Name: Croceicoccus pelagius Ery9
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133013

Type strain:

Species: Croceicoccus pelagius

Strain Designation: Ery9

Culture col. no.: DSM 101479, CGMCC 1.15358

Strain history: <- Y.-H. Wu, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China; Ery9 <- L. Wang

NCBI tax ID(s): 1703341 (species)

SI-ID 404682

DSM 101479

Special Collections

Section

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

colony-forming
Gram-negative
rod-shaped
aerobe
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	*Sphingomonadales*
	Family	*Erythrobacteraceae*
	Genus	*Croceicoccus*
	Species	**Croceicoccus pelagius**
	Full Scientific Name (LPSN)	Croceicoccus pelagius Wu et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25039]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97

[Ref.: #25039]	Cell length	1.0-1.4 µm

[Ref.: #25039]	Cell width	0.3-0.5 µm

[Ref.: #25039]	Cell shape	rod-shaped

[Ref.: #25039]	Motility	no

[Ref.: #25039]	Colony size	1.0-2.0 mm
[Ref.: #25039]	Colony color	yellow
[Ref.: #25039]	Colony shape	circular
[Ref.: #25039]	Incubation period	3 days
[Ref.: #25039]	Cultivation medium used	MA agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

MA agar

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Culture medium growth

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Culture medium

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

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #24801]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24801]	growth	30 °C
[Ref.: #25039]	growth	15-45 °C
[Ref.: #25039]	optimum	30-37 °C

	pH	Kind of pH		pH
[Ref.: #25039]			optimum	7
[Ref.: #25039]			growth	5.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25039]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %90.579
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25039]		NaCl		growth	0-10.0	%(w/v)
[Ref.: #25039]		NaCl		optimum	3	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25039]	adipate ChEBI	-	carbon source
[Ref.: #25039]	adipate ChEBI	-	energy source
[Ref.: #25039]	alpha-lactose ChEBI	-	builds acid from
[Ref.: #25039]	cellobiose ChEBI	+	builds acid from
[Ref.: #25039]	citrate ChEBI	+	carbon source
[Ref.: #25039]	D-fructose ChEBI	-	builds acid from
[Ref.: #25039]	D-galactose ChEBI	-	builds acid from
[Ref.: #25039]	D-glucose ChEBI	+	carbon source
[Ref.: #25039]	D-glucose ChEBI	+	energy source
[Ref.: #25039]	D-mannitol ChEBI	+	carbon source
[Ref.: #25039]	D-mannitol ChEBI	+	energy source
[Ref.: #25039]	D-mannose ChEBI	-	carbon source
[Ref.: #25039]	D-mannose ChEBI	-	energy source
[Ref.: #25039]	D-mannose ChEBI	-	builds acid from
[Ref.: #25039]	D-ribose ChEBI	-	builds acid from
[Ref.: #25039]	D-xylose ChEBI	-	builds acid from
[Ref.: #25039]	decanoate ChEBI	+	carbon source
[Ref.: #25039]	decanoate ChEBI	+	energy source
[Ref.: #25039]	esculin ChEBI	+	hydrolysis
[Ref.: #25039]	ethanol ChEBI	-	builds acid from
[Ref.: #25039]	gelatin ChEBI	-	hydrolysis
[Ref.: #25039]	glucose ChEBI	+	builds acid from
[Ref.: #25039]	L-arabinose ChEBI	-	carbon source
[Ref.: #25039]	L-arabinose ChEBI	-	energy source
[Ref.: #25039]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #25039]	malate ChEBI	-	carbon source
[Ref.: #25039]	malate ChEBI	-	energy source
[Ref.: #25039]	malate ChEBI	+	energy source
[Ref.: #25039]	malate ChEBI	+	carbon source
[Ref.: #25039]	maltose ChEBI	+	carbon source
[Ref.: #25039]	maltose ChEBI	+	energy source
[Ref.: #25039]	maltose ChEBI	+	builds acid from
[Ref.: #25039]	mannitol ChEBI	-	builds acid from
[Ref.: #25039]	melezitose ChEBI	-	builds acid from
[Ref.: #25039]	myo-inositol ChEBI	-	builds acid from
[Ref.: #25039]	nitrate ChEBI	+	reduction
[Ref.: #25039]	peptone	+	carbon source
[Ref.: #25039]	peptone	+	energy source
[Ref.: #25039]	phenylacetate ChEBI	-	carbon source
[Ref.: #25039]	phenylacetate ChEBI	-	energy source
[Ref.: #25039]	potassium gluconate ChEBI	-	carbon source
[Ref.: #25039]	potassium gluconate ChEBI	-	energy source
[Ref.: #25039]	raffinose ChEBI	-	builds acid from
[Ref.: #25039]	ribitol ChEBI	-	builds acid from
[Ref.: #25039]	sodium citrate ChEBI	-	carbon source
[Ref.: #25039]	sodium citrate ChEBI	-	energy source
[Ref.: #25039]	sorbitol ChEBI	-	builds acid from
[Ref.: #25039]	sorbose ChEBI	-	builds acid from
[Ref.: #25039]	starch ChEBI	-	hydrolysis
[Ref.: #25039]	sucrose ChEBI	-	builds acid from
[Ref.: #25039]	trehalose ChEBI	-	builds acid from
[Ref.: #25039]	tryptone	+	carbon source
[Ref.: #25039]	tryptone	+	energy source
[Ref.: #25039]	tryptophan ChEBI	-	energy source
[Ref.: #25039]	tween 40 ChEBI	-	hydrolysis
[Ref.: #25039]	yeast extract	+	carbon source
[Ref.: #25039]	yeast extract	+	energy source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #25039]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #25039]	cephalexin ChEBI	yes	30	µg (disc)
[Ref.: #25039]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #25039]	erythromycin ChEBI	yes	10	µg (disc)
[Ref.: #25039]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #25039]	nalidixic acid ChEBI				yes	30	µg (disc)
[Ref.: #25039]	neomycin ChEBI	yes	30	µg (disc)
[Ref.: #25039]	nitrofurantoin ChEBI	yes	300	µg (disc)
[Ref.: #25039]	novobiocin ChEBI	yes	30	µg (disc)
[Ref.: #25039]	penicillin ChEBI	yes	10	Unit (disc)
[Ref.: #25039]	polymyxin b ChEBI				yes	300	Unit (disc)
[Ref.: #25039]	rifampicin ChEBI	yes	5	µg (disc)
[Ref.: #25039]	streptomycin ChEBI				yes	10	µg (disc)
[Ref.: #25039]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #25039]	vancomycin ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25039]		acetoin ChEBI	yes
[Ref.: #25039]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #25039]		acetoin ChEBI	+
[Ref.: #25039]		indole ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #25039]	acid phosphatase	+	3.1.3.2
[Ref.: #25039]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25039]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25039]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25039]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25039]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25039]	arginine dihydrolase	+	3.5.3.6
[Ref.: #25039]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #25039]	beta-galactosidase	-	3.2.1.23
[Ref.: #25039]	beta-glucosidase	-	3.2.1.21
[Ref.: #25039]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25039]	catalase	+	1.11.1.6
[Ref.: #25039]	cystine arylamidase	+	3.4.11.3
[Ref.: #25039]	esterase (C 4)	+
[Ref.: #25039]	esterase lipase (C 8)	-
[Ref.: #25039]	leucine arylamidase	+	3.4.11.1
[Ref.: #25039]	lipase (C 14)	-
[Ref.: #25039]	lysine decarboxylase	-	4.1.1.18
[Ref.: #25039]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25039]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25039]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #25039]	trypsin	-	3.4.21.4
[Ref.: #25039]	tryptophan deaminase	+	4.1.99.1
[Ref.: #25039]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25039]	urease	-	3.5.1.5
[Ref.: #25039]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #24801]	Sample type/isolated from	surface seawater
[Ref.: #24801]	Geographic location (country and/or sea, region)	Atlantic Ocean (24° 10' S 5° 29' E)
[Ref.: #24801]	Geographic location	-24.1667°/5.4833°

