Name: Hydrocarboniclastica marina Soil36-7
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 166146

Type strain:

Species: Hydrocarboniclastica marina

Strain Designation: Soil36-7

Culture col. no.: MCCC 1A12105, KCTC 62334

NCBI tax ID(s): 2259620 (species)

Section

Hydrocarboniclastica marina Soil36-7 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from deep-sea surface sediment.

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	*Alteromonadales*
	Family	*Alteromonadaceae*
	Genus	*Hydrocarboniclastica*
	Species	**Hydrocarboniclastica marina**
	Full Scientific Name (LPSN)	Hydrocarboniclastica marina Dong et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #67894]	Gram stain	negative

[Ref.: #67894]	Cell length	2.3-2.8 µm

[Ref.: #67894]	Cell width	0.5-0.8 µm

[Ref.: #67894]	Cell shape	rod-shaped

[Ref.: #67894]	Motility	yes

[Ref.: #67894]	Flagellum arrangement	monotrichous, polar

[Ref.: #67894]	Colony size	2-3 mm
[Ref.: #67894]	Colony color	yellowish
[Ref.: #67894]	Colony shape	circular
[Ref.: #67894]	Incubation period	3 days
[Ref.: #67894]	Cultivation medium used	Marine agar (MA)

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #67894]			growth	4-40 °C
[Ref.: #67894]			optimum	28-32 °C

[Ref.: #67894]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #67894]			optimum	7-8
[Ref.: #67894]			growth	5-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67894]

Oxygen tolerance

aerobe

[Ref.: #67894]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #67894]		NaCl		growth	1-12	%(w/v)
[Ref.: #67894]		NaCl		optimum	3-6	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #67894]	adipate ChEBI	-	assimilation
[Ref.: #67894]	amygdalin ChEBI	-	builds acid from
[Ref.: #67894]	citrate ChEBI	+	assimilation
[Ref.: #67894]	D-glucose ChEBI	+	assimilation
[Ref.: #67894]	D-glucose ChEBI	+	builds acid from
[Ref.: #67894]	D-glucose ChEBI	+	fermentation
[Ref.: #67894]	D-mannitol ChEBI	-	assimilation
[Ref.: #67894]	D-mannitol ChEBI	-	builds acid from
[Ref.: #67894]	D-mannose ChEBI	-	assimilation
[Ref.: #67894]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #67894]	decanoate ChEBI	-	assimilation
[Ref.: #67894]	esculin ChEBI	-	hydrolysis
[Ref.: #67894]	gelatin ChEBI	-	hydrolysis
[Ref.: #67894]	L-arabinose ChEBI	-	assimilation
[Ref.: #67894]	L-arabinose ChEBI	-	builds acid from
[Ref.: #67894]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #67894]	malate ChEBI	-	assimilation
[Ref.: #67894]	maltose ChEBI	+	assimilation
[Ref.: #67894]	melibiose ChEBI	+	builds acid from
[Ref.: #67894]	myo-inositol ChEBI	-	builds acid from
[Ref.: #67894]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #67894]	nitrate ChEBI	+	reduction
[Ref.: #67894]	phenylacetate ChEBI	-	assimilation
[Ref.: #67894]	potassium gluconate ChEBI	-	assimilation
[Ref.: #67894]	sodium citrate ChEBI	+	assimilation
[Ref.: #67894]	sucrose ChEBI	-	builds acid from
[Ref.: #67894]	tween 80 ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #67894]	acetoin ChEBI	yes
[Ref.: #67894]	hydrogen sulfide ChEBI	no
[Ref.: #67894]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #67894]		acetoin ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #67894]	2-nitrophenyl beta-D-galactopyranoside	-	3.2.1.52
[Ref.: #67894]	acid phosphatase	+	3.1.3.2
[Ref.: #67894]	alkaline phosphatase	+	3.1.3.1
[Ref.: #67894]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #67894]	alpha-fucosidase	-	3.2.1.51
[Ref.: #67894]	alpha-galactosidase	-	3.2.1.22
[Ref.: #67894]	alpha-glucosidase	-	3.2.1.20
[Ref.: #67894]	alpha-mannosidase	-	3.2.1.24
[Ref.: #67894]	arginine dihydrolase	-	3.5.3.6
[Ref.: #67894]	beta-galactosidase	-	3.2.1.23
[Ref.: #67894]	beta-glucosidase	-	3.2.1.21
[Ref.: #67894]	beta-glucuronidase	-	3.2.1.31
[Ref.: #67894]	catalase	+	1.11.1.6
[Ref.: #67894]	cystine arylamidase	-	3.4.11.3
[Ref.: #67894]	cytochrome oxidase	+	1.9.3.1
[Ref.: #67894]	esterase (C 4)	+
[Ref.: #67894]	esterase Lipase (C 8)	+
[Ref.: #67894]	gelatinase	-
[Ref.: #67894]	leucine arylamidase	+	3.4.11.1
[Ref.: #67894]	lipase (C 14)	+
[Ref.: #67894]	lysine decarboxylase	-	4.1.1.18
[Ref.: #67894]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #67894]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #67894]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #67894]	trypsin	-	3.4.21.4
[Ref.: #67894]	tryptophan decarboxylase	-	4.1.1.27
[Ref.: #67894]	urease	-	3.5.1.5
[Ref.: #67894]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #67894]

