Name: Desulfopila aestuarii DSM 18488
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 4031

Type strain:

Species: Desulfopila aestuarii

Culture col. no.: DSM 18488, JCM 14042, MSL 86

Strain history: A. Ueki MSL86.

NCBI tax ID(s): 1121416 (strain), 231440 (species)

SI-ID 297179

DSM 18488, JCM 14042

Section

Desulfopila aestuarii DSM 18488 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from estuarine sediment.

Gram-negative
motile
rod-shaped
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Deltaproteobacteria*
	Order	*Desulfobacterales*
	Family	*Desulfobulbaceae*
	Genus	*Desulfopila*
	Species	**Desulfopila aestuarii**
	Full Scientific Name (LPSN)	Desulfopila aestuarii Suzuki et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #23207]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #23207]	Cell length	1.9-3.8 µm

[Ref.: #23207]	Cell width	0.7-1.2 µm

[Ref.: #23207]	Cell shape	rod-shaped

[Ref.: #23207]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.821

[Ref.: #23207]	Flagellum arrangement	polar

[Ref.: #23207]	Colony color	greyish
[Ref.: #23207]	Cultivation medium used	slant media

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7557]

Culture medium

DESULFOPILA MSL86 MEDIUM (DSMZ Medium 1068)

[Ref.: #7557]

Culture medium growth

[Ref.: #7557]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7557]

Culture medium composition

expand / minimize

[Ref.: #23207]

Culture medium

slant media

[Ref.: #23207]

Culture medium growth

		Temperature
[Ref.: #7557]	growth	30 °C
[Ref.: #23207]	growth	10-40 °C
[Ref.: #23207]	optimum	35 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #7557]	Temperature range	mesophilic
[Ref.: #23207]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #23207]			optimum	7.5-7.6
[Ref.: #23207]			growth	6.3-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7557]	Oxygen tolerance	anaerobe
[Ref.: #23207]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.446

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.98

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23207]		NaCl		growth	0-5	%(w/v)
[Ref.: #23207]		NaCl		optimum	1	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23207]	acetate ChEBI	-	electron acceptor
[Ref.: #23207]	alanine ChEBI	-	electron acceptor
[Ref.: #23207]	aspartate ChEBI	-	electron acceptor
[Ref.: #23207]	butanol ChEBI	+	electron donor
[Ref.: #23207]	butyrate ChEBI	-	electron acceptor
[Ref.: #23207]	ethanol ChEBI	+	electron donor
[Ref.: #23207]	formate ChEBI	+	electron donor
[Ref.: #23207]	fumarate ChEBI	-	electron acceptor
[Ref.: #23207]	fumarate ChEBI	+	electron donor
[Ref.: #23207]	glutamate ChEBI	-	electron acceptor
[Ref.: #23207]	glycerol ChEBI	+	electron donor
[Ref.: #23207]	glycine ChEBI	-	electron acceptor
[Ref.: #23207]	hydrogen sulfide ChEBI	-	electron acceptor
[Ref.: #23207]	lactate ChEBI	+	electron donor
[Ref.: #23207]	malate ChEBI	-	electron acceptor
[Ref.: #23207]	methanol ChEBI	-	electron acceptor
[Ref.: #23207]	propanol ChEBI	+	electron donor
[Ref.: #23207]	propionate ChEBI	-	electron acceptor
[Ref.: #23207]	pyruvate ChEBI	+	electron donor
[Ref.: #23207]	serine ChEBI	-	electron acceptor
[Ref.: #23207]	succinate ChEBI	-	electron acceptor
[Ref.: #23207]	sulfite ChEBI	-	electron acceptor
[Ref.: #23207]	thiosulfate ChEBI	-	electron acceptor
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #23207]		catalase	-	1.11.1.6
[Ref.: #23207]		cytochrome oxidase	-	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	CO2 fixation in Crenarchaeota	100	9 of 9
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	alanine metabolism	96.55	28 of 29
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	lipid A biosynthesis	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]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	lysine metabolism	76.19	32 of 42
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	oxidative phosphorylation	71.43	65 of 91
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	degradation of sugar acids	52	13 of 25
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #7557]	Sample type/isolated from	estuarine sediment
[Ref.: #7557]	Geographic location (country and/or sea, region)	Yamagata
[Ref.: #7557]	Country	Japan
[Ref.: #7557]	Country ISO 3 Code	JPN
[Ref.: #7557]	Continent	Asia

