Name: Arenimonas terrae R29
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 164486

Type strain:

Species: Arenimonas terrae

Strain Designation: R29

Culture col. no.: JCM 33216, KACC 19896

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; R29.

NCBI tax ID(s): 2546226 (species)

Section

Arenimonas terrae R29 is an obligate aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Orchard soil in Hwasun.

colony-forming
Gram-negative
mesophilic
obligate 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	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Arenimonas*
	Species	**Arenimonas terrae**
	Full Scientific Name (LPSN)	Arenimonas terrae Han et al. 2020

Information on morphological and physiological properties Morphology

[Ref.: #69518]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #69518]	Cell length	0.8-1.6 µm

[Ref.: #69518]	Cell width	0.3-0.4 µm

[Ref.: #69518]	Cell shape	rod-shaped

[Ref.: #69518]	Motility	no

[Ref.: #69518]	Colony color	yellowish
[Ref.: #69518]	Colony shape	circular
[Ref.: #69518]	Incubation period	3 days
[Ref.: #69518]	Cultivation medium used	R2A MEDIUM (DSMZ Medium 830)

Information on culture and growth conditions Culture and growth conditions

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium

LB (Luria-Bertani) MEDIUM

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Culture medium growth

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Culture medium

Marine agar (MA)

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Culture medium growth

		Temperature
[Ref.: #67770]	growth	30 °C
[Ref.: #69518]	growth	15.0-40.0 °C
[Ref.: #69518]	optimum	30 °C

[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #69518]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #69518]			growth	7.0-9.0

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

obligate aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.994
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #69518]		NaCl	no	growth	0.5	%(w/v)

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Observation

quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69518]	adipate ChEBI	-	assimilation
[Ref.: #69518]	casein	+	hydrolysis
[Ref.: #69518]	D-glucose ChEBI	-	assimilation
[Ref.: #69518]	D-mannitol ChEBI	-	assimilation
[Ref.: #69518]	D-mannose ChEBI	-	assimilation
[Ref.: #69518]	dodecanoate ChEBI	-	assimilation
[Ref.: #69518]	esculin ChEBI	-	hydrolysis
[Ref.: #69518]	gelatin ChEBI	+	hydrolysis
[Ref.: #69518]	glucose ChEBI	-	fermentation
[Ref.: #69518]	L-arabinose ChEBI	-	assimilation
[Ref.: #69518]	malate ChEBI	-	assimilation
[Ref.: #69518]	maltose ChEBI	-	assimilation
[Ref.: #69518]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #69518]	nitrate ChEBI	-	reduction
[Ref.: #69518]	phenylacetate ChEBI	-	assimilation
[Ref.: #69518]	potassium gluconate ChEBI	-	assimilation
[Ref.: #69518]	sodium citrate ChEBI	-	assimilation
[Ref.: #69518]	starch ChEBI	-	hydrolysis
[Ref.: #69518]	tween 20 ChEBI	-	hydrolysis
[Ref.: #69518]	tween 80 ChEBI	-	hydrolysis
[Ref.: #69518]	tyrosine ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #69518]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #69518]	acid phosphatase	+	3.1.3.2
[Ref.: #69518]	alkaline phosphatase	+	3.1.3.1
[Ref.: #69518]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #69518]	alpha-fucosidase	-	3.2.1.51
[Ref.: #69518]	alpha-galactosidase	+	3.2.1.22
[Ref.: #69518]	alpha-glucosidase	-	3.2.1.20
[Ref.: #69518]	alpha-mannosidase	-	3.2.1.24
[Ref.: #69518]	arginine dihydrolase	+	3.5.3.6
[Ref.: #69518]	beta-galactosidase	-	3.2.1.23
[Ref.: #69518]	beta-glucosidase	-	3.2.1.21
[Ref.: #69518]	beta-glucuronidase	-	3.2.1.31
[Ref.: #69518]	catalase	+	1.11.1.6
[Ref.: #69518]	cystine arylamidase	+	3.4.11.3
[Ref.: #69518]	cytochrome oxidase	+	1.9.3.1
[Ref.: #69518]	esterase (C 4)	+
[Ref.: #69518]	esterase Lipase (C 8)	+
[Ref.: #69518]	leucine arylamidase	+	3.4.11.1
[Ref.: #69518]	lipase (C 14)	+
[Ref.: #69518]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #69518]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #69518]	trypsin	+	3.4.21.4
[Ref.: #69518]	urease	+	3.5.1.5
[Ref.: #69518]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #69518]

Fatty acid	Percentage
iso-C15:0	37.7
iso-C16:0	20
C18:1 w7c / C18:1 w6c	9.3
iso-C11:0 3-OH	5
iso-C14:0	4.9
C16:0	4.5
iso-C17:0	2.6
C16:1 w7c / C16:1 w6c	2.6
iso-C11:0	2.2
iso-C15:0F	1.8
iso-C15:1 H / C13:0 3OH	1.8
C18:0	1.3
anteiso-C15:0	1.2

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

[Ref.: #67770]	Sample type/isolated from	Orchard soil in Hwasun
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #69518]	Sample type/isolated from	orchard soil sample
[Ref.: #69518]	Geographic location (country and/or sea, region)	Hwasun
[Ref.: #69518]	Country	Republic of Korea
[Ref.: #69518]	Country ISO 3 Code	KOR
[Ref.: #69518]	Continent	Asia
[Ref.: #69518]	Geographic location	34.9990°/126.9620°
[Ref.: #69518]	Enrichment culture	R2A
[Ref.: #69518]	Enrichment culture duration	3 days
[Ref.: #69518]	Enrichment culture temperature	30 ̊C
[Ref.: #69518]	Isolation/enrichment procedure	serial dilution using phospate buffered saline(137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, pH 7.2)
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence MK397782 (>99% sequence identity) for Arenimonas from Microbeatlas

Aquatic Samples	235
Soil Samples	900
Animal Samples	133
Plant Samples	48
Total Samples	1316

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.: #67770]	Arenimonas terrae 16S ribosomal RNA gene, partial sequence	MK397782	1462	ENA	2546226 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Arenimonas terrae R29	GCA_006265115	scaffold	GenBank	2546226 tax ID
[Ref.: #69518]	genome sequence	SMDR00000000		GenBank	2546226 tax ID

[Ref.: #67770]	GC-content	64.9 mol%	genome sequence analysis
[Ref.: #69518]	GC-content	69.8 mol%	genome sequence analysis

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: Arenimonas terrae R29 NCBI: GCA_006265115.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Arenimonas terrae R29 NCBI: GCA_006265115.1
[Ref.: #69480]	motile	no	52.147	no
[Ref.: #69480]	flagellated	no	87.702	no
[Ref.: #69480]	gram-positive	no	98.504	no
[Ref.: #69480]	anaerobic	no	98.758	no
[Ref.: #69480]	aerobic	yes	90.807	no
[Ref.: #69480]	halophile	no	95.32	no
[Ref.: #69480]	spore-forming	no	97.903	no
[Ref.: #69480]	glucose-util	yes	83.754	no
[Ref.: #69480]	thermophile	no	98.007	no
[Ref.: #69480]	glucose-ferment	no	92.109	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 33216, KACC 19896

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Arenimonas terrae sp. nov., isolated from orchard soil.	Han DM, Chun BH, Kim HM, Khan SA, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.003785	2020	*

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 )

#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 .

#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 )

#69518

Dong Min Han, Byung Hee Chun, Hyung Min Kim, Shehzad Abid Khan, Che Ok Jeon: Arenimonas terrae sp. nov., isolated from orchard soil. IJSEM 70: 2020 ( DOI 10.1099/ijsem.0.003785 )

* These data were automatically processed and therefore are not curated

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