Lichenihabitans psoromatis (KCCM 43293, JCM 33311, PAMC 29148)

Name: Lichenihabitans psoromatis (KCCM 43293, JCM 33311, PAMC 29148)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164516

Type strain

Culture col. no. KCCM 43293 JCM 33311 PAMC 29148

NCBI tax ID(s) 2528642

Special Collections JCM Literature strains

History Y. M. Lee; KOPRI, South Korea; PAMC 29148.

Links

Lichenihabitans psoromatis JCM 33311 is a facultative anaerobe, chemoheterotroph, psychrophilic prokaryote that forms circular colonies and was isolated from Lichen, Psoroma antarcticum.

Gram-negative rod-shaped colony-forming facultative anaerobe chemoheterotroph psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 132257

JCM 33311

@ref 20215

Last LPSN update 2026-02-09 11:39:52

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Lichenihabitantaceae

Genus Lichenihabitans

Species Lichenihabitans psoromatis

Full scientific name Lichenihabitans psoromatis Noh et al. 2019

BacDive ID	Other strains from **Lichenihabitans psoromatis** (1)	Type strain
164515	L. psoromatis JCM 33310, KCCM 43292

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
68043	negative	0.9-3.4 µm	0.9-1.6 µm	rod-shaped
125438	negative					97.815

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
68043	pink	circular	14 days	Reasoner's 2A agar (R2A)

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	15	psychrophilic
68043	positive	growth	4-20	psychrophilic
68043	positive	optimum	15	psychrophilic

Culture pH

@ref	Ability	Type	PH
68043	positive	optimum	6.5
68043	positive	growth	5.5-7.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
68043	facultative anaerobe
125439	obligate aerobe	98.9

Nutrition type

68043

Typechemoheterotroph

Spore formation

@ref	Spore formation	Confidence
125439		92.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68043	NaCl	positive	optimum	0 %(w/v)

