Name: Hydrocarboniphaga effusa AP103
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17658

Type strain:

Species: Hydrocarboniphaga effusa

Strain Designation: AP103

Culture col. no.: DSM 16095, ATCC BAA-332

Strain history: <- G. J. Zylstra; AP103

NCBI tax ID(s): 243629 (species)

SI-ID 101323

ATCC BAA-332, DSM 16095

Section

Hydrocarboniphaga effusa AP103 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

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	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Nevskiales*
	Family	*Nevskiaceae*
	Genus	*Hydrocarboniphaga*
	Species	**Hydrocarboniphaga effusa**
	Full Scientific Name (LPSN)	Hydrocarboniphaga effusa Palleroni et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #30166]	Gram stain	negative

[Ref.: #30166]	Cell length	1.2 µm

[Ref.: #30166]	Cell width	0.8 µm

[Ref.: #30166]	Cell shape	rod-shaped

[Ref.: #30166]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6290]

Culture medium

LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)

[Ref.: #6290]

Culture medium growth

[Ref.: #6290]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6290]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6290]			growth	30 °C
[Ref.: #30166]			optimum	28 °C

[Ref.: #6290]	Temperature range	mesophilic
[Ref.: #30166]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30166]

Oxygen tolerance

aerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30166]	arginine ChEBI	+	carbon source
[Ref.: #30166]	asparagine ChEBI	+	carbon source
[Ref.: #30166]	aspartate ChEBI	+	carbon source
[Ref.: #30166]	ethanol ChEBI	+	carbon source
[Ref.: #30166]	glutamate ChEBI	+	carbon source
[Ref.: #30166]	glycerol ChEBI	+	carbon source
[Ref.: #30166]	histidine ChEBI	+	carbon source
[Ref.: #30166]	lactate ChEBI	+	carbon source
[Ref.: #30166]	leucine ChEBI	+	carbon source
[Ref.: #30166]	malate ChEBI	+	carbon source
[Ref.: #30166]	mannitol ChEBI	+	carbon source
[Ref.: #30166]	mannose ChEBI	+	carbon source
[Ref.: #30166]	phenylalanine ChEBI	+	carbon source
[Ref.: #30166]	propionate ChEBI	+	carbon source
[Ref.: #30166]	pyruvate ChEBI	+	carbon source
[Ref.: #30166]	rhamnose ChEBI	+	carbon source
[Ref.: #30166]	ribitol ChEBI	+	carbon source
[Ref.: #30166]	succinate ChEBI	+	carbon source
[Ref.: #30166]	sucrose ChEBI	+	carbon source
[Ref.: #30166]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity
[Ref.: #30166]		gelatinase	+

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

[Ref.: #6290]	Sample type/isolated from	soil
[Ref.: #6290]	Geographic location (country and/or sea, region)	New Jersey
[Ref.: #6290]	Country	USA
[Ref.: #6290]	Country ISO 3 Code	USA
[Ref.: #6290]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY363245 (>99% sequence identity) for Hydrocarboniphaga effusa subclade from Microbeatlas

Aquatic Samples	1243
Soil Samples	488
Animal Samples	941
Plant Samples	237
Total Samples	2909

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

[Ref.: #6290]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #6290]	Hydrocarboniphaga effusa strain AP103 16S ribosomal RNA gene, partial sequence	AY363245	1477	ENA	1172194 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Hydrocarboniphaga effusa AP103	GCA_000271305	contig	GenBank	1172194 tax ID	*
[Ref.: #66792]	Hydrocarboniphaga effusa AP103	1172194.9	wgs	PATRIC	1172194 tax ID	*
[Ref.: #66792]	Hydrocarboniphaga effusa AP103	2521172591	draft	JGI IMG/M	1172194 tax ID	*

[Ref.: #6290]	GC-content	60 mol%
[Ref.: #30166]	GC-content	60.5 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: Hydrocarboniphaga effusa AP103 PATRIC: 1172194.9
[Ref.: #69480]	motile	yes	83.195	yes
[Ref.: #69480]	gram-positive	no	98.868	yes
[Ref.: #69480]	anaerobic	no	99.375	no
[Ref.: #69480]	aerobic	yes	96.364	yes
[Ref.: #69480]	halophile	no	92.088	no
[Ref.: #69480]	spore-forming	no	95.629	no
[Ref.: #69480]	flagellated	no	62.889	no
[Ref.: #69480]	thermophile	no	96.252	yes
[Ref.: #69480]	glucose-util	yes	77.093	no
[Ref.: #69480]	glucose-ferment	no	93.356	no

Availability in culture collections External links

[Ref.: #6290]

Culture collection no.

DSM 16095, ATCC BAA-332

[Ref.: #86649]

SI-ID 101323

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Solimonas soli gen. nov., sp. nov., isolated from soil of a ginseng field.	Kim MK, Kim YJ, Cho DH, Yi TH, Soung NK, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.64938-0	2007	*
Genetics	Genome sequence of n-alkane-degrading Hydrocarboniphaga effusa strain AP103T (ATCC BAA-332T).	Chang HK, Zylstra GJ, Chae JC	J Bacteriol	10.1128/JB.01017-12	2012	*
Phylogeny	Fontimonas thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a freshwater hot spring, and proposal of Solimonadaceae fam. nov. to replace Sinobacteraceae Zhou et al. 2008.	Losey NA, Stevenson BS, Verbarg S, Rudd S, Moore ERB, Lawson PA	Int J Syst Evol Microbiol	10.1099/ijs.0.037127-0	2012	*
Phylogeny	Panacagrimonas perspica gen. nov., sp. nov., a novel member of Gammaproteobacteria isolated from soil of a ginseng field.	Im WT, Liu QM, Yang JE, Kim MS, Kim SY, Lee ST, Yi TH	J Microbiol	10.1007/s12275-010-0067-0	2010	*
Phylogeny	Hydrocarboniphaga daqingensis sp. nov., isolated from a freshwater lake.	Liu Y, Song XF, Jiang JT, Liu YH, Xu CJ, Li H, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.019380-0	2010	*
Metabolism	Profiling mechanisms of alkane hydroxylase activity in vivo using the diagnostic substrate norcarane.	Rozhkova-Novosad EA, Chae JC, Zylstra GJ, Bertrand EM, Alexander-Ozinskas M, Deng D, Moe LA, van Beilen JB, Danahy M, Groves JT, Austin RN	Chem Biol	10.1016/j.chembiol.2006.12.007	2007	*
Phylogeny	Hydrocarboniphaga effusa gen. nov., sp. nov., a novel member of the gamma-Proteobacteria active in alkane and aromatic hydrocarbon degradation.	Palleroni NJ, Port AM, Chang HK, Zylstra GJ	Int J Syst Evol Microbiol	10.1099/ijs.0.03016-0	2004	*

References

#6290

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16095

#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 )

#30166

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26516 (see below)

#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) .

#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) .

#86649

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-ID101323.1 )

#26516

IJSEM 1203 2004 ( DOI 10.1099/ijs.0.03016-0 , PubMed 15280292 )

* These data were automatically processed and therefore are not curated

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