Name: Desulfosarcina widdelii PP31
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140360

Type strain:

Species: Desulfosarcina widdelii

Strain Designation: PP31

Culture col. no.: DSM 103921, JCM 31729

Strain history: M. Watanabe; Hokkaido Univ., Japan; PP31.

NCBI tax ID(s): 947919 (species)

SI-ID 404068

DSM 103921

Special Collections

Section

When using BacDive for research please cite our paper

Desulfosarcina widdelii PP31 is an anaerobe, Gram-negative, motile bacterium that was isolated from oil-polluted marine sediment, p-xylene-degrading sulfate-reducing enrichment culture.

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

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Deltaproteobacteria*
	Order	*Desulfobacterales*
	Family	*Desulfobacteraceae*
	Genus	*Desulfosarcina*
	Species	**Desulfosarcina widdelii**
	Full Scientific Name (LPSN)	Desulfosarcina widdelii Watanabe et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43887]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.7
[Ref.: #125438]	Gram stain	negative Confidence in %96.889

[Ref.: #43887]	Cell length	6.0-27.5 µm

[Ref.: #43887]	Cell width	0.8 µm

[Ref.: #43887]	Cell shape	rod-shaped

[Ref.: #43887]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43887]

Culture medium

Basal medium

[Ref.: #43887]

Culture medium growth

[Ref.: #43887]

Culture medium composition

expand / minimize

[Ref.: #42967]

Culture medium

DESULFUROMUSA MEDIUM (DSMZ Medium 195a)

[Ref.: #42967]

Culture medium growth

[Ref.: #42967]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42967]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #42967]	growth	28 °C
[Ref.: #43887]	growth	20-37 °C
[Ref.: #43887]	optimum	28 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #43887]			optimum	7.3-7.8
[Ref.: #43887]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43887]

Oxygen tolerance

anaerobe

[Ref.: #43887]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43887]	acetate ChEBI	+	carbon source
[Ref.: #43887]	acetate ChEBI	+	electron donor
[Ref.: #43887]	benzene ChEBI	-	electron donor
[Ref.: #43887]	benzoate ChEBI	+	carbon source
[Ref.: #43887]	benzoate ChEBI	+	electron donor
[Ref.: #43887]	butyrate ChEBI	+	carbon source
[Ref.: #43887]	butyrate ChEBI	+	electron donor
[Ref.: #43887]	elemental sulfur ChEBI	+	electron acceptor
[Ref.: #43887]	ethanol ChEBI	-	electron donor
[Ref.: #43887]	formate ChEBI	+	carbon source
[Ref.: #43887]	formate ChEBI	+	electron donor
[Ref.: #43887]	fumarate ChEBI	+	carbon source
[Ref.: #43887]	fumarate ChEBI	+	electron donor
[Ref.: #43887]	fumarate ChEBI	+	fermentation
[Ref.: #43887]	glucose ChEBI	-	electron donor
[Ref.: #43887]	hexane ChEBI	-	electron donor
[Ref.: #43887]	lactate ChEBI	-	electron donor
[Ref.: #43887]	lactate ChEBI	-	fermentation
[Ref.: #43887]	malate ChEBI	+	fermentation
[Ref.: #43887]	nitrate ChEBI	-	electron acceptor
[Ref.: #43887]	phenol ChEBI	-	electron donor
[Ref.: #43887]	propionate ChEBI	+	carbon source
[Ref.: #43887]	propionate ChEBI	+	electron donor
[Ref.: #43887]	pyruvate ChEBI	+	carbon source
[Ref.: #43887]	pyruvate ChEBI	+	electron donor
[Ref.: #43887]	succinate ChEBI	+	carbon source
[Ref.: #43887]	succinate ChEBI	+	electron donor
[Ref.: #43887]	sulfate ChEBI	+	carbon source
[Ref.: #43887]	sulfate ChEBI	+	electron acceptor
[Ref.: #43887]	sulfate ChEBI	+	electron donor
[Ref.: #43887]	sulfite ChEBI	-	electron acceptor
[Ref.: #43887]	thiosulfate ChEBI	+	electron acceptor
[Ref.: #43887]	toluene ChEBI	-	electron donor
[Ref.: #43887]	xylene ChEBI	-	electron donor
[Ref.: #43887]	xylene ChEBI	+	carbon source
[Ref.: #43887]	xylene ChEBI	+	electron donor
[Ref.: #43887]	yeast extract	+	carbon source
[Ref.: #43887]	yeast extract	+	electron donor
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43887]

