Name: Abyssibacter profundi OUC007
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 159837

Type strain:

Species: Abyssibacter profundi

Strain Designation: OUC007

Culture col. no.: KCTC 52933, MCCC 1K03450, JCM 32025

Strain history: <- Min Yu, Ocean Univ. of China

NCBI tax ID(s): 2182787 (species)

Special Collections

Section

Abyssibacter profundi OUC007 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from the seawater at a depth of 1000 m in the Mariana Trench at station MT1.

colony-forming
Gram-negative
motile
rod-shaped
aerobe
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	*Nevskiales*
	Family	*Salinisphaeraceae*
	Genus	*Abyssibacter*
	Species	**Abyssibacter profundi**
	Full Scientific Name (LPSN)	Abyssibacter profundi Zhou et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66716]	Gram stain	negative

[Ref.: #66716]	Cell length	1.7-1.9 µm

[Ref.: #66716]	Cell width	0.4-0.6 µm

[Ref.: #66716]	Cell shape	rod-shaped

[Ref.: #66716]	Motility	yes

[Ref.: #66716]	Flagellum arrangement	polar

[Ref.: #66716]	Colony size	1-2 mm
[Ref.: #66716]	Colony color	transparent
[Ref.: #66716]	Colony shape	circular
[Ref.: #66716]	Incubation period	3 days
[Ref.: #66716]	Cultivation medium used	Marine agar (MA)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #66716]

Culture medium

Marine agar (MA)

[Ref.: #66716]

