Strain identifier
BacDive ID: 5477
Type strain:
Species: Aequorivita sublithincola
Strain Designation: 9-3
Strain history: CIP <- 2017, DSMZ <- J. Bowman, Tasmania Univ., Tasmania, Australia: strain 9-3 <- M. Smith
NCBI tax ID(s): 746697 (strain), 101385 (species)
General
@ref: 5266
BacDive-ID: 5477
DSM-Number: 14238
keywords: genome sequence, Bacteria, obligate aerobe, chemoheterotroph, psychrophilic, Gram-negative, filament-shaped
description: Aequorivita sublithincola 9-3 is an obligate aerobe, chemoheterotroph, psychrophilic bacterium that was isolated from quartz stone sublith.
NCBI tax id
NCBI tax id | Matching level |
---|---|
746697 | strain |
101385 | species |
strain history
@ref | history |
---|---|
5266 | <- J. P. Bowman; 9-3 <- M. Smith |
123346 | CIP <- 2017, DSMZ <- J. Bowman, Tasmania Univ., Tasmania, Australia: strain 9-3 <- M. Smith |
doi: 10.13145/bacdive5477.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Aequorivita
- species: Aequorivita sublithincola
- full scientific name: Aequorivita sublithincola Bowman and Nichols 2002
@ref: 5266
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Aequorivita
species: Aequorivita sublithincola
full scientific name: Aequorivita sublithincola Bowman and Nichols 2002
strain designation: 9-3
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
43341 | negative | 0.5-20 µm | 0.4-0.5 µm | filament-shaped | no | |
69480 | negative | 99.991 | ||||
123346 | negative | rod-shaped | no |
colony morphology
@ref | colony color |
---|---|
43341 | orange |
123346 |
pigmentation
@ref | production | name |
---|---|---|
43341 | no | Flexirubin-Type |
123346 | yes | Flexirubin |
multimedia
- @ref: 66793
- multimedia content: EM_DSM_14238_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5266 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
42118 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
123346 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5266 | positive | growth | 2-10 | psychrophilic |
42118 | positive | growth | 25 | mesophilic |
43341 | positive | growth | -2-25 | |
123346 | positive | growth | 15-25 | psychrophilic |
123346 | no | growth | 5 | psychrophilic |
123346 | no | growth | 30 | mesophilic |
123346 | no | growth | 37 | mesophilic |
123346 | no | growth | 41 | thermophilic |
123346 | no | growth | 45 | thermophilic |
culture pH
- @ref: 43341
- ability: positive
- type: optimum
- pH: 7-7.5
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
43341 | obligate aerobe |
123346 | microaerophile |
nutrition type
- @ref: 43341
- type: chemoheterotroph
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.996 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43341 | NaCl | positive | growth | 6 % |
43341 | NaCl | inconsistent | growth | 10 % |
43341 | NaCl | no | growth | 12-99 % |
123346 | NaCl | no | growth | 0 % |
123346 | NaCl | no | growth | 2 % |
123346 | NaCl | no | growth | 4 % |
123346 | NaCl | no | growth | 6 % |
123346 | NaCl | no | growth | 8 % |
123346 | NaCl | no | growth | 10 % |
observation
@ref | observation |
---|---|
43341 | fermentation of sugars and alcohols |
43341 | hydrolysis of polysaccharides |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
43341 | casein | - | hydrolysis | |
43341 | cellulose | - | degradation | 62968 |
43341 | elastin | - | hydrolysis | 4767 |
43341 | esculin | - | hydrolysis | 4853 |
43341 | gelatin | + | hydrolysis | 5291 |
43341 | L-tyrosine | + | hydrolysis | 17895 |
43341 | starch | - | hydrolysis | 28017 |
43341 | tributyrin | - | hydrolysis | 35020 |
43341 | uric acid | - | degradation | 27226 |
43341 | xanthine | - | degradation | 15318 |
43341 | xylan | - | degradation | 37166 |
123346 | esculin | - | hydrolysis | 4853 |
123346 | hippurate | - | hydrolysis | 606565 |
123346 | nitrate | - | reduction | 17632 |
123346 | nitrite | - | reduction | 16301 |
123346 | malonate | - | assimilation | 15792 |
123346 | nitrate | - | respiration | 17632 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43341 | 15688 | acetoin | no |
43341 | 35581 | indole | no |
123346 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
43341 | 15688 | acetoin | - | |
123346 | 15688 | acetoin | - | |
123346 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43341 | alkaline phosphatase | + | 3.1.3.1 |
