Strain identifier
BacDive ID: 159837
Type strain:
Species: Abyssibacter profundi
Strain Designation: OUC007
Strain history: <- Min Yu, Ocean Univ. of China
NCBI tax ID(s): 2182787 (species)
General
@ref: 66716
BacDive-ID: 159837
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, colony-forming
description: Abyssibacter profundi OUC007 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from the seawater at a depth of 1000 m in the Mariana Trench at station MT1.
NCBI tax id
- NCBI tax id: 2182787
- Matching level: species
strain history
@ref | history |
---|---|
67770 | M. Yu; Coll. of Mar. Life Sci., Ocean Univ. of China, China; OUC007. |
67771 | <- Min Yu, Ocean Univ. of China |
doi: 10.13145/bacdive159837.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Nevskiales
- family: Salinisphaeraceae
- genus: Abyssibacter
- species: Abyssibacter profundi
- full scientific name: Abyssibacter profundi Zhou et al. 2018
@ref: 66716
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Nevskiales
family: Salinisphaeraceae
genus: Abyssibacter
species: Abyssibacter profundi
strain designation: OUC007
type strain: yes
Morphology
cell morphology
- @ref: 66716
- gram stain: negative
- cell length: 1.7-1.9 µm
- cell width: 0.4-0.6 µm
- cell shape: rod-shaped
- motility: yes
- flagellum arrangement: polar
colony morphology
- @ref: 66716
- colony size: 1-2 mm
- colony color: transparent
- colony shape: circular
- incubation period: 3 days
- medium used: Marine agar (MA)
Culture and growth conditions
culture medium
- @ref: 66716
- name: Marine agar (MA)
- growth: yes
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
66716 | positive | optimum | 37 | mesophilic |
66716 | positive | growth | 10-45 | |
67770 | positive | growth | 37 | mesophilic |
67771 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
66716 | positive | optimum | 7.0-8.0 | |
66716 | positive | growth | 7.0-9.0 | alkaliphile |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
66716 | aerobe |
67771 | aerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
66716 | NaCl | positive | growth | 0-7 %(w/v) |
66716 | NaCl | positive | optimum | 2-3 %(w/v) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
66716 | 16024 | D-mannose | - | assimilation |
66716 | 16899 | D-mannitol | - | assimilation |
66716 | 17128 | adipate | - | assimilation |
66716 | 17306 | maltose | - | assimilation |
66716 | 17634 | D-glucose | - | assimilation |
66716 | 18401 | phenylacetate | - | assimilation |
66716 | 25115 | malate | - | assimilation |
66716 | 27689 | decanoate | - | assimilation |
66716 | 30849 | L-arabinose | - | assimilation |
66716 | 32032 | potassium gluconate | - | assimilation |
66716 | 53258 | sodium citrate | - | assimilation |
66716 | 59640 | N-acetylglucosamine | - | assimilation |
66716 | 6731 | melezitose | - | builds acid from |
66716 | 12936 | D-galactose | - | builds acid from |
66716 | 15443 | inulin | - | builds acid from |
66716 | 15824 | D-fructose | - | builds acid from |
66716 | 15963 | ribitol | - | builds acid from |
66716 | 16024 | D-mannose | - | builds acid from |
66716 | 16443 | D-tagatose | - | builds acid from |
66716 | 16634 | raffinose | - | builds acid from |
66716 | 16813 | galactitol | - | builds acid from |
66716 | 16899 | D-mannitol | - | builds acid from |
66716 | 16988 | D-ribose | - | builds acid from |
66716 | 17057 | cellobiose | - | builds acid from |
66716 | 17108 | D-arabinose | - | builds acid from |
66716 | 17113 | erythritol | - | builds acid from |
66716 | 17151 | xylitol | - | builds acid from |
66716 | 17266 | L-sorbose | - | builds acid from |
66716 | 17268 | myo-inositol | - | builds acid from |
66716 | 17306 | maltose | - | builds acid from |
