Name: Persicirhabdus sediminis YM20-087
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17212

Type strain:

Species: Persicirhabdus sediminis

Strain Designation: YM20-087

Culture col. no.: DSM 22463, KCTC 22039, MBIC 08313

Strain history: <- JW Yoon, Tokyo Univ. <- Y Matsuo, MBI

NCBI tax ID(s): 1122952 (strain), 454144 (species)

SI-ID 401548

DSM 22463

Special Collections

Section

Persicirhabdus sediminis YM20-087 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

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	*Verrucomicrobiota*
	Class	*Verrucomicrobiia*
	Order	*Verrucomicrobiales*
	Family	*Verrucomicrobiaceae*
	Genus	*Persicirhabdus*
	Species	**Persicirhabdus sediminis**
	Full Scientific Name (LPSN)	Persicirhabdus sediminis Yoon et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32455]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #32455]	Cell length	1.25 µm

[Ref.: #32455]	Cell width	0.65 µm

[Ref.: #32455]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #32455]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #32455]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16352]

Culture medium

HALF STRENGTH R2A MEDIUM IN 75% SEAWATER (DSMZ Medium 1320)

[Ref.: #16352]

Culture medium growth

[Ref.: #16352]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16352]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16352]	growth	21 °C
[Ref.: #32455]	growth	20-30 °C
[Ref.: #32455]	optimum	25 °C
[Ref.: #67771]	growth	25-30 °C

	pH	Kind of pH		pH
[Ref.: #32455]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32455]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #32455]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32455]		NaCl		growth	<2.5	%

[Ref.: #67771]

Observation

quinones: MK-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32455]	arabinose ChEBI	+	carbon source
[Ref.: #32455]	dextrin ChEBI	+	carbon source
[Ref.: #32455]	nitrate ChEBI	+	reduction
[Ref.: #32455]	trehalose ChEBI	+	carbon source
[Ref.: #32455]	tween 80 ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32455]	acid phosphatase	+	3.1.3.2
[Ref.: #32455]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32455]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #16352]	Sample type/isolated from	marine sediment
[Ref.: #16352]	Geographic location (country and/or sea, region)	Chiba, Shore of Sodegaura-Kaihinkouen (35°27'17.0'' N 139°57'03.8'' E)
[Ref.: #16352]	Country	Japan
[Ref.: #16352]	Country ISO 3 Code	JPN
[Ref.: #16352]	Continent	Asia
[Ref.: #16352]	Geographic location	35.4547°/139.9510°

[Ref.: #67771]	Sample type/isolated from	From marine sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	shore of Sodegaura-Kaihinkouen(35Â°27'17.0'' N 139Â°57'03.8'' E), Chiba
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	35.4547°/139.9510°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB331886 (>99% sequence identity) for Persicirhabdus sediminis subclade from Microbeatlas

Aquatic Samples	1261
Soil Samples	42
Animal Samples	241
Plant Samples	7
Total Samples	1551

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

[Ref.: #16352]

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.: #16352]	Persicirhabdus sediminis gene for 16S rRNA, partial sequence, strain: YM20-087	AB331886	1480	GenBank ENA	1122952 tax ID

[Ref.: #16352]

GC-content

50.4 mol%

Availability in culture collections External links

[Ref.: #16352]

Culture collection no.

DSM 22463, KCTC 22039, MBIC 08313

[Ref.: #86211]

SI-ID 401548

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Oceaniferula marina gen.nov., sp.nov., an anti-fluoroquinolone bacterium isolated from marine sediment.	Jin CB, Feng X, Zou QH, Ye MQ, Du ZJ	Antonie Van Leeuwenhoek	10.1007/s10482-021-01645-0	2021	*
Phylogeny	Description of Persicirhabdus sediminis gen. nov., sp. nov., Roseibacillus ishigakijimensis gen. nov., sp. nov., Roseibacillus ponti sp. nov., Roseibacillus persicicus sp. nov., Luteolibacter pohnpeiensis gen. nov., sp. nov. and Luteolibacter algae sp. nov., six marine members of the phylum 'Verrucomicrobia', and emended descriptions of the class Verrucomicrobiae, the order Verrucomicrobiales and the family Verrucomicrobiaceae.	Yoon J, Matsuo Y, Adachi K, Nozawa M, Matsuda S, Kasai H, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.65520-0	2008	*

References

#16352

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22463

#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 )

#32455

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 #28677 (see below)

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#86211

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-ID401548.1 )

#28677

IJSEM 998 2008 ( DOI 10.1099/ijs.0.65520-0 , PubMed 18398209 )

* These data were automatically processed and therefore are not curated

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