Strain identifier

BacDive ID: 132417

Type strain: Yes

Species: Paludisphaera borealis

Strain Designation: PX4

Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; PX4 <- I. S. Kulichevskaya

NCBI tax ID(s): 1387353 (species)

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General

@ref: 24206

BacDive-ID: 132417

DSM-Number: 28747

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, Gram-negative, sphere-shaped, colony-forming

description: Paludisphaera borealis PX4 is an aerobe, chemoorganotroph, Gram-negative bacterium that forms circular colonies and was isolated from boreal Sphagnum peat bog just above the oxic-anoxic interface.

NCBI tax id

  • NCBI tax id: 1387353
  • Matching level: species

strain history

  • @ref: 24206
  • history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; PX4 <- I. S. Kulichevskaya

doi: 10.13145/bacdive132417.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/planctomycetota
  • domain: Bacteria
  • phylum: Planctomycetota
  • class: Planctomycetia
  • order: Isosphaerales
  • family: Isosphaeraceae
  • genus: Paludisphaera
  • species: Paludisphaera borealis
  • full scientific name: Paludisphaera borealis Kulichevskaya et al. 2016

@ref: 24206

domain: Bacteria

phylum: Planctomycetes

class: Planctomycetia

order: Isosphaerales

family: Isosphaeraceae

genus: Paludisphaera

species: Paludisphaera borealis

full scientific name: Paludisphaera borealis Kulichevskaya et al. 2016

strain designation: PX4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
43814negative1.5-2.5 µmsphere-shapedno
69480negative99.994

colony morphology

  • @ref: 43814
  • colony size: 1-3 mm
  • colony color: Bright-pink
  • colony shape: circular
  • medium used: Agar-solidified M31

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43814Agar-solidified M31yes
24206PALUDISPHAERA BOREALIS MEDIUM (PX4) (DSMZ Medium 1557)yeshttps://mediadive.dsmz.de/medium/1557Name: PALUDISPHAERA BOREALIS MEDIUM (PX4) (DSMZ Medium 1557) Composition: Agar 18.0 g/l N-Acetylglucosamine 1.0 g/l MgSO4 x 7 H2O 0.594 g/l Na-ampicillin 0.2 g/l Nitrilotriacetic acid 0.2 g/l KH2PO4 0.1 g/l Glucose 0.1 g/l Yeast extract 0.1 g/l Peptone 0.1 g/l CaCl2 x 2 H2O 0.0668 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43814positivegrowth6-30
43814positiveoptimum15-25
24206positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43814positivegrowth3.5-6.5acidophile
43814positiveoptimum5-5.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43814
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 43814
  • type: chemoorganotroph

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.931

halophily

  • @ref: 43814
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-0.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4381416449alanine-assimilation
4381429016arginine-assimilation
4381422653asparagine-assimilation
4381435391aspartate-assimilation
4381416150benzoate-assimilation
4381427689decanoate-assimilation
4381416947citrate-assimilation
4381415356cysteine-assimilation
4381415748D-glucuronate-assimilation
4381424996lactate-assimilation
4381425115malate-assimilation
4381416236ethanol-assimilation
4381416842formaldehyde-assimilation
4381415740formate-assimilation
4381433984fucose-assimilation
4381429806fumarate-assimilation
4381428300glutamine-assimilation
4381417859glutaric acid-assimilation
4381417754glycerol-assimilation
4381415428glycine-assimilation
4381427570histidine-assimilation
4381424898isoleucine-assimilation
4381416283L-cystine-assimilation
4381425017leucine-assimilation
4381479285leucrose-assimilation
4381425094lysine-assimilation
4381429864mannitol-assimilation
438146731melezitose-assimilation
4381417790methanol-assimilation
4381416811methionine-assimilation
4381436405norleucine-assimilation
4381418257ornithine-assimilation
4381428044phenylalanine-assimilation
4381426271proline-assimilation
4381417272propionate-assimilation
4381416634raffinose-assimilation
4381417822serine-assimilation
4381427922sorbose-assimilation
4381428017starch-assimilation
4381430929tartrate-assimilation
4381426986threonine-assimilation
4381427897tryptophan-assimilation
4381418186tyrosine-assimilation
4381416199urea-assimilation
4381427266valine-assimilation
43814casein-hydrolysis
4381462968cellulose-hydrolysis
4381417029chitin-hydrolysis
4381437397chondroitin sulfate-hydrolysis
438145181fucoidan-hydrolysis
438146364laminarin-hydrolysis
43814peptone-hydrolysis
4381427941pullulan-hydrolysis
4381428017starch-hydrolysis
4381417057cellobiose+carbon source
4381428757fructose+carbon source
4381428260galactose+carbon source
4381417234glucose+carbon source
4381417716lactose+carbon source
4381417306maltose+carbon source
4381437684mannose+carbon source
4381428053melibiose+carbon source
43814506227N-acetylglucosamine+carbon source
4381415361pyruvate+carbon source
4381426546rhamnose+carbon source
4381433942ribose+carbon source
4381417814salicin+carbon source
4381430031succinate+carbon source
4381417992sucrose+carbon source
4381427082trehalose+carbon source
4381418222xylose+carbon source
438144853esculin+hydrolysis
438145291gelatin+hydrolysis
4381485248gellan gum+hydrolysis
438146452lichenin+hydrolysis
438149215spectinomycin+hydrolysis
4381437166xylan+hydrolysis
4381416449alanine+nitrogen source
4381416134ammonia+nitrogen source
4381422653asparagine+nitrogen source
43814506227N-acetylglucosamine+nitrogen source
4381417632nitrate+nitrogen source
43814peptone+nitrogen source
4381427266valine+nitrogen source
43814yeast extract+nitrogen source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4381417833gentamicinyesyes10000 µg (disc)
438146104kanamycinyesyes30000 µg (disc)
438147507neomycinyesyes10000 µg (disc)
4381428971ampicillinyesyes10000 µg (disc)
4381417076streptomycinyesyes10000 µg (disc)
4381417698chloramphenicolyesyes30000 µg (disc)
438146472lincomycinyesyes10000 µg (disc)
4381428368novobiocinyesyes30000 µg (disc)

