Strain identifier
BacDive ID: 140483
Type strain: 
Species: Noviherbaspirillum autotrophicum
Strain history: S. Ishii TSA66.
NCBI tax ID(s): 709839 (species)
version 8.1 (current version)
General
@ref: 43245
BacDive-ID: 140483
DSM-Number: 25787
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, colony-forming
description: Noviherbaspirillum autotrophicum JCM 17723 is a facultative anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from rice paddy soil under denitrification-inducing conditions.
NCBI tax id
- NCBI tax id: 709839
- Matching level: species
strain history
- @ref: 67770
- history: S. Ishii TSA66.
doi: 10.13145/bacdive140483.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Oxalobacteraceae
- genus: Noviherbaspirillum
- species: Noviherbaspirillum autotrophicum
- full scientific name: Noviherbaspirillum autotrophicum Ishii et al. 2017
@ref: 43245
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Noviherbaspirillum
species: Noviherbaspirillum autotrophicum
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
|---|---|---|---|---|---|---|---|
| 43245 | negative | 1.4-2.2 µm | 0.4-0.6 µm | rod-shaped | yes | polar | |
| 69480 | yes | 98.685 | |||||
| 69480 | negative | 99.996 |
colony morphology
- @ref: 43245
- colony color: white
- colony shape: circular
- medium used: R2A
Culture and growth conditions
culture medium
| @ref | name | growth | composition |
|---|---|---|---|
| 43245 | Reasoner's 2A agar (R2A) | yes | |
| 43245 | nutritient agar (NA) | yes | |
| 43245 | trypticase soy agar (TSA) | no | |
| 43245 | DNBNS medium | yes | 100-fold diluted nutrient broth (DNB; Difco) supplemented with 3 mM nitrate and 4.4 mM succinate |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 43245 | positive | optimum | 30 | mesophilic |
| 43245 | positive | growth | 10-42 | |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 43245
- ability: positive
- type: growth
- pH: 5.5-9.0
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 43245
- oxygen tolerance: facultative anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
halophily
- @ref: 43245
- salt: NaCl
- growth: no
- tested relation: growth
- concentration: 1 %(w/v)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43245 | 17632 | nitrate | + | electron acceptor |
| 43245 | 30089 | acetate | + | carbon source |
| 43245 | 17968 | butyrate | + | carbon source |
| 43245 | 24996 | lactate | + | carbon source |
| 43245 | 15361 | pyruvate | + | carbon source |
| 43245 | 30031 | succinate | + | carbon source |
| 43245 | 31011 | valerate | + | carbon source |
| 43245 | 53423 | tween 40 | + | carbon source |
| 43245 | 53426 | tween 80 | + | carbon source |
| 43245 | 28757 | fructose | - | growth |
| 43245 | 28260 | galactose | - | growth |
| 43245 | 17234 | glucose | - | growth |
| 43245 | 17716 | lactose | - | growth |
| 43245 | 17306 | maltose | - | growth |
| 43245 | 37684 | mannose | - | growth |
| 43245 | 30911 | sorbitol | - | growth |
| 43245 | 26546 | rhamnose | - | growth |
| 43245 | 18222 | xylose | - | growth |
| 43245 | 24265 | gluconate | - | growth |
| 43245 | 28885 | butanol | - | growth |
| 43245 | 16236 | ethanol | - | growth |
| 43245 | 62968 | cellulose | - | growth |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 43245 | catalase | + | 1.11.1.6 |
| 43245 | cytochrome oxidase | + | 1.9.3.1 |
| 43245 | urease | - | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 43245 | rice paddy soil under denitrification-inducing conditions | Tokyo | Japan | JPN | Asia |
| 67770 | Rice paddy soil under denitrification-inducing conditions | Tokyo | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_7282.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_3405;97_4180;98_5341;99_7282&stattab=map
- Last taxonomy: Noviherbaspirillum autotrophicum
- 16S sequence: AB542418
- Sequence Identity:
- Total samples: 321
- soil counts: 122
- aquatic counts: 101
- animal counts: 61
- plant counts: 37
Sequence information
16S sequences
- @ref: 43245
- description: Herbaspirillum sp. TSA66 gene for 16S ribosomal RNA, partial sequence, strain: TSA66
- accession: AB542418
- length: 1453
- database: nuccore
- NCBI tax ID: 709839
Genome sequences
- @ref: 67770
- description: Noviherbaspirillum autotrophicum TSA66
- accession: GCA_000818395
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 709839
GC content
- @ref: 67770
- GC-content: 59.9
- method: genome sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 91.834 | yes |
| flagellated | yes | 83.46 | yes |
| gram-positive | no | 99.159 | yes |
| anaerobic | no | 95.938 | yes |
| aerobic | no | 60.085 | yes |
| halophile | no | 95.259 | no |
| spore-forming | no | 95.305 | no |
| glucose-util | no | 75.151 | yes |
| thermophile | no | 98.408 | no |
| glucose-ferment | no | 89.765 | no |
External links
@ref: 43245
culture collection no.: JCM 17723, DSM 25787, TSA 66
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 28629495 | Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov. | Ishii S, Ashida N, Ohno H, Segawa T, Yabe S, Otsuka S, Yokota A, Senoo K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001875 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Denitrification, Fatty Acids/chemistry, Herbaspirillum/*classification/genetics/isolation & purification, *Oryza, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology | Transcriptome |
| Phylogeny | 33956597 | Massilia horti sp. nov. and Noviherbaspirillum arenae sp. nov., two novel soil bacteria of the Oxalobacteraceae. | Peta V, Raths R, Bucking H | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004765 | 2021 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Oxalobacteraceae/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology | Metabolism |
Reference
| @id | authors | title | doi/url | journal | pubmed |
|---|---|---|---|---|---|
| 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 | ||
| 43245 | Satoshi Ishii, Naoaki Ashida, Hiroki Ohno, Takahiro Segawa, Shuhei Yabe, Shigeto Otsuka, Akira Yokota, Keishi Senoo | Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov. | 10.1099/ijsem.0.001875 | IJSEM 67: 1841-1848 2017 | 28629495 |
| 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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 |
| 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/ | ||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |