Strain identifier
BacDive ID: 140255
Type strain:
Species: Pedobacter zeae
Strain Designation: 22
Strain history: <- J. Gao, Beijing Academy of Agriculture and Forestry Science; 22
NCBI tax ID(s): 1737356 (species)
General
@ref: 42862
BacDive-ID: 140255
DSM-Number: 100774
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Pedobacter zeae 22 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized root tissue of maize.
NCBI tax id
- NCBI tax id: 1737356
- Matching level: species
strain history
- @ref: 42862
- history: <- J. Gao, Beijing Academy of Agriculture and Forestry Science; 22
doi: 10.13145/bacdive140255.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Pedobacter
- species: Pedobacter zeae
- full scientific name: Pedobacter zeae Gao et al. 2017
@ref: 42862
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter zeae
full scientific name: Pedobacter zeae Gao et al. 2017
strain designation: 22
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
25201 | negative | 0.6-1.8 µm | 0.2-0.3 µm | rod-shaped | no | |
69480 | no | 91.3 | ||||
69480 | negative | 99.982 |
colony morphology
- @ref: 25201
- colony size: 0.5-1.0 mm
- colony color: pinkish-yellow
- colony shape: circular
- incubation period: 3 days
- medium used: LB agar plates
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
25201 | LB (Luria-Bertani) MEDIUM | yes | ||
25201 | LB agar plates | yes | ||
25201 | nutrient agar (NA) | yes | ||
25201 | Reasoner's 2A agar (R2A) | yes | ||
25201 | tryptic soy agar (TSA) | yes | ||
25201 | Ashby nitrogen-free medium | yes | ||
42862 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
25201 | positive | growth | 15.0-30.0 | |
25201 | positive | optimum | 30 | mesophilic |
42862 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
25201 | positive | growth | 6.0-7.0 |
25201 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 25201
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.994 |
halophily
@ref | salt | tested relation | concentration | growth |
---|---|---|---|---|
25201 | NaCl | optimum | 1 % | |
25201 | NaCl | growth | 0.0-1.0 %(w/v) | positive |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
25201 | 16808 | 2-dehydro-D-gluconate | - | builds acid from |
25201 | 58143 | 5-dehydro-D-gluconate | - | builds acid from |
25201 | 17128 | adipate | - | assimilation |
25201 | 15963 | ribitol | - | builds acid from |
25201 | 18333 | D-arabitol | - | builds acid from |
25201 | 28847 | D-fucose | - | builds acid from |
25201 | 16899 | D-mannitol | - | assimilation |
25201 | 16899 | D-mannitol | - | builds acid from |
25201 | 6731 | melezitose | - | builds acid from |
25201 | 17924 | D-sorbitol | - | builds acid from |
25201 | 27689 | decanoate | - | assimilation |
25201 | 17113 | erythritol | - | builds acid from |
25201 | 16813 | galactitol | - | builds acid from |
25201 | 28066 | gentiobiose | - | builds acid from |
25201 | 24265 | gluconate | - | builds acid from |
25201 | 17754 | glycerol | - | builds acid from |
25201 | 17268 | myo-inositol | - | builds acid from |
25201 | 15443 | inulin | - | builds acid from |
25201 | 18403 | L-arabitol | - | builds acid from |
25201 | 62345 | L-rhamnose | - | builds acid from |
25201 | 62345 | L-rhamnose | - | oxidation |
25201 | 17266 | L-sorbose | - | builds acid from |
25201 | 65328 | L-xylose | - | builds acid from |
25201 | 25115 | malate | - | assimilation |
25201 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
25201 | 17632 | nitrate | - | reduction |
25201 | 17309 | pectin | - | oxidation |
25201 | 18401 | phenylacetate | - | assimilation |
25201 | 32032 | potassium gluconate | - | assimilation |
25201 | 28017 | starch | - | builds acid from |
25201 | 27897 | tryptophan | - | energy source |
