Name: Lichenihabitans psoromatis JCM 33311
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 164516

Type strain:

Species: Lichenihabitans psoromatis

Culture col. no.: JCM 33311, KCCM 43293, PAMC 29148

Strain history: Y. M. Lee; KOPRI, South Korea; PAMC 29148.

NCBI tax ID(s): 2528642 (species)

Special Collections

Other strains from Lichenihabitans psoromatis

Section

Lichenihabitans psoromatis JCM 33311 is a facultative anaerobe, chemoheterotroph, Gram-negative bacterium that forms circular colonies and was isolated from Lichen, Psoroma antarcticum.

colony-forming
Gram-negative
rod-shaped
chemoheterotroph
facultative anaerobe
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	*Lichenihabitantaceae*
	Genus	*Lichenihabitans*
	Species	**Lichenihabitans psoromatis**
	Full Scientific Name (LPSN)	Lichenihabitans psoromatis Noh et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #68043]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.815

[Ref.: #68043]	Cell length	0.9-3.4 µm

[Ref.: #68043]	Cell width	0.9-1.6 µm

[Ref.: #68043]	Cell shape	rod-shaped

[Ref.: #68043]	Motility	no

[Ref.: #68043]	Colony color	pink
[Ref.: #68043]	Colony shape	circular
[Ref.: #68043]	Incubation period	14 days
[Ref.: #68043]	Cultivation medium used	Reasoner's 2A agar (R2A)

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #67770]	growth	15 °C
[Ref.: #68043]	growth	4-20 °C
[Ref.: #68043]	optimum	15 °C

	pH	Kind of pH		pH
[Ref.: #68043]			optimum	6.5
[Ref.: #68043]			growth	5.5-7.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #68043]

Oxygen tolerance

facultative anaerobe

[Ref.: #68043]

Nutrition type

chemoheterotroph

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #68043]		NaCl		optimum	0	%(w/v)