Culture medium growth

		Temperature
[Ref.: #66716]	optimum	37 °C
[Ref.: #66716]	growth	10-45 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #66716]			optimum	7.0-8.0
[Ref.: #66716]			growth	7.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66716]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66716]		NaCl		growth	0-7	%(w/v)
[Ref.: #66716]		NaCl		optimum	2-3	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66716]	2-oxopentanoate ChEBI	+	carbon source
[Ref.: #66716]	4-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #66716]	adipate ChEBI	-	assimilation
[Ref.: #66716]	alginate ChEBI	-	hydrolysis
[Ref.: #66716]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #66716]	amygdalin ChEBI	-	builds acid from
[Ref.: #66716]	arbutin ChEBI	-	builds acid from
[Ref.: #66716]	beta-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #66716]	casein	-	hydrolysis
[Ref.: #66716]	cellobiose ChEBI	-	builds acid from
[Ref.: #66716]	cellulose ChEBI	-	hydrolysis
[Ref.: #66716]	chitin ChEBI	-	hydrolysis
[Ref.: #66716]	cis-aconitate ChEBI	+	carbon source
[Ref.: #66716]	D-arabinose ChEBI	-	builds acid from
[Ref.: #66716]	D-arabitol ChEBI	-	builds acid from
[Ref.: #66716]	D-fructose ChEBI	-	builds acid from
[Ref.: #66716]	D-fucose ChEBI	-	builds acid from
[Ref.: #66716]	D-galactose ChEBI	-	builds acid from
[Ref.: #66716]	D-glucose ChEBI	-	assimilation
[Ref.: #66716]	D-glucose ChEBI	-	builds acid from
[Ref.: #66716]	D-lyxose ChEBI	-	builds acid from
[Ref.: #66716]	D-mannitol ChEBI	-	assimilation
[Ref.: #66716]	D-mannitol ChEBI	-	builds acid from
[Ref.: #66716]	D-mannose ChEBI	-	assimilation
[Ref.: #66716]	D-mannose ChEBI	-	builds acid from
[Ref.: #66716]	D-ribose ChEBI	-	builds acid from
[Ref.: #66716]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #66716]	D-tagatose ChEBI	-	builds acid from
[Ref.: #66716]	D-xylose ChEBI	-	builds acid from
[Ref.: #66716]	decanoate ChEBI	-	assimilation
[Ref.: #66716]	dna ChEBI	-	hydrolysis
[Ref.: #66716]	erythritol ChEBI	-	builds acid from
[Ref.: #66716]	esculin ferric citrate	-	builds acid from
[Ref.: #66716]	galactitol ChEBI	-	builds acid from
[Ref.: #66716]	gelatin ChEBI	+	hydrolysis
[Ref.: #66716]	gentiobiose ChEBI	-	builds acid from
[Ref.: #66716]	glycerol ChEBI	+	builds acid from
[Ref.: #66716]	glycogen ChEBI	-	builds acid from
[Ref.: #66716]	inulin ChEBI	-	builds acid from
[Ref.: #66716]	L-alaninamide ChEBI	+	carbon source
[Ref.: #66716]	L-arabinose ChEBI	-	assimilation
[Ref.: #66716]	L-arabinose ChEBI	-	builds acid from
[Ref.: #66716]	L-arabitol ChEBI	-	builds acid from
[Ref.: #66716]	L-fucose ChEBI	-	builds acid from
[Ref.: #66716]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #66716]	L-sorbose ChEBI	-	builds acid from
[Ref.: #66716]	L-xylose ChEBI	-	builds acid from
[Ref.: #66716]	lactose ChEBI	-	builds acid from
[Ref.: #66716]	malate ChEBI	-	assimilation
[Ref.: #66716]	maltose ChEBI	-	assimilation
[Ref.: #66716]	maltose ChEBI	-	builds acid from
[Ref.: #66716]	melezitose ChEBI	-	builds acid from
[Ref.: #66716]	melibiose ChEBI	+	builds acid from
[Ref.: #66716]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #66716]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #66716]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #66716]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #66716]	monomethyl succinate ChEBI	+	carbon source
[Ref.: #66716]	myo-inositol ChEBI	-	builds acid from
[Ref.: #66716]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #66716]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #66716]	phenylacetate ChEBI	-	assimilation
[Ref.: #66716]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #66716]	potassium 5-dehydro-D-gluconate	-	builds acid from
[Ref.: #66716]	potassium gluconate ChEBI	-	assimilation
[Ref.: #66716]	potassium gluconate ChEBI	+	builds acid from
[Ref.: #66716]	raffinose ChEBI	-	builds acid from
[Ref.: #66716]	ribitol ChEBI	-	builds acid from
[Ref.: #66716]	salicin ChEBI	+	builds acid from
[Ref.: #66716]	sodium citrate ChEBI	-	assimilation
[Ref.: #66716]	starch ChEBI	+	builds acid from
[Ref.: #66716]	starch ChEBI	-	hydrolysis
[Ref.: #66716]	sucrose ChEBI	+	builds acid from
[Ref.: #66716]	trehalose ChEBI	-	builds acid from
[Ref.: #66716]	turanose ChEBI	-	builds acid from
[Ref.: #66716]	tween 20 ChEBI	+	hydrolysis
[Ref.: #66716]	tween 40 ChEBI	+	carbon source
[Ref.: #66716]	tween 40 ChEBI	+	hydrolysis
[Ref.: #66716]	tween 80 ChEBI	+	carbon source
[Ref.: #66716]	tween 80 ChEBI	+	hydrolysis
[Ref.: #66716]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #66716]	acid phosphatase	-	3.1.3.2
[Ref.: #66716]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66716]	alpha-fucosidase	+	3.2.1.51
[Ref.: #66716]	alpha-galactosidase	-	3.2.1.22
[Ref.: #66716]	alpha-glucosidase	-	3.2.1.20
[Ref.: #66716]	alpha-mannosidase	-	3.2.1.24
[Ref.: #66716]	beta-galactosidase	+	3.2.1.23
[Ref.: #66716]	beta-glucosidase	-	3.2.1.21
[Ref.: #66716]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66716]	catalase	-	1.11.1.6
[Ref.: #66716]	cytochrome oxidase	+	1.9.3.1
[Ref.: #66716]	esterase (C 4)	+
[Ref.: #66716]	esterase Lipase (C 8)	+
[Ref.: #66716]	gelatinase	+
[Ref.: #66716]	leucine arylamidase	+	3.4.11.1
[Ref.: #66716]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #66716]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #66716]	trypsin	-	3.4.21.4
[Ref.: #66716]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #66716]

