Desulfonema ishimotonii (DSM 9679, Jade 02)

Name: Desulfonema ishimotonii (DSM 9679, Jade 02)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3990

Type strain

Strain Designation Jade 02

Culture col. no. DSM 9679 Jade 02

NCBI tax ID(s) 45657

Special Collections DSMZ

Links

Desulfonema ishimotonii Jade 02 is an anaerobe, mesophilic prokaryote that was isolated from marine mud.

anaerobe mesophilic 16S sequence

Name and taxonomic classification

SI-ID 48667

DSM 9679

@ref 20215

Last LPSN update 2025-12-16 09:47:42

Domain Pseudomonadati

Phylum Thermodesulfobacteriota

Class Desulfobacteria

Order Desulfobacterales

Family Desulfococcaceae

Genus Desulfonema

Species Desulfonema ishimotonii

Full scientific name Desulfonema ishimotonii corrig. Fukui et al. 2000

Synonyms (1)

Desulfonema ishimotoi

BacDive ID	Other strains from **Desulfonema ishimotonii** (1)	Type strain
3991	D. ishimotonii DSM 9680, Tokyo 01 (type strain)

Morphology

Colony morphology

3606

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3606	DESULFONEMA ISHIMOTOI MEDIUM (DSMZ Medium 739)		Medium recipe at MediaDive	Name: DESULFONEMA ISHIMOTOI MEDIUM (DSMZ Medium 739) Composition: NaCl 24.9252 g/l MgSO4 x 7 H2O 6.77966 g/l MgCl2 x 6 H2O 5.58325 g/l Na-acetate x 3 H2O 2.49252 g/l CaCl2 x 2 H2O 1.39581 g/l Na2CO3 0.997009 g/l KCl 0.717847 g/l AlK(SO4)2 x 12 H2O 0.478564 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.139581 g/l Disodium succinate 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Isobutyric acid Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
3606	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

3606

Oxygen toleranceanaerobe

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	CMP-KDO biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	L-lactaldehyde degradation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	alanine metabolism	82.76	24 of 29
66794	vitamin B12 metabolism	82.35	28 of 34
66794	cellulose degradation	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	lipoate biosynthesis	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	methionine metabolism	76.92	20 of 26
66794	glycolysis	76.47	13 of 17
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	toluene degradation	75	3 of 4
66794	lysine metabolism	73.81	31 of 42
66794	proline metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	photosynthesis	71.43	10 of 14
66794	pyrimidine metabolism	71.11	32 of 45
66794	oxidative phosphorylation	70.33	64 of 91
66794	histidine metabolism	68.97	20 of 29
66794	flavin biosynthesis	66.67	10 of 15
66794	methane metabolism	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	nitrate assimilation	66.67	6 of 9
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	heme metabolism	64.29	9 of 14
66794	isoleucine metabolism	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	O-antigen biosynthesis	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	arginine metabolism	58.33	14 of 24
66794	lipid metabolism	58.06	18 of 31
66794	non-pathway related	57.89	22 of 38
66794	tryptophan metabolism	57.89	22 of 38
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	cysteine metabolism	55.56	10 of 18
66794	sulfate reduction	53.85	7 of 13
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	coenzyme M biosynthesis	50	5 of 10
66794	denitrification	50	1 of 2
66794	degradation of sugar alcohols	50	8 of 16
66794	biotin biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	urea cycle	46.15	6 of 13
66794	degradation of hexoses	44.44	8 of 18
66794	glutathione metabolism	42.86	6 of 14
66794	tyrosine metabolism	42.86	6 of 14
66794	vitamin K metabolism	40	2 of 5
66794	starch degradation	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	ketogluconate metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	pentose phosphate pathway	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	methanogenesis from CO2	33.33	4 of 12
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	phenol degradation	30	6 of 20
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	metabolism of disaccharids	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	ascorbate metabolism	22.73	5 of 22
66794	carotenoid biosynthesis	22.73	5 of 22

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Mud (Sludge)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3606	marine mud	Jadebusen	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence U45992 (>99% sequence identity) for Desulfonema ishimotonii subclade from Microbeatlas

Aquatic Samples	395
Soil Samples	19
Animal Samples	21
Plant Samples	64
Total Samples	499

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3606	1	Risk group (German classification) According to TRBA 466

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
3606	Desulfonema ishimotoei 16S ribosomal RNA gene sequence	U45992	1440		45657

GC content

@ref	GC-content (mol%)	Method
3606	54.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Physiology	Physiology, phylogenetic relationships, and ecology of filamentous sulfate-reducing bacteria (genus desulfonema)	Fukui M, Teske A, Assmus B, Muyzer G, Widdel F	Arch Microbiol	10.1007/s002030050760	1999

References

#3606	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 9679
#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 )
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Desulfonema ishimotonii (DSM 9679, Jade 02)

Name and taxonomic classification

Morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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