Strain identifier
BacDive ID: 13269
Type strain: 
Species: Amycolatopsis tucumanensis
Strain Designation: ABO
Strain history: LMG 24814 <-- M. E. Trujillo strain ABO <-- V. H. Albarracín.
NCBI tax ID(s): 401106 (species)
version 8.1 (current version)
General
@ref: 16011
BacDive-ID: 13269
DSM-Number: 45259
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Amycolatopsis tucumanensis ABO is an aerobe, spore-forming, mesophilic bacterium that was isolated from copper polluted sediments from a drainage channel.
NCBI tax id
- NCBI tax id: 401106
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16011 | <- M. E. Trujillo, Depart. Microbiol. y Gen., Univ. Salamanca, Spain; ABO <- V. H. Albarracin |
| 67770 | LMG 24814 <-- M. E. Trujillo strain ABO <-- V. H. Albarracín. |
doi: 10.13145/bacdive13269.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Amycolatopsis
- species: Amycolatopsis tucumanensis
- full scientific name: Amycolatopsis tucumanensis Albarracín et al. 2010
@ref: 16011
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Amycolatopsis
species: Amycolatopsis tucumanensis
full scientific name: Amycolatopsis tucumanensis Albarracín et al. 2010
strain designation: ABO
type strain: yes
Morphology
cell morphology
- @ref: 29305
- gram stain: positive
- motility: no
pigmentation
- @ref: 29305
- production: yes
multimedia
- @ref: 16011
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45259.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 16011 | N-Z-AMINE-MEDIUM (DSMZ Medium 554) | yes | https://mediadive.dsmz.de/medium/554 | Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water |
| 16011 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16011 | positive | growth | 28 | mesophilic |
| 29305 | positive | growth | 15-55 | |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 29305
- ability: positive
- type: growth
- pH: 05-10
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 29305
- oxygen tolerance: aerobe
spore formation
- @ref: 29305
- spore formation: yes
halophily
- @ref: 29305
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 5 %
observation
- @ref: 67770
- observation: quinones: MK-9(H4), MK-9(H2)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29305 | 16634 | raffinose | + | carbon source |
| 29305 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29305 | catalase | + | 1.11.1.6 |
| 29305 | gelatinase | + |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 16011 | copper polluted sediments (600 mg/kg Cu) from a drainage channel | Tucuman, Ranchillos | Argentina | ARG | Middle and South America |
| 67770 | Groundwater sediment polluted with copper | Tucumán | Argentina | ARG | Middle and South America |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | #Heavy metal |
| #Engineered | #Waste | #Wastewater |
| #Environmental | #Terrestrial | #Geologic |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_1640.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_935;97_1087;98_1297;99_1640&stattab=map
- Last taxonomy: Amycolatopsis
- 16S sequence: DQ886938
- Sequence Identity:
- Total samples: 520
- soil counts: 204
- aquatic counts: 52
- animal counts: 228
- plant counts: 36
Safety information
risk assessment
- @ref: 16011
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16011
- description: Amycolatopsis tucumanensis strain ABO 16S ribosomal RNA gene, partial sequence
- accession: DQ886938
- length: 1488
- database: ena
- NCBI tax ID: 401106
Genome sequences
- @ref: 66792
- description: Amycolatopsis tucumanensis ABO
- accession: GCA_021654135
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 401106
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | no | 97.326 | yes |
| gram-positive | yes | 92.242 | yes |
| anaerobic | no | 99.43 | yes |
| aerobic | yes | 91.864 | yes |
| halophile | no | 86.687 | no |
| spore-forming | yes | 90.925 | yes |
| motile | no | 93.414 | no |
| glucose-ferment | no | 91.029 | no |
| thermophile | no | 97.707 | yes |
| glucose-util | yes | 89.796 | no |
External links
@ref: 16011
culture collection no.: DSM 45259, BCCM 24814, LMG 24814, JCM 17017
straininfo link
- @ref: 82473
- straininfo: 359553
