Name: Marinicella pacifica sw153
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132977

Type strain:

Species: Marinicella pacifica

Strain Designation: sw153

Culture col. no.: DSM 25600, CGMCC 1.12181, JCM 18208

Strain history: X.-H. Zhang sw153.

NCBI tax ID(s): 1171543 (species)

SI-ID 405704

DSM 25600

Special Collections

Section

When using BacDive for research please cite our paper

Marinicella pacifica sw153 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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Marinicellaceae*
	Genus	*Marinicella*
	Species	**Marinicella pacifica**
	Full Scientific Name (LPSN)	Marinicella pacifica Wang et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43959]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %96.833
[Ref.: #125439]	Gram stain	negative Confidence in %95

[Ref.: #43959]	Cell length	1.8-2.2 µm

[Ref.: #43959]	Cell width	0.5 µm

[Ref.: #43959]	Cell shape	rod-shaped

[Ref.: #43959]	Motility	no

[Ref.: #43959]	Colony size	0.4-0.5 mm
[Ref.: #43959]	Colony color	transparent
[Ref.: #43959]	Colony shape	circular
[Ref.: #43959]	Incubation period	2 days
[Ref.: #43959]	Cultivation medium used	Marine agar 2216

Multimedia content

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Marine agar (MA)

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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

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #24765]	growth	28 °C
[Ref.: #43959]	growth	10-42 °C
[Ref.: #43959]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #43959]			optimum	7.5-8.5
[Ref.: #43959]			growth	6.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43959]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %94.8

[Ref.: #125438]	Ability of spore formation	no Confidence in %91.983
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.8

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43959]		NaCl		growth	1-8	%(w/v)
[Ref.: #43959]		NaCl		optimum	2	%(w/v)

[Ref.: #43959]	Observation	quinone Q-8
[Ref.: #67770]	Observation	quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43959]	amygdalin ChEBI	-	builds acid from
[Ref.: #43959]	arabinose ChEBI	-	builds acid from
[Ref.: #43959]	carboxymethylcellulose ChEBI	+	hydrolysis
[Ref.: #43959]	casein	+	hydrolysis
[Ref.: #43959]	cellobiose ChEBI	-	carbon source
[Ref.: #43959]	chitin ChEBI	+	hydrolysis
[Ref.: #43959]	citrate ChEBI	-	carbon source
[Ref.: #43959]	citrate ChEBI	+	carbon source
[Ref.: #43959]	D-fructose ChEBI	+	carbon source
[Ref.: #43959]	D-galactose ChEBI	+	carbon source
[Ref.: #43959]	D-glucosaminic acid ChEBI	-	carbon source
[Ref.: #43959]	D-glucose 6-phosphate ChEBI	-	carbon source
[Ref.: #43959]	D-mannitol ChEBI	-	carbon source
[Ref.: #43959]	D-mannose ChEBI	-	builds acid from
[Ref.: #43959]	D-psicose ChEBI	+	carbon source
[Ref.: #43959]	D-trehalose ChEBI	-	carbon source
[Ref.: #43959]	dna ChEBI	+	hydrolysis
[Ref.: #43959]	gelatin ChEBI	+	hydrolysis
[Ref.: #43959]	glucosamine ChEBI	-	builds acid from
[Ref.: #43959]	glucose ChEBI	-	fermentation
[Ref.: #43959]	glucose 1-phosphate ChEBI	-	carbon source
[Ref.: #43959]	glycerol 1-phosphate ChEBI	-	carbon source
[Ref.: #43959]	lactose ChEBI	-	builds acid from
[Ref.: #43959]	lactulose ChEBI	-	carbon source
[Ref.: #43959]	maltose ChEBI	-	carbon source
[Ref.: #43959]	mannitol ChEBI	-	builds acid from
[Ref.: #43959]	melibiose ChEBI	-	builds acid from
[Ref.: #43959]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43959]	nitrate ChEBI	-	reduction
[Ref.: #43959]	raffinose ChEBI	-	builds acid from
[Ref.: #43959]	raffinose ChEBI	+	carbon source
[Ref.: #43959]	rhamnose ChEBI	-	builds acid from
[Ref.: #43959]	salicin ChEBI	-	builds acid from
[Ref.: #43959]	starch ChEBI	+	hydrolysis
[Ref.: #43959]	sucrose ChEBI	-	builds acid from
[Ref.: #43959]	turanose ChEBI	-	carbon source
[Ref.: #43959]	tween 20 ChEBI	+	hydrolysis
[Ref.: #43959]	tween 40 ChEBI	+	hydrolysis
[Ref.: #43959]	tween 80 ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43959]	acetoin ChEBI	no
[Ref.: #43959]	hydrogen sulfide ChEBI	no
[Ref.: #43959]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #43959]		acetoin ChEBI	-
[Ref.: #43959]		glucose ChEBI		-