66716 | 17634 | D-glucose | - | builds acid from |
66716 | 17716 | lactose | - | builds acid from |
66716 | 17924 | D-sorbitol | - | builds acid from |
66716 | 18287 | L-fucose | - | builds acid from |
66716 | 18305 | arbutin | - | builds acid from |
66716 | 18333 | D-arabitol | - | builds acid from |
66716 | 18403 | L-arabitol | - | builds acid from |
66716 | 27082 | trehalose | - | builds acid from |
66716 | 27613 | amygdalin | - | builds acid from |
66716 | 28066 | gentiobiose | - | builds acid from |
66716 | 28087 | glycogen | - | builds acid from |
66716 | 28847 | D-fucose | - | builds acid from |
66716 | 30849 | L-arabinose | - | builds acid from |
66716 | 32528 | turanose | - | builds acid from |
66716 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
66716 | 59640 | N-acetylglucosamine | - | builds acid from |
66716 | 62318 | D-lyxose | - | builds acid from |
66716 | 62345 | L-rhamnose | - | builds acid from |
66716 | 65327 | D-xylose | - | builds acid from |
66716 | 65328 | L-xylose | - | builds acid from |
66716 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
66716 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
66716 | esculin ferric citrate | - | builds acid from | |
66716 | potassium 2-dehydro-D-gluconate | - | builds acid from | |
66716 | potassium 5-dehydro-D-gluconate | - | builds acid from | |
66716 | 17754 | glycerol | + | builds acid from |
66716 | 17814 | salicin | + | builds acid from |
66716 | 17992 | sucrose | + | builds acid from |
66716 | 28017 | starch | + | builds acid from |
66716 | 28053 | melibiose | + | builds acid from |
66716 | 32032 | potassium gluconate | + | builds acid from |
66716 | 8295 | beta-hydroxybutyrate | + | carbon source |
66716 | 16383 | cis-aconitate | + | carbon source |
66716 | 16724 | 4-hydroxybutyrate | + | carbon source |
66716 | 21217 | L-alaninamide | + | carbon source |
66716 | 28644 | 2-oxopentanoate | + | carbon source |
66716 | 40585 | alpha-cyclodextrin | + | carbon source |
66716 | 51850 | methyl pyruvate | + | carbon source |
66716 | 53423 | tween 40 | + | carbon source |
66716 | 53426 | tween 80 | + | carbon source |
66716 | 75146 | monomethyl succinate | + | carbon source |
66716 | 16991 | dna | - | hydrolysis |
66716 | 17029 | chitin | - | hydrolysis |
66716 | 28017 | starch | - | hydrolysis |
66716 | 58187 | alginate | - | hydrolysis |
66716 | 62968 | cellulose | - | hydrolysis |
66716 | casein | - | hydrolysis | |
66716 | 5291 | gelatin | + | hydrolysis |
66716 | 53423 | tween 40 | + | hydrolysis |
66716 | 53424 | tween 20 | + | hydrolysis |
66716 | 53426 | tween 80 | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
66716 | acid phosphatase | - | 3.1.3.2 |
66716 | alpha-galactosidase | - | 3.2.1.22 |
66716 | alpha-glucosidase | - | 3.2.1.20 |
66716 | alpha-mannosidase | - | 3.2.1.24 |
66716 | beta-glucosidase | - | 3.2.1.21 |
66716 | beta-glucuronidase | - | 3.2.1.31 |
66716 | catalase | - | 1.11.1.6 |
66716 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
66716 | trypsin | - | 3.4.21.4 |
66716 | valine arylamidase | - | |
66716 | alkaline phosphatase | + | 3.1.3.1 |
66716 | alpha-fucosidase | + | 3.2.1.51 |
66716 | beta-galactosidase | + | 3.2.1.23 |
66716 | cytochrome oxidase | + | 1.9.3.1 |
66716 | esterase (C 4) | + | |
66716 | esterase Lipase (C 8) | + | |
66716 | gelatinase | + | |
66716 | leucine arylamidase | + | 3.4.11.1 |
66716 | naphthol-AS-BI-phosphohydrolase | + |
fatty acid profile
fatty acids
@ref fatty acid percentage 66716 C19:1 w6c / C19:0 cyclo 1.03 66716 C10:0 1.05 66716 C11:0 1.22 66716 C20:1 w7c 1.24 66716 C16:1 w5c 1.27 66716 C17:0 10-methyl 1.94 66716 C17:0 2.54 66716 C16:0 4.03 66716 C17:1 w6c 4.25 66716 C18:1 w6c / C18:1 w7c 58.3 66716 C18:0 6.57 66716 C12:0 3OH 6.81 66716 C12:0 7.22 - type of FA analysis: whole cell analysis
