Strain identifier

BacDive ID: 159679

Type strain: Yes

Species: Rhodoluna limnophila

Strain Designation: 27D-LEPI

Strain history: M. W. Hahn; Res. Dept. for Limnol., Univ. of Innsbruck, Austria; 27D-LEPI.

NCBI tax ID(s): 232537 (species)

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General

@ref: 66530

BacDive-ID: 159679

DSM-Number: 107804

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, Gram-positive, rod-shaped, colony-forming

description: Rhodoluna limnophila 27D-LEPI is an aerobe, chemoorganotroph, Gram-positive bacterium that forms circular colonies and was isolated from freshwater.

NCBI tax id

  • NCBI tax id: 232537
  • Matching level: species

strain history

@refhistory
66530<- M. Hahn, University of Innsbruck Research Institute for Limnology; 27D-LEPI <- J. Schmidt
67770M. W. Hahn; Res. Dept. for Limnol., Univ. of Innsbruck, Austria; 27D-LEPI.

doi: 10.13145/bacdive159679.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Rhodoluna
  • species: Rhodoluna limnophila
  • full scientific name: Rhodoluna limnophila Pitt et al. 2019

  • synonyms

    • @ref: 20215
    • synonym: Rhodoluna limnophila

@ref: 66530

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Microbacteriaceae

genus: Rhodoluna

species: Rhodoluna limnophila

full scientific name: Rhodoluna limnophila Hahn 2009

strain designation: 27D-LEPI

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
68248positive0.5 µm0.3 µmrod-shaped
69480no93.5

colony morphology

  • @ref: 68248
  • colony color: light red
  • colony shape: circular
  • medium used: NSY agar

Culture and growth conditions

culture medium

  • @ref: 66530
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: 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

@refgrowthtypetemperature
66530positivegrowth22
67770positivegrowth25
68248positivegrowth6-34

Physiology and metabolism

oxygen tolerance

  • @ref: 68248
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 68248
  • type: chemoorganotroph

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 90.053

halophily

  • @ref: 68248
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-0.4 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6824817309pectin+assimilation
6824878697D-fructose 6-phosphate+assimilation
6824815824D-fructose+assimilation
6824832323glucuronamide+assimilation
6824817925alpha-D-glucose+assimilation
6824817992sucrose+assimilation
6824832528turanose+assimilation
6824813705acetoacetate+assimilation
6824817306maltose+assimilation
6824812936D-galactose+assimilation
6824828053melibiose+assimilation
6824815748D-glucuronate-assimilation
6824818024D-galacturonic acid-assimilation
6824815971L-histidine-assimilation
68248D-lactic acid methyl ester-assimilation
6824816467L-arginine-assimilation
6824828066gentiobiose-assimilation
6824862345L-rhamnose-assimilation
6824815588D-malate-assimilation
6824829985L-glutamate-assimilation
6824815895D-galactonic acid lactone-assimilation
6824817057cellobiose-assimilation
6824817521(-)-quinic acid-assimilation
68248181014-hydroxyphenylacetic acid-assimilation
6824815740formate-assimilation
6824870744glycyl-L-proline-assimilation
68248L-lactate-assimilation
6824818183L-pyroglutamic acid-assimilation
68248645522-hydroxybutyrate-assimilation
68248506227N-acetyl-D-glucosamine-assimilation
6824837657methyl D-glucoside-assimilation
6824828037n-acetyl-D-galactosamine-assimilation
6824817814D-salicin-assimilation
6824833801D-saccharate-assimilation
6824863154N-acetyl-beta-D-mannosamine-assimilation
68248n-acetyl-neuraminic acid-assimilation
6824873706bromosuccinate-assimilation
682485291gelatin-assimilation
6824851850methyl pyruvate-assimilation
6824864552alpha-hydroxybutyrate-assimilation
6824816523D-serine-assimilation
6824817115L-serine-assimilation
682488295beta-hydroxybutyrate-assimilation
6824816947citrate-assimilation
6824814314D-glucose 6-phosphate+/-assimilation
682488391D-gluconate+/-assimilation
6824815589L-malate+/-assimilation
6824817164stachyose+/-assimilation
6824827082trehalose+/-assimilation

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68248C13:00.9
    68248C14:08.4
    68248C16:07
    68248C12:0 iso0.5
    68248C13:0 anteiso3.5
    68248C14:0 iso30.8
    68248C15:0 iso1.6
    68248C15:0 anteiso35.9
    68248C15:1 anteiso A1.6
    68248C16:0 iso7.9
    68248C17:0 anteiso0.8
  • type of FA analysis: whole cell analysis
  • incubation medium: NSY
  • incubation time: 3
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA40
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitudeenrichment culture
66530freshwaterLeopoldskronerweiher, SalzburgAustriaAUTEurope
67770Surface water from the Leopoldskroner Weiher, a small artificial freshwater pondSalzburgAustriaAUTEurope
68248watersurfaceLeopoldskroner Weiher, SalzburgAustriaAUTEurope2017-11-0147.788313.0367NSY agar

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_26189.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1704;97_2040;98_19670;99_26189&stattab=map
  • Last taxonomy: Rhodoluna limnophila subclade
  • 16S sequence: MK951675
  • Sequence Identity:
  • Total samples: 3087
  • soil counts: 110
  • aquatic counts: 2284
  • animal counts: 677
  • plant counts: 16

Sequence information

16S sequences

  • @ref: 66530
  • description: Rhodoluna limnophila strain 27D-LEPI 16S ribosomal RNA gene, partial sequence
  • accession: MK951675
  • length: 1386
  • database: nuccore
  • NCBI tax ID: 232537

Genome sequences

  • @ref: 66792
  • description: Rhodoluna limnophila 27D-LEPI
  • accession: GCA_005845365
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 232537

GC content

@refGC-contentmethod
6824854genome sequence analysis
6777053.7genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes84.123no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no90.197yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes66.389yes
69480spore-formingspore-formingAbility to form endo- or exosporesno90.053no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno86.465no
69480flagellatedmotile2+Ability to perform flagellated movementno93.5no

External links

@ref: 66530

culture collection no.: DSM 107804, JCM 32926

straininfo link

  • @ref: 112150
  • straininfo: 398667

literature

  • topic: Phylogeny
  • Pubmed-ID: 31535962
  • title: Rhodoluna limnophila sp. nov., a bacterium with 1.4 Mbp genome size isolated from freshwater habitats located in Salzburg, Austria.
  • authors: Pitt A, Schmidt J, Koll U, Hahn MW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003720
  • year: 2019
  • mesh: Actinobacteria/*classification/isolation & purification, Austria, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Genome Size, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
66530Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107804Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107804)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68248Alexandra Pitt, Johanna Schmidt, Ulrike Koll and Martin W. HahnRhodoluna limnophila sp. nov., a bacterium with 1.4 Mbp genome size isolated from freshwater habitats located in Salzburg, Austria10.1099/ijsem.0.003720IJSEM 69: 3946-3954 2019
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
112150Reimer, 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 identifiers10.60712/SI-ID398667.1