Nisaea denitrificans (DSM 18348, CIP 109265, OOB 129)

Name: Nisaea denitrificans (DSM 18348, CIP 109265, OOB 129)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13946

Type strain

Strain Designation DR41_21

Culture col. no. DSM 18348 CIP 109265 OOB 129 DR41_21

NCBI tax ID(s) 1122607 390877

Special Collections DSMZ CIP Literature strains

History <- P. Lebaron, Lab. d'Océanographie Biologique de Banyuls, Univ. Pierre et Marie Curie, France; OOB 129 <- L. Intertaglia, Observatoire Océanologique de Banyuls, Laboratoire ARAGO, Univ. Pierre et Marie Curie - Paris 6, France CIP <- 2006, L. Urios, Banyuls sur mer, France: strain OOB 129

Links

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

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

Name and taxonomic classification

SI-ID 359524

CIP 109265,DSM 18348

@ref 20215

Last LPSN update 2026-02-09 11:21:17

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodospirillales

Family Thalassobaculaceae

Genus Nisaea

Species Nisaea denitrificans

Full scientific name Nisaea denitrificans Urios et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31883	negative	2.5 µm	0.9 µm	rod-shaped
118900	negative			rod-shaped
125439	negative				99.7
125438	negative				98

Colony morphology

Pigmentation

31883

Productionyes

Multimedia

@ref:	66793
multimedia content:	EM_DSM_18348_1.jpg
multimedia.multimedia content:	EM_DSM_18348_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_18348_2.jpg
multimedia.multimedia content:	EM_DSM_18348_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_18348_3.jpg
multimedia.multimedia content:	EM_DSM_18348_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_18348_4.jpg
multimedia.multimedia content:	EM_DSM_18348_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_18348_5.jpg
multimedia.multimedia content:	EM_DSM_18348_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7432	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37494	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
118900	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7432	positive	growth	30
31883	positive	growth	15-44
31883	positive	optimum	30
37494	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31883	positive	optimum	6
31883	positive	growth	05-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

31883

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
31883
125439		99.4
125438		93.288

Observation

31883

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31883	30089 ChEBI	acetate	+	carbon source
31883	28757 ChEBI	fructose	+	carbon source
31883	17234 ChEBI	glucose	+	carbon source
118900	17632 ChEBI	nitrate	-	reduction
118900	16301 ChEBI	nitrite	-	reduction
31883	17272 ChEBI	propionate	+	carbon source
31883	16634 ChEBI	raffinose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118900	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
118900	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31883	catalase	+	1.11.1.6
118900	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31883	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
118900	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118900	ornithine decarboxylase	-	4.1.1.17
118900	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
118900	urease	+	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118900	-	+	+	-	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Isolation date
7432	water column	Banyuls-sur-Mer (42° 29' N 3° 08' E)	France	FRA	Europe	42.4833	3.1333 42.4833/3.1333
118900	Environment, Sea water	Banyuls sur mer	France	FRA	Europe			2004

Taxonmaps

69479

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7432	1	Risk group (German classification) According to TRBA 466
118900	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM42650v1 assembly for Nisaea denitrificans DSM 18348	scaffold	GCA_000426505	1122607.5	2524614677	1122607	73.78

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7432	Nisaea denitrificans strain DR41_21 16S ribosomal RNA gene, partial sequence	DQ665838	1292		1122607

GC content

@ref	GC-content (mol%)	Method
7432	60	thermal denaturation, midpoint method (Tm)
31883	60

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nisaea denitrificans DSM 18348
NCBI: GCA_000426505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.40	no
125439	motility	BacteriaNetⓘ	yes	89.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	81.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nisaea denitrificans DSM 18348 DSM 18348
NCBI: GCA_000426505.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	yes
125438	anaerobic	anaerobicⓘ	no	94.25	yes
125438	aerobic	aerobicⓘ	yes	78.87	no
125438	spore-forming	spore-formingⓘ	no	93.29	yes
125438	thermophilic	thermophileⓘ	no	95.71	yes
125438	flagellated	motile2+ⓘ	yes	84.27	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential.	Isokpehi RD, Kim Y, Krejci SE, Trivedi VD.	Microorganisms	10.3390/microorganisms12040791	2024
	Mechanistic insights into the key marine dimethylsulfoniopropionate synthesis enzyme DsyB/DSYB.	Li CY, Crack JC, Newton-Payne S, Murphy ARJ, Chen XL, Pinchbeck BJ, Zhou S, Williams BT, Peng M, Zhang XH, Chen Y, Le Brun NE, Todd JD, Zhang YZ.	mLife	10.1002/mlf2.12030	2022
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 )
#28143	IJSEM 2336 2008 ( DOI 10.1099/ijs.0.64592-0 , PubMed 18842852 )
#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
#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 .
#118900	Collection of Institut Pasteur ; Curators of the CIP; CIP 109265
#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 .
#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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Nisaea denitrificans (DSM 18348, CIP 109265, OOB 129)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000426505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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