Strain identifier
BacDive ID: 158357
Type strain: 
Species: Pleomorphochaeta naphthae
Strain history: R. Grimaud; Lab. Environ. & Microbiol. (EEM)-IPREM-UMR5254 CNRS, France; SEBR 4209.
NCBI tax ID(s): 1895020 (species)
version 8.1 (current version)
General
@ref: 65033
BacDive-ID: 158357
DSM-Number: 104684
keywords: 16S sequence, Bacteria, anaerobe, chemoorganotroph, mesophilic, Gram-negative, sphere-shaped
description: Pleomorphochaeta naphthae DSM 104684 is an anaerobe, chemoorganotroph, mesophilic bacterium that was isolated from production water from an offshore oil well.
NCBI tax id
- NCBI tax id: 1895020
- Matching level: species
strain history
| @ref | history |
|---|---|
| 65033 | <- R. Grimaud; Université de Pau et des Pays de l'Adour CNRS, Pau, FRANCE; SEBR 4209 <- M. Magot {1991} |
| 67770 | R. Grimaud; Lab. Environ. & Microbiol. (EEM)-IPREM-UMR5254 CNRS, France; SEBR 4209. |
doi: 10.13145/bacdive158357.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/spirochaetota
- domain: Bacteria
- phylum: Spirochaetota
- class: Spirochaetia
- order: Spirochaetales
- family: Sphaerochaetaceae
- genus: Pleomorphochaeta
- species: Pleomorphochaeta naphthae
- full scientific name: Pleomorphochaeta naphthae Arroua et al. 2018
@ref: 65033
domain: Bacteria
phylum: Spirochaetes
class: Spirochaetia
order: Spirochaetales
family: Sphaerochaetaceae
genus: Pleomorphochaeta
species: Pleomorphochaeta naphthae
full scientific name: Pleomorphochaeta naphthae Arroua et al. 2018
type strain: yes
Morphology
cell morphology
- @ref: 66757
- gram stain: negative
- cell length: 0.4-1.8 µm
- cell shape: sphere-shaped
- motility: no
Culture and growth conditions
culture medium
- @ref: 65033
- name: PLEOMORPHOCHAETA MEDIUM (DSMZ Medium 1271)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1271
- composition: Name: PLEOMORPHOCHAETA MEDIUM (DSMZ Medium 1271; with strain-specific modifications) Composition: NaCl 24.9252 g/l MgCl2 x 6 H2O 3.98804 g/l Maltose 1.99402 g/l Na2CO3 1.49551 g/l CaCl2 x 2 H2O 0.997009 g/l Yeast extract 0.997009 g/l NH4Cl 0.498504 g/l Na2S x 9 H2O 0.299103 g/l L-Cysteine HCl x H2O 0.299103 g/l KH2PO4 0.0997009 g/l FeCl2 x 4 H2O 0.00199402 g/l NaOH 0.000498504 g/l Na2-EDTA 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l AlCl3 9.97009e-06 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 65033 | positive | growth | 37 | mesophilic |
| 66757 | positive | optimum | 37 | mesophilic |
| 66757 | positive | growth | 25-42 | |
| 67770 | positive | growth | 37 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 66757 | positive | growth | 4.7-8.5 | alkaliphile |
| 66757 | positive | optimum | 6.8-7 |
Physiology and metabolism
oxygen tolerance
- @ref: 66757
- oxygen tolerance: anaerobe
nutrition type
- @ref: 66757
- type: chemoorganotroph
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 66757 | NaCl | positive | growth | 10-60 g/L |
| 66757 | NaCl | positive | optimum | 40 g/L |
observation
| @ref | observation |
|---|---|
| 66757 | Cells are pleomorphic with a spherical shape during exponential growth phase. |
| 66757 | Many cells carry characteristic protrusions. A lipid-containing membranous structure surrounds cell aggregates. |
| 66757 | Yeast extract is required for growth on carbohydrates and cannot be replaced by vitamins. |
| 66757 | End products of D-glucose fermentation are acetate, ethanol, CO2 and H2. |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 66757 | 12936 | D-galactose | + | fermentation |
| 66757 | 15824 | D-fructose | + | fermentation |
| 66757 | 16024 | D-mannose | + | fermentation |
| 66757 | 16634 | raffinose | + | fermentation |
| 66757 | 16988 | D-ribose | + | fermentation |
| 66757 | 17057 | cellobiose | + | fermentation |
| 66757 | 17151 | xylitol | + | fermentation |
| 66757 | 17306 | maltose | + | fermentation |
| 66757 | 17634 | D-glucose | + | fermentation |
| 66757 | 17924 | D-sorbitol | + | fermentation |
| 66757 | 17992 | sucrose | + | fermentation |
| 66757 | 27082 | trehalose | + | fermentation |
| 66757 | 29864 | mannitol | + | fermentation |
| 66757 | 30849 | L-arabinose | + | fermentation |
| 66757 | 65327 | D-xylose | + | fermentation |
| 66757 | 7896 | hexadecanoate | - | growth |