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68043]	2,3-butanediol	-	respiration
[Ref.: #68043]	2-hydroxybutyrate ChEBI	-	respiration
[Ref.: #68043]	2-oxobutanoate ChEBI	-	respiration
[Ref.: #68043]	2-oxoglutarate ChEBI	-	respiration
[Ref.: #68043]	2-oxopentanoate ChEBI	-	respiration
[Ref.: #68043]	3-hydroxybutyrate ChEBI	-	respiration
[Ref.: #68043]	4-hydroxy-L-proline ChEBI	-	respiration
[Ref.: #68043]	4-hydroxybutyrate ChEBI	-	respiration
[Ref.: #68043]	4-hydroxyphenylacetic acid ChEBI	-	respiration
[Ref.: #68043]	acetate ChEBI	-	respiration
[Ref.: #68043]	alpha-cyclodextrin ChEBI	-	respiration
[Ref.: #68043]	alpha-D-glucose ChEBI	+	respiration
[Ref.: #68043]	alpha-lactose ChEBI	-	respiration
[Ref.: #68043]	amygdalin ChEBI	-	builds acid from
[Ref.: #68043]	arbutin ChEBI	-	builds acid from
[Ref.: #68043]	bromosuccinate ChEBI	-	respiration
[Ref.: #68043]	cellobiose ChEBI	+	respiration
[Ref.: #68043]	cellobiose ChEBI	-	builds acid from
[Ref.: #68043]	cis-aconitate ChEBI	-	respiration
[Ref.: #68043]	citrate ChEBI	-	respiration
[Ref.: #68043]	D-alanine ChEBI	-	respiration
[Ref.: #68043]	D-arabinose ChEBI	+	builds acid from
[Ref.: #68043]	D-arabitol ChEBI	+	respiration
[Ref.: #68043]	D-arabitol ChEBI	+	builds acid from
[Ref.: #68043]	D-fructose ChEBI	+	respiration
[Ref.: #68043]	D-fructose ChEBI	+	builds acid from
[Ref.: #68043]	D-fucose ChEBI	+	builds acid from
[Ref.: #68043]	D-galactonic acid lactone ChEBI	+	respiration
[Ref.: #68043]	D-galactose ChEBI	+	respiration
[Ref.: #68043]	D-galactose ChEBI	+/-	builds acid from
[Ref.: #68043]	D-galacturonic acid ChEBI	-	respiration
[Ref.: #68043]	D-glucarate ChEBI	-	respiration
[Ref.: #68043]	D-gluconate ChEBI	+	respiration
[Ref.: #68043]	D-glucosaminic acid ChEBI	-	respiration
[Ref.: #68043]	D-glucose ChEBI	+/-	builds acid from
[Ref.: #68043]	D-glucose 6-phosphate ChEBI	-	respiration
[Ref.: #68043]	D-glucuronate ChEBI	-	respiration
[Ref.: #68043]	D-lyxose ChEBI	+	builds acid from
[Ref.: #68043]	D-mannitol ChEBI	+	respiration
[Ref.: #68043]	D-mannitol ChEBI	+/-	builds acid from
[Ref.: #68043]	D-mannose ChEBI	+	respiration
[Ref.: #68043]	D-mannose ChEBI	+/-	builds acid from
[Ref.: #68043]	D-psicose ChEBI	+	respiration
[Ref.: #68043]	D-ribose ChEBI	+	builds acid from
[Ref.: #68043]	D-serine ChEBI	-	respiration
[Ref.: #68043]	D-sorbitol ChEBI	+	respiration
[Ref.: #68043]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #68043]	D-tagatose ChEBI	+/-	builds acid from
[Ref.: #68043]	D-xylose ChEBI	+	builds acid from
[Ref.: #68043]	dextrin ChEBI	-	respiration
[Ref.: #68043]	dinitrogen oxide ChEBI	-	assimilation
[Ref.: #68043]	DL-carnitine ChEBI	-	respiration
[Ref.: #68043]	erythritol ChEBI	+	respiration
[Ref.: #68043]	erythritol ChEBI	+/-	builds acid from
[Ref.: #68043]	esculin ferric citrate	+	builds acid from
[Ref.: #68043]	ethanolamine ChEBI	-	respiration
[Ref.: #68043]	formaldehyde ChEBI	-	assimilation
[Ref.: #68043]	formate ChEBI	-	assimilation
[Ref.: #68043]	formate ChEBI	-	respiration
[Ref.: #68043]	galactitol ChEBI	-	builds acid from
[Ref.: #68043]	gamma-aminobutyric acid ChEBI	-	respiration
[Ref.: #68043]	gentiobiose ChEBI	-	respiration
[Ref.: #68043]	gentiobiose ChEBI	+/-	builds acid from
[Ref.: #68043]	glucose 1-phosphate ChEBI	-	respiration
[Ref.: #68043]	glucuronamide ChEBI	-	respiration
[Ref.: #68043]	glycerol ChEBI	+	respiration
[Ref.: #68043]	glycerol ChEBI	+	builds acid from
[Ref.: #68043]	glycerol 1-phosphate ChEBI	-	respiration
[Ref.: #68043]	glycogen ChEBI	-	respiration
[Ref.: #68043]	glycogen ChEBI	+	builds acid from
[Ref.: #68043]	glycyl L-aspartic acid ChEBI	-	respiration
[Ref.: #68043]	glycyl-l-glutamate ChEBI	-	respiration
[Ref.: #68043]	inosine ChEBI	-	respiration
[Ref.: #68043]	inulin ChEBI	+/-	builds acid from
[Ref.: #68043]	itaconate ChEBI	-	respiration
[Ref.: #68043]	L-alaninamide ChEBI	+	respiration
[Ref.: #68043]	L-alanine ChEBI	-	respiration
[Ref.: #68043]	L-alanylglycine ChEBI	-	respiration
[Ref.: #68043]	L-arabinose ChEBI	+	respiration