Fatty acid	Percentage
C15:0	25.9
C15:0 anteiso	22.3
C17:0	9.5
C15:1ω6c	6.9
C16:0	6
C17:1ω6c	5.4
C15:0 iso	4.3
C17:1ω8c	4
C14:0	2.8
C16:1ω7c	2.3
C17:0 anteiso	2
C18:0	1.6

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #42967]	Sample type/isolated from	oil-polluted marine sediment, p-xylene-degrading sulfate-reducing enrichment culture
[Ref.: #42967]	Geographic location (country and/or sea, region)	Shuaiba
[Ref.: #42967]	Country	Kuwait
[Ref.: #42967]	Country ISO 3 Code	KWT
[Ref.: #42967]	Continent	Asia

[Ref.: #43887]	Sample type/isolated from	p-xylene degarding sulfate-reducing enrichment culture established from petroleum-contaminated marine sediments of Shuaiba, Kuwait
[Ref.: #43887]	Geographic location (country and/or sea, region)	Shuaiba
[Ref.: #43887]	Country	Kuwait
[Ref.: #43887]	Country ISO 3 Code	KWT
[Ref.: #43887]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Oil-polluted marine sediments of Shuaiba
[Ref.: #67770]	Country	Kuwait
[Ref.: #67770]	Country ISO 3 Code	KWT
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Laboratory	#Lab enrichment
#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB610146 (>99% sequence identity) for Desulfosarcina widdelii from Microbeatlas

Aquatic Samples	12
Soil Samples
Animal Samples
Plant Samples
Total Samples	12

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

[Ref.: #42967]

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.: #42967]	Desulfosarcina widdelii gene for 16S rRNA, partial sequence	AB610146	1485	GenBank ENA	947919 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Desulfosarcina widdelii PP31	GCA_009688965	complete	GenBank ENA	947919 tax ID	*
[Ref.: #66792]	Desulfosarcina widdelii strain PP31	947919.4	complete	PATRIC	947919 tax ID	*
[Ref.: #66792]	Desulfosarcina widdelii PP31	2883713342	complete	JGI IMG/M	947919 tax ID	*

[Ref.: #42967]

GC-content

54.8 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfosarcina widdelii PP31 NCBI: GCA_009688965.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.889	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	74.273	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	70.635	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	81.258	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	89.132	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	69.292	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfosarcina widdelii PP31 NCBI: GCA_009688965
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	65.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	79

Availability in culture collections External links

[Ref.: #42967]

Culture collection no.

DSM 103921, JCM 31729

[Ref.: #96658]

SI-ID 404068

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Desulfosarcina widdelii sp. nov. and Desulfosarcina alkanivorans sp. nov., hydrocarbon-degrading sulfate-reducing bacteria isolated from marine sediment and emended description of the genus Desulfosarcina.	Watanabe M, Higashioka Y, Kojima H, Fukui M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002062	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 )

#42967

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103921

#43887

Miho Watanabe, Yuriko Higashioka, Hisaya Kojima, Manabu Fukui: Desulfosarcina widdelii sp. nov. and Desulfosarcina alkanivorans sp. nov., hydrocarbon-degrading sulfate-reducing bacteria isolated from marine sediment and emended description of the genus Desulfosarcina. IJSEM 67: 2994 - 2997 2017 ( DOI 10.1099/ijsem.0.002062 , PubMed 28820122 )

#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) .

#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 .

#96658

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-ID404068.1 )

#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 .

* These data were automatically processed and therefore are not curated

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