Name: Polycladomyces abyssicola JIR-001
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133878

Type strain:

Species: Polycladomyces abyssicola

Strain Designation: JIR-001

Culture col. no.: JCM 18147, CECT 8074, BCC 72032, NBRC 109429

Strain history: T. Tsubouchi JIR-001.

NCBI tax ID(s): 1125966 (species)

SI-ID 388630

CECT 8074, JCM 18147

Section

Polycladomyces abyssicola JIR-001 is an aerobe, spore-forming, thermophilic bacterium that was isolated from marine sediment.

Gram-positive
spore-forming
aerobe
thermophilic
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Thermoactinomycetaceae*
	Genus	*Polycladomyces*
	Species	**Polycladomyces abyssicola**
	Full Scientific Name (LPSN)	Polycladomyces abyssicola Tsubouchi et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30750]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #30750]	Motility	no

[Ref.: #30750]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30750]	growth	55-73 °C
[Ref.: #30750]	optimum	57.5 °C
[Ref.: #67770]	growth	55 °C

[Ref.: #30750]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.282

	pH	Kind of pH		pH
[Ref.: #30750]			optimum	7.5
[Ref.: #30750]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30750]

Oxygen tolerance

aerobe

[Ref.: #30750]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30750]		NaCl		growth	01-02	%

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30750]	alanine ChEBI	+	carbon source
[Ref.: #30750]	arginine ChEBI	+	carbon source
[Ref.: #30750]	asparagine ChEBI	+	carbon source
[Ref.: #30750]	esculin ChEBI	+	hydrolysis
[Ref.: #30750]	glycerol ChEBI	+	carbon source
[Ref.: #30750]	glycine ChEBI	+	carbon source
[Ref.: #30750]	mannose ChEBI	+	carbon source
[Ref.: #30750]	ribose ChEBI	+	carbon source
[Ref.: #30750]	xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity
[Ref.: #30750]		gelatinase	+

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

[Ref.: #30750]	Sample type/isolated from	marine sediment

[Ref.: #67770]	Sample type/isolated from	Deep-seafloor sediment at a depth of 48 m below the seafloor off the Shimokita Peninsula of Japan in the northwestern Pacific Ocean (water depth 1,180 m)
* 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 AB688114 (>99% sequence identity) for Polycladomyces from Microbeatlas

Aquatic Samples	330
Soil Samples	1194
Animal Samples	93
Plant Samples	291
Total Samples	1908

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.: #30750]	Polycladomyces abyssicola gene for 16S ribosomal RNA, partial sequence	AB688114	1485	GenBank	1125966 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Polycladomyces abyssicola JIR-001	GCA_018326425	complete	GenBank	1125966 tax ID	*
[Ref.: #66792]	Polycladomyces abyssicola strain JIR-001	1125966.3	complete	PATRIC	1125966 tax ID	*

[Ref.: #30750]	GC-content	55.1 mol%
[Ref.: #67770]	GC-content	55.1 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 GenomeNet Sporulation v. 1 based on: Polycladomyces abyssicola JIR-001 NCBI: GCA_018326425.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Polycladomyces abyssicola JIR-001 NCBI: GCA_018326425.1
[Ref.: #69480]	flagellated	no	95.382	no
[Ref.: #69480]	gram-positive	yes	88.491	yes
[Ref.: #69480]	anaerobic	no	95.804	no
[Ref.: #69480]	aerobic	yes	91.207	yes
[Ref.: #69480]	halophile	no	88.287	no
[Ref.: #69480]	spore-forming	yes	92.74	yes
[Ref.: #69480]	thermophile	yes	100	yes
[Ref.: #69480]	glucose-util	yes	91.687	no
[Ref.: #69480]	motile	no	87.994	yes
[Ref.: #69480]	glucose-ferment	no	94.093	no

Availability in culture collections External links

[Ref.: #30750]

Culture collection no.

JCM 18147, CECT 8074, BCC 72032, NBRC 109429

[Ref.: #91630]

SI-ID 388630

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete Genome Sequence of Polycladomyces abyssicola JIR-001(T), Isolated from Hemipelagic Sediment in Deep Seawater.	Tsubouchi T, Kaneko Y	Microbiol Resour Announc	10.1128/MRA.00435-21	2021	*
Phylogeny	Polycladomyces subterraneus sp. nov., isolated from soil in Thailand.	Maneewong N, Sakdapetsiri C, Suriyachadkun C, Shibata C, Tamura T, Tokuyama S, Kitpreechavanich V	Int J Syst Evol Microbiol	10.1099/ijsem.0.002114	2017	*
Phylogeny	Polycladomyces abyssicola gen. nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment.	Tsubouchi T, Shimane Y, Mori K, Usui K, Hiraki T, Tame A, Uematsu K, Maruyama T, Hatada Y	Int J Syst Evol Microbiol	10.1099/ijs.0.043596-0	2012	*

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 )

#30750

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 #27081 (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) .

#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 )

#91630

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-ID388630.1 )

#27081

IJSEM 1972 2013 ( DOI 10.1099/ijs.0.043596-0 , PubMed 23024147 )

* These data were automatically processed and therefore are not curated

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