Nereida ignava (DSM 16309, CCUG 49433, CECT 5292)

Name: Nereida ignava (DSM 16309, CCUG 49433, CECT 5292)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13682

Type strain

Strain Designation 2SM4

Culture col. no. DSM 16309 CCUG 49433 CECT 5292 CIP 108404 2SM4

NCBI tax ID(s) 1122600 282199

Special Collections DSMZ CCUG CIP Literature strains

Links

Nereida ignava 2SM4 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from Mediterranean sea water.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 138022

CCUG 49433,CECT 5292,CIP 108404,DSM 16309

@ref 20215

Last LPSN update 2025-12-16 09:50:09

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Nereida

Species Nereida ignava

Full scientific name Nereida ignava Pujalte et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
31383	negative	2 µm	0.25 µm	rod-shaped
120044	negative			oval-shaped
125438	negative
125439	negative

Colony morphology

@ref	Incubation period
58552	2 days
120044

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6356	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
37429	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
120044	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6356	positive	growth	25	mesophilic
31383	positive	growth	13-28
31383	positive	optimum	20.5	psychrophilic
37429	positive	growth	25	mesophilic
58552	positive	growth	24-26
120044	negative	growth	41
120044	negative	growth	37
120044	negative	growth	5
120044	positive	growth	15-25	psychrophilic
120044	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31383	aerobe
58552	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125438		90.148
125439		98.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31383	NaCl	positive	growth	<8 %
31383	NaCl	positive	optimum	4 %
120044	NaCl		growth	0 %
120044	NaCl		growth	2 %
120044	NaCl		growth	4 %
120044	NaCl		growth	6 %
120044	NaCl		growth	8 %
120044	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31383	30089 ChEBI	acetate	+	carbon source
31383	16947 ChEBI	citrate	+	carbon source
120044	16947 ChEBI	citrate	-	carbon source
120044	4853 ChEBI	esculin	-	hydrolysis
31383	17234 ChEBI	glucose	+	carbon source
120044	606565 ChEBI	hippurate	+	hydrolysis
31383	24996 ChEBI	lactate	+	carbon source
31383	25115 ChEBI	malate	+	carbon source
120044	15792 ChEBI	malonate	-	assimilation
31383	17306 ChEBI	maltose	+	carbon source
31383	29864 ChEBI	mannitol	+	carbon source
31383	37684 ChEBI	mannose	+	carbon source
120044	17632 ChEBI	nitrate	-	builds gas from
120044	17632 ChEBI	nitrate	-	reduction
120044	16301 ChEBI	nitrite	-	builds gas from
120044	16301 ChEBI	nitrite	-	reduction
31383	18257 ChEBI	ornithine	+	carbon source
31383	17272 ChEBI	propionate	+	carbon source
31383	15361 ChEBI	pyruvate	+	carbon source
31383	17822 ChEBI	serine	+	carbon source
31383	30031 ChEBI	succinate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120044	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
120044	15688 ChEBI	acetoin	-
120044	17234 ChEBI	glucose

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120044	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
120044	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
120044	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120044	caseinase	-	3.4.21.50
31383	catalase	+	1.11.1.6
120044	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31383	cytochrome oxidase	+	1.9.3.1
120044	DNase	-
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	+		from API zym
120044	gamma-glutamyltransferase	-	2.3.2.2
120044	gelatinase	-
120044	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
120044	lipase	-
68382	lipase (C 14)	-		from API zym
120044	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
120044	ornithine decarboxylase	-	4.1.1.17
120044	oxidase	+
120044	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
120044	tryptophan deaminase	-
120044	tween esterase	-
120044	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	valine metabolism	100	9 of 9
66794	suberin monomers biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	denitrification	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	octane oxidation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	CMP-KDO biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	lipid A biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	vitamin B12 metabolism	85.29	29 of 34
66794	vitamin B1 metabolism	84.62	11 of 13
66794	proline metabolism	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	methylglyoxal degradation	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	citric acid cycle	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	photosynthesis	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	ketogluconate metabolism	75	6 of 8
66794	lactate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	pentose phosphate pathway	72.73	8 of 11
66794	NAD metabolism	72.22	13 of 18
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	heme metabolism	71.43	10 of 14
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	leucine metabolism	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	tryptophan metabolism	68.42	26 of 38
66794	oxidative phosphorylation	67.03	61 of 91
66794	flavin biosynthesis	66.67	10 of 15
66794	cyanate degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	alanine metabolism	65.52	19 of 29
66794	lipid metabolism	64.52	20 of 31
66794	vitamin B6 metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	propionate fermentation	60	6 of 10
66794	3-phenylpropionate degradation	60	9 of 15
66794	degradation of sugar acids	60	15 of 25
66794	glycolysis	58.82	10 of 17
66794	arginine metabolism	58.33	14 of 24
66794	propanol degradation	57.14	4 of 7
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	tyrosine metabolism	57.14	8 of 14
66794	degradation of pentoses	57.14	16 of 28
66794	cysteine metabolism	55.56	10 of 18
66794	histidine metabolism	55.17	16 of 29
66794	lysine metabolism	54.76	23 of 42
66794	sulfate reduction	53.85	7 of 13
66794	toluene degradation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	glycine metabolism	50	5 of 10
66794	carnitine metabolism	50	4 of 8
66794	chlorophyll metabolism	50	9 of 18
66794	phenylmercury acetate degradation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	urea cycle	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	arachidonic acid metabolism	44.44	8 of 18
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	glycogen metabolism	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	lipoate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	methane metabolism	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	allantoin degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	metabolism of disaccharids	27.27	3 of 11
66794	glycogen biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	biotin biosynthesis	25	1 of 4