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19651731 | Amycolatopsis tucumanensis sp. nov., a copper-resistant actinobacterium isolated from polluted sediments. | Albarracin VH, Alonso-Vega P, Trujillo ME, Amoroso MJ, Abate CM | Int J Syst Evol Microbiol | 10.1099/ijs.0.010587-0 | 2009 | Actinomycetales/*classification/drug effects/genetics, Base Sequence, Copper/*pharmacology, Drug Resistance, Bacterial, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Water Microbiology, *Water Pollution, Chemical | Genetics |
| Metabolism | 20163821 | Bioaugmentation of copper polluted soil microcosms with Amycolatopsis tucumanensis to diminish phytoavailable copper for Zea mays plants. | Albarracin VH, Amoroso MJ, Abate CM | Chemosphere | 10.1016/j.chemosphere.2010.01.038 | 2010 | Actinobacteria/growth & development/*metabolism, Biodegradation, Environmental, Copper/analysis/*metabolism, Soil/analysis, Soil Microbiology, Soil Pollutants/analysis/*metabolism, Zea mays/*metabolism | |
| Metabolism | 23994656 | Production of bioemulsifiers by Amycolatopsis tucumanensis DSM 45259 and their potential application in remediation technologies for soils contaminated with hexavalent chromium. | Colin VL, Castro MF, Amoroso MJ, Villegas LB | J Hazard Mater | 10.1016/j.jhazmat.2013.08.005 | 2013 | Actinomycetales/drug effects/growth & development/*metabolism, Asparagine/pharmacology, Chromium/*chemistry, Emulsifying Agents/*chemistry/*metabolism, Environmental Restoration and Remediation/methods, Glucose/pharmacology, Glycerol/pharmacology, Soil Pollutants/*chemistry, Urea/pharmacology | Biotechnology |
| Metabolism | 25205070 | Enhanced polyaromatic hydrocarbon degradation by adapted cultures of actinomycete strains. | Bourguignon N, Isaac P, Alvarez H, Amoroso MJ, Ferrero MA | J Basic Microbiol | 10.1002/jobm.201400262 | 2014 | Actinobacteria/isolation & purification/*metabolism, Biodegradation, Environmental, Catechol 1,2-Dioxygenase/genetics/metabolism, Culture Media, Glucose/metabolism, Naphthalenes/metabolism, Phenanthrenes/metabolism, Polycyclic Aromatic Hydrocarbons/*metabolism, Pyrenes/metabolism | Cultivation |
| Metabolism | 27785708 | Insights into the degradation capacities of Amycolatopsis tucumanensis DSM 45259 guided by microarray data. | Bourguignon N, Bargiela R, Rojo D, Chernikova TN, de Rodas SA, Garcia-Cantalejo J, Nather DJ, Golyshin PN, Barbas C, Ferrero M, Ferrer M | World J Microbiol Biotechnol | 10.1007/s11274-016-2163-8 | 2016 | Actinobacteria/*genetics/metabolism, Alkanes/metabolism, Bacterial Proteins/*genetics/metabolism, Biodegradation, Environmental, Copper/metabolism, Evolution, Molecular, Metabolism, Oligonucleotide Array Sequence Analysis/*methods, Sequence Analysis, DNA/*methods | Transcriptome |
| Metabolism | 30878660 | Identification of proteins induced by polycyclic aromatic hydrocarbon and proposal of the phenanthrene catabolic pathway in Amycolatopsis tucumanensis DSM 45259. | Bourguignon N, Irazusta V, Isaac P, Estevez C, Maizel D, Ferrero MA | Ecotoxicol Environ Saf | 10.1016/j.ecoenv.2019.02.071 | 2019 | Actinomycetales/drug effects/*metabolism, Bacterial Proteins/*metabolism, Biodegradation, Environmental, Environmental Pollutants/*analysis/metabolism, Metabolic Networks and Pathways/drug effects, Phenanthrenes/analysis/metabolism, Polycyclic Aromatic Hydrocarbons/*analysis/metabolism | Pathogenicity |
| Genetics | 35551685 | Genome sequencing and genomic analysis of Amycolatopsis tucumanensis DSM 45259 applicable in gray, red, and nano-biotechnology. | Guerrero DS, Romero CM, Polti MA, Davila Costa JS | J Basic Microbiol | 10.1002/jobm.202200157 | 2022 | Biotechnology |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16011 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45259) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45259 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 29305 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25719 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 82473 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID359553.1 | StrainInfo: A central database for resolving microbial strain identifiers |