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68043		2,3-butanediol	-	respiration
68043	64552 ChEBI	2-hydroxybutyrate	-	respiration
68043	16763 ChEBI	2-oxobutanoate	-	respiration
68043	16810 ChEBI	2-oxoglutarate	-	respiration
68043	28644 ChEBI	2-oxopentanoate	-	respiration
68043	37054 ChEBI	3-hydroxybutyrate	-	respiration
68043	18240 ChEBI	4-hydroxy-L-proline	-	respiration
68043	16724 ChEBI	4-hydroxybutyrate	-	respiration
68043	18101 ChEBI	4-hydroxyphenylacetic acid	-	respiration
68043	30089 ChEBI	acetate	-	respiration
68043	40585 ChEBI	alpha-cyclodextrin	-	respiration
68043	17925 ChEBI	alpha-D-glucose	+	respiration
68043	36219 ChEBI	alpha-lactose	-	respiration
68043	27613 ChEBI	amygdalin	-	builds acid from
68043	18305 ChEBI	arbutin	-	builds acid from
68043	73706 ChEBI	bromosuccinate	-	respiration
68043	17057 ChEBI	cellobiose	+	respiration
68043	17057 ChEBI	cellobiose	-	builds acid from
68043	16383 ChEBI	cis-aconitate	-	respiration
68043	16947 ChEBI	citrate	-	respiration
68043	15570 ChEBI	D-alanine	-	respiration
68043	17108 ChEBI	D-arabinose	+	builds acid from
68043	18333 ChEBI	D-arabitol	+	respiration
68043	18333 ChEBI	D-arabitol	+	builds acid from
68043	15824 ChEBI	D-fructose	+	respiration
68043	15824 ChEBI	D-fructose	+	builds acid from
68043	28847 ChEBI	D-fucose	+	builds acid from
68043	15895 ChEBI	D-galactonic acid lactone	+	respiration
68043	12936 ChEBI	D-galactose	+	respiration
68043	12936 ChEBI	D-galactose	+/-	builds acid from
68043	18024 ChEBI	D-galacturonic acid	-	respiration
68043	30612 ChEBI	D-glucarate	-	respiration
68043	8391 ChEBI	D-gluconate	+	respiration
68043	17784 ChEBI	D-glucosaminic acid	-	respiration
68043	17634 ChEBI	D-glucose	+/-	builds acid from
68043	14314 ChEBI	D-glucose 6-phosphate	-	respiration
68043	15748 ChEBI	D-glucuronate	-	respiration
68043	62318 ChEBI	D-lyxose	+	builds acid from
68043	16899 ChEBI	D-mannitol	+	respiration
68043	16899 ChEBI	D-mannitol	+/-	builds acid from
68043	16024 ChEBI	D-mannose	+	respiration
68043	16024 ChEBI	D-mannose	+/-	builds acid from
68043	27605 ChEBI	D-psicose	+	respiration
68043	16988 ChEBI	D-ribose	+	builds acid from
68043	16523 ChEBI	D-serine	-	respiration
68043	17924 ChEBI	D-sorbitol	+	respiration
68043	17924 ChEBI	D-sorbitol	-	builds acid from
68043	16443 ChEBI	D-tagatose	+/-	builds acid from
68043	65327 ChEBI	D-xylose	+	builds acid from
68043	23652 ChEBI	dextrin	-	respiration
68043	17045 ChEBI	dinitrogen oxide	-	assimilation
68043	17126 ChEBI	DL-carnitine	-	respiration
68043	17113 ChEBI	erythritol	+	respiration
68043	17113 ChEBI	erythritol	+/-	builds acid from
68043		esculin ferric citrate	+	builds acid from
68043	16000 ChEBI	ethanolamine	-	respiration
68043	16842 ChEBI	formaldehyde	-	assimilation
68043	15740 ChEBI	formate	-	assimilation
68043	15740 ChEBI	formate	-	respiration
68043	16813 ChEBI	galactitol	-	builds acid from
68043	16865 ChEBI	gamma-aminobutyric acid	-	respiration
68043	28066 ChEBI	gentiobiose	-	respiration
68043	28066 ChEBI	gentiobiose	+/-	builds acid from
68043	29042 ChEBI	glucose 1-phosphate	-	respiration
68043	32323 ChEBI	glucuronamide	-	respiration
68043	17754 ChEBI	glycerol	+	respiration
68043	17754 ChEBI	glycerol	+	builds acid from
68043	14336 ChEBI	glycerol 1-phosphate	-	respiration
68043	28087 ChEBI	glycogen	-	respiration
68043	28087 ChEBI	glycogen	+	builds acid from
68043	73804 ChEBI	glycyl L-aspartic acid	-	respiration
68043	73784 ChEBI	glycyl-l-glutamate	-	respiration
68043	17596 ChEBI	inosine	-	respiration
68043	15443 ChEBI	inulin	+/-	builds acid from