[Ref.: #68043]	L-arabinose ChEBI	+	builds acid from
[Ref.: #68043]	L-arabitol ChEBI	-	builds acid from
[Ref.: #68043]	L-asparagine ChEBI	-	respiration
[Ref.: #68043]	L-aspartate ChEBI	-	respiration
[Ref.: #68043]	L-fucose ChEBI	+	respiration
[Ref.: #68043]	L-fucose ChEBI	+	builds acid from
[Ref.: #68043]	L-glutamate ChEBI	-	respiration
[Ref.: #68043]	L-histidine ChEBI	-	respiration
[Ref.: #68043]	L-leucine ChEBI	-	respiration
[Ref.: #68043]	L-ornithine ChEBI	-	respiration
[Ref.: #68043]	L-phenylalanine ChEBI	-	respiration
[Ref.: #68043]	L-proline ChEBI	-	respiration
[Ref.: #68043]	L-pyroglutamate ChEBI	-	respiration
[Ref.: #68043]	L-rhamnose ChEBI	+	respiration
[Ref.: #68043]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #68043]	L-serine ChEBI	-	respiration
[Ref.: #68043]	L-sorbose ChEBI	+/-	builds acid from
[Ref.: #68043]	L-threonine ChEBI	-	respiration
[Ref.: #68043]	L-xylose ChEBI	+	builds acid from
[Ref.: #68043]	lactate ChEBI	+	respiration
[Ref.: #68043]	lactose ChEBI	-	builds acid from
[Ref.: #68043]	lactulose ChEBI	-	respiration
[Ref.: #68043]	malonate ChEBI	-	respiration
[Ref.: #68043]	maltose ChEBI	-	respiration
[Ref.: #68043]	maltose ChEBI	-	builds acid from
[Ref.: #68043]	melezitose ChEBI	+/-	builds acid from
[Ref.: #68043]	melibiose ChEBI	-	respiration
[Ref.: #68043]	melibiose ChEBI	+/-	builds acid from
[Ref.: #68043]	methanol ChEBI	-	assimilation
[Ref.: #68043]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #68043]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #68043]	methyl beta-D-glucopyranoside ChEBI	-	respiration
[Ref.: #68043]	methyl beta-D-xylopyranoside ChEBI	+/-	builds acid from
[Ref.: #68043]	methyl pyruvate ChEBI	+	respiration
[Ref.: #68043]	methylamine ChEBI	-	assimilation
[Ref.: #68043]	monomethyl succinate ChEBI	+	respiration
[Ref.: #68043]	myo-inositol ChEBI	+	respiration
[Ref.: #68043]	myo-inositol ChEBI	-	builds acid from
[Ref.: #68043]	N-acetylgalactosamine ChEBI	-	respiration
[Ref.: #68043]	N-acetylglucosamine ChEBI	-	respiration
[Ref.: #68043]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #68043]	phenylethylamine ChEBI	-	respiration
[Ref.: #68043]	potassium 2-dehydro-D-gluconate	+	builds acid from
[Ref.: #68043]	potassium 5-dehydro-D-gluconate	+	builds acid from
[Ref.: #68043]	potassium gluconate ChEBI	+	builds acid from
[Ref.: #68043]	propionate ChEBI	-	respiration
[Ref.: #68043]	putrescine ChEBI	-	respiration
[Ref.: #68043]	quinate ChEBI	-	respiration
[Ref.: #68043]	raffinose ChEBI	-	respiration
[Ref.: #68043]	raffinose ChEBI	+/-	builds acid from
[Ref.: #68043]	ribitol ChEBI	+	respiration
[Ref.: #68043]	ribitol ChEBI	-	builds acid from
[Ref.: #68043]	salicin ChEBI	-	builds acid from
[Ref.: #68043]	sebacic acid ChEBI	-	respiration
[Ref.: #68043]	starch ChEBI	+	builds acid from
[Ref.: #68043]	succinamate ChEBI	-	respiration
[Ref.: #68043]	succinate ChEBI	+	respiration
[Ref.: #68043]	sucrose ChEBI	-	respiration
[Ref.: #68043]	sucrose ChEBI	+/-	builds acid from
[Ref.: #68043]	thymidine ChEBI	-	respiration
[Ref.: #68043]	trehalose ChEBI	-	respiration
[Ref.: #68043]	trehalose ChEBI	+/-	builds acid from
[Ref.: #68043]	turanose ChEBI	-	respiration
[Ref.: #68043]	turanose ChEBI	+/-	builds acid from
[Ref.: #68043]	tween 40 ChEBI	-	respiration
[Ref.: #68043]	tween 80 ChEBI	-	respiration
[Ref.: #68043]	urea ChEBI	+	hydrolysis
[Ref.: #68043]	uridine ChEBI	-	respiration
[Ref.: #68043]	urocanic acid ChEBI	-	respiration
[Ref.: #68043]	xylitol ChEBI	+	respiration
[Ref.: #68043]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68043]	acid phosphatase	+	3.1.3.2
[Ref.: #68043]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68043]	catalase	+	1.11.1.6
[Ref.: #68043]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68043]	esterase (C 4)	+
[Ref.: #68043]	esterase Lipase (C 8)	+
[Ref.: #68043]	leucine arylamidase	+	3.4.11.1
[Ref.: #68043]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68043]	trypsin	+	3.4.21.4
[Ref.: #68043]	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #68043]