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43959]		catalase	+	1.11.1.6
[Ref.: #43959]		cytochrome oxidase	+	1.9.3.1

Fatty acid profile

Metadata FA analysis

Reference

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Fatty acid	Percentage
C15:0 iso	46.3
C16:1ω6c / C16:1ω7c	19.1
C11:0 iso 3OH	7.1
C11:0 iso	5.6
C16:0	4.9
C16:0 N alcohol	4.1
C15:0 anteiso	3.1
C17:0 iso	1.5
C16:1ω7c alcohol	1.4

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

[Ref.: #24765]	Sample type/isolated from	surface seawater
[Ref.: #24765]	Geographic location (country and/or sea, region)	Pacific Ocean, South Pacific Gyre
[Ref.: #24765]	Geographic location	-39.3167°/-139.8000°

[Ref.: #43959]	Sample type/isolated from	surface seawater of the South Pacific Gyre
[Ref.: #43959]	Geographic location (country and/or sea, region)	South Pacific Gyre
[Ref.: #43959]	Geographic location	-39.3167°/-139.8000°
[Ref.: #43959]	Enrichment culture	Marine agar 2216
[Ref.: #43959]	Enrichment culture duration	7 days
[Ref.: #43959]	Enrichment culture temperature	28 ̊C

[Ref.: #67770]	Sample type/isolated from	Surface seawater of the South Pacific Gyre (39° 19' S 139° 48' W)
[Ref.: #67770]	Geographic location	-39.3167°/-139.8000°
* 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 JQ082140 (>99% sequence identity) for Marinicella pacifica subclade from Microbeatlas

Aquatic Samples	11
Soil Samples
Animal Samples	2
Plant Samples	1
Total Samples	14

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.: #24765]	Marinicella pacifica strain sw153 16S ribosomal RNA gene, partial sequence	JQ082140	1506	GenBank ENA	1171543 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Marinicella pacifica CGMCC 1.12181	GCA_014636635	scaffold	GenBank ENA	1171543 tax ID	*
[Ref.: #66792]	Marinicella pacifica strain CGMCC 1.12181	1171543.3	wgs	PATRIC	1171543 tax ID	*

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GC-content

44.5 mol%

high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Marinicella pacifica CGMCC 1.12181 NCBI: GCA_014636635.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.833	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.137	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	78.024	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	91.983	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	93.731	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	71.329	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Marinicella pacifica CGMCC 1.12181 NCBI: GCA_014636635
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	94.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	95
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	57.5
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.8

Availability in culture collections External links

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Culture collection no.

DSM 25600, CGMCC 1.12181, JCM 18208

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SI-ID 405704

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Marinicella rhabdoformis sp. nov., isolated from coastal sediment.	Zhong YL, Sun XK, Hui JG, Teng HL, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004210	2020	*
Phylogeny	Marinicella sediminis sp. nov., isolated from marine sediment.	Wang XQ, Li CM, Dunlap CA, Rooney AP, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002839	2018	*
Phylogeny	Marinicella pacifica sp. nov., isolated from seawater.	Wang Y, Liu Y, Zhang Z, Zheng Y, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001027	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 )

#24765

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25600

#43959

Yanan Wang, Yan Liu, Zenghu Zhang, Yanfen Zheng, Xiao-Hua Zhang: Marinicella pacifica sp. nov., isolated from seawater. IJSEM 66: 2313 - 2318 2016 ( DOI 10.1099/ijsem.0.001027 , PubMed 26978647 )

#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) .

#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 .

#91253

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-ID405704.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Marinicella pacifica CGMCC 1.12181

Marinicella pacifica CGMCC 1.12181

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