25201 | 17151 | xylitol | - | builds acid from |
25201 | 15589 | L-malate | + | oxidation |
25201 | 27613 | amygdalin | + | builds acid from |
25201 | 18305 | arbutin | + | builds acid from |
25201 | 73706 | bromosuccinate | + | oxidation |
25201 | 17108 | D-arabinose | + | builds acid from |
25201 | 17057 | cellobiose | + | builds acid from |
25201 | 15824 | D-fructose | + | builds acid from |
25201 | 78697 | D-fructose 6-phosphate | + | oxidation |
25201 | 12936 | D-galactose | + | builds acid from |
25201 | 12936 | D-galactose | + | oxidation |
25201 | 8391 | D-gluconate | + | oxidation |
25201 | 17634 | D-glucose | + | assimilation |
25201 | 17634 | D-glucose | + | builds acid from |
25201 | 14314 | D-glucose 6-phosphate | + | oxidation |
25201 | 17716 | lactose | + | builds acid from |
25201 | 62318 | D-lyxose | + | builds acid from |
25201 | 17306 | maltose | + | builds acid from |
25201 | 16024 | D-mannose | + | assimilation |
25201 | 16024 | D-mannose | + | builds acid from |
25201 | 28053 | melibiose | + | builds acid from |
25201 | 16634 | raffinose | + | builds acid from |
25201 | 16988 | D-ribose | + | builds acid from |
25201 | 17992 | sucrose | + | builds acid from |
25201 | 16443 | D-tagatose | + | builds acid from |
25201 | 16551 | D-trehalose | + | builds acid from |
25201 | 32528 | turanose | + | builds acid from |
25201 | 65327 | D-xylose | + | builds acid from |
25201 | 4853 | esculin | + | hydrolysis |
25201 | 4853 | esculin | + | builds acid from |
25201 | 5291 | gelatin | + | hydrolysis |
25201 | 17234 | glucose | + | fermentation |
25201 | 28087 | glycogen | + | builds acid from |
25201 | 30849 | L-arabinose | + | assimilation |
25201 | 30849 | L-arabinose | + | builds acid from |
25201 | 18287 | L-fucose | + | builds acid from |
25201 | 18287 | L-fucose | + | oxidation |
25201 | 15971 | L-histidine | + | oxidation |
25201 | 17115 | L-serine | + | oxidation |
25201 | 17306 | maltose | + | assimilation |
25201 | 320061 | methyl alpha-D-glucopyranoside | + | builds acid from |
25201 | 320061 | methyl alpha-D-glucopyranoside | + | oxidation |
25201 | 43943 | methyl alpha-D-mannoside | + | builds acid from |
25201 | 28037 | N-acetylgalactosamine | + | oxidation |
25201 | 506227 | N-acetylglucosamine | + | assimilation |
25201 | 506227 | N-acetylglucosamine | + | builds acid from |
25201 | 16634 | raffinose | + | oxidation |
25201 | 28077 | rifampicin | + | oxidation |
25201 | 17814 | salicin | + | builds acid from |
25201 | 53258 | sodium citrate | + | assimilation |
25201 | 75228 | sodium lactate | + | oxidation |
25201 | 17164 | stachyose | + | oxidation |
25201 | 27082 | trehalose | + | oxidation |
25201 | 32528 | turanose | + | oxidation |
metabolite production
- @ref: 25201
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 25201
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
25201 | acid phosphatase | + | 3.1.3.2 |
25201 | alkaline phosphatase | + | 3.1.3.1 |
25201 | alpha-chymotrypsin | - | 3.4.21.1 |
25201 | alpha-fucosidase | + | 3.2.1.51 |
25201 | alpha-galactosidase | + | 3.2.1.22 |
25201 | alpha-glucosidase | + | 3.2.1.20 |
25201 | alpha-mannosidase | + | 3.2.1.24 |
25201 | arginine dihydrolase | - | 3.5.3.6 |
25201 | beta-galactosidase | + | 3.2.1.23 |
25201 | beta-glucosidase | + | 3.2.1.21 |
25201 | beta-glucuronidase | + | 3.2.1.31 |
25201 | catalase | + | 1.11.1.6 |
25201 | cystine arylamidase | + | 3.4.11.3 |
25201 | cytochrome oxidase | + | 1.9.3.1 |
25201 | esterase (C 4) | + | |
25201 | esterase Lipase (C 8) | + | |
25201 | leucine arylamidase | + | 3.4.11.1 |
25201 | lipase (C 14) | - | |
25201 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
25201 | naphthol-AS-BI-phosphohydrolase | + | |
