Name: Plesiocystis pacifica Sir-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 10420

Type strain:

Species: Plesiocystis pacifica

Strain Designation: Sir-1

Culture col. no.: DSM 14875, AJ 13960, JCM 11591

Strain history: T. Iizuka SIR-1.

NCBI tax ID(s): 191768 (species)

SI-ID 100867

DSM 14875, JCM 11591

Other strains from Plesiocystis pacifica

P. pacifica SHI-1, DSM 14876, AJ 13393, JCM ...

Section

Plesiocystis pacifica Sir-1 is a mesophilic bacterium that was isolated from semi-dried seagrass .

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	*Deltaproteobacteria*
	Order	*Myxococcales*
	Family	*Nannocystaceae*
	Genus	*Plesiocystis*
	Species	**Plesiocystis pacifica**
	Full Scientific Name (LPSN)	Plesiocystis pacifica Iizuka et al. 2003

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5591]

Culture medium

CY/3 SEAWATER MEDIUM (DSMZ Medium 1602)

[Ref.: #5591]

Culture medium growth

[Ref.: #5591]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5591]

Culture medium composition

expand / minimize

[Ref.: #5591]

Culture medium

VY/4-SWS AGAR (DSMZ Medium 958)

[Ref.: #5591]

Culture medium growth

[Ref.: #5591]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5591]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5591]			growth	30 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #5591]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5591]

Name of produced compound

haloalkane dehalogenase

[Ref.: #67770]

Observation

quinones: MK-8(H₂)

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

[Ref.: #5591]	Sample type/isolated from	semi-dried seagrass (Zostera)
[Ref.: #5591]	Host species	Zostera
[Ref.: #5591]	Geographic location (country and/or sea, region)	Iriomote-Jima Island, Okinawa
[Ref.: #5591]	Country	Japan
[Ref.: #5591]	Country ISO 3 Code	JPN
[Ref.: #5591]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Semi-dried sample of sea grass
[Ref.: #67770]	Geographic location (country and/or sea, region)	Iriomote-jima Island
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Aquatic plant

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB083432 (>99% sequence identity) for Plesiocystis pacifica subclade from Microbeatlas

Aquatic Samples	1671
Soil Samples	471
Animal Samples	937
Plant Samples	59
Total Samples	3138

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

[Ref.: #5591]

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.: #5591]	Plesiocystis pacifica gene for 16S ribosomal RNA	AB083432	1484	ENA	391625 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Plesiocystis pacifica SIR-1	GCA_000170895	contig	GenBank	391625 tax ID	*
[Ref.: #66792]	Plesiocystis pacifica SIR-1	391625.5	wgs	PATRIC	391625 tax ID	*
[Ref.: #66792]	Plesiocystis pacifica SIR-1	640963030	draft	JGI IMG/M	391625 tax ID	*

[Ref.: #5591]

GC-content

69.3 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Plesiocystis pacifica SIR-1 PATRIC: 391625.5
[Ref.: #69480]	gram-positive	no	96.735	no
[Ref.: #69480]	anaerobic	no	96.916	no
[Ref.: #69480]	halophile	yes	54.391	no
[Ref.: #69480]	spore-forming	no	82.277	no
[Ref.: #69480]	glucose-util	yes	77.994	no
[Ref.: #69480]	aerobic	yes	72.833	no
[Ref.: #69480]	motile	no	64.814	no
[Ref.: #69480]	flagellated	no	90.312	no
[Ref.: #69480]	thermophile	no	97.577	yes
[Ref.: #69480]	glucose-ferment	no	86.007	no

Availability in culture collections External links

[Ref.: #5591]

Culture collection no.

DSM 14875, AJ 13960, JCM 11591

[Ref.: #79702]

SI-ID 100867

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites.	Amiri Moghaddam J, Crusemann M, Alanjary M, Harms H, Davila-Cespedes A, Blom J, Poehlein A, Ziemert N, Konig GM, Schaberle TF	Sci Rep	10.1038/s41598-018-34954-y	2018	*
Phylogeny	Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan.	Iizuka T, Jojima Y, Fudou R, Hiraishi A, Ahn JW, Yamanaka S	Int J Syst Evol Microbiol	10.1099/ijs.0.02418-0	2003	*
	New Deoxyenhygrolides from Plesiocystis pacifica Provide Insights into Butenolide Core Biosynthesis.	Hug JJ, Kjaerulff L, Garcia R, Muller R	Mar Drugs	10.3390/md20010072	2022	*

References

#5591

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14875

#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 )

#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) .

#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) .

#79702

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-ID100867.1 )

* These data were automatically processed and therefore are not curated

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Plesiocystis pacifica SIR-1

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