68043	17240 ChEBI	itaconate	-	respiration
68043	21217 ChEBI	L-alaninamide	+	respiration
68043	16977 ChEBI	L-alanine	-	respiration
68043	73786 ChEBI	L-alanylglycine	-	respiration
68043	30849 ChEBI	L-arabinose	+	respiration
68043	30849 ChEBI	L-arabinose	+	builds acid from
68043	18403 ChEBI	L-arabitol	-	builds acid from
68043	17196 ChEBI	L-asparagine	-	respiration
68043	29991 ChEBI	L-aspartate	-	respiration
68043	18287 ChEBI	L-fucose	+	respiration
68043	18287 ChEBI	L-fucose	+	builds acid from
68043	29988 ChEBI	L-glutamate	-	respiration
68043	15971 ChEBI	L-histidine	-	respiration
68043	15603 ChEBI	L-leucine	-	respiration
68043	15729 ChEBI	L-ornithine	-	respiration
68043	17295 ChEBI	L-phenylalanine	-	respiration
68043	17203 ChEBI	L-proline	-	respiration
68043	57606 ChEBI	L-pyroglutamate	-	respiration
68043	62345 ChEBI	L-rhamnose	+	respiration
68043	62345 ChEBI	L-rhamnose	-	builds acid from
68043	17115 ChEBI	L-serine	-	respiration
68043	17266 ChEBI	L-sorbose	+/-	builds acid from
68043	16857 ChEBI	L-threonine	-	respiration
68043	65328 ChEBI	L-xylose	+	builds acid from
68043	24996 ChEBI	lactate	+	respiration
68043	17716 ChEBI	lactose	-	builds acid from
68043	6359 ChEBI	lactulose	-	respiration
68043	15792 ChEBI	malonate	-	respiration
68043	17306 ChEBI	maltose	-	respiration
68043	17306 ChEBI	maltose	-	builds acid from
68043	6731 ChEBI	melezitose	+/-	builds acid from
68043	28053 ChEBI	melibiose	-	respiration
68043	28053 ChEBI	melibiose	+/-	builds acid from
68043	17790 ChEBI	methanol	-	assimilation
68043	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
68043	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
68043	320055 ChEBI	methyl beta-D-glucopyranoside	-	respiration
68043	74863 ChEBI	methyl beta-D-xylopyranoside	+/-	builds acid from
68043	51850 ChEBI	methyl pyruvate	+	respiration
68043	16830 ChEBI	methylamine	-	assimilation
68043	75146 ChEBI	monomethyl succinate	+	respiration
68043	17268 ChEBI	myo-inositol	+	respiration
68043	17268 ChEBI	myo-inositol	-	builds acid from
68043	28800 ChEBI	N-acetylgalactosamine	-	respiration
68043	59640 ChEBI	N-acetylglucosamine	-	respiration
68043	59640 ChEBI	N-acetylglucosamine	-	builds acid from
68043	50048 ChEBI	phenylethylamine	-	respiration
68043		potassium 2-dehydro-D-gluconate	+	builds acid from
68043		potassium 5-dehydro-D-gluconate	+	builds acid from
68043	32032 ChEBI	potassium gluconate	+	builds acid from
68043	17272 ChEBI	propionate	-	respiration
68043	17148 ChEBI	putrescine	-	respiration
68043	26490 ChEBI	quinate	-	respiration
68043	16634 ChEBI	raffinose	-	respiration
68043	16634 ChEBI	raffinose	+/-	builds acid from
68043	15963 ChEBI	ribitol	+	respiration
68043	15963 ChEBI	ribitol	-	builds acid from
68043	17814 ChEBI	salicin	-	builds acid from
68043	41865 ChEBI	sebacic acid	-	respiration
68043	28017 ChEBI	starch	+	builds acid from
68043	143136 ChEBI	succinamate	-	respiration
68043	30031 ChEBI	succinate	+	respiration
68043	17992 ChEBI	sucrose	-	respiration
68043	17992 ChEBI	sucrose	+/-	builds acid from
68043	17748 ChEBI	thymidine	-	respiration
68043	27082 ChEBI	trehalose	-	respiration
68043	27082 ChEBI	trehalose	+/-	builds acid from
68043	32528 ChEBI	turanose	-	respiration
68043	32528 ChEBI	turanose	+/-	builds acid from
68043	53423 ChEBI	tween 40	-	respiration
68043	53426 ChEBI	tween 80	-	respiration
68043	16199 ChEBI	urea	+	hydrolysis
68043	16704 ChEBI	uridine	-	respiration
68043	27248 ChEBI	urocanic acid	-	respiration
68043	17151 ChEBI	xylitol	+	respiration
68043	17151 ChEBI	xylitol	-	builds acid from