Fatty acid	Percentage
C16:0	30.3
C16:1 w6/7c	26.4
C16:0 10-methyl	10.2
C18:1 w7c	6.5
C12:0	6
C18:0	5
C12:0 3OH	3.7
C18:1 w9c	3.2
C14:0 3OH	1.7
C14:0	1

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

[Ref.: #67894]	Sample type/isolated from	deep-sea surface sediment
[Ref.: #67894]	Sampling date	2015-09
[Ref.: #67894]	Geographic location (country and/or sea, region)	deep-sea sediment site MIE-HDU in the north-east of the South China Sea
[Ref.: #67894]	Country	China
[Ref.: #67894]	Country ISO 3 Code	CHN
[Ref.: #67894]	Continent	Asia
[Ref.: #67894]	Geographic location	21.3672°/119.4070°
[Ref.: #67894]	Enrichment culture	R2A agar
[Ref.: #67894]	Enrichment culture duration	7 days
[Ref.: #67894]	Enrichment culture temperature	10 ̊C
[Ref.: #67894]	Isolation/enrichment procedure	the sediment of each layer is resuspended in sterile seawater. Finally, approximately 10-4, 10-5 and 10-6 dilutions of these supernatants are spread onto modified R2A medium plates, and incubated under aerobic conditions at 10°C for 7 days.
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence MH572220 (>99% sequence identity) for Hydrocarboniclastica marina subclade from Microbeatlas

Aquatic Samples	1079
Soil Samples	383
Animal Samples	2136
Plant Samples	115
Total Samples	3713

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.: #67894]	Hydrocarboniclastica marina strain Soil36-7 16S ribosomal RNA gene, partial sequence	MH572220	1524	ENA	2259620 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67894]	Hydrocarboniclastica marina soil36-7	GCA_004851605	complete	GenBank	2259620 tax ID

[Ref.: #67894]

GC-content

57.9 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hydrocarboniclastica marina soil36-7 NCBI: GCA_004851605.1
[Ref.: #69480]	motile	yes	91.679	no
[Ref.: #69480]	flagellated	yes	86.822	yes
[Ref.: #69480]	gram-positive	no	98.44	yes
[Ref.: #69480]	anaerobic	no	97.767	no
[Ref.: #69480]	aerobic	yes	86.464	yes
[Ref.: #69480]	halophile	yes	83.521	no
[Ref.: #69480]	spore-forming	no	94.601	no
[Ref.: #69480]	glucose-util	yes	52.263	no
[Ref.: #69480]	thermophile	no	99.7	no
[Ref.: #69480]	glucose-ferment	no	84.13	yes

Availability in culture collections External links

[Ref.: #67894]

Culture collection no.

MCCC 1A12105, KCTC 62334

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hydrocarboniclastica marina gen. nov., sp. nov., a marine hydrocarbonoclastic bacterium isolated from an in situ enriched hydrocarbon-degrading consortium in sea sediment.	Dong C, Ma T, Liu R, Lai Q, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.003454	2019	*

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 )

#67894

Chunming Dong, Tiantian Ma, Renju Liu, Qiliang Lai, Zongze Shao: Hydrocarboniclastica marina gen. nov., sp. nov., a marine hydrocarbonoclastic bacterium isolated from an in situ enriched hydrocarbon-degrading consortium in sea sediment. IJSEM 69: 2250 - 2257 2019 ( DOI 10.1099/ijsem.0.003454 )

#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) .

* These data were automatically processed and therefore are not curated

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Hydrocarboniclastica marina soil36-7

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