Name: Methanobacterium lacus 17A1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6956

Type strain:

Species: Methanobacterium lacus

Strain Designation: 17A1

Culture col. no.: DSM 24406, JCM 17760

Strain history: G. Borrel 17A1.

NCBI tax ID(s): 877455 (species)

SI-ID 398368

DSM 24406

Other strains from Methanobacterium lacus

M. lacus AL21, DSM 25616

Section

Methanobacterium lacus 17A1 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from deep cold sediment of meromictic lake.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Methanobacteriota*
	Class	*Methanobacteria*
	Order	*Methanobacteriales*
	Family	*Methanobacteriaceae*
	Genus	*Methanobacterium*
	Species	**Methanobacterium lacus**
	Full Scientific Name (LPSN)	Methanobacterium lacus Borrel et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30371]	Gram stain	negative

[Ref.: #30371]	Cell length	8.5 µm

[Ref.: #30371]	Cell shape	rod-shaped

[Ref.: #30371]	Motility	no

[Ref.: #17659]

Incubation period

8-14 days

[Ref.: #30371]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17659]

Culture medium

METHANOBACTERIUM MEDIUM (DSMZ Medium 119)

[Ref.: #17659]

Culture medium growth

[Ref.: #17659]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17659]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17659]	growth	30 °C
[Ref.: #30371]	growth	14-40 °C
[Ref.: #30371]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #17659]	Temperature range	mesophilic
[Ref.: #30371]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30371]			optimum	6.5
[Ref.: #30371]			growth	5-8.6

Information on physiology and metabolism Physiology and metabolism

[Ref.: #17659]

Oxygen tolerance

anaerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30371]		NaCl		optimum	0.58	%

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	coenzyme M biosynthesis	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	methanofuran biosynthesis	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	methanogenesis from CO2	75	9 of 12
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	vitamin B12 metabolism	70.59	24 of 34
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	53.57	15 of 28
[Ref.: #66794]	peptidoglycan biosynthesis	53.33	8 of 15
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	50	4 of 8
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	oxidative phosphorylation	46.15	42 of 91
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	42.86	6 of 14
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	isoprenoid biosynthesis	34.62	9 of 26
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	sulfopterin metabolism	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #17659]	Sample type/isolated from	deep cold sediment of meromictic lake
[Ref.: #17659]	Geographic location (country and/or sea, region)	Lake Pavin, Auvergne
[Ref.: #17659]	Country	France
[Ref.: #17659]	Country ISO 3 Code	FRA
[Ref.: #17659]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Deep sediment of the meromictic Lake Pavin
[Ref.: #67770]	Country	France
[Ref.: #67770]	Country ISO 3 Code	FRA
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment
#Condition	#Psychrophilic (<10°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ110085 (>99% sequence identity) for Methanobacterium lacus subclade from Microbeatlas

Aquatic Samples	319
Soil Samples	375
Animal Samples	6
Plant Samples	20
Total Samples	720

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

[Ref.: #17659]

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.: #17659]	Methanobacterium lacus strain 17A1 16S ribosomal RNA gene, partial sequence	HQ110085	1351	ENA	877455 tax ID

[Ref.: #17659]	GC-content	37 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30371]	GC-content	37 mol%

Availability in culture collections External links

[Ref.: #17659]

Culture collection no.

DSM 24406, JCM 17760

[Ref.: #76418]

SI-ID 398368

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methanobacterium lacus sp. nov., isolated from the profundal sediment of a freshwater meromictic lake.	Borrel G, Joblin K, Guedon A, Colombet J, Tardy V, Lehours AC, Fonty G	Int J Syst Evol Microbiol	10.1099/ijs.0.034538-0	2011	*

References

#17659

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24406

#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 )

#30371

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 #26711 (see below)

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#76418

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-ID398368.1 )

#26711

IJSEM 1625 2012 ( DOI 10.1099/ijs.0.034538-0 , PubMed 21890730 )

* These data were automatically processed and therefore are not curated

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