Strain identifier
BacDive ID: 132518
Type strain:
Species: Arthrobacter deserti
Strain history: <- W. Li, YIM; YIM CS25 <- Z. Yan
NCBI tax ID(s): 1742687 (species)
General
@ref: 24307
BacDive-ID: 132518
DSM-Number: 29935
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive
description: Arthrobacter deserti DSM 29935 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from desert soil.
NCBI tax id
- NCBI tax id: 1742687
- Matching level: species
strain history
- @ref: 24307
- history: <- W. Li, YIM; YIM CS25 <- Z. Yan
doi: 10.13145/bacdive132518.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Micrococcaceae
- genus: Arthrobacter
- species: Arthrobacter deserti
- full scientific name: Arthrobacter deserti Hu et al. 2016
@ref: 24307
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micrococcaceae
genus: Arthrobacter
species: Arthrobacter deserti
full scientific name: Arthrobacter deserti Hu et al. 2016
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | confidence |
---|---|---|---|
43967 | positive | no | |
69480 | positive | 100 |
colony morphology
- @ref: 43967
- colony color: white
- medium used: T5 agar
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
43967 | T5 agar | yes | 0.05 % tryptone, 0.1 % glucose, 0.2 % yeast extract, 0.1 % CaCO3, 0.1 % trace salt, 1.5 % agar, pH 7.0 | |
24307 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water | https://mediadive.dsmz.de/medium/92 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43967 | positive | growth | 15-40 | |
24307 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 43967
- ability: positive
- type: growth
- pH: 6.0-8.0
Physiology and metabolism
oxygen tolerance
- @ref: 43967
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | no | 99.997 |
halophily
- @ref: 43967
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-6 %(w/v)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43967 | 17234 | glucose | - | builds acid from |
43967 | 28017 | starch | - | hydrolysis |
43967 | 53424 | tween 20 | - | hydrolysis |
43967 | 53425 | tween 60 | - | hydrolysis |
43967 | 53426 | tween 80 | - | hydrolysis |
43967 | 17632 | nitrate | - | reduction |
43967 | 17128 | adipate | + | assimilation |
43967 | 27613 | amygdalin | + | assimilation |
43967 | 18305 | arbutin | + | assimilation |
43967 | 16947 | citrate | + | assimilation |
43967 | 17113 | erythritol | + | assimilation |
43967 | 24265 | gluconate | + | assimilation |
43967 | 25115 | malate | + | assimilation |
43967 | 28053 | melibiose | + | assimilation |
43967 | 18401 | phenylacetate | + | assimilation |
43967 | 15588 | D-malate | + | carbon source |
43967 | 15589 | L-malate | + | carbon source |
43967 | 73918 | 3-O-methyl-D-glucose | + | carbon source |
43967 | 30089 | acetate | + | carbon source |
43967 | 13705 | acetoacetate | + | carbon source |
43967 | 17925 | alpha-D-glucose | + | carbon source |
43967 | 73706 | bromosuccinate | + | carbon source |
43967 | 17057 | cellobiose | + | carbon source |
43967 | 16947 | citrate | + | carbon source |
43967 | 18333 | D-arabitol | + | carbon source |
43967 | 15824 | D-fructose | + | carbon source |
43967 | 78697 | D-fructose 6-phosphate | + | carbon source |
43967 | 12936 | D-galactose | + | carbon source |
43967 | 8391 | D-gluconate | + | carbon source |
43967 | 14314 | D-glucose 6-phosphate | + | carbon source |
43967 | 16899 | D-mannitol | + | carbon source |
43967 | 16024 | D-mannose | + | carbon source |
43967 | 23652 | dextrin | + | carbon source |
43967 | 17754 | glycerol | + | carbon source |
43967 | L-alanine 4-nitroanilide | + | carbon source | |
43967 | 30849 | L-arabinose | + | carbon source |
43967 | 16467 | L-arginine | + | carbon source |
43967 | 29985 | L-glutamate | + | carbon source |
43967 | 17115 | L-serine | + | carbon source |
43967 | 17306 | maltose | + | carbon source |
43967 | 320061 | methyl alpha-D-glucopyranoside | + | carbon source |
43967 | 43943 | methyl alpha-D-mannoside | + | carbon source |
43967 | 506227 | N-acetylglucosamine | + | carbon source |
43967 | 17309 | pectin | + | carbon source |
43967 | 17272 | propionate | + | carbon source |
43967 | 26490 | quinate | + | carbon source |
43967 | 16634 | raffinose | + | carbon source |
43967 | 17992 | sucrose | + | carbon source |
43967 | 33954 | tagatose | + | carbon source |
43967 | 27082 | trehalose | + | carbon source |
43967 | 32528 | turanose | + | carbon source |
43967 | 4853 | esculin | + | hydrolysis |
