Name: Idiomarina abyssalis DSM 15222
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6228

Type strain:

Species: Idiomarina abyssalis

Culture col. no.: DSM 15222, ATCC BAA-312, KMM 227, CIP 107408

Strain history: CIP <- 2002, KMM

NCBI tax ID(s): 86102 (species)

SI-ID 93234

ATCC BAA-312, CIP 107408

Section

Idiomarina abyssalis DSM 15222 is a mesophilic, Gram-negative, motile bacterium that was isolated from seawater.

Gram-negative
motile
rod-shaped
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	*Gammaproteobacteria*
	Order	*Alteromonadales*
	Family	*Idiomarinaceae*
	Genus	*Idiomarina*
	Species	**Idiomarina abyssalis**
	Full Scientific Name (LPSN)	Idiomarina abyssalis Ivanova et al. 2000

Information on morphological and physiological properties Morphology

[Ref.: #115984]	Gram stain	negative

[Ref.: #115984]	Cell shape	rod-shaped

[Ref.: #115984]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5765]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #5765]

Culture medium growth

[Ref.: #5765]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5765]

Culture medium composition

expand / minimize

[Ref.: #33123]

Culture medium

Marine agar (MA)

[Ref.: #33123]

Culture medium growth

[Ref.: #33123]

Culture medium composition

expand / minimize

[Ref.: #115984]

Culture medium

CIP Medium 13

[Ref.: #115984]

Culture medium growth

[Ref.: #115984]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #5765]	growth	28 °C
[Ref.: #33123]	growth	25 °C
[Ref.: #115984]	growth	5-41 °C

[Ref.: #5765]	Temperature range	mesophilic
[Ref.: #33123]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #115984]		NaCl		growth	2-10	%
[Ref.: #115984]		NaCl	no	growth	0	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #115984]	citrate ChEBI	-	carbon source
[Ref.: #115984]	esculin ChEBI	-	hydrolysis
[Ref.: #115984]	glucose ChEBI	-	degradation
[Ref.: #115984]	nitrate ChEBI	+	reduction
[Ref.: #115984]	nitrite ChEBI	+	reduction

	Metabolite production	Metabolite	Production
[Ref.: #115984]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #115984]		acetoin ChEBI	-
[Ref.: #115984]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #115984]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #115984]	amylase	-
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #115984]	caseinase	+	3.4.21.50
[Ref.: #115984]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #115984]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #115984]	gelatinase	+
[Ref.: #115984]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #115984]	lipase	+
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #115984]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #115984]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #115984]	oxidase	+
[Ref.: #115984]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #115984]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #115984]	tryptophan deaminase	-
[Ref.: #115984]	tween esterase	+
[Ref.: #115984]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #115984]	10331	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #5765]	Sample type/isolated from	seawater
[Ref.: #5765]	Geographic location (country and/or sea, region)	north-western Pacific Ocean at a depth of 4000–5000 m (8° 20' N, 133° 0' W)
[Ref.: #5765]	Geographic location	8.3333°/-133.0000°

[Ref.: #115984]	Sample type/isolated from	Environment, Deep sea water
[Ref.: #115984]	Country	Pacific Ocean
[Ref.: #115984]	Isolation date	1985
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF052740 (>99% sequence identity) for Idiomarina from Microbeatlas

Aquatic Samples	787
Soil Samples	32
Animal Samples	220
Plant Samples	30
Total Samples	1069

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

[Ref.: #5765]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #115984]	Biosafety level	1	Risk group (French classification)

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.: #5765]	Idiomarina abyssalis strain KM227(EI4) 16S ribosomal RNA gene, partial sequence	AF052740	1465	ENA	86102 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Idiomarina abyssalis KMM 227	GCA_900116625	contig	GenBank	86102 tax ID	*
[Ref.: #66792]	Idiomarina abyssalis KMM 227	GCA_001294685	contig	GenBank	86102 tax ID	*
[Ref.: #66792]	Idiomarina abyssalis strain KMM 227	86102.6	wgs	PATRIC	86102 tax ID	*
[Ref.: #66792]	Idiomarina abyssalis strain KMM 227	86102.5	wgs	PATRIC	86102 tax ID	*
[Ref.: #66792]	Idiomarina abyssalis KMM 227	2642422567	draft	JGI IMG/M	86102 tax ID	*
[Ref.: #66792]	Idiomarina abyssalis KMM 227	2648501134	draft	JGI IMG/M	86102 tax ID	*

[Ref.: #5765]

GC-content

50.4 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Idiomarina abyssalis strain KMM 227 PATRIC: 86102.6
[Ref.: #69480]	motile	yes	90.234	no
[Ref.: #69480]	flagellated	no	53.75	no
[Ref.: #69480]	gram-positive	no	99.208	no
[Ref.: #69480]	anaerobic	no	98.054	no
[Ref.: #69480]	halophile	yes	69.279	no
[Ref.: #69480]	spore-forming	no	97.265	no
[Ref.: #69480]	thermophile	no	98.666	yes
[Ref.: #69480]	glucose-util	yes	84.946	no
[Ref.: #69480]	aerobic	yes	84.474	no
[Ref.: #69480]	glucose-ferment	no	79.75	no

Availability in culture collections External links

[Ref.: #5765]

Culture collection no.

DSM 15222, ATCC BAA-312, KMM 227, CIP 107408

[Ref.: #75707]

SI-ID 93234

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome Sequence of the Deep-Sea Bacterium Idiomarina abyssalis KMM 227T.	Rheaume BA, Mithoefer S, MacLea KS	Genome Announc	10.1128/genomeA.01256-15	2015	*
Phylogeny	Idiomarina aquatica sp. nov., a moderately halophilic bacterium isolated from salterns.	Jose Leon M, Martinez-Checa F, Ventosa A, Sanchez-Porro C	Int J Syst Evol Microbiol	10.1099/ijsem.0.000619	2015	*
Phylogeny	Idiomarina loihiensis sp. nov., a halophilic gamma-Proteobacterium from the Lo'ihi submarine volcano, Hawai'i.	Donachie SP, Hou S, Gregory TS, Malahoff A, Alam M	Int J Syst Evol Microbiol	10.1099/ijs.0.02701-0	2003	*
Phylogeny	Idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the Pacific Ocean, including descriptions of two species, Idiomarina abyssalis sp. nov. and Idiomarina zobellii sp. nov.	Ivanova EP, Romanenko LA, Chun J, Matte MH, Matte GR, Mikhailov VV, Svetashev VI, Huq A, Maugel T, Colwell RR	Int J Syst Evol Microbiol	10.1099/00207713-50-2-901	2000	*

References

#5765

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15222

#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 )

#33123 ; Curators of the CIP;

#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) .

#68382

Automatically annotated from API zym .

#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) .

#75707

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-ID93234.1 )

#115984 Collection of Institut Pasteur ; Curators of the CIP; CIP 107408
* These data were automatically processed and therefore are not curated

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Idiomarina abyssalis strain KMM 227

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