Strain identifier
BacDive ID: 24248
Type strain: 
Species: Nocardioides terrae
Strain Designation: VA15
Strain history: CGMCC 1.7056 <-- J.-Y. Zhang VA15.
NCBI tax ID(s): 574651 (species)
version 8.1 (current version)
General
@ref: 20681
BacDive-ID: 24248
DSM-Number: 28109
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Nocardioides terrae VA15 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from forest soil.
NCBI tax id
- NCBI tax id: 574651
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20681 | <- NBRC <- CGMCC 1.7056 <- J.-Y. Zhang, CAS; VA15 |
| 67770 | CGMCC 1.7056 <-- J.-Y. Zhang VA15. |
doi: 10.13145/bacdive24248.20230509.8.1
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 terrae
- full scientific name: Nocardioides terrae Zhang et al. 2009
@ref: 20681
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides terrae
full scientific name: Nocardioides terrae Zhang et al. 2009
strain designation: VA15
type strain: yes
Morphology
cell morphology
- @ref: 29316
- gram stain: positive
- cell length: 0.65 µm
- cell width: 0.3 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 29316
- production: yes
Culture and growth conditions
culture medium
- @ref: 20681
- 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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20681 | positive | growth | 28 | mesophilic |
| 29316 | positive | growth | 16-34 | |
| 29316 | positive | optimum | 29 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29316 | positive | growth | 5.5-8.5 | alkaliphile |
| 29316 | positive | optimum | 6.2-6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 29316
- oxygen tolerance: aerobe
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29316 | NaCl | positive | growth | 0-1 % |
| 29316 | NaCl | positive | optimum | 0-0.25 % |
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29316 | 17234 | glucose | + | carbon source |
| 29316 | 17306 | maltose | + | carbon source |
| 29316 | 29864 | mannitol | + | carbon source |
| 29316 | 18401 | phenylacetate | + | carbon source |
| 29316 | 4853 | esculin | + | hydrolysis |
| 29316 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29316 | acid phosphatase | + | 3.1.3.2 |
| 29316 | alkaline phosphatase | + | 3.1.3.1 |
| 29316 | catalase | + | 1.11.1.6 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 20681 | forest soil | Changbai Mountain | China | CHN | Asia |
| 67770 | Forest soil from the Changbai Mountains | Heilongjiang Province | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Forest |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_88257.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_3660;97_46516;98_60959;99_88257&stattab=map
- Last taxonomy: Nocardioides terrae subclade
- 16S sequence: FJ423762
- Sequence Identity:
- Total samples: 802
- soil counts: 403
- aquatic counts: 19
- animal counts: 48
- plant counts: 332
Safety information
risk assessment
- @ref: 20681
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20681
- description: Nocardioides terrae strain VA15 16S ribosomal RNA gene, partial sequence
- accession: FJ423762
- length: 1523
- database: ena
- NCBI tax ID: 574651
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Nocardioides terrae strain CGMCC 1.7056 | 574651.3 | wgs | patric | 574651 |
| 66792 | Nocardioides terrae CGMCC 1.7056 | 2617270786 | draft | img | 574651 |
| 67770 | Nocardioides terrae CGMCC 1.7056 | GCA_900112345 | scaffold | ncbi | 574651 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 20681 | 71.6 | |
| 67770 | 71.6 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | yes | 86.911 | no |
| anaerobic | no | 99.062 | yes |
| halophile | no | 96.678 | yes |
| spore-forming | no | 87.689 | no |
| glucose-util | yes | 87.191 | no |
| thermophile | no | 92.899 | yes |
| motile | no | 72.818 | yes |
| flagellated | no | 94.142 | no |
| aerobic | yes | 93.65 | yes |
| glucose-ferment | no | 88.754 | no |
External links
@ref: 20681
culture collection no.: DSM 28109, CGMCC 1.7056, JCM 16799, NBRC 104259
straininfo link
- @ref: 88190
- straininfo: 404232
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19622661 | Nocardioides terrae sp. nov., isolated from forest soil. | Zhang JY, Liu XY, Liu SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.010785-0 | 2009 | Actinomycetales/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Trees/*microbiology | Metabolism |
| Phylogeny | 35834405 | Nocardioides nematodiphilus sp. nov., isolated from rhizosphere of Arabidopsis thaliana. | Zhang XM, Mo WT, Wei YQ, Li X, Ma GM, Yang YS, Wang XJ, Liu JJ, Liu ZY, Zhou XK, Zhang TK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005271 | 2022 | *Actinomycetales, *Arabidopsis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nocardioides, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Soil Microbiology | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||||
| 20681 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28109 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28109) | ||||
| 29316 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 25729 | 28776041 | ||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
| 69479 | João 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 beta | https://microbeatlas.org/ | ||||
| 88190 | Reimer, 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 identifiers | 10.60712/SI-ID404232.1 |