Desulfocicer vacuolatum (DSM 3385, JCM 12295, IbRM)

Name: Desulfocicer vacuolatum (DSM 3385, JCM 12295, IbRM)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3968

Type strain

Strain Designation IbRM

Culture col. no. DSM 3385 JCM 12295 IbRM

NCBI tax ID(s) 1121400 2298

Special Collections DSMZ JCM

History DSMZ <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; IbRM <- F. Widdel {1984} JCM <-- DSM 3385 <-- F. Widdel lbRM.

Links

Desulfocicer vacuolatum IbRM is an anaerobe bacterium that was isolated from marine mud.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 47719

DSM 3385,JCM 12295

@ref 20215

Last LPSN update 2026-05-29 08:25:49

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Desulfobacteria

Order Desulfobacterales

Family Desulfobacteraceae

Genus Desulfocicer

Species Desulfocicer vacuolatum

Full scientific name Desulfocicer vacuolatum (Kuever et al. 2006) Galushko and Kuever 2021

Synonyms (1)

"Desulfobacterium vacuolatum"

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.732
125438	negative	95.383

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1371	DESULFUROMUSA MEDIUM (DSMZ Medium 195a)		Medium recipe at MediaDive	Name: DESULFUROMUSA MEDIUM (DSMZ Medium 195a) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na2-fumarate 2.49252 g/l Na2CO3 1.49551 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 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 Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic 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 Riboflavin 4.98504e-05 g/l Nicotinic 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 Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
1371	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1371	anaerobe
125439	facultative anaerobe	96.467

Spore formation

@ref	Spore formation	Confidence
125439		99.939

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	hydrogen production	100	5 of 5
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	aspartate and asparagine metabolism	100	9 of 9
66794	vitamin B1 metabolism	92.31	12 of 13
66794	palmitate biosynthesis	90.91	20 of 22
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	propanol degradation	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	propionate fermentation	80	8 of 10
66794	methylglyoxal degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	lipoate biosynthesis	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	alanine metabolism	79.31	23 of 29
66794	citric acid cycle	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	purine metabolism	76.6	72 of 94
66794	glycolysis	76.47	13 of 17
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	vitamin B6 metabolism	72.73	8 of 11
66794	lysine metabolism	71.43	30 of 42
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	photosynthesis	71.43	10 of 14
66794	heme metabolism	71.43	10 of 14
66794	pyrimidine metabolism	68.89	31 of 45
66794	cysteine metabolism	66.67	12 of 18
66794	serine metabolism	66.67	6 of 9
66794	nitrate assimilation	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	methane metabolism	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	flavin biosynthesis	66.67	10 of 15
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	arginine metabolism	62.5	15 of 24
66794	gluconeogenesis	62.5	5 of 8
66794	cellulose degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	oxidative phosphorylation	57.14	52 of 91
66794	polyamine pathway	56.52	13 of 23
66794	degradation of sugar alcohols	56.25	9 of 16
66794	non-pathway related	55.26	21 of 38
66794	sulfate reduction	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	ketogluconate metabolism	50	4 of 8
66794	lactate fermentation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	glutathione metabolism	50	7 of 14
66794	pantothenate biosynthesis	50	3 of 6
66794	denitrification	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	tryptophan metabolism	50	19 of 38
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	phenylmercury acetate degradation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	pentose phosphate pathway	45.45	5 of 11
66794	phenol degradation	45	9 of 20
66794	tyrosine metabolism	42.86	6 of 14
66794	vitamin K metabolism	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	Entner Doudoroff pathway	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	cyanate degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	methanogenesis from CO2	33.33	4 of 12
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	myo-inositol biosynthesis	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	degradation of pentoses	28.57	8 of 28
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of sugar acids	28	7 of 25
66794	ascorbate metabolism	27.27	6 of 22
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	vitamin E metabolism	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9

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
1371	marine mud	Venice	Italy	ITA	Europe

Taxonmaps

69479

Global distribution of 16S sequence AF418178 (>99% sequence identity) for Desulfobacterium vacuolatum subclade from Microbeatlas

Aquatic Samples	456
Soil Samples	43
Animal Samples	133
Plant Samples	12
Total Samples	644

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1371	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2681813565 annotated assembly for Desulfocicer vacuolatum DSM 3385	scaffold	GCA_900176365	1121400.3	2681813565	1121400	59.6
66792	MiH-14oct19-180 assembly for Desulfocicer vacuolatum DSM 3385	contig	GCA_945870015	1121400.7		1121400	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
1371	Desulfobacterium vacuolatum DSM 3385 16S ribosomal RNA gene, partial sequence	AF418178	1553		2298
67770	D.vacuolatum 16S ribosomal rRNA	M34408	1383		2298

GC content

1371

GC-content (mol%)45.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2681813565 annotated assembly for Desulfocicer vacuolatum DSM 3385
NCBI: GCA_900176365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	96.47	no
125439	gram_stain	BacteriaNetⓘ	negative	99.73	no
125439	motility	BacteriaNetⓘ	yes	43.60	no
125439	spore_formation	BacteriaNetⓘ	no	99.94	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfobacterium vacuolatum DSM 3385 strain DSM 3385
PATRIC: 1121400.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.38	no
125438	anaerobic	anaerobicⓘ	yes	77.92	yes
125438	spore-forming	spore-formingⓘ	no	84.59	no
125438	aerobic	aerobicⓘ	no	79.93	yes
125438	thermophilic	thermophileⓘ	no	87.92	no
125438	flagellated	motile2+ⓘ	yes	53.25	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities.	Bedard DL, Van Slyke G, Nubel U, Bateson MM, Brumfield S, An YJ, Becraft ED, Wood JM, Thiel V, Ward DM.	Microorganisms	10.3390/microorganisms11122921	2023
Metabolism	Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments.	Ravenschlag K, Sahm K, Knoblauch C, Jorgensen BB, Amann R.	Appl Environ Microbiol	10.1128/aem.66.8.3592-3602.2000	2000
Metabolism	Demethylation of dimethylsulfoniopropionate to 3-S-methylmercaptopropionate by marine sulfate-reducing bacteria.	van der Maarel MJ, Jansen M, Haanstra R, Meijer WG, Hansen TA	Appl Environ Microbiol	10.1128/aem.62.11.3978-3984.1996	1996

References

#1371	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3385
#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 )
#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 )
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#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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Desulfocicer vacuolatum (DSM 3385, JCM 12295, IbRM)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900176365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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