enzymes

@refvalueactivityec
43814acid phosphatase+3.1.3.2
43814esterase (C 4)+
43814esterase Lipase (C 8)+
43814leucine arylamidase+3.4.11.1
43814valine arylamidase+
43814phosphohydrolase+
43814N-acetyl-beta-glucosaminidase+3.2.1.52
43814beta-galactosidase+3.2.1.23
43814alkaline phosphatase-3.1.3.1
43814cystine arylamidase-3.4.11.3
43814lipase (C 14)-
43814trypsin-3.4.21.4
43814chymotrypsin-3.4.4.5
43814alpha-galactosidase-3.2.1.22
43814beta-glucuronidase-3.2.1.31
43814alpha-fucosidase-3.2.1.51
43814alpha-mannosidase-3.2.1.24
43814catalase+1.11.1.6
43814cytochrome oxidase+1.9.3.1
43814urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
24206boreal Sphagnum peat bog just above the oxic-anoxic interfaceSphagnumYaroslavl region (58° 14' N 38° 12' E)RussiaRUSEurope58.233338.2
43814A boreal Sphagnum peat bog in ObukhovskoyeObukhovskoye, Yaroslavl regionRussiaRUSEurope58.2338.2

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Wetland (Swamp)
#Host#Plants#Moss
#Climate#Cold#Tundra
#Host#Plants#Peat moss

taxonmaps

  • @ref: 69479
  • File name: preview.99_6909.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_490;96_3244;97_3982;98_5082;99_6909&stattab=map
  • Last taxonomy: Paludisphaera borealis subclade
  • 16S sequence: KF467528
  • Sequence Identity:
  • Total samples: 1641
  • soil counts: 1225
  • aquatic counts: 250
  • animal counts: 95
  • plant counts: 71

Safety information

risk assessment

  • @ref: 24206
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24206
  • description: Paludisphaera borealis strain PX4 16S ribosomal RNA gene, complete sequence
  • accession: KF467528
  • length: 1503
  • database: ena
  • NCBI tax ID: 1387353

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paludisphaera borealis PX4GCA_001956985completencbi1387353
66792Paludisphaera borealis strain PX41387353.5plasmidpatric1387353
66792Paludisphaera borealis strain PX41387353.4plasmidpatric1387353
66792Paludisphaera borealis strain PX41387353.3completepatric1387353
66792Paludisphaera borealis PX42751185664completeimg1387353

GC content

@refGC-contentmethod
4381466
2420666sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes83no
flagellatedno91.196yes
gram-positiveno96.927yes
anaerobicno97.458yes
aerobicyes90.344yes
halophileno94.933yes
spore-formingno88.484no
glucose-utilyes86.149yes
thermophileno93.921no
motileno63.447no
glucose-fermentno87.579no

External links

@ref: 24206

culture collection no.: DSM 28747, VKM B-2904

straininfo link

  • @ref: 90757
  • straininfo: 400727

literature

  • topic: Phylogeny
  • Pubmed-ID: 26611145
  • title: Paludisphaera borealis gen. nov., sp. nov., a hydrolytic planctomycete from northern wetlands, and proposal of Isosphaeraceae fam. nov.
  • authors: Kulichevskaya IS, Ivanova AA, Suzina NE, Rijpstra WIC, Sinninghe Damste JS, Dedysh SN
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000799
  • year: 2015

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24206Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28747Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28747)
43814Irina S. Kulichevskaya, Anastasia A. Ivanova, Natalia E. Suzina, W. Irene C. Rijpstra, Jaap S. Sinninghe Damste, Svetlana N. DedyshPaludisphaera borealis gen. nov., sp. nov., a hydrolytic planctomycete from northern wetlands, and proposal of Isosphaeraceae fam. nov.10.1099/ijsem.0.000799IJSEM 66: 837-844 201626611145
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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
90757Reimer, 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-ID400727.1