43967 | 5291 | gelatin | + | hydrolysis |
43967 | 53423 | tween 40 | + | hydrolysis |
metabolite production
- @ref: 43967
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
43967 | catalase | + | 1.11.1.6 |
43967 | cytochrome oxidase | - | 1.9.3.1 |
43967 | urease | - | 3.5.1.5 |
43967 | arginine dihydrolase | - | 3.5.3.6 |
43967 | alkaline phosphatase | + | 3.1.3.1 |
43967 | esterase (C 4) | + | |
43967 | esterase Lipase (C 8) | + | |
43967 | phosphatase | + | |
43967 | naphthol-AS-BI-phosphohydrolase | + | |
43967 | alpha-glucosidase | + | 3.2.1.20 |
fatty acid profile
fatty acids
@ref fatty acid percentage 43967 C13:0 anteiso 0.1 43967 C15:0 anteiso 51.4 43967 C17:0 anteiso 8.7 43967 C17:1 anteiso ω9c 4.3 43967 C14:0 0.5 43967 C14:1ω5c 0.1 43967 C15:1ω6c 0.3 43967 C16:0 1.1 43967 C16:1ω7c / C16:1ω7c 1.7 43967 C18:0 0.1 43967 C18:1ω9c 0.1 43967 C14:0 iso 0.5 43967 C15:0 iso 18.9 43967 iso-C15:1 H / C15:1 iH / C13:3 OH 0.9 43967 C16:0 iso 5 43967 C16:1 iso H 1.8 43967 C17:0 iso 2.8 43967 C17:1 iso ω9c / C16:0 10-methyl 2 - type of FA analysis: whole cell analysis
- incubation medium: Tryptic soy agar
- agar/liquid: agar
- incubation temperature: 28
- incubation time: 2
- software version: Sherlock 6.0
- library/peak naming table: ACTINO
- system: MIS MIDI
- method/protocol: Sasser, 1990
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|---|---|
24307 | desert soil | Xinjiang Uyghur Autonomous Region, Turpan desert (42° 12' 33'' N 89° 17' 47'' E) | China | CHN | Asia | 42.2092 | 89.2964 | ||||
43967 | soil sample collected from Turpan desert in Xinjiang Uyghur Autonomous Region, north-western China | desert in Xinjiang Uyghur Autonomous Region | China | CHN | Asia | 42.2092 | 89.2964 | Tryptic soy agar | supplemeted with 100 mg/L nyastatin | 2 weeks | 28 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Desert |
#Environmental | #Terrestrial | #Soil |
#Condition | #Xerophilic |
Safety information
risk assessment
- @ref: 24307
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24307
- description: Arthrobacter sp. YIM CS25 16S ribosomal RNA gene, partial sequence
- accession: KT946776
- length: 1491
- database: ena
- NCBI tax ID: 1742687
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Arthrobacter deserti CGMCC 1.15091 | GCA_012395865 | scaffold | ncbi | 1742687 |
66792 | Arthrobacter deserti strain CGMCC 1.15091 | 1742687.3 | wgs | patric | 1742687 |
66792 | Arthrobacter deserti CGMCC 1.15091 | 2903049818 | draft | img | 1742687 |
GC content
@ref | GC-content | method |
---|---|---|
43967 | 68.3 | thermal denaturation, midpoint method (Tm) |
24307 | 68.3 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 72.546 | yes |
flagellated | no | 93.855 | no |
gram-positive | yes | 90.592 | no |
anaerobic | no | 98.846 | yes |
aerobic | yes | 94.133 | no |
halophile | no | 58.218 | no |
spore-forming | no | 95.665 | no |
glucose-util | yes | 85.1 | yes |
thermophile | no | 97.982 | no |
glucose-ferment | no | 89.656 | no |
External links
@ref: 24307
culture collection no.: DSM 29935, CGMCC 1.15091, KCTC 39544, YIM CS25
straininfo link
- @ref: 90844
- straininfo: 400969
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26908080 | Arthrobacter deserti sp. nov., isolated from a desert soil sample. | Hu QW, Chu X, Xiao M, Li CT, Yan ZF, Hozzein WN, Kim CJ, Zhi XY, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000986 | 2016 | Arthrobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 32886595 | Arthrobacter mobilis sp. nov., a novel actinobacterium isolated from Cholistan desert soil. | Ye JJ, Liu SW, Lu QP, Cheema MT, Abbas M, Sajid I, Huang DL, Sun CH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004431 | 2020 | Arthrobacter/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Pakistan, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | 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 | |||
24307 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29935 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29935) | |||
43967 | Qing-Wen Hu, Xiao Chu, Min Xiao, Chang-Tian Li, Zheng-Fei Yan, Wael N. Hozzein, Chang-Jin Kim, Xiao-Yang Zhi, Wen-Jun Li | Arthrobacter deserti sp. nov., isolated from a desert soil sample | 10.1099/ijsem.0.000986 | IJSEM 66: 2035-2040 2016 | 26908080 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
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 | |||
90844 | 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-ID400969.1 |