Name: Planctopirus limnophila Müller 290
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11940

Type strain:

Species: Planctopirus limnophila

Strain Designation: Müller 290

Culture col. no.: DSM 3776, ATCC 43296, IFAM 1008

Strain history: <- IFAM <- Müller, 290

NCBI tax ID(s): 521674 (strain), 120 (species)

SI-ID 41761

ATCC 43296, DSM 3776

Special Collections

DSMZ

Section

When using BacDive for research please cite our paper

Planctopirus limnophila Müller 290 is a mesophilic bacterium that was isolated from surface water.

mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Planctomycetota*
	Class	*Planctomycetia*
	Order	*Planctomycetales*
	Family	*Planctomycetaceae*
	Genus	*Planctopirus*
	Species	**Planctopirus limnophila**
	Full Scientific Name (LPSN)	Planctopirus limnophila corrig. (Hirsch and Müller 1986) Scheuner et al. 2015

	Synonym	Planctopirus limnophilus
	Synonym	Planctomyces limnophilus

Information on morphological and physiological properties Morphology

[Ref.: #125438]	Gram stain	negative Confidence in %96.489

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1470]

Culture medium

PYGV AGAR (DSMZ Medium 621)

[Ref.: #1470]

Culture medium growth

[Ref.: #1470]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1470]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #1470]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %95.8

[Ref.: #125439]

Ability of spore formation

no Confidence in %90.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	methanofuran biosynthesis	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	66.67	4 of 6
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	polyamine pathway	60.87	14 of 23
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	oxidative phosphorylation	52.75	48 of 91
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	methanogenesis from CO2	41.67	5 of 12
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	vitamin B12 metabolism	23.53	8 of 34
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		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.: #1470]	Sample type/isolated from	surface water
[Ref.: #1470]	Geographic location (country and/or sea, region)	Holstein
[Ref.: #1470]	Country	Germany
[Ref.: #1470]	Country ISO 3 Code	DEU
[Ref.: #1470]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Surface water

What are isolation sources categories?

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

[Ref.: #1470]

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.: #20218]	P.limnophilus 16S rDNA	X62911	1528	GenBank ENA	521674 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Planctopirus limnophila DSM 3776	GCA_000092105	complete	GenBank ENA	521674 tax ID	*
[Ref.: #66792]	Planctomyces limnophilus DSM 3776	521674.6	complete	PATRIC	521674 tax ID	*
[Ref.: #66792]	Planctopirus limnophila DSM 3776	521674.22	plasmid	PATRIC	521674 tax ID	*
[Ref.: #66792]	Planctopirus limnophila DSM 3776	646564559	complete	JGI IMG/M	521674 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Planctopirus limnophila DSM 3776 DSM 3776 NCBI: GCA_000092105.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.489	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	82.026	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	72.316	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	79.709	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	91.468	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	54.59	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Planctomyces limnophilus DSM 3776 PATRIC: 521674.6
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	90.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	54
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	83.2
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	95.8

Availability in culture collections External links

[Ref.: #1470]

Culture collection no.

DSM 3776, ATCC 43296, IFAM 1008

[Ref.: #81153]

SI-ID 41761

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Planctopirus ephydatiae, a novel Planctomycete isolated from a freshwater sponge.	Kohn T, Wiegand S, Boedeker C, Rast P, Heuer A, Jetten MSM, Schuler M, Becker S, Rohde C, Muller RW, Brummer F, Rohde M, Engelhardt H, Jogler M, Jogler C	Syst Appl Microbiol	10.1016/j.syapm.2019.126022	2019	*
Phylogeny	Planctopirus hydrillae sp. nov., an antibiotic producing Planctomycete isolated from the aquatic plant Hydrilla and its whole genome shotgun sequence analysis.	Yadav S, Vaddavalli R, Siripuram S, Eedara RVV, Yadav S, Rabishankar O, Lodha T, Chintalapati S, Chintalapati V	J Antibiot (Tokyo)	10.1038/s41429-018-0035-1	2018	*
Phylogeny	Schlesneria paludicola gen. nov., sp. nov., the first acidophilic member of the order Planctomycetales, from Sphagnum-dominated boreal wetlands.	Kulichevskaya IS, Ivanova AO, Belova SE, Baulina OI, Bodelier PLE, Rijpstra WIC, Sinninghe Damste JS, Zavarzin GA, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijs.0.65157-0	2007	*
Phylogeny	Physical map of the genome of Planctomyces limnophilus, a representative of the phylogenetically distinct planctomycete lineage.	Ward-Rainey N, Rainey FA, Wellington EM, Stackebrandt E	J Bacteriol	10.1128/jb.178.7.1908-1913.1996	1996	*
	Developing Techniques for the Utilization of Planctomycetes As Producers of Bioactive Molecules.	Jeske O, Surup F, Ketteniss M, Rast P, Forster B, Jogler M, Wink J, Jogler C	Front Microbiol	10.3389/fmicb.2016.01242	2016	*
	Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of environmental organisms: the Planctomycetes paradigm.	Cayrou C, Raoult D, Drancourt M	Environ Microbiol Rep	10.1111/j.1758-2229.2010.00176.x	2010	*

References

#1470

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3776

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 )

#81153

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-ID41761.1 )

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* These data were automatically processed and therefore are not curated

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Planctopirus limnophila DSM 3776 DSM 3776

Planctomyces limnophilus DSM 3776

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