, Conway de Macario E, Macario AJ, Ahring BK	Gene	10.1016/s0378-1119(99)00343-1	1999	Amino Acid Sequence, Ammonia/pharmacology, Base Sequence, Cloning, Molecular, DNA Primers, Genes, Archaeal, HSP70 Heat-Shock Proteins/chemistry/genetics, Methanosarcina/drug effects/*genetics, Molecular Sequence Data, Oxidative Stress, Sequence Homology, Amino Acid	Genetics
Enzymology	10719203	Growth kinetics of thermophilic Methanosarcina spp. isolated from full-scale biogas plants treating animal manures.	Mladenovska Z, Ahring BK	FEMS Microbiol Ecol	10.1111/j.1574-6941.2000.tb00687.x	2000
Metabolism	16348788	Carbon Monoxide, Hydrogen, and Formate Metabolism during Methanogenesis from Acetate by Thermophilic Cultures of Methanosarcina and Methanothrix Strains.	Zinder SH, Anguish T	Appl Environ Microbiol	10.1128/aem.58.10.3323-3329.1992	1992
	16535059	Establishment and Characterization of an Anaerobic Thermophilic (55(deg)C) Enrichment Culture Degrading Long-Chain Fatty Acids.	Angelidaki I, Ahring BK	Appl Environ Microbiol	10.1128/aem.61.6.2442-2445.1995	1995
Phylogeny	26763977	Methanosarcina flavescens sp. nov., a methanogenic archaeon isolated from a full-scale anaerobic digester.	Kern T, Fischer MA, Deppenmeier U, Schmitz RA, Rother M	Int J Syst Evol Microbiol	10.1099/ijsem.0.000894	2016
Phylogeny	28473726	Non-autotrophic methanogens dominate in anaerobic digesters.	Kouzuma A, Tsutsumi M, Ishii S, Ueno Y, Abe T, Watanabe K	Sci Rep	10.1038/s41598-017-01752-x	2017	Anaerobiosis, Autotrophic Processes, Bioreactors/microbiology, Contig Mapping, Genes, Archaeal, Methane/metabolism, Methanobacteriaceae/genetics, Methanosarcina/*genetics, Phylogeny, RNA, Ribosomal, 16S/genetics	Metabolism

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
668	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1825)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-1825
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)
76576	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID41920.1	StrainInfo: A central database for resolving microbial strain identifiers