Name: Arenimonas donghaensis HO3-R19
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17444

Type strain:

Species: Arenimonas donghaensis

Strain Designation: HO3-R19

Culture col. no.: DSM 18148, KACC 11381

Strain history: <- B.-Y. Kim; HO3-R19

NCBI tax ID(s): 1121014 (strain), 375061 (species)

SI-ID 396980

DSM 18148

Section

Arenimonas donghaensis HO3-R19 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seashore sand.

Gram-negative
motile
rod-shaped
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	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Arenimonas*
	Species	**Arenimonas donghaensis**
	Full Scientific Name (LPSN)	Arenimonas donghaensis Kwon et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31832]	Gram stain	negative

[Ref.: #31832]	Cell length	2.25 µm

[Ref.: #31832]	Cell width	0.5 µm

[Ref.: #31832]	Cell shape	rod-shaped

[Ref.: #31832]	Motility	yes

[Ref.: #31832]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7407]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7407]

Culture medium growth

[Ref.: #7407]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7407]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7407]	growth	28 °C
[Ref.: #31832]	growth	04-37 °C
[Ref.: #31832]	optimum	28 °C

[Ref.: #7407]	Temperature range	mesophilic
[Ref.: #31832]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31832]			optimum	8
[Ref.: #31832]			growth	07-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31832]

Oxygen tolerance

aerobe

[Ref.: #31832]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31832]		NaCl		growth	0-3	%
[Ref.: #31832]		NaCl		optimum	1.5	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31832]		gelatin ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #31832]	acid phosphatase	+	3.1.3.2
[Ref.: #31832]	alkaline phosphatase	+	3.1.3.1
[Ref.: #31832]	catalase	+	1.11.1.6
[Ref.: #31832]	cytochrome oxidase	+	1.9.3.1
[Ref.: #31832]	gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	purine metabolism	79.79	75 of 94
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	heme metabolism	50	7 of 14
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	45.45	5 of 11
[Ref.: #66794]	d-mannose degradation	44.44	4 of 9
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	oxidative phosphorylation	37.36	34 of 91
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
		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.: #7407]	Sample type/isolated from	seashore sand
[Ref.: #7407]	Geographic location (country and/or sea, region)	Pohang
[Ref.: #7407]	Country	Republic of Korea
[Ref.: #7407]	Country ISO 3 Code	KOR
[Ref.: #7407]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Sandy
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ411038 (>99% sequence identity) for Arenimonas donghaensis subclade from Microbeatlas

Aquatic Samples	569
Soil Samples	497
Animal Samples	143
Plant Samples	92
Total Samples	1301

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

[Ref.: #7407]

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.: #7407]	Arenimonas donghaensis strain HO3-R19 16S ribosomal RNA gene, partial sequence	DQ411038	1499	ENA	375061 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Arenimonas donghaensis DSM 18148 = HO3-R19	GCA_000743535	contig	GenBank	1121014 tax ID	*
[Ref.: #66792]	Arenimonas donghaensis DSM 18148 = HO3-R19	1121014.3	wgs	PATRIC	1121014 tax ID	*
[Ref.: #66792]	Arenimonas donghaensis DSM 18148, HO3-R19	2597489983	complete	JGI IMG/M	1121014 tax ID	*
[Ref.: #66792]	Arenimonas donghaensis DSM 18148, HO3-R19	2574179743	draft	JGI IMG/M	1121014 tax ID	*

[Ref.: #31832]

GC-content

65 mol%

Availability in culture collections External links

[Ref.: #7407]

Culture collection no.

DSM 18148, KACC 11381

[Ref.: #86440]

SI-ID 396980

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Arenimonas caeni sp. nov., isolated from activated sludge.	Liu H, Ren L, Lu P, Sun L, Zhu G	Int J Syst Evol Microbiol	10.1099/ijsem.0.002937	2018	*
Phylogeny	Arenimonas halophila sp. nov., isolated from soil.	Kanjanasuntree R, Kim JH, Yoon JH, Sukhoom A, Kantachote D, Kim W	Int J Syst Evol Microbiol	10.1099/ijsem.0.002801	2018	*
Phylogeny	Arenimonas soli sp. nov., isolated from saline-alkaline soil.	Xu L, Sun JQ, Liu X, Liu XZ, Qiao MQ, Wu XL	Int J Syst Evol Microbiol	10.1099/ijsem.0.002026	2017	*
Phylogeny	Arenimonas alkanexedens sp. nov., isolated from a frozen soil sample.	Zhu J, Wang HM, Zhang Q, Dong WW, Kong DL, Wang YW, Song JL, Jiang X, Zhao SM, Zhang W, Ruan ZY	Antonie Van Leeuwenhoek	10.1007/s10482-017-0876-9	2017	*
Phylogeny	Arenimonas aestuarii sp. nov., isolated from estuary sediment.	Jeong HI, Jin HM, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.000913	2016	*
Phylogeny	Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China.	Zhang SY, Xiao W, Xia YS, Wang YX, Cui XL, Zhang NM	Antonie Van Leeuwenhoek	10.1007/s10482-015-0409-3	2015	*
Phylogeny	Arenimonas daechungensis sp. nov., isolated from the sediment of a eutrophic reservoir.	Huy H, Jin L, Lee YK, Lee KC, Lee JS, Yoon JH, Ahn CY, Oh HM	Int J Syst Evol Microbiol	10.1099/ijs.0.035410-0	2012	*
Phylogeny	Arenimonas malthae sp. nov., a gammaproteobacterium isolated from an oil-contaminated site.	Young CC, Kampfer P, Ho MJ, Busse HJ, Huber BE, Arun AB, Shen FT, Lai WA, Rekha PD	Int J Syst Evol Microbiol	10.1099/ijs.0.64975-0	2007	*
Phylogeny	Arenimonas donghaensis gen. nov., sp. nov., isolated from seashore sand.	Kwon SW, Kim BY, Weon HY, Baek YK, Go SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64457-0	2007	*
	High quality draft genomic sequence of Arenimonas donghaensis DSM 18148(T).	Chen F, Wang H, Cao Y, Li X, Wang G	Stand Genomic Sci	10.1186/s40793-015-0055-4	2015	*

References

#7407

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18148

#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 )

#31832

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 #28098 (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 .

#86440

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-ID396980.1 )

#28098

IJSEM 954 2007 ( DOI 10.1099/ijs.0.64457-0 , PubMed 17473240 )

* These data were automatically processed and therefore are not curated

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