Nisaea denitrificans DR41_21 | Type strain | DSM 18348, CIP 109265, OOB 129 | BacDiveID:13946

Strain identifier

BacDive ID: 13946

Type strain:

Species: Nisaea denitrificans

Strain Designation: DR41_21

Culture col. no.: DSM 18348, CIP 109265, OOB 129

Strain history: CIP <- 2006, L. Urios, Banyuls sur mer, France: strain OOB 129

NCBI tax ID(s): 1122607 (strain), 390877 (species)

SI-ID 359524

CIP 109265, DSM 18348

Section

Nisaea denitrificans DR41_21 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from water column.

Gram-negative
motile
rod-shaped
aerobe
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	*Alphaproteobacteria*
	Order	*Rhodospirillales*
	Family	*Thalassobaculaceae*
	Genus	*Nisaea*
	Species	**Nisaea denitrificans**
	Full Scientific Name (LPSN)	Nisaea denitrificans Urios et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #31883]	Gram stain	negative
[Ref.: #118900]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #31883]	Cell length	2.5 µm

[Ref.: #31883]	Cell width	0.9 µm

[Ref.: #31883]	Cell shape	rod-shaped
[Ref.: #118900]	Cell shape	rod-shaped

[Ref.: #31883]	Motility	yes
[Ref.: #118900]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.085

Pigment production

yes

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

Marine agar (MA)

Culture medium growth

Culture medium composition

expand / minimize

[Ref.: #118900]

Culture medium

CIP Medium 13

[Ref.: #118900]

Culture medium growth

[Ref.: #118900]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #7432]			growth	30 °C
[Ref.: #31883]			growth	15-44 °C
[Ref.: #31883]			optimum	30 °C
[Ref.: #37494]			growth	30 °C

[Ref.: #7432]	Temperature range	mesophilic
[Ref.: #31883]	Temperature range	mesophilic
[Ref.: #37494]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31883]			optimum	6
[Ref.: #31883]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

Oxygen tolerance

aerobe

[Ref.: #31883]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

Observation

aggregates in chains

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31883]		acetate ChEBI	+	carbon source
[Ref.: #31883]		fructose ChEBI	+	carbon source
[Ref.: #31883]		glucose ChEBI	+	carbon source
[Ref.: #118900]		nitrate ChEBI	-	reduction
[Ref.: #118900]		nitrite ChEBI	-	reduction
[Ref.: #31883]		propionate ChEBI	+	carbon source
[Ref.: #31883]		raffinose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #118900]		indole ChEBI	no

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #68382]		acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #118900]		alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]		alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]		alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]		alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]		alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]		alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]		alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]		beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]		beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]		beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31883]		catalase	+	1.11.1.6
[Ref.: #118900]		catalase	+	1.11.1.6
[Ref.: #68382]		cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31883]		cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]		esterase (C 4)	+		* from API zym
[Ref.: #68382]		esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]		leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]		lipase (C 14)	-		* from API zym
[Ref.: #118900]		lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]		N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]		naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118900]		ornithine decarboxylase	-	4.1.1.17
[Ref.: #118900]		oxidase	+
[Ref.: #68382]		trypsin	-	3.4.21.4	* from API zym
[Ref.: #118900]		urease	+	3.5.1.5
[Ref.: #68382]		valine arylamidase	+		* from API zym
		Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #118900]	11750	-	+	+	-	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #7432]	Sample type/isolated from	water column
[Ref.: #7432]	Geographic location (country and/or sea, region)	Banyuls-sur-Mer (42° 29' N 3° 08' E)
[Ref.: #7432]	Country	France
[Ref.: #7432]	Country ISO 3 Code	FRA
[Ref.: #7432]	Continent	Europe
[Ref.: #7432]	Geographic location	42.4833°/3.1333°

[Ref.: #118900]	Sample type/isolated from	Environment, Sea water
[Ref.: #118900]	Geographic location (country and/or sea, region)	Banyuls sur mer
[Ref.: #118900]	Country	France
[Ref.: #118900]	Country ISO 3 Code	FRA
[Ref.: #118900]	Continent	Europe
[Ref.: #118900]	Isolation date	2004
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

-

What are isolation sources categories?

Global distribution of 16S sequence DQ665838 (>99% sequence identity) for Nisaea from Microbeatlas

Aquatic Samples	2179
Soil Samples	68
Animal Samples	120
Plant Samples	23
Total Samples	2390

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

[Ref.: #7432]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118900]	Biosafety level	1	Risk group (French classification)

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.: #7432]	Nisaea denitrificans strain DR41_21 16S ribosomal RNA gene, partial sequence	DQ665838	1292	ENA	1122607 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nisaea denitrificans DSM 18348	GCA_000426505	scaffold	GenBank	1122607 tax ID	*
[Ref.: #66792]	Nisaea denitrificans DSM 18348	1122607.5	wgs	PATRIC	1122607 tax ID	*
[Ref.: #66792]	Nisaea denitrificans DSM 18348	2524614677	draft	JGI IMG/M	1122607 tax ID	*

[Ref.: #7432]	GC-content	60 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #31883]	GC-content	60 mol%

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: Nisaea denitrificans DSM 18348 DSM 18348 NCBI: GCA_000426505.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nisaea denitrificans DSM 18348 DSM 18348 NCBI: GCA_000426505.1
[Ref.: #69480]	motile	yes	88.39	yes
[Ref.: #69480]	flagellated	yes	73.468	no
[Ref.: #69480]	gram-positive	no	98.878	yes
[Ref.: #69480]	anaerobic	no	98.65	no
[Ref.: #69480]	aerobic	yes	88.74	yes
[Ref.: #69480]	halophile	yes	65.588	no
[Ref.: #69480]	spore-forming	no	95.3	yes
[Ref.: #69480]	glucose-util	yes	86.464	yes
[Ref.: #69480]	thermophile	no	92.624	yes
[Ref.: #69480]	glucose-ferment	no	91.67	no

Availability in culture collections External links

Culture collection no.

DSM 18348, CIP 109265, OOB 129

SI-ID 359524

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nisaea sediminum sp. nov., a heavy metal resistant bacterium isolated from marine sediment in the East China Sea.	Zhu S, Cheng Y, Guo C, Xie F, Jung D, Zhang W, He S	Antonie Van Leeuwenhoek	10.1007/s10482-021-01665-w	2021	*
Phylogeny	Nisaea denitrificans gen. nov., sp. nov. and Nisaea nitritireducens sp. nov., two novel members of the class Alphaproteobacteria from the Mediterranean Sea.	Urios L, Michotey V, Intertaglia L, Lesongeur F, Lebaron P	Int J Syst Evol Microbiol	10.1099/ijs.0.64592-0	2008	*

References

#7432

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18348

#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 )

#31883

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 #28143 (see below)

#37494 ; Curators of the CIP;

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#68382

Automatically annotated from API zym .

#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 )

#83119

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-ID359524.1 )

#118900 Collection of Institut Pasteur ; Curators of the CIP; CIP 109265

#28143

IJSEM 2336 2008 ( DOI 10.1099/ijs.0.64592-0 , PubMed 18842852 )

* These data were automatically processed and therefore are not curated

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