Strain identifier
BacDive ID: 131253
Type strain: 
Species: Microvirga lotononidis
Strain history: <- HAMBI; HAMBI 3237 <- K. Lindström, HAMBI; LMG 26455 <- A. Willems, LMG; WSM3557 <- J.K. Ardley, Murdoch University, Australia; CB 1322 <- A. McInnes, CB <- W.C. Verboom
NCBI tax ID(s): 864069 (species)
version 9 (current version)
General
@ref: 22480
BacDive-ID: 131253
DSM-Number: 28906
keywords: 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Microvirga lotononidis DSM 28906 is an aerobe, Gram-negative, motile bacterium that was isolated from Lotononis angolensis, nitrogen-fixing nodule.
NCBI tax id
- NCBI tax id: 864069
- Matching level: species
strain history
- @ref: 22480
- history: <- HAMBI; HAMBI 3237 <- K. Lindström, HAMBI; LMG 26455 <- A. Willems, LMG; WSM3557 <- J.K. Ardley, Murdoch University, Australia; CB 1322 <- A. McInnes, CB <- W.C. Verboom
doi: 10.13145/bacdive131253.20240510.9
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Methylobacteriaceae
- genus: Microvirga
- species: Microvirga lotononidis
- full scientific name: Microvirga lotononidis Ardley et al. 2012
@ref: 22480
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Microvirga
species: Microvirga lotononidis
full scientific name: Microvirga lotononidis Ardley et al. 2012
type strain: yes
Morphology
cell morphology
- @ref: 30397
- gram stain: negative
- cell length: 1.6 µm
- cell width: 0.45 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 30397
- production: yes
Culture and growth conditions
culture medium
- @ref: 22480
- name: MODIFIED YMA MEDIUM (HAMBI) (DSMZ Medium 1545)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1545
- composition: Name: MODIFIED YMA MEDIUM (HAMBI) (DSMZ Medium 1545) Composition: Agar 20.0 g/l Mannitol 10.0 g/l Yeast extract 2.5 g/l K2HPO4 x 3 H2O 0.6 g/l MgSO4 x 7 H2O 0.2 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 22480 | positive | growth | 28 |
| 30397 | positive | growth | 15-45 |
| 30397 | positive | optimum | 41 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30397 | positive | growth | 5.5-9.5 | alkaliphile |
| 30397 | positive | optimum | 7.75 |
Physiology and metabolism
oxygen tolerance
- @ref: 30397
- oxygen tolerance: aerobe
spore formation
- @ref: 30397
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30397 | NaCl | positive | growth | 0-2 % |
| 30397 | NaCl | positive | optimum | 0.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30397 | 30089 | acetate | + | carbon source |
| 30397 | 22599 | arabinose | + | carbon source |
| 30397 | 17057 | cellobiose | + | carbon source |
| 30397 | 28757 | fructose | + | carbon source |
| 30397 | 17234 | glucose | + | carbon source |
| 30397 | 29987 | glutamate | + | carbon source |
| 30397 | 17754 | glycerol | + | carbon source |
| 30397 | 29864 | mannitol | + | carbon source |
| 30397 | 30031 | succinate | + | carbon source |
| 30397 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30397 | catalase | + | 1.11.1.6 |
| 30397 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 22480
- sample type: Lotononis angolensis, nitrogen-fixing nodule
- geographic location: Chibala (Fort Jameson)
- country: Zambia
- origin.country: ZMB
- continent: Africa
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root nodule |
taxonmaps
- @ref: 69479
- File name: preview.99_2142.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_1174;97_1377;98_1672;99_2142&stattab=map
- Last taxonomy: Microvirga
- 16S sequence: HM362432
- Sequence Identity:
- Total samples: 475
- soil counts: 307
- aquatic counts: 74
- animal counts: 70
- plant counts: 24
Safety information
risk assessment
- @ref: 22480
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 30397 | Microvirga lotononidis strain WSM3557 16S ribosomal RNA gene, partial sequence | HM362432 | 1457 | nuccore | 864069 |
| 22480 | Dictyostelium discoideum strain QS38 anonymous locus 06_2763183 genomic sequence | HM362332 | 531 | nuccore | 44689 |
| 124043 | Microvirga lotononidis partial 16S rRNA gene, strain HAMBI 3237 | LT899968 | 1386 | nuccore | 864069 |
GC content
- @ref: 30397
- GC-content: 62.8-63
External links
@ref: 22480
culture collection no.: DSM 28906, HAMBI 3237, LMG 26455, WSM 3557, CB 1322
straininfo link
- @ref: 89697
- straininfo: 377578
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22199210 | Microvirga lupini sp. nov., Microvirga lotononidis sp. nov. and Microvirga zambiensis sp. nov. are alphaproteobacterial root-nodule bacteria that specifically nodulate and fix nitrogen with geographically and taxonomically separate legume hosts. | Ardley JK, Parker MA, De Meyer SE, Trengove RD, O'Hara GW, Reeve WG, Yates RJ, Dilworth MJ, Willems A, Howieson JG | Int J Syst Evol Microbiol | 10.1099/ijs.0.035097-0 | 2011 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fabaceae/*microbiology, Fatty Acids/analysis, Methylobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nitrogen Fixation, *Phylogeny, Plant Root Nodulation, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Texas, Zambia | Genetics |
| Genetics | 25197439 | Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T.). | Reeve W, Ardley J, Tian R, De Meyer S, Terpolilli J, Melino V, Tiwari R, Yates R, O'Hara G, Howieson J, Ninawi M, Zhang X, Bruce D, Detter C, Tapia R, Han C, Wei CL, Huntemann M, Han J, Chen IM, Mavromatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Pati A, Goodwin L, Woyke T, Kyrpides N | Stand Genomic Sci | 10.4056/sigs.4548266 | 2013 | ||
| Genetics | 26749561 | Microvirga massiliensis sp. nov., the human commensal with the largest genome. | Caputo A, Lagier JC, Azza S, Robert C, Mouelhi D, Fournier PE, Raoult D | Microbiologyopen | 10.1002/mbo3.329 | 2016 | Adolescent, Alphaproteobacteria/classification/*genetics, Bacterial Typing Techniques, Computational Biology/methods, France, Gastrointestinal Microbiome/genetics, *Genome, Bacterial, *Genomics/methods, Humans, Male, Metagenome, Metagenomics/methods, Molecular Sequence Annotation, Phenotype, Phylogeny, Sequence Analysis, DNA | Phylogeny |
| Phylogeny | 31177347 | Microvirga calopogonii sp. nov., a novel alphaproteobacterium isolated from a root nodule of Calopogonium mucunoides in Southwest China. | Wang F, Yang L, Deng J, Liu X, Lu Y, Chen W, Wu J | Antonie Van Leeuwenhoek | 10.1007/s10482-019-01285-5 | 2019 | China, Fabaceae/*microbiology, Genome, Bacterial, Genomics/methods, Methylobacteriaceae/chemistry/*classification/genetics/*isolation & purification, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Soil Microbiology, Symbiosis, Whole Genome Sequencing | Genetics |
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 | ||||
| 22480 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28906 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28906) | ||||
| 30397 | 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 | 26734 | 28776041 | ||
| 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 | ||
| 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/ | ||||
| 89697 | 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-ID377578.1 | ||||
| 124043 | Dr. Isabel Schober, Dr. Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy |