Name: Paracoccus aestuariivivens GHD-30
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140807

Type strain:

Species: Paracoccus aestuariivivens

Strain Designation: GHD-30

Culture col. no.: KCTC 52214, NBRC 111993

NCBI tax ID(s): 1820333 (species)

Section

Paracoccus aestuariivivens GHD-30 is a Gram-negative, pleomorphic-shaped bacterium that forms circular colonies and was isolated from a tidal flat at Gangwha Island on the Yellow Sea.

colony-forming
Gram-negative
pleomorphic-shaped
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	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Paracoccus*
	Species	**Paracoccus aestuariivivens**
	Full Scientific Name (LPSN)	Paracoccus aestuariivivens Park et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43591]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.978

[Ref.: #43591]	Cell length	0.4-1.5 µm

[Ref.: #43591]	Cell width	0.4-0.7 µm

[Ref.: #43591]	Cell shape	pleomorphic-shaped

[Ref.: #43591]	Motility	no

[Ref.: #43591]	Colony size	1-2 mm
[Ref.: #43591]	Colony color	Yellowish white
[Ref.: #43591]	Colony shape	circular
[Ref.: #43591]	Incubation period	3 days
[Ref.: #43591]	Cultivation medium used	MA agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43591]

Culture medium

Marine agar (MA)

[Ref.: #43591]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #43591]		growth	15-45 °C
[Ref.: #43591]	no	growth	10 °C
[Ref.: #43591]	no	growth	50 °C
[Ref.: #43591]		optimum	30 °C

[Ref.: #43591]	Temperature range	psychrophilic
[Ref.: #43591]	Temperature range	thermophilic
[Ref.: #43591]	Temperature range	mesophilic

	Kind of pH		pH
[Ref.: #43591]		optimum	6.5-7.5
[Ref.: #43591]		growth	5
[Ref.: #43591]	no	growth	4.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43591]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43591]		NaCl		growth	0-8	%(w/v)
[Ref.: #43591]		NaCl		optimum	2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43591]	acetate ChEBI	+	carbon source
[Ref.: #43591]	acetate ChEBI	+	energy source
[Ref.: #43591]	benzoate ChEBI	-	carbon source
[Ref.: #43591]	benzoate ChEBI	-	energy source
[Ref.: #43591]	casein	+	hydrolysis
[Ref.: #43591]	cellobiose ChEBI	+	carbon source
[Ref.: #43591]	cellobiose ChEBI	+	energy source
[Ref.: #43591]	citrate ChEBI	+	carbon source
[Ref.: #43591]	citrate ChEBI	+	energy source
[Ref.: #43591]	D-fructose ChEBI	+	carbon source
[Ref.: #43591]	D-fructose ChEBI	+	energy source
[Ref.: #43591]	D-galactose ChEBI	+	carbon source
[Ref.: #43591]	D-galactose ChEBI	+	energy source
[Ref.: #43591]	D-glucose ChEBI	+	carbon source
[Ref.: #43591]	D-glucose ChEBI	+	energy source
[Ref.: #43591]	D-mannose ChEBI	+	carbon source
[Ref.: #43591]	D-mannose ChEBI	+	energy source
[Ref.: #43591]	D-trehalose ChEBI	+	carbon source
[Ref.: #43591]	D-trehalose ChEBI	+	energy source
[Ref.: #43591]	D-xylose ChEBI	+	carbon source
[Ref.: #43591]	D-xylose ChEBI	+	energy source
[Ref.: #43591]	esculin ChEBI	+	hydrolysis
[Ref.: #43591]	formate ChEBI	-	carbon source
[Ref.: #43591]	formate ChEBI	-	energy source
[Ref.: #43591]	gelatin ChEBI	-	hydrolysis
[Ref.: #43591]	hypoxanthine ChEBI	+	hydrolysis
[Ref.: #43591]	L-arabinose ChEBI	+	carbon source
[Ref.: #43591]	L-arabinose ChEBI	+	energy source
[Ref.: #43591]	L-glutamate ChEBI	-	carbon source
[Ref.: #43591]	L-glutamate ChEBI	-	energy source
[Ref.: #43591]	L-malate ChEBI	+	carbon source
[Ref.: #43591]	L-malate ChEBI	+	energy source
[Ref.: #43591]	L-tyrosine ChEBI	+	hydrolysis
[Ref.: #43591]	maltose ChEBI	-	carbon source
[Ref.: #43591]	maltose ChEBI	-	energy source
[Ref.: #43591]	nitrate ChEBI	+	reduction
[Ref.: #43591]	pyruvate ChEBI	+	carbon source
[Ref.: #43591]	pyruvate ChEBI	+	energy source
[Ref.: #43591]	salicin ChEBI	-	carbon source
[Ref.: #43591]	salicin ChEBI	-	energy source
[Ref.: #43591]	starch ChEBI	-	hydrolysis
[Ref.: #43591]	succinate ChEBI	+	carbon source
[Ref.: #43591]	succinate ChEBI	+	energy source
[Ref.: #43591]	sucrose ChEBI	+	carbon source
[Ref.: #43591]	sucrose ChEBI	+	energy source
[Ref.: #43591]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43591]	urea ChEBI	+	hydrolysis
[Ref.: #43591]	xanthine ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43591]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #43591]	carbenicillin ChEBI	yes	100	µg (disc)
[Ref.: #43591]	cephalothin ChEBI	yes	30	µg (disc)
[Ref.: #43591]	chloramphenicol ChEBI	yes	100	µg (disc)
[Ref.: #43591]	gentamicin ChEBI	yes	30	µg (disc)
[Ref.: #43591]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #43591]	lincomycin ChEBI				yes	15	µg (disc)
[Ref.: #43591]	neomycin ChEBI	yes	30	µg (disc)
[Ref.: #43591]	novobiocin ChEBI	yes	5	µg (disc)
[Ref.: #43591]	oleandomycin ChEBI	yes	15	µg (disc)
[Ref.: #43591]	penicillin g ChEBI	yes	20	Unit (disc)
[Ref.: #43591]	polymyxin b ChEBI	yes	100	Unit (disc)
[Ref.: #43591]	streptomycin ChEBI	yes	50	µg (disc)
[Ref.: #43591]	tetracycline ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #43591]	acid phosphatase	+	3.1.3.2
[Ref.: #43591]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43591]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43591]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43591]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43591]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43591]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43591]	beta-galactosidase	-	3.2.1.23
[Ref.: #43591]	beta-glucosidase	-	3.2.1.21
[Ref.: #43591]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43591]	catalase	+	1.11.1.6
[Ref.: #43591]	cystine arylamidase	+	3.4.11.3
[Ref.: #43591]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43591]	esterase (C 4)	+
[Ref.: #43591]	esterase Lipase (C 8)	+
[Ref.: #43591]	leucine arylamidase	+	3.4.11.1
[Ref.: #43591]	lipase (C 14)	-
[Ref.: #43591]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43591]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43591]	trypsin	-	3.4.21.4
[Ref.: #43591]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43591]

Fatty acid	Percentage	ECL
C18:1ω6c / C18:1ω7c	33.5
C16:0	26
C16:1ω6c / C16:1ω7c	19.8
C12:0	5.8
C14:0	5.5
C12:0aldehyde / unknown ECL 10.928	4.8	10928
C18:0	1.1

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

[Ref.: #43591]	Sample type/isolated from	a tidal flat at Gangwha Island on the Yellow Sea
[Ref.: #43591]	Geographic location (country and/or sea, region)	Gangwha Island
[Ref.: #43591]	Country	Republic of Korea
[Ref.: #43591]	Country ISO 3 Code	KOR
[Ref.: #43591]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Tidal flat

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU696538 (>99% sequence identity) for Paracoccus from Microbeatlas

Aquatic Samples	49
Soil Samples	19
Animal Samples	103
Plant Samples	2
Total Samples	173

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.: #43591]	16S rRNA gene sequence	KU696538		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paracoccus aestuariivivens NBRC 111993	GCA_009711225	contig	GenBank	1820333 tax ID	*
[Ref.: #66792]	Paracoccus aestuariivivens strain NBRC 111993	1820333.3	wgs	PATRIC	1820333 tax ID	*

[Ref.: #43591]

GC-content

62 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Paracoccus aestuariivivens strain NBRC 111993 PATRIC: 1820333.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paracoccus aestuariivivens strain NBRC 111993 PATRIC: 1820333.3
[Ref.: #69480]	motile	no	62.294	no
[Ref.: #69480]	gram-positive	no	98.161	yes
[Ref.: #69480]	anaerobic	no	98.724	no
[Ref.: #69480]	aerobic	yes	92.933	no
[Ref.: #69480]	halophile	no	80.603	no
[Ref.: #69480]	spore-forming	no	96.902	yes
[Ref.: #69480]	glucose-util	yes	90.996	yes
[Ref.: #69480]	flagellated	no	89.055	no
[Ref.: #69480]	thermophile	no	98.679	no
[Ref.: #69480]	glucose-ferment	no	86.955	no

Availability in culture collections External links

[Ref.: #43591]

Culture collection no.

KCTC 52214, NBRC 111993

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Polyphasic taxonomic analysis of Paracoccus ravus sp. nov., an alphaproteobacterium isolated from marine sediment.	Yoon J, Maharjan S, Choi H	FEMS Microbiol Lett	10.1093/femsle/fnz184	2019	*
Phylogeny	Paracoccus sordidisoli sp. nov., isolated from an agricultural field contaminated with hexachlorocyclohexane isomers.	Singh AK, Kohli P, Mahato NK, Lal R	Int J Syst Evol Microbiol	10.1099/ijsem.0.002289	2017	*
Phylogeny	Paracoccus aestuariivivens sp. nov., isolated from a tidal flat.	Park S, Yoon SY, Jung YT, Won SM, Park DS, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001133	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 )

#43591

Sooyeon Park, Sun Young Yoon, Yong-Taek Jung, Sung-Min Won, Doo-Sang Park, Jung-Hoon Yoon: Paracoccus aestuariivivens sp. nov., isolated from a tidal flat. IJSEM 66: 2992 - 2998 2016 ( DOI 10.1099/ijsem.0.001133 , PubMed 27150589 )

#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 )

* These data were automatically processed and therefore are not curated

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Paracoccus aestuariivivens strain NBRC 111993

Paracoccus aestuariivivens strain NBRC 111993

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