Strain identifier

BacDive ID: 17487

Type strain: Yes

Species: Lysobacter niabensis

Strain Designation: GH34-4

Strain history: CIP <- 2007, DSMZ <- KACC <- H. Y. Weon, RDA, Suwon, Korea: strain GH34-4

NCBI tax ID(s): 380628 (species)

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General

@ref: 7454

BacDive-ID: 17487

DSM-Number: 18244

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, ovoid-shaped

description: Lysobacter niabensis GH34-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from green house soil.

NCBI tax id

  • NCBI tax id: 380628
  • Matching level: species

strain history

@refhistory
7454<- S.-W. Kwon, GH34-4 <- H.-Y. Weon
121286CIP <- 2007, DSMZ <- KACC <- H. Y. Weon, RDA, Suwon, Korea: strain GH34-4

doi: 10.13145/bacdive17487.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Lysobacter
  • species: Lysobacter niabensis
  • full scientific name: Lysobacter niabensis Weon et al. 2007

@ref: 7454

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter niabensis

full scientific name: Lysobacter niabensis Weon et al. 2007

strain designation: GH34-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31837negative3.5 µm0.5 µmovoid-shaped
121286negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7454R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
37776MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
121286CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7454positivegrowth25mesophilic
31837positivegrowth05-37
31837positiveoptimum28mesophilic
37776positivegrowth30mesophilic

culture pH

@refabilitytypepH
31837positivegrowth05-08
31837positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31837aerobe
121286obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
31837NaClpositivegrowth0-1 %
31837NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12128617632nitrate-reduction
12128616301nitrite-reduction

metabolite production

  • @ref: 121286
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31837catalase+1.11.1.6
31837gelatinase+
31837cytochrome oxidase+1.9.3.1
121286oxidase+
121286catalase+1.11.1.6
121286urease-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
121286-+++-++-++++---+++--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7454green house soilRepublic of KoreaKORAsia
121286Environment, Greenhouse soil cultivated with cucumberRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Greenhouse
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2870.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_1523;97_1817;98_2224;99_2870&stattab=map
  • Last taxonomy: Lysobacter
  • 16S sequence: DQ462461
  • Sequence Identity:
  • Total samples: 53688
  • soil counts: 37305
  • aquatic counts: 5500
  • animal counts: 3985
  • plant counts: 6898

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74541Risk group (German classification)
1212861Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31837
  • description: Lysobacter niabensis strain GH34-4 16S ribosomal RNA gene, partial sequence
  • accession: DQ462461
  • length: 1477
  • database: nuccore
  • NCBI tax ID: 380628

GC content

  • @ref: 31837
  • GC-content: 62.5

External links

@ref: 7454

culture collection no.: DSM 18244, CIP 109589, KACC 11587

straininfo link

  • @ref: 86485
  • straininfo: 297239

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17329782Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea.Weon HY, Kim BY, Kim MK, Yoo SH, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64473-02007DNA, Bacterial, DNA, Ribosomal, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Soil Microbiology, Xanthomonadaceae/chemistry/*classification/genetics/isolation & purificationGenetics
Phylogeny19329586Lysobacter oryzae sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.).Aslam Z, Yasir M, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.000588-02009Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny25406233Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil.Ngo HTT, Won K, Du J, Son HM, Park Y, Kook M, Kim KY, Jin FX, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.067397-02014Aglaia/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lysobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny25828767Lysobacter fragariae sp. nov. and Lysobacter rhizosphaerae sp. nov. isolated from rhizosphere of strawberry plant.Singh H, Du J, Ngo HT, Won K, Yang JE, Kim KY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0439-x2015Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fragaria/*microbiology, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Plant Roots/microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny26025168Lysobacter tyrosinelyticus sp. nov. isolated from Gyeryongsan national park soil.Du J, Singh H, Ngo HT, Won K, Kim KY, Yi THJ Microbiol10.1007/s12275-015-4729-92015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Parks, Recreational, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Phylogeny26763907Lysobacter terricola sp. nov., isolated from greenhouse soil.Kim SJ, Ahn JH, Weon HY, Hong SB, Seok SJ, Kim JS, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0008932016
Phylogeny27377971Lysobacter humi sp. nov., a bacterium isolated from rice field.Akter S, Huq MA, Yi THArch Microbiol10.1007/s00203-016-1262-02016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Lysobacter/*classification/genetics/growth & development/*isolation & purification, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/metabolismTranscriptome
Phylogeny27521144Lysobacter rhizophilus sp. nov., isolated from rhizosphere soil of mugunghwa, the national flower of South Korea.Yan ZF, Trinh H, Moya G, Lin P, Li CT, Kook MC, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0014222016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hibiscus/*microbiology, Lysobacter/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny34061342Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil.Kim KR, Kim KH, Khan SA, Kim HM, Han DM, Jeon COJ Microbiol10.1007/s12275-021-1156-y2021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Lysobacter/classification/genetics/*isolation & purification, Phospholipids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil/chemistry, *Soil MicrobiologyMetabolism
Phylogeny35076363Lysobacter terrestris sp. nov., isolated from soil.Woo CY, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0052042022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Lysobacter/classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7454Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18244)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18244
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
31837Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2810328776041
37776Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7350
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
86485Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297239.1StrainInfo: A central database for resolving microbial strain identifiers
121286Curators of the CIPCollection of Institut Pasteur (CIP 109589)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109589