| 66757 | 15361 | pyruvate | - | growth |
| 66757 | 15963 | ribitol | - | growth |
| 66757 | 16150 | benzoate | - | growth |
| 66757 | 16236 | ethanol | - | growth |
| 66757 | 16411 | acetic acid | - | growth |
| 66757 | 17108 | D-arabinose | - | growth |
| 66757 | 17268 | myo-inositol | - | growth |
| 66757 | 17272 | propionate | - | growth |
| 66757 | 17578 | toluene | - | growth |
| 66757 | 17716 | lactose | - | growth |
| 66757 | 17754 | glycerol | - | growth |
| 66757 | 17790 | methanol | - | growth |
| 66757 | 17968 | butyrate | - | growth |
| 66757 | 24996 | lactate | - | growth |
| 66757 | 25115 | malate | - | growth |
| 66757 | 27338 | xylene | - | growth |
| 66757 | 28087 | glycogen | - | growth |
| 66757 | 29806 | fumarate | - | growth |
| 66757 | 30031 | succinate | - | growth |
| 66757 | 45296 | hexadecane | - | growth |
| 66757 | 53258 | citric acid | - | growth |
| 66757 | 62345 | L-rhamnose | - | growth |
| 66757 | 77393 | tripalmitin | - | growth |
| 66757 | casamino acids | - | growth | |
| 66757 | peptone | - | growth | |
| 66757 | yeast extract | - | growth |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 66757 | catalase | - | 1.11.1.6 |
| 66757 | cytochrome oxidase | - | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature | isolation procedure |
|---|---|---|---|---|---|---|---|---|---|---|
| 65033 | production water from an offshore oil well | Emraude off shore oil field, well number BB 325 | Republic of the Congo | COG | Africa | |||||
| 66757 | sample of production water from an oil field from a non-water-flooded oil reservoir (300m depth, 35-40°C and 40 g l-1 NaCL concentration) | Republic of the Congo | COG | Africa | SEM medium | contained biotrypcase (15 g l-1), yeast extract (10 g l-1), glucose (2.5 g l-1) and minerals replicating the composition of the produced water | 3 weeks | 37 | Enrichment and isolation were performed underanoxic conditions by inoculating 2 ml of the produced water sample into serum bottles containing 18 ml SEM medium and incubated without shaking at 37°C. Strain SEBR 4209T was purified by successive streaking on SEM agar plates in anaerobiosis as described previously. | |
| 67770 | Production water from an oil field | Republic of the Congo | COG | Africa |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | #Oil (Fuel) |
| #Engineered | #Industrial | #Plant (Factory) |
| #Engineered | #Built environment | #Water reservoir (Aquarium/pool) |
Sequence information
16S sequences
- @ref: 65033
- description: Sphaerochaeta sp. SEBR 4209 strain SEBR4209 16S ribosomal RNA gene, partial sequence
- accession: KX791435
- length: 1373
- database: ena
- NCBI tax ID: 1895020
GC content
| @ref | GC-content | method |
|---|---|---|
| 65033 | 29.6 | |
| 66757 | 29.6 | high performance liquid chromatography (HPLC) |
External links
@ref: 65033
culture collection no.: DSM 104684, JCM 31871, SEBR 4209
straininfo link
- @ref: 111162
- straininfo: 400755
literature
- topic: Phylogeny
- Pubmed-ID: 30307390
- title: Pleomorphochaeta naphthae sp. nov., a new anaerobic fermentative bacterium isolated from an oil field.
- authors: Arroua B, Grimaud R, Hirschler-Rea A, Bouriat P, Magot M, Urios L, Ranchou-Peyruse A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.003048
- year: 2018
- mesh: Bacterial Typing Techniques, Base Composition, Congo, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Oil and Gas Fields/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spirochaetaceae/*classification/genetics/isolation & purification
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | catalogue | 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 | |||
| 65033 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104684 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104684) | |||
| 66757 | Boussad Arroua, Regis Grimaud, Agnes Hirschler-Rea, Patrick Bouriat, Michel Magot, Laurent Urios, Anthony Ranchou-Peyruse | Pleomorphochaeta naphthae sp. nov., a new anaerobic fermentative bacterium isolated from an oil field | 10.1099/ijsem.0.003048 | IJSEM 68: 3747-3753 2018 | 30307390 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 111162 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID400755.1 |