Strain identifier
BacDive ID: 13390
Type strain:
Species: Pseudonocardia zijingensis
Strain Designation: 6330
Strain history: CIP <- 2002, JCM <- 2001, Z. Liu: strain 6330
NCBI tax ID(s): 153376 (species)
General
@ref: 12079
BacDive-ID: 13390
DSM-Number: 44774
keywords: 16S sequence, Bacteria, mesophilic, Gram-positive, rod-shaped
description: Pseudonocardia zijingensis 6330 is a mesophilic, Gram-positive, rod-shaped bacterium that was isolated from soil sample.
NCBI tax id
- NCBI tax id: 153376
- Matching level: species
strain history
@ref | history |
---|---|
12079 | <- CGMCC <- Z. Liu; 6330 |
67770 | Z. Liu 6330. |
124031 | CIP <- 2002, JCM <- 2001, Z. Liu: strain 6330 |
doi: 10.13145/bacdive13390.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Pseudonocardia
- species: Pseudonocardia zijingensis
- full scientific name: Pseudonocardia zijingensis Huang et al. 2002
@ref: 12079
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Pseudonocardia
species: Pseudonocardia zijingensis
full scientific name: Pseudonocardia zijingensis Huang et al. 2002
strain designation: 6330
type strain: yes
Morphology
cell morphology
- @ref: 124031
- gram stain: positive
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12079 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water |
34377 | MEDIUM 275 - for Actinomadura rugatobispora and Actinomadura verrucosospora | yes | Distilled water make up to (1000.000 ml);Sodium chloride (1.000 g);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Ammonium sulphate (2.000 g);Starch maize (10.000 g);Calcium carbonate (2.000 g);Trace salt solution - M00447 (1.000 ml) | |
124031 | CIP Medium 275 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=275 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
12079 | positive | growth | 28 | mesophilic |
34377 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
124031 | positive | growth | 25-41 | |
124031 | no | growth | 10 | psychrophilic |
124031 | no | growth | 45 | thermophilic |
Physiology and metabolism
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
124031 | NaCl | positive | growth | 0 % |
124031 | NaCl | no | growth | 2 % |
124031 | NaCl | no | growth | 4 % |
124031 | NaCl | no | growth | 6 % |
124031 | NaCl | no | growth | 8 % |
124031 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | - | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | - | builds acid from | 16024 |
68371 | D-fructose | - | builds acid from | 15824 |
68371 | D-glucose | - | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
68369 | malate | - | assimilation | 25115 |
68369 | adipate | - | assimilation | 17128 |
68369 | decanoate | - | assimilation | 27689 |
68369 | gluconate | - | assimilation | 24265 |
68369 | N-acetylglucosamine | - | assimilation | 59640 |
68369 | D-mannitol | - | assimilation | 16899 |
68369 | D-mannose | - | assimilation | 16024 |
68369 | L-arabinose | - | assimilation | 30849 |
68369 | D-glucose | - | assimilation | 17634 |
68369 | gelatin | - | hydrolysis | 5291 |
68369 | esculin | + | hydrolysis | 4853 |
68369 | urea | - | hydrolysis | 16199 |
68369 | arginine | - | hydrolysis | 29016 |
68369 | D-glucose | - | fermentation | 17634 |
68369 | tryptophan | - | energy source | 27897 |
68369 | nitrate | + | reduction | 17632 |
124031 | esculin | - | hydrolysis | 4853 |
124031 | hippurate | - | hydrolysis | 606565 |
124031 | nitrate | - | reduction | 17632 |
124031 | nitrite | - | reduction | 16301 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
124031 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test | methylred-test |
---|---|---|---|---|---|
68369 | 35581 | indole | - | ||
124031 | 15688 | acetoin | - | ||
124031 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
124031 | oxidase | - | |
124031 | alcohol dehydrogenase | - | 1.1.1.1 |
124031 | gelatinase | - | |
124031 | catalase | + | 1.11.1.6 |
124031 | gamma-glutamyltransferase | - | 2.3.2.2 |
124031 | lysine decarboxylase | - | 4.1.1.18 |
124031 | ornithine decarboxylase | - | 4.1.1.17 |
124031 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
124031 | tryptophan deaminase | - | |
124031 | urease | - | 3.5.1.5 |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
12079 | - | + | +/- | +/- | - | + | +/- | - | - | - | - | - | - | + | - | +/- | - | - | - | - |
124031 | - | - | + | + | - | + | - | + | - | - | + | + | - | + | - | + | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
12079 | + | - | - | - | - | + | - | + | - | - | - | - | - | +/- | - | - | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
124031 | - | - | - | +/- | +/- | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | +/- |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
12079 | soil sample | Yunnan Province, Zijing Mountain | China | CHN | Asia |
67770 | Soil | Zijing Mountain, Yunnan Province | China | CHN | Asia |
124031 | Environment, Soil | Zijing moutain, Yunnan | China | CHN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
12079 | 1 | Risk group (German classification) |
124031 | 2 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20218
- description: Pseudonocardia zijingensis 16S ribosomal RNA gene, partial sequence
- accession: AF325725
- length: 1422
- database: ena
- NCBI tax ID: 153376
GC content
- @ref: 67770
- GC-content: 70.9
- method: thermal denaturation, midpoint method (Tm)
External links
@ref: 12079
culture collection no.: DSM 44774, AS 4.1545, CIP 107621, JCM 11117, BCRC 16328, CGMCC 4.1545
straininfo link
- @ref: 82587
- straininfo: 100894
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12054266 | Proposal to combine the genera Actinobispora and Pseudonocardia in an emended genus Pseudonocardia, and description of Pseudonocardia zijingensis sp. nov.. | Huang Y, Wang L, Lu Z, Hong L, Liu Z, Tan GYA, Goodfellow M | Int J Syst Evol Microbiol | 10.1099/00207713-52-3-977 | 2002 | Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 20827574 | Pseudonocardia sichuanensis sp. nov., a novel endophytic actinomycete isolated from the root of Jatropha curcas L. | Qin S, Xing K, Fei SM, Lin Q, Chen XM, Cao CL, Sun Y, Wang Y, Li WJ, Jiang JH | Antonie Van Leeuwenhoek | 10.1007/s10482-010-9504-7 | 2010 | Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Cell Wall/chemistry, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Jatropha/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 20971834 | Pseudonocardia kunmingensis sp. nov., an actinobacterium isolated from surface-sterilized roots of Artemisia annua L. | Zhao GZ, Li J, Huang HY, Zhu WY, Park DJ, Kim CJ, Xu LH, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.027607-0 | 2010 | Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Artemisia annua/*microbiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
12079 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44774) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44774 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
34377 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5077 | ||||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
82587 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100894.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
124031 | Curators of the CIP | Collection of Institut Pasteur (CIP 107621) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107621 |