Strain identifier
BacDive ID: 11946
Type strain: 
Species: Zavarzinella formosa
Strain Designation: A10
Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; A10 <- I. S. Kulichevskaya
NCBI tax ID(s): 1123508 (strain), 360055 (species)
version 8.1 (current version)
General
@ref: 8394
BacDive-ID: 11946
DSM-Number: 19928
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, ovoid-shaped
description: Zavarzinella formosa A10 is an aerobe, psychrophilic, ovoid-shaped bacterium that was isolated from Sphagnum peat bog Bakchar .
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1123508 | strain |
| 360055 | species |
strain history
- @ref: 8394
- history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; A10 <- I. S. Kulichevskaya
doi: 10.13145/bacdive11946.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/planctomycetota
- domain: Bacteria
- phylum: Planctomycetota
- class: Planctomycetia
- order: Gemmatales
- family: Gemmataceae
- genus: Zavarzinella
- species: Zavarzinella formosa
- full scientific name: Zavarzinella formosa Kulichevskaya et al. 2009
@ref: 8394
domain: Bacteria
phylum: Planctomycetes
class: Planctomycetia
order: Planctomycetales
family: Gemmataceae
genus: Zavarzinella
species: Zavarzinella formosa
full scientific name: Zavarzinella formosa Kulichevskaya et al. 2009 emend. Scheuner et al. 2014
strain designation: A10
type strain: yes
Morphology
cell morphology
| @ref | cell length | cell width | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|---|---|
| 28947 | 2.85 µm | 2.25 µm | ovoid-shaped | no | ||
| 69480 | negative | 99.902 |
pigmentation
- @ref: 28947
- production: yes
Culture and growth conditions
culture medium
- @ref: 8394
- name: ZAVARZINELLA FORMOSA MEDIUM (DSMZ Medium 1196)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1196
- composition: Name: ZAVARZINELLA FORMOSA MEDIUM (DSMZ Medium 1196) Composition: Agar 15.0 g/l N-Acetylglucosamine 1.0 g/l Glucose 0.5 g/l KH2PO4 0.1 g/l MgSO4 x 7 H2O 0.1 g/l Peptone 0.1 g/l Yeast extract 0.1 g/l Casamino acids 0.1 g/l CaCl2 x 6 H2O 0.05 g/l NaCl 0.01 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l MnSO4 x H2O 0.000154 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 8394 | positive | growth | 20 | psychrophilic |
| 28947 | positive | growth | 10-30 | |
| 28947 | positive | optimum | 22.5 | psychrophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 28947 | positive | growth | 3.8-7.2 | acidophile |
| 28947 | positive | optimum | 5.75 |
Physiology and metabolism
oxygen tolerance
- @ref: 28947
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.973 |
halophily
- @ref: 28947
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <0.6 %
observation
- @ref: 28947
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28947 | 17057 | cellobiose | + | carbon source |
| 28947 | 28260 | galactose | + | carbon source |
| 28947 | 17234 | glucose | + | carbon source |
| 28947 | 17716 | lactose | + | carbon source |
| 28947 | 17306 | maltose | + | carbon source |
| 28947 | 506227 | N-acetylglucosamine | + | carbon source |
| 28947 | 15361 | pyruvate | + | carbon source |
| 28947 | 16634 | raffinose | + | carbon source |
| 28947 | 26546 | rhamnose | + | carbon source |
| 28947 | 33942 | ribose | + | carbon source |
| 28947 | 17814 | salicin | + | carbon source |
| 28947 | 17992 | sucrose | + | carbon source |
| 28947 | 27082 | trehalose | + | carbon source |
| 28947 | 18222 | xylose | + | carbon source |
| 28947 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 28947 | acid phosphatase | + | 3.1.3.2 |
| 28947 | alkaline phosphatase | + | 3.1.3.1 |
| 28947 | catalase | + | 1.11.1.6 |
| 28947 | gelatinase | + | |
| 28947 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 8394
- sample type: Sphagnum peat bog Bakchar (at a depth of 10-20 cm)
- host species: Sphagnum
- geographic location: West Siberia
- country: Russia
- origin.country: RUS
- continent: Asia
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Peat moss
taxonmaps
- @ref: 69479
- File name: preview.99_86967.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5462;96_24657;97_30877;98_60150;99_86967&stattab=map
- Last taxonomy: Zavarzinella formosa subclade
- 16S sequence: AM162406
- Sequence Identity:
- Total samples: 150
- soil counts: 62
- aquatic counts: 76
- animal counts: 12
Safety information
risk assessment
- @ref: 8394
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8394
- description: Zavarzinella formosa partial 16S rRNA gene, type strain A10T
- accession: AM162406
- length: 1426
- database: ena
- NCBI tax ID: 360055
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Zavarzinella formosa DSM 19928 | GCA_000255705 | scaffold | ncbi | 1123508 |
| 66792 | Zavarzinella formosa DSM 19928 | 1123508.3 | wgs | patric | 1123508 |
| 66792 | Zavarzinella formosa DSM 19928 | 2548877000 | draft | img | 1123508 |
| 66792 | Zavarzinella formosa DSM 19928 TH-08apr19-96 | GCA_945906165 | contig | ncbi | 1123508 |
| 66792 | Zavarzinella formosa DSM 19928 strain TH-08apr19-96 | 1123508.8 | wgs | patric | 1123508 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8394 | 62.3 | |
| 28947 | 62.5 | |
| 8394 | 59 | sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 65.604 | no |
| flagellated | no | 89.215 | yes |
| gram-positive | no | 97.014 | no |
| anaerobic | no | 97.148 | no |
| aerobic | yes | 88.141 | yes |
| halophile | no | 94.824 | no |
| spore-forming | no | 86.943 | no |
| glucose-util | yes | 87.587 | yes |
| thermophile | no | 99.206 | yes |
| glucose-ferment | no | 86.296 | no |
External links
@ref: 8394
culture collection no.: DSM 19928, VKM B-2478
straininfo link
- @ref: 81159
- straininfo: 360725
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19196778 | Zavarzinella formosa gen. nov., sp. nov., a novel stalked, Gemmata-like planctomycete from a Siberian peat bog. | Kulichevskaya IS, Baulina OI, Bodelier PL, Rijpstra WI, Damste JS, Dedysh SN | Int J Syst Evol Microbiol | 10.1099/ijs.0.002378-0 | 2009 | Bacteria/chemistry/*classification/genetics/ultrastructure, Fatty Acids/analysis, Lipids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Siberia, *Soil, *Soil Microbiology, Species Specificity | Genetics |
| Genetics | 22740668 | Genome sequences of three species in the family Planctomycetaceae. | Guo M, Han X, Jin T, Zhou L, Yang J, Li Z, Chen J, Geng B, Zou Y, Wan D, Li D, Dai W, Wang H, Chen Y, Ni P, Fang C, Yang R | J Bacteriol | 10.1128/JB.00639-12 | 2012 | Gene Expression Regulation, Bacterial/physiology, *Genome, Bacterial, Molecular Sequence Data, Planctomycetales/classification/*genetics, Species Specificity | Phylogeny |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 8394 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19928) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19928 | |||
| 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 | |||
| 28947 | 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 | 25386 | 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) | |||
| 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 81159 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID360725.1 | StrainInfo: A central database for resolving microbial strain identifiers |