Desulfocucumis palustris (DSM 102911, NBRC 112242, NAW-5)

Name: Desulfocucumis palustris (DSM 102911, NBRC 112242, NAW-5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140353

Type strain

Strain Designation NAW-5

Culture col. no. DSM 102911 NBRC 112242 NAW-5

NCBI tax ID(s) 1898651

Special Collections DSMZ Literature strains

History <- M. Watanabe, Hokkaido University, Sapporo, Japan; NAW-5 <- M. Watanabe {2016}

Links

Desulfocucumis palustris NAW-5 is an obligate anaerobe, spore-forming, Gram-negative bacterium that was isolated from marsh soil.

spore-forming Gram-negative motile rod-shaped obligate anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 408151

NBRC 112242,DSM 102911

@ref 20215

Last LPSN update 2026-02-09 11:33:35

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Peptococcaceae

Genus Desulfocucumis

Species Desulfocucumis palustris

Full scientific name Desulfocucumis palustris Watanabe et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Flagellum arrangement
43451	negative	3-4 µm	1 µm	rod-shaped		peritrichous

Colony morphology

@ref	Colony color	Medium used
43451	pale brown	Basal medium

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43451	Basal medium
42960	PELOTOMACULUM MEDIUM (DSMZ Medium 960)		Medium recipe at MediaDive	Name: PELOTOMACULUM MEDIUM (DSMZ Medium 960; with strain-specific modifications) Composition: Na2CO3 1.49701 g/l NH4Cl 0.538922 g/l Na acetate 0.499002 g/l Yeast extract 0.499002 g/l Na2S x 9 H2O 0.299401 g/l L-Cysteine HCl x H2O 0.299401 g/l MgCl2 x 6 H2O 0.199601 g/l KH2PO4 0.139721 g/l Nitrilotriacetic acid 0.0127745 g/l NaCl 0.000998004 g/l FeCl2 x 4 H2O 0.000998004 g/l Sodium resazurin 0.000499002 g/l CaCl2 x 2 H2O 9.98004e-05 g/l NiCl2 x 6 H2O 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l ZnCl2 9.98004e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Na2WO4 x 2 H2O 3.99202e-05 g/l CoCl2 x 6 H2O 2.99401e-05 g/l Na2MoO4 x 2 H2O 2.99401e-05 g/l Na2SeO3 x 5 H2O 2.99401e-05 g/l CuCl2 1.99601e-05 g/l Biotin 1.99601e-05 g/l Folic acid 1.99601e-05 g/l H3BO3 9.98004e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
42960	positive	growth	28
43451	positive	growth	18-48
43451	positive	optimum	32-37

Culture pH

@ref	Ability	Type	PH
43451	positive	optimum	6.2-7.3
43451	positive	growth	5.8-8.4

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43451	obligate anaerobe
125439	anaerobe	99.9

Spore formation

43451

Spore formationyes

Halophily

@ref	Halophily level	Salt	Growth	Tested relation	Concentration
43451		NaCl	positive	growth	0-2.1 %
43451	non-halophilic	NaCl	positive	optimum	0 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43451	30089 ChEBI	acetate	+	assimilation
43451	16150 ChEBI	benzoate	+	assimilation
43451	17968 ChEBI	butyrate	+	assimilation
43451	33403 ChEBI	elemental sulfur	+	electron acceptor
43451	29034 ChEBI	ferric iron	-	electron acceptor
43451	15740 ChEBI	formate	+	assimilation
43451	29806 ChEBI	fumarate	+	assimilation
43451	17234 ChEBI	glucose	-	assimilation
43451	48944 ChEBI	isobutyrate	+	assimilation
43451	24996 ChEBI	lactate	+	assimilation
43451	17632 ChEBI	nitrate	-	electron acceptor
43451	16301 ChEBI	nitrite	-	electron acceptor
43451	17272 ChEBI	propionate	+	assimilation
43451	15361 ChEBI	pyruvate	+	assimilation
43451	16189 ChEBI	sulfate	+	electron acceptor
43451	17359 ChEBI	sulfite	-	electron acceptor
43451	16094 ChEBI	thiosulfate	+	electron acceptor