Enzymes

@ref	Value	Activity	Ec
68043	acid phosphatase	+	3.1.3.2
68043	alkaline phosphatase	+	3.1.3.1
68043	catalase	+	1.11.1.6
68043	cytochrome oxidase	+	1.9.3.1
68043	esterase (C 4)	+
68043	esterase Lipase (C 8)	+
68043	leucine arylamidase	+	3.4.11.1
68043	naphthol-AS-BI-phosphohydrolase	+
68043	trypsin	+	3.4.21.4
68043	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@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

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
67770	Lichen, Psoroma antarcticum	Psoroma antarcticum	King George Island	Antarctica	ATA	Antarctica
68043	lichen, Psoroma antarcticum		King George Island, Antarctica				-62.24	-58.7433 -62.24/-58.7433

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
68043	ASM432363v1 assembly for Lichenihabitans psoromatis PAMC 29148	complete	GCA_004323635	2528642.3	2873554119	2528642	97.96

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
68043	Lichenihabitans psoromatis strain PAMC29148 16S ribosomal RNA gene, partial sequence	MK344722	1413		2528642

GC content

@ref	GC-content (mol%)	Method
67770	63.1	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Lichenihabitans psoromatis PAMC 29148
NCBI: GCA_004323635

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.90	no
125439	motility	BacteriaNetⓘ	no	58.70	no
125439	gram_stain	BacteriaNetⓘ	negative	88.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizobiales bacterium PAMC 29148
PATRIC: 2528642.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.82	yes
125438	anaerobic	anaerobicⓘ	no	94.46	yes
125438	spore-forming	spore-formingⓘ	no	88.28	no
125438	aerobic	aerobicⓘ	yes	79.54	yes
125438	thermophilic	thermophileⓘ	no	96.32	yes
125438	flagellated	motile2+ⓘ	yes	60.47	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Biotechnology	Lichens and Health-Trends and Perspectives for the Study of Biodiversity in the Antarctic Ecosystem.	Prado T, Degrave WMS, Duarte GF.	J Fungi (Basel)	10.3390/jof11030198	2025
	Diversity and Physiological Characteristics of Antarctic Lichens-Associated Bacteria.	Noh HJ, Park Y, Hong SG, Lee YM.	Microorganisms	10.3390/microorganisms9030607	2021
Metabolism	Bacteriomic Profiles of Rock-Dwelling Lichens from the Venezuelan Guiana Shield and the South African Highveld Plateau.	He Z, Naganuma T, Melville HIAS.	Microorganisms	10.3390/microorganisms12020290	2024
Phylogeny	Microbial occurrence and symbiont detection in a global sample of lichen metagenomes.	Tagirdzhanova G, Saary P, Cameron ES, Allen CCG, Garber AI, Escandon DD, Cook AT, Goyette S, Nogerius VT, Passo A, Mayrhofer H, Holien H, Tonsberg T, Stein LY, Finn RD, Spribille T.	PLoS Biol	10.1371/journal.pbio.3002862	2024
	Microbiome in Cladonia squamosa Is Vertically Stratified According to Microclimatic Conditions.	Noh HJ, Lee YM, Park CH, Lee HK, Cho JC, Hong SG.	Front Microbiol	10.3389/fmicb.2020.00268	2020
Genetics	What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen.	Greshake Tzovaras B, Segers FHID, Bicker A, Dal Grande F, Otte J, Anvar SY, Hankeln T, Schmitt I, Ebersberger I.	Genome Biol Evol	10.1093/gbe/evaa049	2020
	A novel bacteriobiont of the Arctic lichen Flavocetraria nivalis, Lichenifustis flavocetrariae gen. nov, sp. nov. demonstrating hydrolytic properties and containing a full set of the Calvin-Benson-Bassham cycle genes.	Pankratov TA, Samylina OS, Tikhonova EN, Ianutsevich EA, Avtukh AN, Lee YM.	Arch Microbiol	10.1007/s00203-023-03577-x	2023
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 )
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Lichenihabitans psoromatis (KCCM 43293, JCM 33311, PAMC 29148)

Name and taxonomic classification