Strain identifier

BacDive ID: 132482

Type strain: Yes

Species: Nocardioides zeicaulis

Strain Designation: JM-601

Strain history: CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-601

NCBI tax ID(s): 1776857 (species)

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General

@ref: 24271

BacDive-ID: 132482

DSM-Number: 101604

keywords: 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, rod-shaped, colony-forming

description: Nocardioides zeicaulis JM-601 is an obligate aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from stem tissue of healthy 10-week-old, field-grown maize , isolated as an endophyte.

NCBI tax id

  • NCBI tax id: 1776857
  • Matching level: species

strain history

@refhistory
24271<- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; JM-601 <- J. McInroy
67770CCM 8654 <-- S. P. Glaeser; Justus-Liebig-Univ. Giessen, Germany; JM-601 <-- J. A. McInroy; Auburn Univ., USA.
124030CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-601

doi: 10.13145/bacdive132482.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides zeicaulis
  • full scientific name: Nocardioides zeicaulis Kämpfer et al. 2016

@ref: 24271

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides zeicaulis

full scientific name: Nocardioides zeicaulis Kämpfer et al. 2016

strain designation: JM-601

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
43685positive1.5-2-5 µm0.9-1.5 µmrod-shapedno
124030positiverod-shapedno

colony morphology

  • @ref: 43685
  • colony size: 0.5 mm
  • colony color: Yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: TSA agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24271TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
42168MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
43685Trypticase Soy Agar (TSA)no
43685Trypticase Soy Agar (TSA)yes
24271R2A 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
124030CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
42168positivegrowth30mesophilic
43685positivegrowth10-37
43685positiveoptimum28mesophilic
24271positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
43685positivegrowth5.5-8
43685positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43685
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 43685
  • type of spore: endospore
  • spore formation: no

halophily

  • @ref: 43685
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 1-3 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4368517128adipate-assimilation
4368518305arbutin-assimilation
4368527689decanoate-assimilation
4368515963ribitol-assimilation
4368517924D-sorbitol-assimilation
4368525115malate-assimilation
4368517268myo-inositol-assimilation
4368528037N-acetylgalactosamine-assimilation
43685506227N-acetylglucosamine-assimilation
4368518401phenylacetate-assimilation
4368533942ribose-assimilation
4368517814salicin-assimilation
4368553258sodium citrate-assimilation
4368517057cellobiose-builds acid from
4368515963ribitol-builds acid from
4368518333D-arabitol-builds acid from
4368517634D-glucose-builds acid from
4368516899D-mannitol-builds acid from
4368517924D-sorbitol-builds acid from
4368565327D-xylose-builds acid from
4368516813galactitol-builds acid from
4368517113erythritol-builds acid from
4368530849L-arabinose-builds acid from
4368562345L-rhamnose-builds acid from
4368517716lactose-builds acid from
4368517306maltose-builds acid from
4368528053melibiose-builds acid from
4368517268myo-inositol-builds acid from
4368516634raffinose-builds acid from
4368517814salicin-builds acid from
4368517992sucrose-builds acid from
4368527082trehalose-builds acid from
4368527613amygdalin-fermentation
4368517234glucose-fermentation
4368528087glycogen-fermentation
4368517268myo-inositol-fermentation
4368530849L-arabinose-fermentation
4368517716lactose-fermentation
4368517306maltose-fermentation
4368529864mannitol-fermentation
4368528053melibiose-fermentation
4368526546rhamnose-fermentation
4368533942ribose-fermentation
4368530911sorbitol-fermentation
4368517992sucrose-fermentation
4368518222xylose-fermentation
4368517057cellobiose+assimilation
4368515824D-fructose+assimilation
4368512936D-galactose+assimilation
4368518391D-gluconate+assimilation
4368517634D-glucose+assimilation
4368516024D-mannose+assimilation
4368565327D-xylose+assimilation
4368517234glucose+assimilation
4368530849L-arabinose+assimilation
4368562345L-rhamnose+assimilation
4368517306maltose+assimilation
4368528053melibiose+assimilation
4368517992sucrose+assimilation
4368527082trehalose+assimilation
4368517632nitrate+reduction

metabolite production

@refChebi-IDmetaboliteproduction
4368516136hydrogen sulfideno
4368535581indoleno

enzymes

@refvalueactivityec
43685catalase+1.11.1.6
43685cytochrome oxidase-1.9.3.1
43685alkaline phosphatase+3.1.3.1
43685esterase Lipase (C 8)+
43685leucine arylamidase+3.4.11.1
43685cystine arylamidase+3.4.11.3
43685valine arylamidase+
43685alpha-glucosidase+3.2.1.20
43685protease+
43685N-acetyl-beta-glucosaminidase-3.2.1.52
43685alpha-mannosidase-3.2.1.24
43685alpha-fucosidase-3.2.1.51
43685arginine dihydrolase-3.5.3.6
43685urease-3.5.1.5
43685lysine decarboxylase-4.1.1.18
43685ornithine decarboxylase-4.1.1.17
43685tryptophan deaminase-4.1.99.1
43685gelatinase-
43685pyrazinamidase-3.5.1.B15
43685alpha-galactosidase+3.2.1.22
43685beta-galactosidase+/-3.2.1.23
43685amylase+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
24271stem tissue of healthy 10-week-old, field-grown maize (Zea mays, cultivar 'Sweet Belle'), isolated as an endophyteZea maysAlabama, Tallassee Plant Breeding Unit facility, E.V. Smith Research CenterUSAUSANorth America
43685isolated as an endophyte of stem tissue of healthy maize (Zea mays)Plant Breeding Unit facility, E. V. Smith Research Center, Tallassee, AlabamaUSAUSANorth America1990-07
67770Stem tissue of healthy 10-week-old, field-grown maize (Zea mays, cultivar 'Sweet Belle') at the Plant Breeding Unit facility, E.V. Smith Research CenterZea maysTallassee, ALUSAUSANorth America
124030Field grown maize, stem-endopyteTallassee, Alabama, USAUnited States of AmericaUSANorth America1990-05-02

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Stem (Branch)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
242711Risk group (German classification)
1240301Risk group (French classification)

Sequence information

16S sequences

  • @ref: 24271
  • description: Nocardioides zeicaulis strain JM-601 16S ribosomal RNA gene, partial sequence
  • accession: KU201963
  • length: 1425
  • database: ena
  • NCBI tax ID: 1776857

External links

@ref: 24271

culture collection no.: DSM 101604, CCM 8654, CIP 110980, JCM 32381

straininfo link

  • @ref: 90813
  • straininfo: 403774

literature

  • topic: Phylogeny
  • Pubmed-ID: 26867539
  • title: Nocardioides zeicaulis sp. nov., an endophyte actinobacterium of maize.
  • authors: Kampfer P, Glaeser SP, McInroy JA, Busse HJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000959
  • year: 2016
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Alabama, Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Stems/microbiology, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology
  • topic2: Enzymology

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
24271Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101604Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101604)
42168Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/34587
43685Peter Kämpfer, Stefanie P. Glaeser, John A. McInroy, Hans-Jürgen BusseNocardioides zeicaulis sp. nov., an endophyte actinobacterium of maize10.1099/ijsem.0.000959IJSEM 66: 1869-1874 201626867539
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
90813Reimer, 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-ID403774.1
124030Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110980Collection of Institut Pasteur (CIP 110980)