[Ref.: #25039]	Sample type/isolated from	surface seawater
[Ref.: #25039]	Geographic location (country and/or sea, region)	Atlantic Ocean (24° 10' S 5° 29' E)
[Ref.: #25039]	Country	Atlantic Ocean
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

What are isolation sources categories?

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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

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

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Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #24801]	Croceicoccus pelagius strain Ery9 16S ribosomal RNA gene, complete sequence	KT383844	1477	GenBank ENA	1703341 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Croceicoccus pelagius Ery9	GCA_001661915	scaffold	GenBank ENA	1703341 tax ID	*
[Ref.: #66792]	Croceicoccus pelagius CGMCC 1.15358	GCA_014642495	contig	GenBank ENA	1703341 tax ID	*
[Ref.: #66792]	Croceicoccus pelagius strain CGMCC 1.15358	1703341.5	wgs	PATRIC	1703341 tax ID	*
[Ref.: #66792]	Croceicoccus pelagius Ery9	2832283248	draft	JGI IMG/M	1703341 tax ID	*

[Ref.: #25039]	GC-content	62.8 mol%	genome sequence analysis
[Ref.: #24801]	GC-content	62.8 mol%	sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Croceicoccus pelagius Ery9 NCBI: GCA_001661915.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Croceicoccus pelagius Ery9 NCBI: GCA_001661915.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.382	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	89.016	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.579	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.668	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	59.243	no

Availability in culture collections External links

[Ref.: #24801]

Culture collection no.

DSM 101479, CGMCC 1.15358

[Ref.: #91287]

SI-ID 404682

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 .

#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 )

#91287

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-ID404682.1 )

* These data were automatically processed and therefore are not curated

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