- incubation medium: MA
- agar/liquid: agar
- incubation temperature: 28
- incubation time: 3
- software version: Sherlock 6.1
- library/peak naming table: RTSBA6
- system: MIS MIDI
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | sampling date | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture temperature | isolation procedure |
---|---|---|---|---|---|---|---|---|---|---|---|
66716 | the seawater at a depth of 1000 m in the Mariana Trench at station MT1 | 2015-11 | 1000 m in the Mariana Trench at station MT1 in the western Pacific Ocean, an average of 200 km to the east of the Mariana Islands, in the Western Pacific | Philippines | PHL | Asia | 11.3839 | 142.5 | marine agar | 28 | The seawater samples were spread on marine agar 2216E plates and incubated atroom temperature (approximately 28°C) on board and 28°C in the laboratory. |
67770 | Seawater at a depth of 1000 m in the Mariana Trench | ||||||||||
67771 | From 1000m sea water | Marianas Trench of Pacific Ocean | International waters |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_68188.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16084;96_28507;97_35926;98_46423;99_68188&stattab=map
- Last taxonomy: Abyssibacter profundi subclade
- 16S sequence: KY612316
- Sequence Identity:
- Total samples: 649
- soil counts: 2
- aquatic counts: 620
- animal counts: 26
- plant counts: 1
Sequence information
16S sequences
- @ref: 66716
- description: Oceanococcus sp. strain OUC007 16S ribosomal RNA gene, partial sequence
- accession: KY612316
- length: 1502
- database: ena
- NCBI tax ID: 2182787
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Abyssibacter profundi OUC007 | 2831460164 | draft | img | 2182787 |
67770 | Abyssibacter profundi OUC007 | GCA_003151135 | contig | ncbi | 2182787 |
GC content
- @ref: 66716
- GC-content: 63.1
- method: genome sequence analysis
External links
@ref: 66716
culture collection no.: KCTC 52933, MCCC 1K03450, JCM 32025
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 30204582 | Abyssibacter profundi gen. nov., sp. nov., a marine bacterium isolated from seawater of the Mariana Trench. | Zhou S, Ren Q, Li Y, Liu J, Wang X, Wu Y, Zhang Y, Zhang XH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002999 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Pacific Ocean, Phosphatidylethanolamines/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water Microbiology | Transcriptome |
Phylogeny | 33034549 | Salifodinibacter halophilus gen. nov., sp. nov., a halophilic gammaproteobacterium in the family Salinisphaeraceae isolated from a salt mine in the Colombian Andes. | Parada-Pinilla MP, Diaz-Cardenas C, Lopez G, Diaz-Riano JI, Gonzalez LN, Restrepo S, Trujillo ME, Baena S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004490 | 2020 | Bacterial Typing Techniques, Base Composition, Colombia, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Genome Size, Geologic Sediments/microbiology, *Mining, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Water Microbiology | 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 | ||
66716 | Shun Zhou, Qiaomeng Ren, Yuying Li, Jiwen Liu, Xiaolei Wang, Yanhong Wu, Yulin Zhang, Xiao-hua Zhang | Abyssibacter profundi gen. nov., sp. nov., a marine bacterium isolated from seawater of the Mariana Trench | 10.1099/ijsem.0.002999 | IJSEM 68: 3423-3429 2018 | 30204582 |
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 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||
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/ |