Strain identifier
BacDive ID: 14222
Type strain:
Species: Rhizorhapis suberifaciens
Strain Designation: CA1, EY 2404, Ca 1
Strain history: CIP <- 1998, A.H.C. van Bruggen, Univ. California, Davis, CA, USA: strain Ca 1 <- C. Waters
NCBI tax ID(s): 1219056 (strain), 13656 (species)
General
@ref: 3170
BacDive-ID: 14222
DSM-Number: 7465
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, plant pathogen
description: Rhizorhapis suberifaciens CA1 is a mesophilic, Gram-negative plant pathogen that was isolated from Lactuca sativa, corky roots.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1219056 | strain |
13656 | species |
strain history
@ref | history |
---|---|
3170 | <- LMG <- A. van Bruggen Univ. California, USA |
67770 | ATCC 49355 <-- A. H. C. van Bruggen CR-CA1 <-- R. Michelmore <-- C. Waters. |
123343 | CIP <- 1998, A.H.C. van Bruggen, Univ. California, Davis, CA, USA: strain Ca 1 <- C. Waters |
doi: 10.13145/bacdive14222.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Rhizorhapis
- species: Rhizorhapis suberifaciens
- full scientific name: Rhizorhapis suberifaciens (van Bruggen et al. 1990) Francis et al. 2014
synonyms
@ref synonym 20215 Sphingobium suberifaciens 20215 Rhizomonas suberifaciens 20215 Sphingomonas suberifaciens
@ref: 3170
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Rhizorhapis
species: Rhizorhapis suberifaciens
full scientific name: Rhizorhapis suberifaciens (van Bruggen et al. 1990) Francis et al. 2014
strain designation: CA1, EY 2404, Ca 1
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.998 | ||
123343 | negative | rod-shaped | yes |
pigmentation
- @ref: 123343
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3170 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
3170 | RHIZOMONAS SUBERIFACIENS MEDIUM (DSMZ Medium 726) | yes | https://mediadive.dsmz.de/medium/726 | Name: RHIZOMONAS SUBERIFACIENS MEDIUM (DSMZ Medium 726) Composition: Agar 11.0 g/l Enzymatic digest of casein 5.0 g/l Glucose 2.5 g/l K2HPO4 x 3 H2O 1.3 g/l MgSO4 x 7 H2O 0.5 g/l KNO3 0.5 g/l Ca(NO3)2 x 4 H2O 0.06 g/l Distilled water |
36403 | MEDIUM 254 - for Rhizomonas suberifaciens | yes | Distilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.500 g);Glucose (2.500 g);Potassium nitrate (0.500 g);Calcium nitrate tetrahydrate (0.060g);Di Potassium monohydrogenophosphate (1.000 g);Casein hydrolysate acid hydrolysed vitamin | |
123343 | CIP Medium 254 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=254 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3170 | positive | growth | 28 | mesophilic |
36403 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 26 | mesophilic |
123343 | positive | growth | 25-30 | mesophilic |
123343 | no | growth | 5 | psychrophilic |
123343 | no | growth | 10 | psychrophilic |
123343 | no | growth | 37 | mesophilic |
123343 | no | growth | 41 | thermophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.99 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
123343 | NaCl | positive | growth | 0 % |
123343 | NaCl | no | growth | 2 % |
123343 | NaCl | no | growth | 4 % |
123343 | NaCl | no | growth | 6 % |
123343 | NaCl | no | growth | 8 % |
123343 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | + | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
123343 | 16947 | citrate | - | carbon source |
123343 | 4853 | esculin | + | hydrolysis |
123343 | 17632 | nitrate | + | reduction |
123343 | 16301 | nitrite | - | reduction |
antibiotic resistance
- @ref: 123343
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
123343 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
123343 | oxidase | + | |
123343 | beta-galactosidase | + | 3.2.1.23 |
123343 | alcohol dehydrogenase | - | 1.1.1.1 |
123343 | gelatinase | - | |
123343 | catalase | + | 1.11.1.6 |
123343 | lysine decarboxylase | - | 4.1.1.18 |
123343 | ornithine decarboxylase | - | 4.1.1.17 |
123343 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
123343 | tryptophan deaminase | - | |
123343 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123343 | - | + | + | + | - | + | + | - | + | - | + | - | - | + | - | + | + | - | - | - |
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 | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3170 | + | - | - | - | - | + | - | + | - | + | - | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
3170 | Lactuca sativa, corky roots | Lactuca sativa | California | USA | USA | North America |
67770 | Lettuce roots | CA | USA | USA | North America | |
123343 | Plant, Corked lettuce roots | California | United States of America | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_87530.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_36340;97_46181;98_60493;99_87530&stattab=map
- Last taxonomy: Rhizorhapis suberifaciens subclade
- 16S sequence: KF437561
- Sequence Identity:
- Total samples: 24368
- soil counts: 12941
- aquatic counts: 5886
- animal counts: 2084
- plant counts: 3457
Safety information
risk assessment
@ref | pathogenicity plant | biosafety level | biosafety level comment |
