Name: Methanococcoides burtonii ACE-M
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7060

Type strain:

Species: Methanococcoides burtonii

Strain Designation: ACE-M

Culture col. no.: DSM 6242, NBRC 107633

Strain history: <- P. D. Franzmann, ACE-M

NCBI tax ID(s): 259564 (strain), 29291 (species)

SI-ID 48128

DSM 6242

Section

Methanococcoides burtonii ACE-M is an anaerobe, psychrophilic, Gram-negative archaeon that was isolated from Ace Lake water at 24 m depth.

Gram-negative
anaerobe
psychrophilic
16S sequence
Archaea
genome sequence

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	"Methanomicrobia"
	Order	*Methanosarcinales*
	Family	*Methanosarcinaceae*
	Genus	*Methanococcoides*
	Species	**Methanococcoides burtonii**
	Full Scientific Name (LPSN)	Methanococcoides burtonii Franzmann et al. 1993

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.973

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2553]

Culture medium

METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c)

[Ref.: #2553]

Culture medium growth

[Ref.: #2553]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2553]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2553]			growth	21 °C

[Ref.: #2553]

Temperature range

psychrophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2553]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %98.943

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	methanofuran biosynthesis	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[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]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	methanogenesis from CO2	75	9 of 12
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	vitamin B12 metabolism	64.71	22 of 34
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutamate and glutamine metabolism	60.71	17 of 28
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	tetrahydrofolate 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]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	non-pathway related	47.37	18 of 38
[Ref.: #66794]	oxidative phosphorylation	47.25	43 of 91
[Ref.: #66794]	peptidoglycan biosynthesis	46.67	7 of 15
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	lysine metabolism	45.24	19 of 42
[Ref.: #66794]	alanine metabolism	44.83	13 of 29
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	tryptophan metabolism	39.47	15 of 38
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		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.: #2553]	Sample type/isolated from	Ace Lake water at 24 m depth
[Ref.: #2553]	Continent	Australia and Oceania
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Lake (large)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X65537 (>99% sequence identity) for Methanococcoides burtonii subclade from Microbeatlas

Aquatic Samples	101
Soil Samples
Animal Samples
Plant Samples	1
Total Samples	102

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

[Ref.: #2553]

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.: #20218]	M.burtonii gene for 16S rRNA	X65537	1476	ENA	29291 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methanococcoides burtonii DSM 6242	GCA_000013725	complete	GenBank	259564 tax ID	*
[Ref.: #66792]	Methanococcoides burtonii DSM 6242	637000161	complete	JGI IMG/M	259564 tax ID	*
[Ref.: #66792]	Methanococcoides burtonii DSM 6242	259564.15	complete	PATRIC	259564 tax ID	*

[Ref.: #2553]

GC-content

39.6 mol%

thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Methanococcoides burtonii DSM 6242 DSM 6242 NCBI: GCA_000013725.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methanococcoides burtonii DSM 6242 DSM 6242 NCBI: GCA_000013725.1
[Ref.: #69480]	motile	no	90.32	no
[Ref.: #69480]	flagellated	no	96.483	no
[Ref.: #69480]	gram-positive	no	96.72	no
[Ref.: #69480]	anaerobic	yes	98.063	yes
[Ref.: #69480]	halophile	no	80.102	no
[Ref.: #69480]	spore-forming	no	94.59	no
[Ref.: #69480]	thermophile	no	93.863	yes
[Ref.: #69480]	glucose-util	yes	74.871	no
[Ref.: #69480]	aerobic	no	93.934	yes
[Ref.: #69480]	glucose-ferment	no	65.937	no

Availability in culture collections External links

[Ref.: #2553]

Culture collection no.

DSM 6242, NBRC 107633

[Ref.: #76517]

SI-ID 48128

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methanococcoides orientis sp. nov., a methylotrophic methanogen isolated from sediment of the East China Sea.	Liang L, Sun Y, Dong Y, Ahmad T, Chen Y, Wang J, Wang F	Int J Syst Evol Microbiol	10.1099/ijsem.0.005384	2022	*
Phylogeny	Methanococcoides vulcani sp. nov., a marine methylotrophic methanogen that uses betaine, choline and N,N-dimethylethanolamine for methanogenesis, isolated from a mud volcano, and emended description of the genus Methanococcoides.	L'Haridon S, Chalopin M, Colombo D, Toffin L	Int J Syst Evol Microbiol	10.1099/ijs.0.058289-0	2014	*
Metabolism	Recombinant production, crystallization and preliminary X-ray analysis of PCNA from the psychrophilic archaeon Methanococcoides burtonii DSM 6242.	Byrne-Steele ML, Hughes RC, Ng JD	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309109037075	2009	*
Stress	Analysis of the AAA+ chaperone clpB gene and stress-response expression in the halophilic methanogenic archaeon Methanohalophilus portucalensis.	Shih CJ, Lai MC	Microbiology (Reading)	10.1099/mic.0.2007/007633-0	2007	*

References

#2553

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6242

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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) .

#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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76517

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-ID48128.1 )

* These data were automatically processed and therefore are not curated

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Methanococcoides burtonii DSM 6242 DSM 6242

Methanococcoides burtonii DSM 6242 DSM 6242

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