Name: Rurimicrobium arvi J107-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158542

Type strain:

Species: Rurimicrobium arvi

Strain Designation: J107-1

Culture col. no.: KEMB 9005-549, KACC 19167, JCM 31921

Strain history: J. Kim; Kyonggi Univ., South Korea; J107-1.

NCBI tax ID(s): 2049916 (species)

Section

Rurimicrobium arvi J107-1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from farmland soil.

colony-forming
Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Rurimicrobium*
	Species	**Rurimicrobium arvi**
	Full Scientific Name (LPSN)	Rurimicrobium arvi Dahal et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #65590]	Gram stain	negative

[Ref.: #65590]	Cell length	0.5-0.65 µm

[Ref.: #65590]	Cell width	0.4-0.55 µm

[Ref.: #65590]	Cell shape	rod-shaped
[Ref.: #65590]	Cell shape	coccus-shaped

[Ref.: #65590]	Motility	no

[Ref.: #65590]	Colony size	1-2 mm
[Ref.: #65590]	Colony color	yellow
[Ref.: #65590]	Colony shape	circular
[Ref.: #65590]	Incubation period	4 days
[Ref.: #65590]	Cultivation medium used	R2A

[Ref.: #65590]	Pigment production	no
[Ref.: #65590]	Pigment name	flexirubin-type pigments

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

tryptone soy agar

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Culture medium growth

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Culture medium

veal infusion agar

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Culture medium growth

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Culture medium

sulphide indole motility medium

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Culture medium

sorbitol MacConkey agar

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Culture medium growth

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Culture medium

brain heart infusion agar

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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

PDA

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Culture medium growth

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Culture medium

MCA

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Culture medium growth

		Temperature
[Ref.: #65590]	growth	15-42 °C
[Ref.: #65590]	optimum	20-37 °C
[Ref.: #67770]	growth	30 °C

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Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #65590]			optimum	7-8.5
[Ref.: #65590]			growth	5.5-9

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

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Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65590]		NaCl		optimum	0	%
[Ref.: #65590]		NaCl		growth	0-0.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65590]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #65590]	casein	+	hydrolysis
[Ref.: #65590]	chitin ChEBI	-	hydrolysis
[Ref.: #65590]	dna ChEBI	-	hydrolysis
[Ref.: #65590]	esculin ferric citrate	-	hydrolysis
[Ref.: #65590]	gelatin ChEBI	-	hydrolysis
[Ref.: #65590]	glucose ChEBI	-	fermentation
[Ref.: #65590]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #65590]	nitrate ChEBI	-	reduction
[Ref.: #65590]	starch ChEBI	-	hydrolysis
[Ref.: #65590]	tryptophan ChEBI	-	energy source
[Ref.: #65590]	tween 40 ChEBI	-	hydrolysis
[Ref.: #65590]	tween 60 ChEBI	-	hydrolysis
[Ref.: #65590]	tween 80 ChEBI	-	hydrolysis
[Ref.: #65590]	tyrosine ChEBI	+	hydrolysis
[Ref.: #65590]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #65590]	acetoin ChEBI	no
[Ref.: #65590]	hydrogen sulfide ChEBI	no
[Ref.: #65590]	indole ChEBI	no

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #65590]	acetoin ChEBI	-
[Ref.: #65590]	glucose ChEBI		-
[Ref.: #65590]	indole ChEBI			-

	Enzyme	Enzyme activity	EC number
[Ref.: #65590]	acid phosphatase	+	3.1.3.2
[Ref.: #65590]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65590]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65590]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65590]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65590]	alpha-glucosidase	-	3.2.1.20
[Ref.: #65590]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65590]	beta-galactosidase	-	3.2.1.23
[Ref.: #65590]	beta-glucosidase	-	3.2.1.21
[Ref.: #65590]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65590]	catalase	+	1.11.1.6
[Ref.: #65590]	cystine arylamidase	+	3.4.11.3
[Ref.: #65590]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65590]	esterase (C 4)	+
[Ref.: #65590]	esterase Lipase (C 8)	+
[Ref.: #65590]	leucine arylamidase	+	3.4.11.1
[Ref.: #65590]	lipase (C 14)	-
[Ref.: #65590]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65590]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65590]	trypsin	-	3.4.21.4
[Ref.: #65590]	tryptophan deaminase	-	4.1.99.1
[Ref.: #65590]	urease	-	3.5.1.5
[Ref.: #65590]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

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Fatty acid	Percentage
C15:0 iso	33.8
iso-C15:1 G	28.7
iso-C17:0 3-OH	15.6
C17:0 iso	8.8
iso-C15:0 3-OH	3.9
iso-C15:1ω9c	3
C13:0 iso	2
C16:0	1.5
C16:1ω7c and/or C16:1ω6c	0.8
C17:1 iso ω10c	0.3
iso-C14:0 3-OH	0.3
C16:0 3OH	0.3
C14:0	0.3
iso-C16:0 3-OH	0.2
C17:0 anteiso	0.2
C18:0	0.2
C10:0 iso	0.1

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

[Ref.: #65590]	Sample type/isolated from	farmland soil
[Ref.: #65590]	Geographic location (country and/or sea, region)	Suwon, Gyeonggi-Do
[Ref.: #65590]	Country	Republic of Korea
[Ref.: #65590]	Country ISO 3 Code	KOR
[Ref.: #65590]	Continent	Asia
[Ref.: #65590]	Geographic location	37.2772°/126.9960°
[Ref.: #65590]	Enrichment culture	R2A broth

[Ref.: #67770]	Sample type/isolated from	Farmland soil at Suwon
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Field

What are isolation sources categories?

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Global distribution of 16S sequence KY233200 (>99% sequence identity) for Rurimicrobium arvi subclade from Microbeatlas

Aquatic Samples	507
Soil Samples	421
Animal Samples	114
Plant Samples	315
Total Samples	1357

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.: #65590]	16S rRNA gene sequence	KY233200		GenBank

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GC-content

47.8 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

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Culture collection no.

KEMB 9005-549, KACC 19167, JCM 31921

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rurimicrobium arvi gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from farmland soil.	Dahal RH, Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002452	2017	*

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 )

#65590

Ram Hari Dahal, Dhiraj Kumar Chaudhary, Jaisoo Kim: Rurimicrobium arvi gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from farmland soil. IJSEM 67: 5235 - 5243 2017 ( DOI 10.1099/ijsem.0.002452 , PubMed 29072559 )

#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 .

* These data were automatically processed and therefore are not curated

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