Name: Halodesulfovibrio marinisediminis NMRC 101113
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 4153

Type strain:

Species: Halodesulfovibrio marinisediminis

Strain Designation: NMRC 101113, C/L 2

Culture col. no.: DSM 17456, JCM 14577, NBRC 101113

Strain history: S. Takii C/L2.

NCBI tax ID(s): 1121457 (strain), 458711 (species)

SI-ID 401170

DSM 17456

Section

Halodesulfovibrio marinisediminis NMRC 101113 is an anaerobe, mesophilic, vibrio-shaped bacterium that was isolated from anoxic coastal sediment, highly eutrophic area.

vibrio-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	*Desulfovibrionales*
	Family	*Desulfovibrionaceae*
	Genus	*Halodesulfovibrio*
	Species	**Halodesulfovibrio marinisediminis**
	Full Scientific Name (LPSN)	Halodesulfovibrio marinisediminis (Takii et al. 2008) Shivani et al. 2017

Synonym

Desulfovibrio marinisediminis

Information on morphological and physiological properties Morphology

[Ref.: #32597]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #32597]	Cell length	1-3.5 µm
[Ref.: #25150]	Cell length	1.0-3.5 µm

[Ref.: #32597]	Cell width	0.7-1 µm
[Ref.: #25150]	Cell width	0.7-0.1 µm

[Ref.: #32597]	Cell shape	coccus-shaped
[Ref.: #25150]	Cell shape	vibrio-shaped

[Ref.: #32597]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.269

[Ref.: #32597]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6996]

Culture medium

DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c)

[Ref.: #6996]

Culture medium growth

[Ref.: #6996]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6996]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6996]	growth	37 °C
[Ref.: #25150]	optimum	37 °C
[Ref.: #25150]	growth	15.0-40.0 °C
[Ref.: #32597]	growth	15-40 °C
[Ref.: #32597]	optimum	37 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #6996]	Temperature range	mesophilic
[Ref.: #25150]	Temperature range	mesophilic
[Ref.: #32597]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

		pH
[Ref.: #25150]	optimum	7.5
[Ref.: #32597]	optimum	7.5
[Ref.: #25150]	growth	6.3-8.6
[Ref.: #32597]	growth	6.3-8.6

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6996]	Oxygen tolerance	anaerobe
[Ref.: #25150]	Oxygen tolerance	obligate anaerobe
[Ref.: #32597]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.998

[Ref.: #32597]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.993

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25150]		NaCl		optimum	1.5-3.5	%(w/v)
[Ref.: #25150]		NaCl		growth	0.05-3.5	%(w/v)

[Ref.: #32597]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: MK-6(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25150]	acetate ChEBI	+	electron donor
[Ref.: #25150]	aspartate ChEBI	+	electron donor
[Ref.: #32597]	aspartate ChEBI	+	carbon source
[Ref.: #25150]	benzoate ChEBI	-	electron donor
[Ref.: #25150]	cysteine ChEBI	-	electron donor
[Ref.: #25150]	gelatin ChEBI	-	hydrolysis
[Ref.: #25150]	glycerol ChEBI	+	electron donor
[Ref.: #32597]	glycerol ChEBI	+	carbon source
[Ref.: #25150]	serine ChEBI	+	electron donor
[Ref.: #32597]	succinate ChEBI	+	carbon source
[Ref.: #25150]	sulfite ChEBI	+	electron acceptor
[Ref.: #25150]	tryptophan ChEBI	-	energy source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25150]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test
[Ref.: #25150]		indole ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25150]	catalase	+	1.11.1.6
[Ref.: #32597]	catalase	+	1.11.1.6
[Ref.: #25150]	tryptophan deaminase	-	4.1.99.1

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

[Ref.: #6996]	Sample type/isolated from	anoxic coastal sediment, highly eutrophic area
[Ref.: #6996]	Geographic location (country and/or sea, region)	Tokyo Bay
[Ref.: #6996]	Country	Japan
[Ref.: #6996]	Country ISO 3 Code	JPN
[Ref.: #6996]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Coastal marine sediment from the eutrophic Tokyo Bay
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB353727 (>99% sequence identity) for Halodesulfovibrio from Microbeatlas

Aquatic Samples	424
Soil Samples	30
Animal Samples	382
Plant Samples	43
Total Samples	879

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

[Ref.: #6996]

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.: #6996]	Desulfovibrio marinisediminis gene for 16S rRNA, partial sequence	AB353727	1533	ENA	1121457 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Halodesulfovibrio marinisediminis DSM 17456	GCA_900129975	scaffold	GenBank	1121457 tax ID
[Ref.: #66792]	Halodesulfovibrio marinisediminis DSM 17456	1121457.4	wgs	PATRIC	1121457 tax ID	*
[Ref.: #66792]	Halodesulfovibrio marinisediminis DSM 17456	2585428071	draft	JGI IMG/M	1121457 tax ID	*

[Ref.: #6996]	GC-content	46.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #25150]	GC-content	45 mol%	genome sequence analysis
[Ref.: #32597]	GC-content	46.2 mol%
[Ref.: #6996]	GC-content	45 mol%	sequence analysis

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: Halodesulfovibrio marinisediminis DSM 17456 DSM 17456 NCBI: GCA_900129975.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halodesulfovibrio marinisediminis DSM 17456 PATRIC: 1121457.4
[Ref.: #69480]	motile	yes	92.354	no
[Ref.: #69480]	flagellated	yes	54.012	no
[Ref.: #69480]	gram-positive	no	99.215	no
[Ref.: #69480]	anaerobic	yes	98.925	yes
[Ref.: #69480]	aerobic	no	98.658	no
[Ref.: #69480]	halophile	no	66.013	no
[Ref.: #69480]	spore-forming	no	95.044	yes
[Ref.: #69480]	thermophile	no	98.653	no
[Ref.: #69480]	glucose-util	no	52.865	no
[Ref.: #69480]	glucose-ferment	no	72.615	no

Availability in culture collections External links

[Ref.: #6996]

Culture collection no.

DSM 17456, JCM 14577, NBRC 101113

[Ref.: #73654]

SI-ID 401170

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Desulfovibrio oceani subsp. oceani sp. nov., subsp. nov. and Desulfovibrio oceani subsp. galateae subsp. nov., novel sulfate-reducing bacteria isolated from the oxygen minimum zone off the coast of Peru.	Finster KW, Kjeldsen KU	Antonie Van Leeuwenhoek	10.1007/s10482-009-9403-y	2009	*
Phylogeny	Desulfovibrio marinisediminis sp. nov., a novel sulfate-reducing bacterium isolated from coastal marine sediment via enrichment with Casamino acids.	Takii S, Hanada S, Hase Y, Tamaki H, Uyeno Y, Sekiguchi Y, Matsuura K	Int J Syst Evol Microbiol	10.1099/ijs.0.65750-0	2008	*

References

#6996

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17456

#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 )

#25150

Y. S. Shivani, Y.,Sasikala, C.,Ramana, C. V.: Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp. IJSEM 67: 87 - 93 2017 ( DOI 10.1099/ijsem.0.001574 , PubMed 27902290 )

#32597

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28810 (see below)

#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 .

#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 )

#73654

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-ID401170.1 )

#28810

IJSEM 2433 2008 ( DOI 10.1099/ijs.0.65750-0 , PubMed 18842870 )

* These data were automatically processed and therefore are not curated

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Halodesulfovibrio marinisediminis DSM 17456 DSM 17456

Halodesulfovibrio marinisediminis DSM 17456

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