25201 | trypsin | + | 3.4.21.4 |
25201 | tryptophan deaminase | - | 4.1.99.1 |
25201 | urease | - | 3.5.1.5 |
25201 | valine arylamidase | + |
fatty acid profile
fatty acids
@ref fatty acid percentage 25201 C15:0 anteiso 0.5 25201 C13:1 at 12-13 0.4 25201 C14:0 2.6 25201 C14:0 2OH 0.3 25201 C14:1ω5c 0.3 25201 C15:1ω6c 0.6 25201 C16:0 0.8 25201 C16:0 3OH 0.8 25201 C16:1ω5c 1.4 25201 C16:1ω7c / C16:1ω6c 31.4 25201 C18:1ω5c 0.4 25201 C19:1ω11c / C19:1ω9c 4.1 25201 C11:0 iso 0.4 25201 C13:0 iso 0.3 25201 C15:0 iso 37 25201 C15:0 iso 3OH 3 25201 C15:1 iso F 0.2 25201 C15:1 iso h / C13:0 3OH 1 25201 C16:0 iso 3OH 0.9 25201 C17:0 iso 0.2 25201 C17:0 iso 3OH 7.9 25201 C17:1 iso I /C17:1 anteiso B 0.9 25201 C17:1 iso ω9c / C16:0 10-methyl 4.5 - type of FA analysis: whole cell analysis
- incubation medium: TSA medium
- incubation temperature: 28
- incubation time: 3
- library/peak naming table: TSBA 6
- system: MIS MIDI
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|
25201 | surface-sterilized root tissue of maize | Fangshan District of Beijing | Republic of China | CHN | Asia | Ashby nitrogen-free medium | 3 days | 28 |
42862 | surface-sterilized root tissue of maize | Fangshan District of Beijing | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root (Rhizome) |
#Host Body-Site | #Plant | #Sterilized plant part |
Safety information
risk assessment
- @ref: 42862
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
25201 | Pedobacter sp. 22 16S ribosomal RNA gene, partial sequence | KR610524.2 | 1480 | nuccore | 1737356 |
42862 | Pedobacter zeae strain 22 16S ribosomal RNA gene, partial sequence | KR610524 | 1480 | ena | 1737356 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pedobacter zeae CGMCC 1.15287 | GCA_014641575 | scaffold | ncbi | 1737356 |
66792 | Pedobacter zeae DSM 100774 | GCA_014196715 | scaffold | ncbi | 1737356 |
66792 | Pedobacter zeae strain CGMCC 1.15287 | 1737356.4 | wgs | patric | 1737356 |
66792 | Pedobacter zeae strain DSM 100774 | 1737356.3 | wgs | patric | 1737356 |
66792 | Pedobacter zeae DSM 100774 | 2829961646 | draft | img | 1737356 |
GC content
@ref | GC-content | method |
---|---|---|
25201 | 40.7-41.7 | thermal denaturation, midpoint method (Tm) |
42862 | 41.2 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 96.876 | yes |
gram-positive | no | 97.069 | yes |
anaerobic | no | 99.493 | yes |
aerobic | yes | 86.489 | no |
halophile | no | 96.575 | yes |
spore-forming | no | 93.936 | no |
thermophile | no | 98.51 | yes |
glucose-util | yes | 90.039 | yes |
motile | no | 90.126 | yes |
glucose-ferment | no | 88.093 | no |
External links
@ref: 42862
culture collection no.: DSM 100774, CGMCC 1.15287
straininfo link
- @ref: 96563
- straininfo: 407605
literature
- topic: Phylogeny
- Pubmed-ID: 27902277
- title: Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root.
- authors: Gao JL, Sun P, Mao XJ, Du YL, Liu BY, Sun JG
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001603
- year: 2017
- mesh: Bacterial Typing Techniques, Base Composition, Beijing, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology
- topic2: Enzymology
Reference
@id | authors | title | doi/url | journal | pubmed | catalogue |
---|---|---|---|---|---|---|
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 | |||
25201 | J. L. S. Gao, P.,Mao, X. J.,Du, Y. L.,Liu, B. Y.,Sun, J. G. | Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root | 10.1099/ijsem.0.001603 | IJSEM 67: 231-236 2017 | 27902277 | |
42862 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100774 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100774) | |||
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 | |||
96563 | 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-ID407605.1 |