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
120044	-	-	-	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6356	Mediterranean sea water	near Valencia	Spain	ESP	Europe
58552	Oyster meat	Valencia	Spain	ESP	Europe
120044	Environment, Sea water	Valencia	Spain	ESP	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ748748 (>99% sequence identity) for Nereida ignava subclade from Microbeatlas

Aquatic Samples	12489
Soil Samples	272
Animal Samples	376
Plant Samples	83
Total Samples	13220

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6356	1	Risk group (German classification) According to TRBA 466
120044	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	IMG-taxon 2599185238 annotated assembly for Nereida ignava DSM 16309	contig	GCA_900114125	1122600.3	2599185238	1122600	72.37
66792	N.ignavaCECT5292_PROKKA assembly for Nereida ignava CECT 5292	contig	GCA_001404155	282199.9	2706794653	282199	64.58
66792	N.ignavaCECT5292_MIRA assembly for Nereida ignava CECT 5292	contig	GCA_001049735	282199.8		282199	63.84

Genome browser: GCA_900114125

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Nereida ignava strain CECT5292 16S ribosomal RNA gene, partial sequence	DQ915613	1307		282199
6356	Nereida ignava 16S rRNA gene, type strain 2SM4T	AJ748748	1455		282199

GC content

6356

GC-content (mol%)56

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nereida ignava DSM 16309
NCBI: GCA_900114125

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.00	no
125439	gram_stain	BacteriaNetⓘ	negative	98.90	no
125439	motility	BacteriaNetⓘ	yes	77.30	no
125439	spore_formation	BacteriaNetⓘ	no	98.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nereida ignava DSM 16309
PATRIC: 1122600.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	yes
125438	anaerobic	anaerobicⓘ	no	93.60	yes
125438	spore-forming	spore-formingⓘ	no	90.15	no
125438	aerobic	aerobicⓘ	yes	85.25	yes
125438	thermophilic	thermophileⓘ	no	93.79	yes
125438	flagellated	motile2+ⓘ	no	52.45	no

Literature

Title	Authors	Journal	DOI	Year
Characteristics and Evolutionary Analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from Streamlined Plasmids to Chromids.	Liu Y, Zheng Q, Lin W, Jiao N.	mSystems	10.1128/msystems.00358-19	2019
Draft Genome Sequence of Nereida sp. Strain MMG025, Isolated from Giant Kelp.	Alker AT, Hern NA, Ali MA, Baez MI, Baswell BC, Baxter BI, Blitz A, Calimlim TM, Chevalier CA, Eguia CA, Esparza T, Fuller AE, Gwynn CJ, Hedin AL, Johnson RA, Kaur M, Laxina RT, Lee K, Maguire PN, Martelino IF, Melendez JA, Navarro JJ, Navarro JN, Osborn JM, Padilla MR, Peralta ND, Pureza JLR, Rojas JJ, Romo TR, Sakha M, Salcedo GJ, Sims KA, Trieu TH, Niesman IR, Shikuma NJ.	Microbiol Resour Announc	10.1128/mra.00122-22	2022
Draft genomic sequence of Nereida ignava CECT 5292(T), a marine bacterium of the family Rhodobacteraceae.	Arahal DR, Pujalte MJ, Rodrigo-Torres L	Stand Genomic Sci	10.1186/s40793-016-0141-2	2016
Description and Comparative Genomics of Algirhabdus cladophorae gen. nov., sp. nov., a Novel Aerobic Anoxygenic Phototrophic Bacterial Epibiont Associated with the Green Alga Cladophora stimpsonii.	Nedashkovskaya O, Baldaev S, Ivaschenko A, Bystritskaya E, Zhukova N, Eremeev V, Kukhlevskiy A, Kurilenko V, Isaeva M.	Life (Basel)	10.3390/life15030331	2025
Nereida ignava gen. nov., sp. nov., a novel aerobic marine alpha-proteobacterium that is closely related to uncultured Prionitis (alga) gall symbionts.	Pujalte MJ, Macian MC, Arahal DR, Ludwig W, Schleifer KH, Garay E	Int J Syst Evol Microbiol	10.1099/ijs.0.63442-0	2005

References

#6356	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16309
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#31383	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 #27695 (see below)
#37429	; Curators of the CIP;
#58552	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 49433
#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 )
#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 .
#120044	Collection of Institut Pasteur ; Curators of the CIP; CIP 108404
#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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Nereida ignava (DSM 16309, CCUG 49433, CECT 5292)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900114125

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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