---|---|---|---|
3170 | yes | 1 | Risk group (German classification) |
123343 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
3170 | Sphingomonas suberifaciens gene for 16S rRNA, partial sequence | D13737 | 1415 | ena | 1219056 |
3170 | Rhizorhapis suberifaciens NBRC 15211 16S ribosomal RNA gene, partial sequence | KF437561 | 1453 | ena | 1219056 |
67770 | Sphingomonas suberifaciens gene for 16S rRNA, partial sequence, strain: NBRC 15211 | AB680813 | 1414 | ena | 1219056 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhizorhapis suberifaciens DSM 7465 | GCA_014200045 | scaffold | ncbi | 13656 |
66792 | Rhizorhapis suberifaciens strain DSM 7465 | 13656.4 | wgs | patric | 13656 |
66792 | Rhizorhapis suberifaciens DSM 7465 | 2829787817 | draft | img | 13656 |
GC content
@ref | GC-content | method |
---|---|---|
3170 | 59 | |
67770 | 58.6-59.2 | Buoyant density centrifugation (BD) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 83.622 | no |
gram-positive | no | 97.579 | no |
anaerobic | no | 98.101 | no |
aerobic | yes | 83.327 | no |
halophile | no | 96.734 | no |
spore-forming | no | 90.832 | no |
glucose-util | yes | 79.631 | no |
thermophile | no | 93.353 | yes |
motile | yes | 71.851 | no |
glucose-ferment | no | 93.127 | yes |
External links
@ref: 3170
culture collection no.: DSM 7465, ATCC 49355, CIP 105429, ICMP 12535, JCM 8521, LMG 11026, LMG 17323, NBRC 15211, NCPPB 3629, IFO 15211, LMG 15574, LMG 15591, LMG 9830
straininfo link
- @ref: 83381
- straininfo: 4820
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 8186095 | Phylogenetic evidence for Sphingomonas and Rhizomonas as nonphotosynthetic members of the alpha-4 subclass of the Proteobacteria. | Takeuchi M, Sawada H, Oyaizu H, Yokota A | Int J Syst Bacteriol | 10.1099/00207713-44-2-308 | 1994 | Bacteriochlorophylls/analysis, Base Sequence, DNA, Bacterial/*genetics, DNA, Ribosomal/*genetics, Fatty Acids/analysis, Gram-Negative Bacteria/chemistry/*classification/genetics, Lipids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 10385200 | Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas. | Yabuuchi E, Kosako Y, Naka T, Suzuki S, Yano I | Microbiol Immunol | 10.1111/j.1348-0421.1999.tb02414.x | 1999 | Base Composition, DNA, Bacterial, DNA, Ribosomal, Genotype, Glycosphingolipids/analysis, Gram-Negative Aerobic Bacteria/chemistry/*classification/genetics, Microbial Sensitivity Tests, Phylogeny, RNA, Ribosomal, 16S | Genetics |
Phylogeny | 22561591 | Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov. | Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ, Tindall BJ, Sproer C, Overmann J | Int J Syst Evol Microbiol | 10.1099/ijs.0.040105-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Fresh Water, Molecular Sequence Data, Myristic Acids/analysis, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, *Water Microbiology | Genetics |
Phylogeny | 24436067 | Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. | Francis IM, Jochimsen KN, De Vos P, van Bruggen AHC | Int J Syst Evol Microbiol | 10.1099/ijs.0.058909-0 | 2014 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lettuce/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Diseases/*microbiology, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification | Genetics |
Phylogeny | 24647265 | Novel primers and PCR protocols for the specific detection and quantification of Sphingobium suberifaciens in situ. | Bull CT, Goldman PH, Martin KJ | Mol Cell Probes | 10.1016/j.mcp.2014.03.001 | 2014 | Bacterial Typing Techniques/methods, DNA Primers/*genetics, DNA, Bacterial/chemistry/*genetics, Genetic Variation, Lettuce/microbiology, Molecular Sequence Data, Plant Roots/microbiology, Polymerase Chain Reaction/*methods, RNA, Ribosomal, 16S/*genetics, Reproducibility of Results, Sequence Analysis, DNA, Soil Microbiology, Species Specificity, Sphingomonadaceae/classification/*genetics | Genetics |
Phylogeny | 25385991 | Sphingobium subterraneum sp. nov., isolated from ground water. | Lee JC, Kim SG, Whang KS | Int J Syst Evol Microbiol | 10.1099/ijs.0.069708-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Groundwater/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistry | Genetics |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
3170 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7465) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-7465 | |
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 | |
36403 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17448 | ||
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) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68369 | Automatically annotated from API 20NE | |||
68382 | Automatically annotated from API zym | |||
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 | |
83381 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID4820.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
123343 | Curators of the CIP | Collection of Institut Pasteur (CIP 105429) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105429 |