Croceicoccus marinus (CGMCC 1.6776, JCM 14846, E4A9)

Name: Croceicoccus marinus (CGMCC 1.6776, JCM 14846, E4A9)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133445

Type strain

Strain Designation E4A9

Culture col. no. CGMCC 1.6776 JCM 14846 E4A9

NCBI tax ID(s) 450378

Special Collections JCM Literature strains

History JCM <-- X.-W. Xu E4A9.

Links

Croceicoccus marinus E4A9 is an aerobe, Gram-negative, motile bacterium that was isolated from marine sediment.

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

Name and taxonomic classification

SI-ID 393330

JCM 14846

@ref 20215

Last LPSN update 2026-05-29 08:38:05

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Croceicoccus

Species Croceicoccus marinus

Full scientific name Croceicoccus marinus Xu et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29022	negative	0.8-1.0 µm	0.8-1.0 µm	coccus-shaped
125438	negative				96.733
125439	negative				95.725

Pigmentation

29022

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29022	positive	growth	04-42
29022	positive	optimum	25
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
29022	positive	optimum	7
29022	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29022	aerobe
125439	obligate aerobe	97.56

Spore formation

@ref	Spore formation	Confidence
29022
125439		98.82

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29022	NaCl	positive	growth	0-10 %
29022	NaCl	positive	optimum	0.5 %

Observation

@ref	Observation
29022	aggregates in clumps
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29022	30089 ChEBI	acetate	+	carbon source
29022	16449 ChEBI	alanine	+	carbon source
29022	4853 ChEBI	esculin	+	hydrolysis
29022	16236 ChEBI	ethanol	+	carbon source
29022	17234 ChEBI	glucose	+	carbon source
29022	29987 ChEBI	glutamate	+	carbon source
29022	17754 ChEBI	glycerol	+	carbon source
29022	27570 ChEBI	histidine	+	carbon source
29022	24996 ChEBI	lactate	+	carbon source
29022	25115 ChEBI	malate	+	carbon source
29022	17306 ChEBI	maltose	+	carbon source
29022	37684 ChEBI	mannose	+	carbon source
29022	17272 ChEBI	propionate	+	carbon source
29022	15361 ChEBI	pyruvate	+	carbon source
29022	17822 ChEBI	serine	+	carbon source
29022	30031 ChEBI	succinate	+	carbon source
29022	17992 ChEBI	sucrose	+	carbon source
29022	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29022	catalase	+	1.11.1.6
29022	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	quinate degradation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	glycine betaine biosynthesis	100	5 of 5
66794	factor 420 biosynthesis	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	propionate fermentation	90	9 of 10
66794	CO2 fixation in Crenarchaeota	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	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	d-xylose degradation	81.82	9 of 11
66794	threonine metabolism	80	8 of 10
66794	gallate degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	3-phenylpropionate degradation	80	12 of 15
66794	citric acid cycle	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	serine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	chorismate metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	degradation of sugar acids	76	19 of 25
66794	alanine metabolism	75.86	22 of 29
66794	purine metabolism	75.53	71 of 94
66794	CMP-KDO biosynthesis	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	metabolism of disaccharids	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	glutathione metabolism	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	octane oxidation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	tryptophan metabolism	63.16	24 of 38
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	urea cycle	61.54	8 of 13
66794	methionine metabolism	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	myo-inositol biosynthesis	60	6 of 10
66794	lysine metabolism	59.52	25 of 42
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	degradation of pentoses	57.14	16 of 28
66794	polyamine pathway	56.52	13 of 23
66794	d-mannose degradation	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	kanosamine biosynthesis II	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	selenocysteine biosynthesis	50	3 of 6
66794	carotenoid biosynthesis	50	11 of 22
66794	ribulose monophosphate pathway	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	arginine metabolism	50	12 of 24
66794	cyclohexanol degradation	50	2 of 4
66794	sulfopterin metabolism	50	2 of 4
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	oxidative phosphorylation	45.05	41 of 91
66794	phenol degradation	45	9 of 20
66794	lipid A biosynthesis	44.44	4 of 9
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	vitamin B12 metabolism	44.12	15 of 34
66794	ascorbate metabolism	40.91	9 of 22
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	arachidonic acid metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	methanogenesis from CO2	25	3 of 12
66794	carnitine metabolism	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type
29022	marine sediment
67770	Deep sea sediment sample collected from a polymetallic nodule region in the East Pacific Ocean

Taxonmaps

69479

Global distribution of 16S sequence LC508796 (>99% sequence identity) for Sphingomonadales from Microbeatlas

Aquatic Samples	59
Soil Samples	23
Animal Samples	6
Plant Samples	0
Total Samples	88

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM166167v2 assembly for Croceicoccus marinus E4A9	complete	GCA_001661675	450378.4	2827117550	450378	90.83

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29022	Sphingomonadaceae bacterium E4A9 16S ribosomal RNA gene, partial sequence	EF623998	1450		450378
67770	Croceicoccus marinus JCM 14846 gene for 16S ribosomal RNA, partial sequence	LC508796	1411		450378

GC content

@ref	GC-content (mol%)	Method
29022	71.5
67770	64.5	genome sequence analysis
67770	71.3-71.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM166167v2 assembly for Croceicoccus marinus E4A9
NCBI: GCA_001661675

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.56	no
125439	gram_stain	BacteriaNetⓘ	negative	95.73	no
125439	motility	BacteriaNetⓘ	yes	45.53	no
125439	spore_formation	BacteriaNetⓘ	no	98.82	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Croceicoccus marinus E4A9
NCBI: GCA_001661675.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.73	yes
125438	anaerobic	anaerobicⓘ	no	94.90	yes
125438	aerobic	aerobicⓘ	yes	88.34	no
125438	spore-forming	spore-formingⓘ	no	88.39	no
125438	thermophilic	thermophileⓘ	no	96.73	no
125438	flagellated	motile2+ⓘ	yes	67.13	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae.	Xu XW, Wu YH, Wang CS, Wang XG, Oren A, Wu M	Int J Syst Evol Microbiol	10.1099/ijs.0.004267-0	2009

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 )
#25452	IJSEM 2247 2009 ( DOI 10.1099/ijs.0.004267-0 , PubMed 19620383 )
#29022	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 #25452
#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 )
#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 .
#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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Croceicoccus marinus (CGMCC 1.6776, JCM 14846, E4A9)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001661675

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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