Strain identifier
BacDive ID: 158594
Type strain:
Species: Stakelama algicida
Strain history: J. Kim; Kyonggi Univ., South Korea; Yeonmyeong 1-13.
NCBI tax ID(s): 1715649 (species)
General
@ref: 65307
BacDive-ID: 158594
keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Stakelama algicida KEMB 9005-324 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface seawater.
NCBI tax id
- NCBI tax id: 1715649
- Matching level: species
strain history
- @ref: 67770
- history: J. Kim; Kyonggi Univ., South Korea; Yeonmyeong 1-13.
doi: 10.13145/bacdive158594.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Stakelama
- species: Stakelama algicida
- full scientific name: Stakelama algicida Kristyanto et al. 2018
@ref: 65307
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Stakelama
species: Stakelama algicida
type strain: yes
Morphology
cell morphology
- @ref: 65307
- gram stain: negative
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 65307
- colony size: 1-1.2 mm
- colony color: yellow
- colony shape: circular
- medium used: R2A
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
65307 | Reasoner's 2A agar (R2A) | yes |
65307 | Marine agar (MA) | yes |
65307 | tryptic soy agar | yes |
65307 | Nutrient agar (NA) | yes |
65307 | LB (Luria-Bertani) MEDIUM | yes |
65307 | MacConkey agar | no |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
65307 | positive | growth | 5-39 | |
65307 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
65307 | positive | growth | 5-10 | alkaliphile |
65307 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 65307
- oxygen tolerance: aerobe
spore formation
- @ref: 65307
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
65307 | NaCl | positive | growth | 0-11 % |
65307 | NaCl | positive | optimum | 0 % |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
65307 | 17128 | adipate | - | assimilation |
65307 | 27613 | amygdalin | - | fermentation |
65307 | 27613 | amygdalin | + | builds acid from |
65307 | 22599 | arabinose | - | fermentation |
65307 | 27689 | decanoate | - | assimilation |
65307 | casein | - | hydrolysis | |
65307 | 17057 | cellobiose | + | builds acid from |
65307 | 16947 | citrate | - | assimilation |
65307 | 15963 | ribitol | - | builds acid from |
65307 | 17108 | D-arabinose | - | builds acid from |
65307 | 18333 | D-arabitol | - | builds acid from |
65307 | 15824 | D-fructose | - | builds acid from |
65307 | 17634 | D-glucose | + | assimilation |
65307 | 17634 | D-glucose | + | builds acid from |
65307 | 62318 | D-lyxose | - | builds acid from |
65307 | 16899 | D-mannitol | - | assimilation |
65307 | 16899 | D-mannitol | - | builds acid from |
65307 | 16024 | D-mannose | - | assimilation |
65307 | 16024 | D-mannose | - | builds acid from |
65307 | 16988 | D-ribose | - | builds acid from |
65307 | 17924 | D-sorbitol | - | builds acid from |
65307 | 16443 | D-tagatose | - | builds acid from |
65307 | 16991 | dna | - | hydrolysis |
65307 | 16813 | galactitol | - | builds acid from |
65307 | 17113 | erythritol | - | builds acid from |
65307 | 4853 | esculin | + | hydrolysis |
65307 | 5291 | gelatin | - | hydrolysis |
65307 | 28066 | gentiobiose | + | builds acid from |
65307 | 17234 | glucose | - | fermentation |
65307 | 17754 | glycerol | - | builds acid from |
65307 | 28087 | glycogen | - | builds acid from |
65307 | 17268 | myo-inositol | - | builds acid from |
65307 | 17268 | myo-inositol | - | fermentation |
65307 | 15443 | inulin | - | builds acid from |
65307 | 30849 | L-arabinose | + | assimilation |
65307 | 18403 | L-arabitol | - | builds acid from |
65307 | 18287 | L-fucose | - | builds acid from |
65307 | 62345 | L-rhamnose | - | builds acid from |
65307 | 17266 | L-sorbose | - | builds acid from |
65307 | 65328 | L-xylose | - | builds acid from |
65307 | 25115 | malate | + | assimilation |
65307 | 17306 | maltose | - | assimilation |
65307 | 17306 | maltose | - | builds acid from |
65307 | 29864 | mannitol | - | fermentation |
65307 | 6731 | melezitose | - | builds acid from |
65307 | 28053 | melibiose | - | builds acid from |
65307 | 28053 | melibiose | - | fermentation |
65307 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
65307 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
65307 | 37657 | methyl D-glucoside | - | builds acid from |
65307 | 506227 | N-acetylglucosamine | - | builds acid from |
65307 | 506227 | N-acetylglucosamine | + | assimilation |
65307 | 18401 | phenylacetate | - | assimilation |
65307 | potassium 2-dehydro-D-gluconate | - | builds acid from | |
65307 | potassium 5-dehydro-D-gluconate | - | builds acid from | |
65307 | 32032 | potassium gluconate | - | assimilation |
65307 | 32032 | potassium gluconate | - | builds acid from |
65307 | 16634 | raffinose | - | builds acid from |
65307 | 26546 | rhamnose | - | fermentation |
65307 | 53258 | sodium citrate | - | assimilation |
65307 | 30911 | sorbitol | - | fermentation |
65307 | 28017 | starch | - | hydrolysis |
65307 | 17992 | sucrose | - | fermentation |
65307 | 27082 | trehalose | + | builds acid from |
65307 | 32528 | turanose | - | builds acid from |
65307 | 53426 | tween 80 | + | hydrolysis |
65307 | 16199 | urea | - | hydrolysis |
65307 | 17151 | xylitol | - | builds acid from |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant | resistance conc. |
---|---|---|---|---|---|---|---|
65307 | 17833 | gentamicin | yes | yes | 10 µg (disc) | ||
65307 | 28077 | rifampicin | yes | yes | 10 µg (disc) | ||
65307 | 17076 | streptomycin | yes | yes | 10 µg (disc) | ||
65307 | 17334 | penicillin | yes | yes | 10 µg (disc) | ||
65307 | 28971 | ampicillin | yes | yes | 30 µg (disc) | ||
65307 | 6104 | kanamycin | yes | yes | 30 µg (disc) | ||
65307 | 27902 | tetracycline | yes | yes | 31 µg (disc) | ||
65307 | 45924 | trimethoprim | yes | yes | 32 µg (disc) | ||
65307 | 7507 | neomycin | yes | yes | 33 µg (disc) | ||
65307 | 28368 | novobiocin | yes | yes | 34 µg (disc) | ||
65307 | 17698 | chloramphenicol | yes | yes | 100 µg (disc) | ||
65307 | 100147 | nalidixic acid | yes | yes | 30 µg (disc) | ||
65307 | 27641 | cycloheximide | yes | yes | 30 µg (disc) | ||
65307 | 9332 | sulfamethoxazole | yes | yes | 30 µg (disc) |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
65307 | 15688 | acetoin | no |
65307 | 16136 | hydrogen sulfide | no |
65307 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | methylred-test | voges-proskauer-test |
---|---|---|---|---|
65307 | 17234 | glucose | - | |
65307 | 15688 | acetoin | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
65307 | catalase | + | 1.11.1.6 |
65307 | cytochrome oxidase | + | 1.9.3.1 |
65307 | alkaline phosphatase | + | 3.1.3.1 |
65307 | esterase (C 4) | + | |
65307 | esterase Lipase (C 8) | + | |
65307 | leucine arylamidase | + | 3.4.11.1 |
65307 | valine arylamidase | + | |
65307 | cystine arylamidase | + | 3.4.11.3 |
65307 | trypsin | + | 3.4.21.4 |
65307 | acid phosphatase | + | 3.1.3.2 |
65307 | naphthol-AS-BI-phosphohydrolase | + | |
65307 | beta-glucosidase | + | 3.2.1.21 |
65307 | beta-glucuronidase | + | 3.2.1.31 |
65307 | beta-galactosidase | + | 3.2.1.23 |
65307 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
65307 | lysine decarboxylase | - | 4.1.1.18 |
65307 | arginine dihydrolase | - | 3.5.3.6 |
65307 | ornithine decarboxylase | - | 4.1.1.17 |
65307 | lipase (C 14) | - | |
65307 | alpha-chymotrypsin | - | 3.4.21.1 |
65307 | alpha-galactosidase | - | 3.2.1.22 |
65307 | alpha-glucosidase | - | 3.2.1.20 |
65307 | alpha-mannosidase | - | 3.2.1.24 |
65307 | alpha-fucosidase | - | 3.2.1.51 |
fatty acid profile
fatty acids
@ref fatty acid percentage 65307 C16:0 13.3 65307 C18:1ω7c 71.4 65307 C19:0 cyclo ω8c 2.7 65307 C14:0 2OH 8.3 65307 C16:1ω7c and/or C16:1ω6c 2.3 - type of FA analysis: whole cell analysis
- incubation medium: R2A
- agar/liquid: agar
- incubation temperature: 30
- incubation time: 2
- software version: Sherlock 6.2B
- library/peak naming table: TSBA6
- system: MIS MIDI
- cutoff value:
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 | isolation procedure |
---|---|---|---|---|---|---|---|---|---|---|---|---|
65307 | surface seawater | Geoje Island in the South Sea | Republic of Korea | KOR | Asia | 35.3072 | 128.667 | ZoBell agar | 5 g peptone, 1 g yeast extract, 0.01 g FePO 4 .4H 2 O, 15 g agar, 750 ml aged seawater, 250 ml distilled water, pH 7.2 | 7 days | 25 | The sample was filtered through a membrane filter with 0.22 µm pore size and spread-plated on ZoBell agar |
67770 | Surface seawater collected from Geoje Island in the South Sea | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Surface water |
taxonmaps
- @ref: 69479
- File name: preview.99_102787.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_20001;97_24846;98_31470;99_102787&stattab=map
- Last taxonomy: Stakelama algicida
- 16S sequence: KR054617
- Sequence Identity:
- Total samples: 92
- soil counts: 10
- aquatic counts: 42
- animal counts: 6
- plant counts: 34
Sequence information
16S sequences
- @ref: 65307
- description: 16S rRNA gene sequence
- accession: KR054617
- database: nuccore
GC content
- @ref: 67770
- GC-content: 65.1
- method: high performance liquid chromatography (HPLC)
External links
@ref: 65307
culture collection no.: KEMB 9005-324, JCM 31498, Yeonmyeong 1-13
literature
- topic: Phylogeny
- Pubmed-ID: 29205132
- title: Stakelama algicida sp. nov., novel algicidal species of the family Sphingomonadaceae isolated from seawater.
- authors: Kristyanto S, Chaudhary DK, Kim J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002506
- year: 2017
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry, *Water Microbiology
- topic2: Transcriptome
Reference
@id | authors | title | doi/url | 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 | ||
65307 | Sylvia Kristyanto, Dhiraj Kumar Chaudhary, Jaisoo Kim | Stakelama algicida sp. nov., novel algicidal species of the family Sphingomonadaceae isolated from seawater | 10.1099/ijsem.0.002506 | IJSEM 68: 317-323 2018 | 29205132 |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |