Name: Aquibium oceanicum B7
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140989

Type strain:

Species: Aquibium oceanicum

Strain Designation: B7

Culture col. no.: KCTC 42783, MCCC 1K02305

Strain history: <- Dildar, Zhejiang Univ.

NCBI tax ID(s): 1670800 (species)

Section

Aquibium oceanicum B7 is an aerobe, Gram-negative, oval-shaped bacterium that forms circular colonies and was isolated from From sea water from the East China Sea.

colony-forming
Gram-negative
oval-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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Phyllobacteriaceae*
	Genus	*Aquibium*
	Species	**Aquibium oceanicum**
	Full Scientific Name (LPSN)	Aquibium oceanicum (Fu et al. 2017) Kim et al. 2022

Synonym

Mesorhizobium oceanicum

Information on morphological and physiological properties Morphology

[Ref.: #43876]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.985

[Ref.: #43876]	Cell length	0.8-1.0 µm

[Ref.: #43876]	Cell width	0.4-0.6 µm

[Ref.: #43876]	Cell shape	oval-shaped

[Ref.: #43876]	Motility	no

[Ref.: #43876]	Colony size	1.0-2.0 mm
[Ref.: #43876]	Colony color	light yellow
[Ref.: #43876]	Colony shape	circular
[Ref.: #43876]	Incubation period	4 days
[Ref.: #43876]	Cultivation medium used	Marine agar 2216

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43876]

Culture medium

Marine agar (MA)

[Ref.: #43876]

Culture medium growth

[Ref.: #43876]

Culture medium

Yeast mannitol agar

[Ref.: #43876]

Culture medium growth

		Temperature
[Ref.: #43876]	growth	25-40 °C
[Ref.: #43876]	optimum	35 °C
[Ref.: #67771]	growth	35 °C

[Ref.: #43876]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43876]			optimum	7
[Ref.: #43876]			growth	5.5-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43876]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %96
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43876]		NaCl		growth	0-8	%(w/v)
[Ref.: #43876]		NaCl		optimum	3	%(w/v)

[Ref.: #43876]

Observation

quinone Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43876]	adipate ChEBI	+/-	carbon source
[Ref.: #43876]	casamino acids	-	carbon source
[Ref.: #43876]	casein	+	hydrolysis
[Ref.: #43876]	citrate ChEBI	+	carbon source
[Ref.: #43876]	D-glucose ChEBI	+	carbon source
[Ref.: #43876]	D-mannitol ChEBI	+	carbon source
[Ref.: #43876]	D-mannose ChEBI	+	carbon source
[Ref.: #43876]	decanoate ChEBI	-	assimilation
[Ref.: #43876]	esculin ChEBI	-	hydrolysis
[Ref.: #43876]	gelatin ChEBI	+/-	hydrolysis
[Ref.: #43876]	glucose ChEBI	-	fermentation
[Ref.: #43876]	L-arabinose ChEBI	+	carbon source
[Ref.: #43876]	malate ChEBI	+	carbon source
[Ref.: #43876]	maltose ChEBI	+	carbon source
[Ref.: #43876]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #43876]	nitrate ChEBI	+/-	reduction
[Ref.: #43876]	nitrite ChEBI	-	reduction
[Ref.: #43876]	peptone	-	carbon source
[Ref.: #43876]	phenylacetate ChEBI	-	assimilation
[Ref.: #43876]	polypeptone	+	carbon source
[Ref.: #43876]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43876]	soyton	+	carbon source
[Ref.: #43876]	starch ChEBI	-	hydrolysis
[Ref.: #43876]	tryptone	-	carbon source
[Ref.: #43876]	tween 20 ChEBI	-	hydrolysis
[Ref.: #43876]	tween 40 ChEBI	+	hydrolysis
[Ref.: #43876]	tween 60 ChEBI	+	hydrolysis
[Ref.: #43876]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43876]	tyrosine ChEBI	-	hydrolysis
[Ref.: #43876]	urea ChEBI	+	hydrolysis
[Ref.: #43876]	yeast extract	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43876]	acetoin ChEBI	no
[Ref.: #43876]	hydrogen sulfide ChEBI	no
[Ref.: #43876]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #43876]		acetoin ChEBI	-
[Ref.: #43876]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #43876]	6-phospho-beta-galactosidase	-	3.2.1.85
[Ref.: #43876]	acid phosphatase	+/-	3.1.3.2
[Ref.: #43876]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43876]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43876]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43876]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43876]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #43876]	beta-glucosidase	-	3.2.1.21
[Ref.: #43876]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43876]	catalase	+	1.11.1.6
[Ref.: #43876]	chymotrypsin	-	3.4.4.5
[Ref.: #43876]	cystine arylamidase	-	3.4.11.3
[Ref.: #43876]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43876]	esterase (C 4)	+
[Ref.: #43876]	esterase Lipase (C 8)	+
[Ref.: #43876]	leucine arylamidase	-	3.4.11.1
[Ref.: #43876]	lipase (C 14)	-
[Ref.: #43876]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43876]	naphthol-AS-BI-phosphohydrolase	+/-
[Ref.: #43876]	trypsin	+	3.4.21.4
[Ref.: #43876]	valine arylamidase	+/-
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen biosynthesis	100	4 of 4
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	4-hydroxyphenylacetate degradation	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	methionine metabolism	88.46	23 of 26
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	tryptophan metabolism	86.84	33 of 38
[Ref.: #66794]	pyrimidine metabolism	86.67	39 of 45
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	d-xylose degradation	81.82	9 of 11
[Ref.: #66794]	creatinine degradation	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	phenol degradation	80	16 of 20
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	oxidative phosphorylation	68.13	62 of 91
[Ref.: #66794]	degradation of sugar acids	68	17 of 25
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	androgen and estrogen metabolism	56.25	9 of 16
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #67771]	Sample type/isolated from	From sea water from the East China Sea
[Ref.: #67771]	Geographic location (country and/or sea, region)	Zhejiang
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #43876]	Sample type/isolated from	deep seawater (at a depth of 1.0 km) in South China Sea
[Ref.: #43876]	Sampling date	2012-08
[Ref.: #43876]	Geographic location (country and/or sea, region)	South China Sea
[Ref.: #43876]	Country	China
[Ref.: #43876]	Country ISO 3 Code	CHN
[Ref.: #43876]	Continent	Asia
[Ref.: #43876]	Geographic location	15.2333°/117.2830°
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

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.: #43876]	16S rRNA gene sequence	KT157593		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Aquibium oceanicum B7	GCA_001889605	complete	GenBank	1670800 tax ID	*
[Ref.: #66792]	Mesorhizobium sp. B7	1670800.3	complete	PATRIC	1670800 tax ID	*
[Ref.: #66792]	Mesorhizobium oceanicum B7	2728369379	complete	JGI IMG/M	1670800 tax ID	*

[Ref.: #43876]

GC-content

65.1 mol%

genome sequence analysis

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: Mesorhizobium oceanicum B7 NCBI: GCA_001889605.1
[Ref.: #69481]	spore-forming	no	96	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Mesorhizobium oceanicum B7 NCBI: GCA_001889605.1
[Ref.: #69480]	flagellated	no	80.957	yes
[Ref.: #69480]	gram-positive	no	97.224	yes
[Ref.: #69480]	anaerobic	no	98.065	yes
[Ref.: #69480]	aerobic	yes	94.574	yes
[Ref.: #69480]	halophile	no	76.324	no
[Ref.: #69480]	spore-forming	no	96.279	no
[Ref.: #69480]	glucose-util	yes	89.222	yes
[Ref.: #69480]	thermophile	no	96.474	yes
[Ref.: #69480]	motile	yes	77.185	yes
[Ref.: #69480]	glucose-ferment	no	91.417	yes

Availability in culture collections External links

[Ref.: #43876]

Culture collection no.

KCTC 42783, MCCC 1K02305

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Aquibium microcysteis gen. nov., sp. nov., isolated from a Microcystis aeruginosa culture and reclassification of Mesorhizobium carbonis as Aquibium carbonis comb. nov. and Mesorhizobium oceanicum as Aquibium oceanicum comb. nov.	Kim M, Kim W, Park W	Int J Syst Evol Microbiol	10.1099/ijsem.0.005230	2022	*
Phylogeny	Mesorhizobium oceanicum sp. nov., isolated from deep seawater.	Fu GY, Yu XY, Zhang CY, Zhao Z, Wu D, Su Y, Wang RJ, Han SB, Wu M, Sun C	Int J Syst Evol Microbiol	10.1099/ijsem.0.002009	2017	*

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 )

#43876

Ge-yi Fu, Xiao-yun Yu, Chong-ya Zhang, Zhe Zhao, Dildar Wu, Yue Su, Rui-jun Wang, Shuai-bo Han, Min Wu, Cong Sun: Mesorhizobium oceanicum sp. nov., isolated from deep seawater. IJSEM 67: 2739 - 2745 2017 ( DOI 10.1099/ijsem.0.002009 , PubMed 28853693 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

* These data were automatically processed and therefore are not curated

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Mesorhizobium oceanicum B7

Mesorhizobium oceanicum B7

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