43341 | esterase | - | |
43341 | esterase | + | |
43341 | lysine decarboxylase | - | 4.1.1.18 |
43341 | arginine dihydrolase | - | 3.5.3.6 |
43341 | ornithine decarboxylase | - | 4.1.1.17 |
43341 | alpha-arabinosidase | - | 3.2.1.55 |
43341 | alpha-fucosidase | - | 3.2.1.51 |
43341 | beta-glucosidase | - | 3.2.1.21 |
43341 | beta-galactosidase | - | 3.2.1.23 |
43341 | 6-phospho-beta-galactosidase | - | 3.2.1.85 |
43341 | beta-glucuronidase | - | 3.2.1.31 |
43341 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
43341 | lipase | - | |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
123346 | oxidase | - | |
123346 | beta-galactosidase | + | 3.2.1.23 |
123346 | alcohol dehydrogenase | - | 1.1.1.1 |
123346 | gelatinase | +/- | |
123346 | amylase | - | |
123346 | DNase | - | |
123346 | caseinase | - | 3.4.21.50 |
123346 | catalase | + | 1.11.1.6 |
123346 | tween esterase | + | |
123346 | gamma-glutamyltransferase | + | 2.3.2.2 |
123346 | lecithinase | - | |
123346 | lipase | - | |
123346 | lysine decarboxylase | - | 4.1.1.18 |
123346 | ornithine decarboxylase | - | 4.1.1.17 |
123346 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
123346 | tryptophan deaminase | - | |
123346 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123346 | - | + | + | + | - | + | + | - | + | + | + | + | - | - | - | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | continent | enrichment culture | isolation procedure | country | origin.country | isolation date |
---|---|---|---|---|---|---|---|---|
5266 | quartz stone sublith | Vestfold Hills | Australia and Oceania | |||||
43341 | quartz stone aublithic material | marine agar (Difco, Oxoid) | sublithic biomass is scraped , vortexed and then diluted in trypicase soy broth | |||||
123346 | Quartz stone sublim | Vestfold hills | Antarctica | Antarctica | ATA | 1998 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Geologic
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
5266 | 1 | Risk group (German classification) |
123346 | 1 | Risk group (French classification) |
Sequence information
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Aequorivita sublithincola DSM 14238 | GCA_000265385 | complete | ncbi | 746697 |
66792 | Aequorivita sublithincola DSM 14238 | 746697.3 | complete | patric | 746697 |
66792 | Aequorivita sublithincola QSSC9-3, DSM 14238 | 2509276063 | complete | img | 746697 |
GC content
- @ref: 5266
- GC-content: 36-37
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 88.927 | yes |
flagellated | no | 95.907 | yes |
gram-positive | no | 98.355 | no |
anaerobic | no | 99.32 | yes |
aerobic | yes | 92.635 | no |
halophile | yes | 79.618 | yes |
spore-forming | no | 94.585 | no |
thermophile | no | 99.73 | yes |
glucose-util | yes | 79.335 | no |
glucose-ferment | no | 91.452 | no |
External links
@ref: 5266
culture collection no.: DSM 14238, ACAM 643, CIP 107454, LMG 21432
straininfo link
- @ref: 74965
- straininfo: 86436
literature
- topic: Phylogeny
- Pubmed-ID: 12361255
- title: Aequorivita gen. nov., a member of the family Flavobacteriaceae isolated from terrestrial and marine Antarctic habitats.
- authors: Bowman JP, Nichols DS
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-52-5-1533
- year: 2002
- mesh: Antarctic Regions, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gram-Negative Aerobic Rods and Cocci/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Seawater/microbiology
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5266 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14238) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14238 | |||
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 | |||
42118 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/4891 | ||||
43341 | 10.1007/978-0-387-68572-4 | |||||
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) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68382 | Automatically annotated from API zym | |||||
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 | |||
74965 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID86436.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123346 | Curators of the CIP | Collection of Institut Pasteur (CIP 107454) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107454 |