Name: Palleronia aestuarii Y26
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13857

Type strain:

Species: Palleronia aestuarii

Strain Designation: Y26

Culture col. no.: DSM 22009

Strain history: <- C. O. Jeon, Chung-Ang Univ., Seoul, Republic of Korea; Y26 <-

NCBI tax ID(s): 568105 (species)

SI-ID 112294

DSM 22009, KACC 13705

Section

Palleronia aestuarii Y26 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

coccus-shaped
Gram-negative
motile
aerobe
mesophilic
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	*Roseobacteraceae*
	Genus	*Palleronia*
	Species	**Palleronia aestuarii**
	Full Scientific Name (LPSN)	Palleronia aestuarii (Kim et al. 2010) Barnier et al. 2022

Synonym

Hwanghaeicola aestuarii

Information on morphological and physiological properties Morphology

[Ref.: #29791]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #29791]	Cell length	0.8-1.2 µm

[Ref.: #29791]	Cell width	0.8-1.2 µm

[Ref.: #29791]	Cell shape	coccus-shaped

[Ref.: #29791]	Motility	yes

[Ref.: #29791]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16100]

Culture medium

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

[Ref.: #16100]

Culture medium growth

[Ref.: #16100]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16100]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16100]	growth	28 °C
[Ref.: #29791]	growth	15-35 °C
[Ref.: #29791]	optimum	25-30 °C

[Ref.: #16100]	Temperature range	mesophilic
[Ref.: #29791]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29791]			optimum	6.5-7.5
[Ref.: #29791]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29791]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29791]		NaCl		growth	1.5-6	%
[Ref.: #29791]		NaCl		optimum	02-03	%

[Ref.: #29791]

Observation

aggregates in chains

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29791]		esculin ChEBI	+	hydrolysis

	Metabolite production	Metabolite	Production
[Ref.: #29791]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #29791]		indole ChEBI	+

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29791]		catalase	+	1.11.1.6
[Ref.: #29791]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	allantoin degradation	100	9 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	glycogen biosynthesis	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	degradation of sugar acids	92	23 of 25
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	pyrimidine metabolism	88.89	40 of 45
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	carnitine metabolism	87.5	7 of 8
[Ref.: #66794]	degradation of sugar alcohols	87.5	14 of 16
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	degradation of pentoses	78.57	22 of 28
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	chlorophyll metabolism	72.22	13 of 18
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	degradation of hexoses	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	ascorbate metabolism	59.09	13 of 22
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
		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.: #16100]	Sample type/isolated from	tidal flat sediment
[Ref.: #16100]	Geographic location (country and/or sea, region)	Taean coast
[Ref.: #16100]	Country	Republic of Korea
[Ref.: #16100]	Country ISO 3 Code	KOR
[Ref.: #16100]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ230842 (>99% sequence identity) for Hwanghaeicola aestuarii subclade from Microbeatlas

Aquatic Samples	65
Soil Samples	92
Animal Samples	15
Plant Samples	2
Total Samples	174

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

[Ref.: #16100]

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.: #16100]	Hwanghaeicola aestuarii strain Y26 16S ribosomal RNA gene, partial sequence	FJ230842	1350	ENA	568105 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Palleronia aestuarii DSM 22009	GCA_003253995	scaffold	GenBank	568105 tax ID	*
[Ref.: #66792]	Hwanghaeicola aestuarii strain DSM 22009	568105.3	wgs	PATRIC	568105 tax ID	*
[Ref.: #66792]	Hwanghaeicola aestuarii DSM 22009	2593339276	draft	JGI IMG/M	568105 tax ID	*

[Ref.: #16100]	GC-content	61.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29791]	GC-content	61 mol%

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: Hwanghaeicola aestuarii DSM 22009 NCBI: GCA_003253995.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hwanghaeicola aestuarii DSM 22009 NCBI: GCA_003253995.1
[Ref.: #69480]	flagellated	no	88.94	no
[Ref.: #69480]	gram-positive	no	97.502	no
[Ref.: #69480]	anaerobic	no	95.984	no
[Ref.: #69480]	halophile	yes	58.422	no
[Ref.: #69480]	spore-forming	no	95.745	no
[Ref.: #69480]	aerobic	yes	90.972	yes
[Ref.: #69480]	glucose-util	yes	88.882	no
[Ref.: #69480]	thermophile	no	96.408	yes
[Ref.: #69480]	motile	yes	63.523	yes
[Ref.: #69480]	glucose-ferment	no	90.365	no

Availability in culture collections External links

[Ref.: #16100]

Culture collection no.

DSM 22009

[Ref.: #83033]

SI-ID 112294

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hwanghaeicola aestuarii gen. nov., sp. nov., a moderately halophilic bacterium isolated from a tidal flat of the Yellow Sea.	Kim JM, Jung JY, Chae HB, Park W, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.021048-0	2010	*

References

#16100

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22009

#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 )

#29791

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 #26169 (see below)

#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 )

#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 )

#83033

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-ID112294.1 )

#26169

IJSEM 2877 2010 ( DOI 10.1099/ijs.0.021048-0 , PubMed 20081009 )

* These data were automatically processed and therefore are not curated

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Hwanghaeicola aestuarii DSM 22009

Hwanghaeicola aestuarii DSM 22009

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