Fatty acid	Percentage
C18:1 w6c / C18:1 w7c	58.3
C12:0	7.22
C12:0 3OH	6.81
C18:0	6.57
C17:1 w6c	4.25
C16:0	4.03
C17:0	2.54
C17:0 10-methyl	1.94
C16:1 w5c	1.27
C20:1 w7c	1.24
C11:0	1.22
C10:0	1.05
C19:1 w6c / C19:0 cyclo	1.03

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

[Ref.: #66716]	Sample type/isolated from	the seawater at a depth of 1000 m in the Mariana Trench at station MT1
[Ref.: #66716]	Sampling date	2015-11
[Ref.: #66716]	Geographic location (country and/or sea, region)	1000 m in the Mariana Trench at station MT1 in the western Pacific Ocean, an average of 200 km to the east of the Mariana Islands, in the Western Pacific
[Ref.: #66716]	Country	Philippines
[Ref.: #66716]	Country ISO 3 Code	PHL
[Ref.: #66716]	Continent	Asia
[Ref.: #66716]	Geographic location	11.3839°/142.5000°
[Ref.: #66716]	Enrichment culture	marine agar
[Ref.: #66716]	Enrichment culture temperature	28 ̊C
[Ref.: #66716]	Isolation/enrichment procedure	The seawater samples were spread on marine agar 2216E plates and incubated atroom temperature (approximately 28°C) on board and 28°C in the laboratory.

[Ref.: #67770]	Sample type/isolated from	Seawater at a depth of 1000 m in the Mariana Trench

[Ref.: #67771]	Sample type/isolated from	From 1000m sea water
[Ref.: #67771]	Geographic location (country and/or sea, region)	Marianas Trench of Pacific Ocean
[Ref.: #67771]	Country	International waters
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KY612316 (>99% sequence identity) for Abyssibacter profundi subclade from Microbeatlas

Aquatic Samples	620
Soil Samples	2
Animal Samples	26
Plant Samples	1
Total Samples	649

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.: #66716]	Abyssibacter profundi strain OUC007 16S ribosomal RNA gene, partial sequence	KY612316	1502	GenBank ENA	2182787 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Abyssibacter profundi OUC007	GCA_003151135	contig	GenBank ENA	2182787 tax ID
[Ref.: #66792]	Abyssibacter profundi OUC007	2831460164	draft	JGI IMG/M	2182787 tax ID	*

[Ref.: #66716]

GC-content

63.1 mol%

genome sequence analysis

Availability in culture collections External links

[Ref.: #66716]

Culture collection no.

KCTC 52933, MCCC 1K03450, JCM 32025

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Salifodinibacter halophilus gen. nov., sp. nov., a halophilic gammaproteobacterium in the family Salinisphaeraceae isolated from a salt mine in the Colombian Andes.	Parada-Pinilla MP, Diaz-Cardenas C, Lopez G, Diaz-Riano JI, Gonzalez LN, Restrepo S, Trujillo ME, Baena S	Int J Syst Evol Microbiol	10.1099/ijsem.0.004490	2020	*
Phylogeny	Abyssibacter profundi gen. nov., sp. nov., a marine bacterium isolated from seawater of the Mariana Trench.	Zhou S, Ren Q, Li Y, Liu J, Wang X, Wu Y, Zhang Y, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002999	2018	*

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 )

#66716

Shun Zhou, Qiaomeng Ren, Yuying Li, Jiwen Liu, Xiaolei Wang, Yanhong Wu, Yulin Zhang, Xiao-hua Zhang: Abyssibacter profundi gen. nov., sp. nov., a marine bacterium isolated from seawater of the Mariana Trench. IJSEM 68: 3423 - 3429 2018 ( DOI 10.1099/ijsem.0.002999 , PubMed 30204582 )

#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;
#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 .

* These data were automatically processed and therefore are not curated

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