Croceicoccus pelagius (DSM 101479, CGMCC 1.15358, Ery9)

Name: Croceicoccus pelagius (DSM 101479, CGMCC 1.15358, Ery9)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133013

Type strain

Strain Designation Ery9

Culture col. no. DSM 101479 CGMCC 1.15358 Ery9

NCBI tax ID(s) 1703341

Special Collections DSMZ Literature strains

History DSMZ <- Y.-H. Wu, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China; Ery9 <- L. Wang

Links

Croceicoccus pelagius Ery9 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface seawater.

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 404682

DSM 101479

@ref 20215

Last LPSN update 2026-05-29 08:37:59

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Croceicoccus

Species Croceicoccus pelagius

Full scientific name Croceicoccus pelagius Wu et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
25039	negative	1.0-1.4 µm	0.3-0.5 µm	rod-shaped
125439	negative				96.87
125438	negative				97

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25039	1.0-2.0 mm	yellow	circular	3 days	MA agar

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
25039	MA agar
24801	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

Culture temp

@ref	Growth	Type	Temperature (°C)
24801	positive	growth	30
25039	positive	growth	15-45
25039	positive	optimum	30-37

Culture pH

@ref	Ability	Type	PH	PH range
25039	positive	optimum	7
25039	positive	growth	5.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25039	aerobe
125439	obligate aerobe	98.186

Spore formation

@ref	Spore formation	Confidence
125439		99.149
125438		90.579

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25039	NaCl	positive	growth	0-10.0 %(w/v)
25039	NaCl		optimum	3 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25039	17128 ChEBI	adipate	-	carbon source
25039	17128 ChEBI	adipate	-	energy source
25039	36219 ChEBI	alpha-lactose	-	builds acid from
25039	17057 ChEBI	cellobiose	+	builds acid from
25039	16947 ChEBI	citrate	+	carbon source
25039	15824 ChEBI	D-fructose	-	builds acid from
25039	12936 ChEBI	D-galactose	-	builds acid from
25039	17634 ChEBI	D-glucose	+	carbon source
25039	17634 ChEBI	D-glucose	+	energy source
25039	16899 ChEBI	D-mannitol	+	carbon source
25039	16899 ChEBI	D-mannitol	+	energy source
25039	16024 ChEBI	D-mannose	-	carbon source
25039	16024 ChEBI	D-mannose	-	energy source
25039	16024 ChEBI	D-mannose	-	builds acid from
25039	16988 ChEBI	D-ribose	-	builds acid from
25039	65327 ChEBI	D-xylose	-	builds acid from
25039	27689 ChEBI	decanoate	+	carbon source
25039	27689 ChEBI	decanoate	+	energy source
25039	4853 ChEBI	esculin	+	hydrolysis
25039	16236 ChEBI	ethanol	-	builds acid from
25039	5291 ChEBI	gelatin	-	hydrolysis
25039	17234 ChEBI	glucose	+	builds acid from
25039	30849 ChEBI	L-arabinose	-	carbon source
25039	30849 ChEBI	L-arabinose	-	energy source
25039	62345 ChEBI	L-rhamnose	-	builds acid from
25039	25115 ChEBI	malate	-	carbon source
25039	25115 ChEBI	malate	-	energy source
25039	25115 ChEBI	malate	+	energy source
25039	25115 ChEBI	malate	+	carbon source
25039	17306 ChEBI	maltose	+	carbon source
25039	17306 ChEBI	maltose	+	energy source
25039	17306 ChEBI	maltose	+	builds acid from
25039	29864 ChEBI	mannitol	-	builds acid from
25039	6731 ChEBI	melezitose	-	builds acid from
25039	17268 ChEBI	myo-inositol	-	builds acid from
25039	17632 ChEBI	nitrate	+	reduction
25039		peptone	+	carbon source
25039		peptone	+	energy source
25039	18401 ChEBI	phenylacetate	-	carbon source
25039	18401 ChEBI	phenylacetate	-	energy source
25039	32032 ChEBI	potassium gluconate	-	carbon source
25039	32032 ChEBI	potassium gluconate	-	energy source
25039	16634 ChEBI	raffinose	-	builds acid from
25039	15963 ChEBI	ribitol	-	builds acid from
25039	53258 ChEBI	sodium citrate	-	carbon source
25039	53258 ChEBI	sodium citrate	-	energy source
25039	30911 ChEBI	sorbitol	-	builds acid from
25039	27922 ChEBI	sorbose	-	builds acid from
25039	28017 ChEBI	starch	-	hydrolysis
25039	17992 ChEBI	sucrose	-	builds acid from
25039	27082 ChEBI	trehalose	-	builds acid from
25039		tryptone	+	carbon source
25039		tryptone	+	energy source
25039	27897 ChEBI	tryptophan	-	energy source
25039	53423 ChEBI	tween 40	-	hydrolysis
25039		yeast extract	+	carbon source
25039		yeast extract	+	energy source