Fatty acid	Percentage
C18:1 w7c / C18:1 w6c	39.7
C16:1 w7c / C16:1 w6c	25.2
C19:0 cyclo w8c	11.9
C18:0	4.7
C12:0	4.4
C16:0	3.8
C18:1 w7c 11-Methyl	3.3
C18:0 3OH	3.3
C14:0 3OH/C16:1 ISO I	2.9
C14:0	0.8

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

[Ref.: #67770]	Sample type/isolated from	Lichen, Psoroma antarcticum
[Ref.: #67770]	Host species	Psoroma antarcticum
[Ref.: #67770]	Geographic location (country and/or sea, region)	King George Island
[Ref.: #67770]	Country	Antarctica
[Ref.: #67770]	Country ISO 3 Code	ATA
[Ref.: #67770]	Continent	Antarctica

[Ref.: #68043]	Sample type/isolated from	lichen, Psoroma antarcticum
[Ref.: #68043]	Geographic location (country and/or sea, region)	King George Island, Antarctica
[Ref.: #68043]	Geographic location	-62.2400°/-58.7433°
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence MK344722 (>99% sequence identity) for Lichenihabitans psoromatis subclade from Microbeatlas

Aquatic Samples	194
Soil Samples	709
Animal Samples	178
Plant Samples	370
Total Samples	1451

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.: #68043]	Lichenihabitans psoromatis strain PAMC29148 16S ribosomal RNA gene, partial sequence	MK344722	1413	GenBank ENA	2528642 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #68043]	Lichenihabitans psoromatis PAMC 29148	GCA_004323635	complete	GenBank ENA	2528642 tax ID
[Ref.: #66792]	Rhizobiales bacterium PAMC 29148	2528642.3	complete	PATRIC	2528642 tax ID	*

[Ref.: #67770]

GC-content

63.1 mol%

genome sequence analysis

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhizobiales bacterium PAMC 29148 PATRIC: 2528642.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizobiales bacterium PAMC 29148 PATRIC: 2528642.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.815	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.455	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.278	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	79.542	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.319	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	60.473	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 33311, KCCM 43293, PAMC 29148

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lichenihabitans psoromatis gen. nov., sp. nov., a member of a novel lineage (Lichenihabitantaceae fam. nov.) within the order of Rhizobiales isolated from Antarctic lichen.	Noh HJ, Baek K, Hwang CY, Shin SC, Hong SG, Lee YM	Int J Syst Evol Microbiol	10.1099/ijsem.0.003695	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 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68043

Hyun-Ju Noh, Kiwoon Baek, Chung Yeon Hwang, Seung Chul Shin, Soon Gyu Hong, Yung Mi Lee: Lichenihabitans psoromatis gen. nov., sp. nov., a member of a novel lineage (Lichenihabitantaceae fam. nov.) within the order of Rhizobiales isolated from Antarctic lichen. IJSEM 69: 3837 - 3842 2019 ( DOI 10.1099/ijsem.0.003695 )

#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) .

#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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Rhizobiales bacterium PAMC 29148

Rhizobiales bacterium PAMC 29148

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Change proposal