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	aspartate and asparagine metabolism	100	9 of 9
66794	glycogen metabolism	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	L-lactaldehyde degradation	100	3 of 3
66794	propanol degradation	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	glycine betaine biosynthesis	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	alanine metabolism	75.86	22 of 29
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	coenzyme A metabolism	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	photosynthesis	71.43	10 of 14
66794	starch degradation	70	7 of 10
66794	threonine metabolism	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	oxidative phosphorylation	67.03	61 of 91
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	valine metabolism	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	NAD metabolism	66.67	12 of 18
66794	serine metabolism	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	citric acid cycle	64.29	9 of 14
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	pyrimidine metabolism	62.22	28 of 45
66794	leucine metabolism	61.54	8 of 13
66794	sulfate reduction	61.54	8 of 13
66794	phenylalanine metabolism	61.54	8 of 13
66794	hydrogen production	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	non-pathway related	57.89	22 of 38
66794	lysine metabolism	57.14	24 of 42
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	chorismate metabolism	55.56	5 of 9
66794	pentose phosphate pathway	54.55	6 of 11
66794	purine metabolism	51.06	48 of 94
66794	suberin monomers biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	tetrahydrofolate metabolism	50	7 of 14
66794	toluene degradation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	butanoate fermentation	50	2 of 4
66794	lipid metabolism	48.39	15 of 31
66794	flavin biosynthesis	46.67	7 of 15
66794	urea cycle	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	vitamin B12 metabolism	44.12	15 of 34
66794	polyamine pathway	43.48	10 of 23
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	cysteine metabolism	38.89	7 of 18
66794	gluconeogenesis	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	glutathione metabolism	35.71	5 of 14
66794	degradation of pentoses	35.71	10 of 28
66794	methionine metabolism	34.62	9 of 26
66794	histidine metabolism	34.48	10 of 29
66794	sphingosine metabolism	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	pantothenate biosynthesis	33.33	2 of 6
66794	tryptophan metabolism	31.58	12 of 38
66794	isoprenoid biosynthesis	30.77	8 of 26
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	arginine metabolism	29.17	7 of 24
66794	tyrosine metabolism	28.57	4 of 14
66794	degradation of hexoses	27.78	5 of 18
66794	d-xylose degradation	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	C4 and CAM-carbon fixation	25	2 of 8
66794	carnitine metabolism	25	2 of 8
66794	vitamin E metabolism	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	CMP-KDO biosynthesis	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	heme metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Wetland (Swamp)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
42960	marsh soil	Hokkaido Prefectural Natural Park, Nopporo Forest Park	Japan	JPN	Asia
43451	Marsh soil from Nopporo Forest Park	Sapporo, Hokkaido	Japan	JPN	Asia	43.068	141.519 43.068/141.519

Taxonmaps

69479

Global distribution of 16S sequence LC183909 (>99% sequence identity) for Desulfocucumis palustris subclade from Microbeatlas

Aquatic Samples	7
Soil Samples	2
Animal Samples
Plant Samples	4
Total Samples	13

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42960	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM293387v1 assembly for Desulfocucumis palustris NAW-5	contig	GCA_002933875	1898651.6	2788500037	1898651	21.49

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42960	Desulfocucumis palustris gene for 16S ribosomal RNA, partial sequence, strain: NAW-5	LC183909	1442		1898651

GC content

@ref	GC-content (mol%)	Method
42960	46.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfocucumis palustris NAW-5
NCBI: GCA_002933875

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	61.60	no
125439	motility	BacteriaNetⓘ	yes	50.90	no
125439	gram_stain	BacteriaNetⓘ	variable	59.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.90	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Desulfocucumis palustris gen. nov., sp. nov., a mesophilic sulfate reducer belonging to Desulfotomaculum subcluster Ig.	Watanabe M, Kojima H, Fukui M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002005	2017

References

#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 )
#42960	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102911
#43451	Miho Watanabe, Hisaya Kojima, Manabu Fukui: Desulfocucumis palustris gen. nov., sp. nov., a mesophilic sulfate reducer belonging to Desulfotomaculum subcluster Ig. IJSEM 67: 2679 - 2682 2017 ( DOI 10.1099/ijsem.0.002005 , PubMed 28786781 )
#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 .
#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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Desulfocucumis palustris (DSM 102911, NBRC 112242, NAW-5)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002933875

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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