[Ref.: #23207]	Sample type/isolated from	estuarine sediment located in the Sea around the Japanese islands

[Ref.: #67770]	Sample type/isolated from	Estuarine sediment in the Sea of Japan around the Japanese Islands
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Brackish
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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

[Ref.: #7557]

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.: #7557]	Desulfopila aestuarii gene for 16S ribosomal RNA, partial sequence	AB110542	1471	ENA	231440 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Desulfopila aestuarii DSM 18488	GCA_900143695	contig	GenBank	1121416 tax ID
[Ref.: #66792]	Desulfopila aestuarii DSM 18488	1121416.3	wgs	PATRIC	1121416 tax ID	*
[Ref.: #66792]	Desulfopila aestuarii DSM 18488	2582581262	draft	JGI IMG/M	1121416 tax ID	*
[Ref.: #66792]	Desulfopila aestuarii DSM 18488 MiH-14oct19-162	GCA_945863875	contig	GenBank	1121416 tax ID	*
[Ref.: #66792]	Desulfopila aestuarii DSM 18488 strain MiH-14oct19-162	1121416.5	wgs	PATRIC	1121416 tax ID	*

[Ref.: #7557]	GC-content	54.4 mol%
[Ref.: #23207]	GC-content	54.4 mol%	high performance liquid chromatography (HPLC)

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: Desulfopila aestuarii DSM 18488 PATRIC: 1121416.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Desulfopila aestuarii DSM 18488 PATRIC: 1121416.3
[Ref.: #69480]	motile	yes	89.121	yes
[Ref.: #69480]	flagellated	yes	67.059	yes
[Ref.: #69480]	gram-positive	no	98.891	yes
[Ref.: #69480]	anaerobic	yes	91.686	yes
[Ref.: #69480]	aerobic	no	94.741	yes
[Ref.: #69480]	halophile	no	91.558	yes
[Ref.: #69480]	spore-forming	no	92.978	no
[Ref.: #69480]	glucose-util	yes	61.427	no
[Ref.: #69480]	thermophile	no	98.609	yes
[Ref.: #69480]	glucose-ferment	no	83.582	no

Availability in culture collections External links

[Ref.: #7557]

Culture collection no.

DSM 18488, JCM 14042, MSL 86

[Ref.: #73536]

SI-ID 297179

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	A sulfate-reducing bacterial genus, Desulfosediminicola gen. nov., comprising two novel species cultivated from tidal-flat sediments.	Song J, Hwang J, Kang I, Cho JC	Sci Rep	10.1038/s41598-021-99469-5	2021	*
Phylogeny	Desulfopila inferna sp. nov., a sulfate-reducing bacterium isolated from the subsurface of a tidal sand-flat.	Gittel A, Seidel M, Kuever J, Galushko AS, Cypionka H, Konneke M	Int J Syst Evol Microbiol	10.1099/ijs.0.015644-0	2009	*
Phylogeny	Desulfopila aestuarii gen. nov., sp. nov., a Gram-negative, rod-like, sulfate-reducing bacterium isolated from an estuarine sediment in Japan.	Suzuki D, Ueki A, Amaishi A, Ueki K	Int J Syst Evol Microbiol	10.1099/ijs.0.64600-0	2007	*

References

#7557

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18488

#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 )

#23207

Daisuke Suzuki, Atsuko Ueki, Aya Amaishi, Katsuji Ueki: Desulfopila aestuarii gen. nov., sp. nov., a Gram-negative, rod-like, sulfate-reducing bacterium isolated from an estuarine sediment in Japan. IJSEM 57: 520 - 526 2007 ( DOI 10.1099/ijs.0.64600-0 , PubMed 17329777 )

#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;

#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 )

#73536

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-ID297179.1 )

* These data were automatically processed and therefore are not curated

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