Name: Abyssibacter profundi OUC007
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/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)

Section

Abyssibacter profundi OUC007 is an aerobe, mesophilic, Gram-negative 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
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Nevskiales*
	Family	*Salinisphaeraceae*
	Genus	*Abyssibacter*
	Species	**Abyssibacter profundi**
	Full Scientific Name (PNU)	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

[Ref.: #66716]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	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]	Oceanococcus sp. strain OUC007 16S ribosomal RNA gene, partial sequence	KY612316	1502	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	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

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Abyssibacter profundi in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF