Strain identifier
BacDive ID: 7218
Type strain: 
Species: Methylocystis hirsuta
Strain history: <- A. S. Lindner, Dept. Environmental Engineering Sci., Univ. Florida, USA; CSC1 <- S. M. Henry and D. Grbic-Galic, Dept. Civil Engineering, Stanford Univ., USA
NCBI tax ID(s): 369798 (species)
version 8.1 (current version)
General
@ref: 7564
BacDive-ID: 7218
DSM-Number: 18500
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Methylocystis hirsuta DSM 18500 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from uncontaminated groundwater aquifer in the mid-1980s from Moffett Naval Air Station.
NCBI tax id
- NCBI tax id: 369798
- Matching level: species
strain history
- @ref: 7564
- history: <- A. S. Lindner, Dept. Environmental Engineering Sci., Univ. Florida, USA; CSC1 <- S. M. Henry and D. Grbic-Galic, Dept. Civil Engineering, Stanford Univ., USA
doi: 10.13145/bacdive7218.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Methylocystaceae
- genus: Methylocystis
- species: Methylocystis hirsuta
- full scientific name: Methylocystis hirsuta Lindner et al. 2007
@ref: 7564
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylocystaceae
genus: Methylocystis
species: Methylocystis hirsuta
full scientific name: Methylocystis hirsuta Lindner et al. 2007
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | motility | confidence |
|---|---|---|---|---|---|
| 31857 | negative | 0.85 µm | 0.45 µm | no | |
| 69480 | negative | 99.998 |
Culture and growth conditions
culture medium
- @ref: 7564
- name: METHYLOSARCINA QUISQUILLARUM AND M. FIBRATA MEDIUM (DSMZ Medium 921)
- growth: yes
- link: https://mediadive.dsmz.de/medium/921
- composition: Name: METHYLOSARCINA QUISQUILLARUM AND M. FIBRATA MEDIUM (DSMZ Medium 921) Composition: Agar 15.0 g/l MgSO4 x 6 H2O 1.0 g/l KNO3 1.0 g/l Na2HPO4 x 12 H2O 0.716 g/l KH2PO4 0.26 g/l CaCl2 x 2 H2O 0.2 g/l CuSO4 x 5 H2O 0.001 g/l FeSO4 x 7 H2O 0.0005 g/l ZnSO4 x 7 H2O 0.0004 g/l Fe(III)-EDTA 0.00038 g/l Na2MoO4 x 2 H2O 0.00026 g/l Na2-EDTA 0.00025 g/l CoCl2 x 6 H2O 5e-05 g/l MnCl2 x 4 H2O 2e-05 g/l H3BO3 1.5e-05 g/l NiCl2 x 6 H2O 1e-05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 31857 | positive | optimum | 30 | mesophilic |
| 7564 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 31857 | positive | growth | 5.0-8.0 |
| 31857 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 31857
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.908 |
observation
- @ref: 31857
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31857 | 22653 | asparagine | + | carbon source |
| 31857 | 35391 | aspartate | + | carbon source |
| 31857 | 18257 | ornithine | + | carbon source |
| 31857 | 17148 | putrescine | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31857 | catalase | + | 1.11.1.6 |
| 31857 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 7564
- sample type: uncontaminated groundwater aquifer in the mid-1980s from Moffett Naval Air Station
- geographic location: California, Mountain View
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Groundwater
taxonmaps
- @ref: 69479
- File name: preview.99_302.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_208;97_227;98_256;99_302&stattab=map
- Last taxonomy: Methylocystis
- 16S sequence: DQ364433
- Sequence Identity:
- Total samples: 1645
- soil counts: 493
- aquatic counts: 940
- animal counts: 169
- plant counts: 43
Safety information
risk assessment
- @ref: 7564
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7564
- description: Methylocystis hirsuta strain CSC1 16S ribosomal RNA gene, partial sequence
- accession: DQ364433
- length: 1450
- database: ena
- NCBI tax ID: 369798
Genome sequences
- @ref: 66792
- description: Methylocystis hirsuta strain CSC1
- accession: 369798.5
- assembly level: wgs
- database: patric
- NCBI tax ID: 369798
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.088 | yes |
| anaerobic | no | 96.462 | yes |
| halophile | no | 95.924 | no |
| spore-forming | no | 94.781 | no |
| glucose-util | yes | 71.193 | no |
| aerobic | yes | 75.881 | yes |
| motile | no | 87.868 | no |
| flagellated | no | 96.386 | yes |
| thermophile | no | 97.596 | yes |
| glucose-ferment | no | 93.726 | no |
External links
@ref: 7564
culture collection no.: DSM 18500, ATCC BAA 1344, CSC 1
straininfo link
- @ref: 76670
- straininfo: 298315
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17684277 | Methylocystis hirsuta sp. nov., a novel methanotroph isolated from a groundwater aquifer. | Lindner AS, Pacheco A, Aldrich HC, Costello Staniec A, Uz I, Hodson DJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.64541-0 | 2007 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fresh Water/*microbiology, Methylocystaceae/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Genetics |
| Metabolism | 30548837 | Genome sequence of Methylocystis hirsuta CSC1, a polyhydroxyalkanoate producing methanotroph. | Bordel S, Rodriguez E, Munoz R | Microbiologyopen | 10.1002/mbo3.771 | 2018 | Bacterial Proteins/genetics/metabolism, Base Sequence, *Genome, Bacterial, Methane/metabolism, Methylocystaceae/classification/*genetics/isolation & purification/metabolism, Oxygenases/genetics/metabolism, Plasmids/genetics, Polyhydroxyalkanoates/*biosynthesis | Genetics |
| Biotechnology | 31862586 | Elucidating the influence of environmental factors on biogas-based polyhydroxybutyrate production by Methylocystis hirsuta CSC1. | Rodriguez Y, Firmino PIM, Arnaiz E, Lebrero R, Munoz R | Sci Total Environ | 10.1016/j.scitotenv.2019.135136 | 2019 | *Biofuels, Bioreactors, Methane, *Methylocystaceae | |
| Phylogeny | 34913862 | Methylocystis silviterrae sp.nov., a high-affinity methanotrophic bacterium isolated from the boreal forest soil. | Tikhonova EN, Grouzdev DS, Avtukh AN, Kravchenko IK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005166 | 2021 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Methylocystaceae/classification/isolation & purification, Moscow, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Taiga, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7564 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18500) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18500 | |||
| 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 | |||
| 31857 | 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 | 28120 | 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 | |||
| 76670 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID298315.1 | StrainInfo: A central database for resolving microbial strain identifiers |