Strain identifier
BacDive ID: 24801
Type strain:
Species: Melioribacter roseus
Strain Designation: P3M-2
Strain history: O. A. Podosokorskaya P3M-2.
NCBI tax ID(s): 1134405 (species)
General
@ref: 21273
BacDive-ID: 24801
DSM-Number: 23840
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, organotroph, thermophilic, Gram-negative, motile, rod-shaped
description: Melioribacter roseus P3M-2 is a facultative anaerobe, organotroph, thermophilic bacterium that was isolated from microbial mat from the wooden surface of a chute under the flow of thermal water coming out of a 2775-m-deep oil exploration well.
NCBI tax id
- NCBI tax id: 1134405
- Matching level: species
strain history
@ref | history |
---|---|
21273 | <- O. A. Podosocorskaya, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; P3M-2 |
67770 | O. A. Podosokorskaya P3M-2. |
doi: 10.13145/bacdive24801.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/chlorobiota
- domain: Bacteria
- phylum: Chlorobiota
- class: Ignavibacteria
- order: Ignavibacteriales
- family: Melioribacteraceae
- genus: Melioribacter
- species: Melioribacter roseus
- full scientific name: Melioribacter roseus Podosokorskaya et al. 2013
@ref: 21273
domain: Bacteria
phylum: Chlorobi
class: Ignavibacteria
order: Melioribacteraceae, not assigned to order
family: Melioribacteraceae
genus: Melioribacter
species: Melioribacter roseus
full scientific name: Melioribacter roseus Podosokorskaya et al. 2013
strain designation: P3M-2
type strain: yes
Morphology
cell morphology
- @ref: 43396
- gram stain: negative
- cell length: 0.65-10 µm
- cell width: 0.25-0.35 µm
- cell shape: rod-shaped
- motility: yes
- flagellum arrangement: polar
pigmentation
- @ref: 43396
- production: yes
- name: carotenoid-type
Culture and growth conditions
culture medium
- @ref: 21273
- name: IGNAVIBACTERIA MEDIUM (DSMZ Medium 1374)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1374
- composition: Name: IGNAVIBACTERIA MEDIUM (DSMZ Medium 1374) Composition: Na2SO4 3.9604 g/l Yeast extract 1.9802 g/l NaCl 0.990099 g/l KCl 0.49505 g/l MgCl2 x 6 H2O 0.39604 g/l Na2S x 9 H2O 0.29703 g/l NH4Cl 0.247525 g/l KH2PO4 0.19802 g/l CaCl2 x 2 H2O 0.0990099 g/l NaHCO3 0.0990099 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.000776238 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.000391089 g/l CoCl2 x 6 H2O 0.000235644 g/l ZnSO4 x 7 H2O 0.000142178 g/l Pyridoxine hydrochloride 9.90099e-05 g/l MnCl2 x 4 H2O 9.80198e-05 g/l Na2SeO4 9.36634e-05 g/l Riboflavin 4.95049e-05 g/l Thiamine-HCl x 2 H2O 4.95049e-05 g/l D-Calcium pantothenate 4.95049e-05 g/l Nicotinic acid 4.95049e-05 g/l p-Aminobenzoic acid 4.95049e-05 g/l Lipoic acid 4.95049e-05 g/l Na2WO4 x 2 H2O 3.26733e-05 g/l Na2MoO4 x 2 H2O 2.37624e-05 g/l Biotin 1.9802e-05 g/l Folic acid 1.9802e-05 g/l H3BO3 5.94059e-06 g/l CuCl2 x 2 H2O 1.78218e-06 g/l Vitamin B12 9.90099e-07 g/l HCl Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
21273 | positive | growth | 47 | thermophilic |
43396 | positive | optimum | 52-55 | thermophilic |
43396 | positive | growth | 35-60 | |
67770 | positive | growth | 55 | thermophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43396 | positive | growth | 6-8.7 | alkaliphile |
43396 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 43396
- oxygen tolerance: facultative anaerobe
nutrition type
- @ref: 43396
- type: organotroph
spore formation
- @ref: 43396
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43396 | NaCl | positive | optimum | 6 g/L |
43396 | NaCl | no | growth | 60 g/L |
observation
- @ref: 67770
- observation: quinones: MK-7
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43396 | 62968 | cellulose | + | assimilation |
43396 | 30089 | acetate | + | assimilation |
43396 | 2511 | agarose | + | assimilation |
43396 | 22599 | arabinose | + | assimilation |
43396 | 29125 | arsenate | + | reduction |
43396 | beef extract | + | assimilation | |
43396 | 28885 | butanol | - | assimilation |
43396 | 85146 | carboxymethylcellulose | + | assimilation |
43396 | 17057 | cellobiose | + | assimilation |
43396 | 52071 | dextran | + | assimilation |
43396 | 15379 | dioxygen | + | reduction |
43396 | 24996 | lactate | - | assimilation |
43396 | 16236 | ethanol | - | assimilation |
43396 | ferrihydrite | + | reduction | |
43396 | 15740 | formate | + | assimilation |
43396 | 28757 | fructose | + | assimilation |
43396 | 28260 | galactose | - | assimilation |
43396 | 495056 | gamma-cyclodextrin | + | assimilation |
43396 | 5291 | gelatin | + | assimilation |
43396 | 17234 | glucose | + | assimilation |
43396 | 28087 | glycogen | + | assimilation |
43396 | 17716 | lactose | + | assimilation |
43396 | 6452 | lichenin | + | assimilation |
43396 | 6457 | lignin | - | assimilation |
43396 | 17306 | maltose | + | assimilation |
43396 | 29864 | mannitol | - | assimilation |
43396 | 37684 | mannose | + | assimilation |
43396 | 16301 | nitrite | + | reduction |
43396 | 17309 | pectin | - | assimilation |
43396 | peptone | + | assimilation | |
43396 | 28831 | propanol | - | assimilation |
43396 | 17272 | propionate | - | assimilation |
43396 | 15361 | pyruvate | - | assimilation |
43396 | 26546 | rhamnose | + | assimilation |
43396 | 33942 | ribose | + | assimilation |
43396 | 30911 | sorbitol | - | assimilation |
43396 | 28017 | starch | + | assimilation |
43396 | 17992 | sucrose | - | assimilation |
43396 | 41253 | tetradecane | - | assimilation |
43396 | 27082 | trehalose | + | assimilation |
43396 | 10057 | xanthan | + | assimilation |
43396 | 37166 | xylan | + | assimilation |
43396 | 18222 | xylose | + | assimilation |
43396 | yeast extract | + | required for growth | |
43396 | yeast extract | + | assimilation |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43396 | 30089 | acetate | yes |
43396 | 16526 | carbon dioxide | yes |
43396 | 18276 | dihydrogen | yes |
43396 | 24996 | DL-lactate | yes |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43396 | catalase | +/- | 1.11.1.6 |
43396 | cytochrome oxidase | +/- | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
21273 | microbial mat from the wooden surface of a chute under the flow of thermal water coming out of a 2775-m-deep oil exploration well | Tomsk region, Parabel’ district, west bank of Ob River | Russia | RUS | Asia |
67770 | Microbial mat developing on the wooden surface of a chute under the flow of hot water emerging from a 2775-m-deep oil exploration well in Tomsk region | Western Siberia | Russia | RUS |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | ||
#Environmental | #Aquatic | |
#Environmental | #Microbial community | #Microbial mat |
taxonmaps
- @ref: 69479
- File name: preview.99_1771.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_252;96_1004;97_1170;98_1398;99_1771&stattab=map
- Last taxonomy: Melioribacter roseus subclade
- 16S sequence: JQ292917
- Sequence Identity:
- Total samples: 1473
- soil counts: 172
- aquatic counts: 843
- animal counts: 435
- plant counts: 23
Safety information
risk assessment
- @ref: 21273
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21273
- description: Melioribacter roseus strain P3M-2 16S ribosomal RNA gene, partial sequence
- accession: JQ292917
- length: 1539
- database: ena
- NCBI tax ID: 1191523
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Melioribacter roseus P3M-2 | GCA_000279145 | complete | ncbi | 1191523 |
66792 | Melioribacter roseus P3M-2 | 1191523.3 | complete | patric | 1191523 |
GC content
@ref | GC-content | method |
---|---|---|
21273 | 41.3 | sequence analysis |
43396 | 41 | |
67770 | 41 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 79.665 | yes |
flagellated | no | 83.563 | no |
gram-positive | no | 98.421 | yes |
anaerobic | no | 86.738 | yes |
aerobic | no | 81.889 | no |
halophile | no | 88.221 | yes |
spore-forming | no | 94.626 | yes |
thermophile | yes | 99.999 | yes |
glucose-util | yes | 87.098 | yes |
glucose-ferment | no | 71.536 | no |
External links
@ref: 21273
culture collection no.: DSM 23840, JCM 17771, VKM B-2668
straininfo link
- @ref: 88623
- straininfo: 406506
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23297868 | Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria, and a proposal of a novel bacterial phylum Ignavibacteriae. | Podosokorskaya OA, Kadnikov VV, Gavrilov SN, Mardanov AV, Merkel AY, Karnachuk OV, Ravin NV, Bonch-Osmolovskaya EA, Kublanov IV | Environ Microbiol | 10.1111/1462-2920.12067 | 2013 | Bacteria, Anaerobic/genetics, Chlorobi/*classification/genetics/*physiology/ultrastructure, Ferric Compounds, Genome, Bacterial/genetics, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Rec A Recombinases/genetics, Russia, Species Specificity | Genetics |
Metabolism | 23301019 | Genomic analysis of Melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within Bacteriodetes/Chlorobi group. | Kadnikov VV, Mardanov AV, Podosokorskaya OA, Gavrilov SN, Kublanov IV, Beletsky AV, Bonch-Osmolovskaya EA, Ravin NV | PLoS One | 10.1371/journal.pone.0053047 | 2013 | Bacteria, Anaerobic/genetics, Bacteroidetes/*genetics, Base Composition, Carbohydrate Metabolism, Electron Transport, *Genome, Bacterial, Genomics, Hydrolysis, Likelihood Functions, Metabolic Networks and Pathways, Photosynthesis, *Phylogeny, Polysaccharides/metabolism, Proteome/analysis, RNA, Ribosomal/metabolism, Ribosomes/metabolism, Transcription, Genetic | Genetics |
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 | |||
21273 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23840 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23840) | |||
43396 | Olga A. Podosokorskaya, Vitaly V. Kadnikov, Sergey N. Gavrilov, Andrey V. Mardanov, Alexander Y. Merkel, Olga V. Karnachuk, Nikolay V. Ravin, Elizaveta A. Bonch-Osmolovskaya, Ilya V. Kublanov | Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria, and a proposal of a novel bacterial phylum Ignavibacteriae | 10.1111/1462-2920.12067 | Environ. Microbiol. 15: 1759-1771 2013 | 23297868 | |
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/ | ||||
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/ | |||
88623 | 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-ID406506.1 |