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
25039	28971	ampicillin	10 µg (disc)
25039	3534	cephalexin	30 µg (disc)
25039	17698	chloramphenicol	30 µg (disc)
25039	48923	erythromycin	10 µg (disc)
25039	6104	kanamycin	30 µg (disc)
25039	100147	nalidixic acid		30 µg (disc)
25039	7507	neomycin	30 µg (disc)
25039	71415	nitrofurantoin	300 µg (disc)
25039	28368	novobiocin	30 µg (disc)
25039	17334	penicillin	10 Unit (disc)
25039	8309	polymyxin b		300 Unit (disc)
25039	28077	rifampicin	5 µg (disc)
25039	17076	streptomycin		10 µg (disc)
25039	27902	tetracycline	30 µg (disc)
25039	28001	vancomycin	30 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25039	15688 ChEBI	acetoin
25039	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
25039	15688 ChEBI	acetoin	+
25039	35581 ChEBI	indole		-

Enzymes

@ref	Value	Activity	Ec
25039	acid phosphatase	+	3.1.3.2
25039	alkaline phosphatase	+	3.1.3.1
25039	alpha-chymotrypsin	-	3.4.21.1
25039	alpha-galactosidase	-	3.2.1.22
25039	alpha-glucosidase	+	3.2.1.20
25039	alpha-mannosidase	-	3.2.1.24
25039	arginine dihydrolase	+	3.5.3.6
25039	beta-D-fucosidase	-	3.2.1.38
25039	beta-galactosidase	-	3.2.1.23
25039	beta-glucosidase	-	3.2.1.21
25039	beta-glucuronidase	-	3.2.1.31
25039	catalase	+	1.11.1.6
25039	cystine arylamidase	+	3.4.11.3
25039	esterase (C 4)	+
25039	esterase lipase (C 8)	-
25039	leucine arylamidase	+	3.4.11.1
25039	lipase (C 14)	-
25039	lysine decarboxylase	-	4.1.1.18
25039	N-acetyl-beta-glucosaminidase	-	3.2.1.52
25039	naphthol-AS-BI-phosphohydrolase	+
25039	ornithine decarboxylase	-	4.1.1.17
25039	trypsin	-	3.4.21.4
25039	tryptophan deaminase	+	4.1.99.1
25039	tryptophan deaminase	-	4.1.99.1
25039	urease	-	3.5.1.5
25039	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Latitude	Longitude	Country
24801	surface seawater	Atlantic Ocean (24° 10' S 5° 29' E)	-24.1667	5.4833 -24.1667/5.4833
25039	surface seawater	Atlantic Ocean (24° 10' S 5° 29' E)			Atlantic Ocean

Taxonmaps

69479

Global distribution of 16S sequence KT383844 (>99% sequence identity) for Croceicoccus from Microbeatlas

Aquatic Samples	1073
Soil Samples	222
Animal Samples	88
Plant Samples	94
Total Samples	1477

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24801	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM166191v1 assembly for Croceicoccus pelagius Ery9	scaffold	GCA_001661915	1703341.3	2832283248	1703341	66.69
66792	ASM1464249v1 assembly for Croceicoccus pelagius CGMCC 1.15358	contig	GCA_014642495	1703341.5	8065897586	1703341	66.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24801	Croceicoccus pelagius strain Ery9 16S ribosomal RNA gene, complete sequence	KT383844	1477		1703341
124043	Croceicoccus pelagius strain CGMCC 1.15358 16S ribosomal RNA gene, partial sequence.	MT760080	1311		1703341

GC content

@ref	GC-content (mol%)	Method
25039	62.8	genome sequence analysis
24801	62.8	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM166191v1 assembly for Croceicoccus pelagius Ery9
NCBI: GCA_001661915

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.19	no
125439	gram_stain	BacteriaNetⓘ	negative	96.87	no
125439	spore_formation	BacteriaNetⓘ	no	99.15	no
125439	motility	BacteriaNetⓘ	yes	42.72	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Croceicoccus pelagius Ery9
NCBI: GCA_001661915.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	yes
125438	anaerobic	anaerobicⓘ	no	95.38	yes
125438	aerobic	aerobicⓘ	yes	89.02	yes
125438	spore-forming	spore-formingⓘ	no	90.58	no
125438	thermophilic	thermophileⓘ	no	96.67	yes
125438	flagellated	motile2+ⓘ	no	59.24	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Croceicoccus ponticola sp. nov., a lipolytic bacterium isolated from seawater.	Park S, Won SM, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003301	2019
Phylogeny	Croceicoccus pelagius sp. nov. and Croceicoccus mobilis sp. nov., isolated from marine environments.	Wu YH, Li GY, Jian SL, Cheng H, Huo YY, Wang CS, Shao ZZ, Xu XW	Int J Syst Evol Microbiol	10.1099/ijsem.0.001381	2016

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 )
#24801	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101479
#25039	Y. H. L. Wu, G. Y.,Jian, S. L.,Cheng, H.,Huo, Y. Y.,Wang, C. S.,Shao, Z. Z.,Xu, X. W.: Croceicoccus pelagius sp. nov. and Croceicoccus mobilis sp. nov., isolated from marine environments. IJSEM 66: 4506 - 4511 2016 ( DOI 10.1099/ijsem.0.001381 , PubMed 27503117 )
#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) .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 pelagius (DSM 101479, CGMCC 1.15358, Ery9)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001661915

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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