Name: Methylibium petroleiphilum PM1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134120

Type strain:

Species: Methylibium petroleiphilum

Strain Designation: PM1

Culture col. no.: ATCC BAA-1232, LMG 22953

NCBI tax ID(s): 105560 (species)

SI-ID 135175

LMG 22953, ATCC BAA-1232

Section

Methylibium petroleiphilum PM1 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from compost biofilter.

Gram-negative
motile
rod-shaped
facultative 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	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	[Burkholderiales, not assigned to family]
	Genus	*Methylibium*
	Species	**Methylibium petroleiphilum**
	Full Scientific Name (LPSN)	Methylibium petroleiphilum Nakatsu et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31430]	Gram stain	negative

[Ref.: #31430]	Cell length	01-02 µm

[Ref.: #31430]	Cell width	0.5 µm

[Ref.: #31430]	Cell shape	rod-shaped

[Ref.: #31430]	Motility	yes

[Ref.: #31430]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #31430]			growth	25-30 °C
[Ref.: #31430]			optimum	30 °C

[Ref.: #31430]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #31430]			optimum	6.5
[Ref.: #31430]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31430]

Oxygen tolerance

facultative aerobe

[Ref.: #31430]

Ability of spore formation

[Ref.: #31430]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31430]	acetate ChEBI	+	carbon source
[Ref.: #31430]	alanine ChEBI	+	carbon source
[Ref.: #31430]	asparagine ChEBI	+	carbon source
[Ref.: #31430]	ethanol ChEBI	+	carbon source
[Ref.: #31430]	nitrate ChEBI	+	reduction
[Ref.: #31430]	pyruvate ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31430]		cytochrome oxidase	+	1.9.3.1
[Ref.: #31430]		urease	+	3.5.1.5

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

[Ref.: #31430]	Sample type/isolated from	compost biofilter
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Composting
#Engineered	#Bioremediation	#Biofilter

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF176594 (>99% sequence identity) for Methylibium petroleiphilum subclade from Microbeatlas

Aquatic Samples	73
Soil Samples	14
Animal Samples	22
Plant Samples	4
Total Samples	113

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.: #31430]	Methylibium petroleiphilum PM1 16S ribosomal RNA gene, partial sequence; 16S-23S intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF176594	2208	GenBank	420662 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methylibium petroleiphilum PM1	GCA_000015725	complete	GenBank	420662 tax ID	*
[Ref.: #66792]	Methylibium petroleiphilum PM1	420662.15	complete	PATRIC	420662 tax ID	*
[Ref.: #66792]	Methylibium petroleiphilum PM1	420662.29	plasmid	PATRIC	420662 tax ID	*
[Ref.: #66792]	Methylibium petroleiphilum PM1	640069319	complete	JGI IMG/M	420662 tax ID	*

[Ref.: #31430]

GC-content

69 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: Methylibium petroleiphilum PM1 PM1 NCBI: GCA_000015725.1
[Ref.: #69480]	motile	yes	87.498	no
[Ref.: #69480]	flagellated	yes	73.039	no
[Ref.: #69480]	gram-positive	no	99.01	no
[Ref.: #69480]	anaerobic	no	96.048	no
[Ref.: #69480]	halophile	no	95.108	no
[Ref.: #69480]	spore-forming	no	95.54	yes
[Ref.: #69480]	thermophile	no	97.267	yes
[Ref.: #69480]	glucose-util	no	55.237	no
[Ref.: #69480]	aerobic	yes	85.01	no
[Ref.: #69480]	glucose-ferment	no	91.215	no

Availability in culture collections External links

[Ref.: #31430]

Culture collection no.

ATCC BAA-1232, LMG 22953

[Ref.: #91722]

SI-ID 135175

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Hydrocarbon degrading microbial communities in bench scale aerobic biobarriers for gasoline contaminated groundwater treatment.	Daghio M, Tatangelo V, Franzetti A, Gandolfi I, Papacchini M, Careghini A, Sezenna E, Saponaro S, Bestetti G	Chemosphere	10.1016/j.chemosphere.2015.02.022	2015	*
Phylogeny	Methylibium subsaxonicum spec. nov., a betaproteobacterium Isolated from a hardwater rivulet.	Stackebrandt E, Fruhling A, Cousin S, Brambilla E, Lunsdorf H, Verbarg S	Curr Microbiol	10.1007/s00284-007-9095-3	2008	*
Phylogeny	Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria.	Nakatsu CH, Hristova K, Hanada S, Meng XY, Hanson JR, Scow KM, Kamagata Y	Int J Syst Evol Microbiol	10.1099/ijs.0.63524-0	2006	*

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 )

#31430

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 #27736 (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) .

#91722

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-ID135175.1 )

#27736

IJSEM 983 2006 ( DOI 10.1099/ijs.0.63524-0 , PubMed 16627642 )

* 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 Methylibium petroleiphilum in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Methylibium petroleiphilum PM1 PM1

Change proposal

Change proposal