Psychromicrobium silvestre (DSM 102047, LMG 29369, AK20-18)

Name: Psychromicrobium silvestre (DSM 102047, LMG 29369, AK20-18)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133081

Type strain

Strain Designation AK20-18

Culture col. no. DSM 102047 LMG 29369 AK20-18

NCBI tax ID(s) 1645614

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Psychromicrobium silvestre AK20-18 is an aerobe, Gram-variable, rod-shaped prokaryote that was isolated from alpine forest soil.

Gram-variable rod-shaped aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406036

LMG 29369,DSM 102047

@ref 20215

Last LPSN update 2025-12-16 10:01:41

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Psychromicrobium

Species Psychromicrobium silvestre

Full scientific name Psychromicrobium silvestre Schumann et al. 2017

BacDive ID	Other strains from **Psychromicrobium silvestre** (1)	Type strain
133080	P. silvestre AM20-54, DSM 102046, LMG 29368

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
25235	variable	0.9-1.1 µm	0.5-0.6 µm	rod-shaped
25235				coccus-shaped
125438					93.5

Colony morphology

@ref	Colony size	Colony color	Incubation period	Medium used
25235	1 mm	creamy white	4 days	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
25235	Reasoner's 2A agar (R2A)
25235	nutritient agar (NA)		0.5 % peptone, 0.3 % meat extract, 1.5 % agar; pH 7
25235	trypticase soy agar (TSA)		1.5 % casein peptone, 0.5 % soy peptone, 0.5 % sodium chloride, 1.5 % agar; pH 7
24869	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24869	positive	growth	25	mesophilic
25235	positive	growth	5-30
25235	positive	optimum	20-30
25235	negative	growth	35

Culture pH

@ref	Ability	Type	PH	PH range
25235	positive	optimum	6.0-7.0
25235	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
25235	aerobe
25235	microaerophile

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25235	NaCl	positive	growth	0.0-5.0 %(w/v)
25235	NaCl		optimum	0.0-3.0 %(w/v)

Murein

@ref	Murein short key	Type
24869	A11.27	A3alpha L-Lys-L-Thr-L-Ala₂

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25235	17128 ChEBI	adipate	-	assimilation
25235	62968 ChEBI	cellulose	-	hydrolysis
25235	17029 ChEBI	chitin	-	assimilation
25235	17634 ChEBI	D-glucose	+	assimilation
25235	16899 ChEBI	D-mannitol	+	assimilation
25235	16024 ChEBI	D-mannose	+	assimilation
25235	27689 ChEBI	decanoate	+	assimilation
25235	16991 ChEBI	dna	-	hydrolysis
25235	4853 ChEBI	esculin	+	hydrolysis
25235	5291 ChEBI	gelatin	+	hydrolysis
25235	17234 ChEBI	glucose	-	fermentation
25235	30849 ChEBI	L-arabinose	-	assimilation
25235	17716 ChEBI	lactose	+	assimilation
25235	25115 ChEBI	malate	+	assimilation
25235	17306 ChEBI	maltose	+	assimilation
25235	17632 ChEBI	nitrate	-	reduction
25235	18401 ChEBI	phenylacetate	+	assimilation
25235	32032 ChEBI	potassium gluconate	+	assimilation
25235		skimmed milk	+	hydrolysis
25235	53258 ChEBI	sodium citrate	+	assimilation
25235	28017 ChEBI	starch	-	hydrolysis
25235	53426 ChEBI	tween 80	+	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25235	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Methylred-test
25235	17234 ChEBI	glucose	-

Enzymes

@ref	Value	Activity	Ec
25235	acid phosphatase	+	3.1.3.2
25235	alkaline phosphatase	+	3.1.3.1
25235	alpha-chymotrypsin	-	3.4.21.1
25235	alpha-fucosidase	-	3.2.1.51
25235	alpha-galactosidase	-	3.2.1.22
25235	alpha-glucosidase	+	3.2.1.20
25235	alpha-mannosidase	+	3.2.1.24
25235	amylase	-
25235	arginine dihydrolase	-	3.5.3.6
25235	beta-galactosidase	+	3.2.1.23
25235	beta-glucosidase	+	3.2.1.21
25235	beta-glucuronidase	-	3.2.1.31
25235	catalase	+	1.11.1.6
25235	cellulase	-	3.2.1.4
25235	cystine arylamidase	-	3.4.11.3
25235	cytochrome oxidase	-	1.9.3.1
25235	DNase	-
25235	esterase Lipase (C 8)	+
25235	leucine arylamidase	+	3.4.11.1
25235	lipase (C 14)	+
25235	naphthol-AS-BI-phosphohydrolase	+
25235	pyrazinamidase	+	3.5.1.B15
25235	pyrrolidonyl arylamidase	+	3.4.19.3
25235	trypsin	+	3.4.21.4
25235	urease	-	3.5.1.5
25235	valine arylamidase	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Climate	#Cold	#Alpine
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture temperature
24869	alpine forest soil	South Tyrol, Klobenstein/Ritten (46° 32' 38.1'' N 011° 28' 16.1'' E)	Italy	ITA	Europe	46.5439	11.4711 46.5439/11.4711
25235	forest soil collected in Klo- benstein/Ritten at 1200 m above sea level							R2A agar	amended with cycloheximide	20

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24869	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1340829v1 assembly for Psychromicrobium silvestre DSM 102047	contig	GCA_013408295	1645614.3	2821010246	1645614	76.54

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24869	Psychromicrobium silvestre strain AK20-18 16S ribosomal RNA gene, partial sequence	KP899144	1368		1645614
124043	Psychromicrobium silvestre strain DSM 102047 16S ribosomal RNA gene, partial sequence.	MG831935	1491		1645614

GC content

@ref	GC-content (mol%)	Method
24869	59.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Psychromicrobium silvestre DSM 102047
NCBI: GCA_013408295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	81.00	no
125439	motility	BacteriaNetⓘ	no	85.50	no
125439	gram_stain	BacteriaNetⓘ	positive	67.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	77.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Psychromicrobium silvestre strain DSM 102047
PATRIC: 1645614.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	76.54	yes
125438	anaerobic	anaerobicⓘ	no	98.29	yes
125438	spore-forming	spore-formingⓘ	no	76.16	no
125438	aerobic	aerobicⓘ	yes	86.49	no
125438	thermophilic	thermophileⓘ	no	96.83	yes
125438	flagellated	motile2+ⓘ	no	93.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Psychromicrobium lacuslunae sp. nov., isolated from a high altitude lake.	Kiran S, Schumann P, Busse HJ, Sproer C, Rana A, Pal M, Korpole S, Tewari R, Gulati A	Int J Syst Evol Microbiol	10.1099/ijsem.0.002997	2018
Phylogeny	Psychromicrobium silvestre gen. nov., sp. nov., an actinobacterium isolated from alpine forest soils.	Schumann P, Zhang DC, Franca L, Albuquerque L, da Costa MS, Margesin R	Int J Syst Evol Microbiol	10.1099/ijsem.0.001677	2017

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 )
#24869	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102047
#25235	P. Z. Schumann, De-Chao,França, Luís,Albuquerque, Luciana,da Costa, Milton S,Margesin, Rosa: Psychromicrobium silvestre gen. nov., sp. nov., an actinobacterium isolated from alpine forest soils. IJSEM 67: 640 - 645 2017 ( DOI 10.1099/ijsem.0.001677 , PubMed 27902317 )
#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) .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Psychromicrobium silvestre (DSM 102047, LMG 29369, AK20-18)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Murein

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013408295

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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