Strain identifier

BacDive ID: 11654

Type strain: Yes

Species: Paenibacillus uliginis

Strain Designation: N3/975

Strain history: CIP <- 2011, U. Behrendt, ZALF, Münchenberg, Germany: strain N3/975

NCBI tax ID(s): 1313296 (strain), 683737 (species)

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General

@ref: 15998

BacDive-ID: 11654

DSM-Number: 21861

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, Gram-positive, rod-shaped

description: Paenibacillus uliginis N3/975 is a facultative anaerobe, spore-forming, Gram-positive bacterium that was isolated from fen peat soil of a nitrogen fertilization long-term experiment.

NCBI tax id

NCBI tax idMatching level
1313296strain
683737species

strain history

@refhistory
333552011, U. Behrendt, ZALF, Münchenberg, Germany: strain N3/975
15998<- U. Behrendt, Leibniz-Centre Agricultural Landscape Res. (ZALF), Müncheberg, Germany; N3/975
123711CIP <- 2011, U. Behrendt, ZALF, Münchenberg, Germany: strain N3/975

doi: 10.13145/bacdive11654.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Paenibacillus
  • species: Paenibacillus uliginis
  • full scientific name: Paenibacillus uliginis Behrendt et al. 2011

@ref: 15998

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus uliginis

full scientific name: Paenibacillus uliginis Behrendt et al. 2011

strain designation: N3/975

type strain: yes

Morphology

cell morphology

  • @ref: 123711
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15998CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 0.01 g/l Distilled water
33355MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123711CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
15998positivegrowth30
33355positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 123711
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 91.148

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
123711nitrate-reduction17632
123711nitrite-reduction16301

metabolite production

  • @ref: 123711
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123711oxidase+
123711catalase+1.11.1.6
123711urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123711-----+---+---+--+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123711+---+--+/--+/-++/-+-------+++-+++++/-+/-+/-+--+/-++-+/-+------+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
15998fen peat soil of a nitrogen fertilization long-term experimentBrandenburg, PaulinenaueGermanyDEUEurope
123711Environment, Soil, fen peat grasslandPaulinenaueGermanyDEUEurope2008

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Wetland (Swamp)

taxonmaps

  • @ref: 69479
  • File name: preview.99_51448.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_295;97_2107;98_2587;99_51448&stattab=map
  • Last taxonomy: Paenibacillus uliginis
  • 16S sequence: FN556467
  • Sequence Identity:
  • Total samples: 539
  • soil counts: 92
  • aquatic counts: 8
  • animal counts: 14
  • plant counts: 425

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
159981Risk group (German classification)
1237111Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15998
  • description: Paenibacillus uliginis partial 16S rRNA gene, type strain N3/975T
  • accession: FN556467
  • length: 1510
  • database: nuccore
  • NCBI tax ID: 1313296

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus uliginis N3/975GCA_900177425chromosomencbi1313296
66792Paenibacillus uliginis N3/9752529292568draftimg1313296

GC content

  • @ref: 15998
  • GC-content: 45.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes60.179no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.345yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes55.286no
69480spore-formingspore-formingAbility to form endo- or exosporesyes91.148no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.569no
69480flagellatedmotile2+Ability to perform flagellated movementyes86.296no

External links

@ref: 15998

culture collection no.: DSM 21861, LMG 24790, CIP 110295

straininfo link

  • @ref: 80878
  • straininfo: 359369

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20813476Characterization of heterotrophic nitrifying bacteria with respiratory ammonification and denitrification activity--description of Paenibacillus uliginis sp. nov., an inhabitant of fen peat soil and Paenibacillus purispatii sp. nov., isolated from a spacecraft assembly clean room.Behrendt U, Schumann P, Stieglmeier M, Pukall R, Augustin J, Sproer C, Schwendner P, Moissl-Eichinger C, Ulrich ASyst Appl Microbiol10.1016/j.syapm.2010.07.0042010*Air Microbiology, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Denitrification, Environment, Controlled, Molecular Sequence Data, *Nitrification, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil Microbiology, SpacecraftGenetics
Phylogeny25288280Paenibacillus lemnae sp. nov., an endophytic bacterium of duckweed (Lemna aequinoctialis).Kittiwongwattana C, Thawai CInt J Syst Evol Microbiol10.1099/ijs.0.067876-02014Araceae/*microbiology, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, ThailandGenetics
Phylogeny35059831Konateibacter massiliensis gen. nov. sp. nov. and Paenibacillus faecalis sp. nov., Two New Species Isolated from the Stool Samples of Infants Suffering from Marasmus.Sarr M, Tall ML, Ben Khedher M, Pham TP, Mbaye B, Camara A, Armstrong N, Chartier C, Fadlane A, Sokhna C, Raoult D, Tidjani Alou M, Million MCurr Microbiol10.1007/s00284-021-02757-62022DNA, Bacterial/genetics, Humans, *Paenibacillus/genetics, Phylogeny, *Protein-Energy Malnutrition, RNA, Ribosomal, 16S/geneticsPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15998Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21861)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21861
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
33355Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8139
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
80878Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID359369.1StrainInfo: A central database for resolving microbial strain identifiers
123711Curators of the CIPCollection of Institut Pasteur (CIP 110295)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110295