Candidatus Melainobacteriota
 | A request that this article title be changed to Melainabacteria is under discussion. Please do not move this article until the discussion is closed. |
| Melainabacteria | |
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| SEM of Chlorella sorokiniana and attached Vampirovibrio chlorellavorus cells.
Scale bar, 5.0 μm. | |
Scientific classification 
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| Domain: | Bacteria |
| Kingdom: | Bacillati |
| Clade: | Cyanobacteria/Melainabacteria clade |
| Phylum: | "Candidatus Melainobacteriota" corrig. Di Rienzi et al. 2013 in Oren & Göker 2023[1] |
| Class: | Vampirovibrionophyceae corrig. Strunecký and Mareš 2023 |
| Orders and genera[2] | |
| Synonyms | |
"Candidatus Melainobacteriota" is a monotypic phylum of bacteria that is the sister phylum of the phylum Cyanobacteriota (named under the Botanical Code).[1] It has one class Vampirovibrionophyceae.
Vampirovibrio chlorellavorus is the only species of the phylum that has been grown in cell culture.[7] Candidatus species of melainabacteria have been discovered through DNA and RNA sequence analysis of samples from soil, the human gut, and various aquatic habitats such as groundwater. By analyzing genomes of melainabacteria, predictions are possible about their cell structure and metabolic abilities. The deduced structure of the bacterial cell is similar to cyanobacteria in being surrounded by two membranes.[8] It differs from cyanobacteria in its predicted ability to move by flagella (like gram-negative flagella), though some members (e.g. Gastranaerophilales) appear to lack flagella.[8] It is predicted that melainabacteria are not able to perform photosynthesis, but obtain energy by fermentation.
Treatments
[edit]Melainabacteria has been treated as:
- The phylum "Candidatus Melainabacteria" when its DNA was discovered in 2013.[9]
- The class "Candidatus Melainabacteria" under Cyanobacteria in Soo et al. (2014).[10]
- The phylum "Candidatus Melainobacteriota", the 2013 name corrected to match new bacteriological rules.[1]
- The class Vampirovibriophyceae under Cyanobacteria in Strunecký and Mareš 2023, with the corrected spelling Vampirovibrionophyceae.[2]
- The class "Vampirovibrionia" under Cyanobacteria in 2023.[11]
It was not realized until 2015 that this group actually includes one cultured bacterium.[12] Names proposed prior to this point are written under the assumption that they describe an uncultured group and are Candidatus. Names proposed without Candidatus after this point use the cultured species in the description. Removal of the Candidatus prefix does not happen automatically; instead, an author must make a separate valid publication.[13]
Treating this group as a phylum would place it at the same taxonomic rank as Cyanobacteriota.[14]
Phylogeny
[edit]| 16S rRNA based LTP_10_2024[15][16][17] | 120 marker proteins based GTDB 09-RS220[18][19][20] | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Classification
[edit]- Phylum "Ca. Melainobacteriota" corrig. Di Rienzi et al. 2013
- Class Vampirovibrionophyceae Strunecký and Mareš 2023 (ACD20)
- Order "Caenarcanales" corrig. Soo et al. 2014 ["Caenarcaniphilales" Soo et al. 2014]
- Family "Caenarcanaceae" Chuvochina et al. 2023
- Genus "Ca. Caenarcanum" Soo et al. 2014
- "Ca. C. bioreactoricola" Soo et al. 2014
- Genus "Ca. Caenarcanum" Soo et al. 2014
- Family "Caenarcanaceae" Chuvochina et al. 2023
- Order Vampirovibrionales Chuvochina et al. 2024
- Family Vampirovibrionaceae Chuvochina et al. 2024
- Genus Vampirovibrio Gromov & Mamkayeva 1972 ex Gromov & Mamkaeva 1980
- V. chlorellavorus Gromov & Mamkayeva 1972 ex Gromov & Mamkaeva 1980
- Genus Vampirovibrio Gromov & Mamkayeva 1972 ex Gromov & Mamkaeva 1980
- Family Vampirovibrionaceae Chuvochina et al. 2024
- Order "Ca. Gastranaerophilales" Soo et al. 2014
- Family "Adamsellaceae" Pallen, Rodriguez-R & Alikhan 2022 [CAJFVJ01]
- Family "RUG14156"
- Genus "Ca. Galligastranaerophilus" Gilroy et al. 2021
- "Ca. G. faecipullorum" Gilroy et al. 2021
- "Ca. G. gallistercoris" Gilroy et al. 2021
- "Ca. G. intestinavium" Gilroy et al. 2021
- "Ca. G. intestinigallinarum" Gilroy et al. 2021
- Genus "Ca. Galligastranaerophilus" Gilroy et al. 2021
- Family "Gastranaerophilaceae" Gilroy et al. 2021
- Genus "Ca. Avigastranaerophilus" Gilroy et al. 2021
- "Ca. A. faecigallinarum" Gilroy et al. 2021
- Genus "Ca. Gastranaerophilus" Soo et al. 2014
- "Ca. G. phascolarctosicola" Soo et al. 2014
- "Ca. G. termiticola" Utami et al. 2018
- Genus "Ca. Limenecus" Gilroy et al. 2021
- "Ca. L. avicola" Gilroy et al. 2021
- Genus "Ca. Scatenecus" Gilroy et al. 2021
- "Ca. S. faecavius" Gilroy et al. 2021
- Genus "Ca. Scatousia" Gilroy et al. 2021
- "Ca. S. excrementigallinarum" Gilroy et al. 2021
- "Ca. S. excrementipullorum" Gilroy et al. 2021
- Genus "Ca. Spyradomonas" Gilroy et al. 2021
- "Ca. S. excrementavium" Gilroy et al. 2021
- Genus "Ca. Stercorousia" Gilroy et al. 2021
- "Ca. S. faecigallinarum" Gilroy et al. 2021
- Genus "Ca. Avigastranaerophilus" Gilroy et al. 2021
- Order "Caenarcanales" corrig. Soo et al. 2014 ["Caenarcaniphilales" Soo et al. 2014]
- Class Vampirovibrionophyceae Strunecký and Mareš 2023 (ACD20)
Ecological niche
[edit]Melainabacteria nucleic acids can be found in a range of environments, including soil, water, and animal habitats. They can be often be found in the gut of humans and in the respiratory tract, oral environments, and skin surface, though rarely. Melainabacteria nucleic acids are often found in natural environments such as groundwater aquifers and lake sediment, soil, bioreactor,[7] and the aphotic zone of aquatic environments such as lake sediment and aquifers.[7] Cyanobacteria bloom in freshwater systems as a result of excess nutrients and high temperatures, resulting in a scum on the water surface that resembles spilled paint.[7] Because melainabacteria is a type of Cyanobacteria, it has raised concern because melainabacteria thrive in groundwater systems. The genomes of melainabacteria were found to be bigger when found in aquifer systems and algal cultivation ponds than when in the mammalian gut environment.[7]
Origin
[edit]The Great Oxygenation Event (GOE) increased the abundance of oxygen in the atmosphere. [21][22] Bacteria that existed before the GEO did not rely on oxygen, such as the billion-year-old cyanobacteria. Melainabacteria do not photosynthesize.[23] Cyanobacteria produced atmospheric oxygen and supported the development of early plant cells.[24]
Genome
[edit]The genomes of melainabacteria organisms isolated from ground water indicate that the organism has the capacity to fix nitrogen. Melainabacteria are predicted to lack linked electron transport chains, but have multiple methods to generate a membrane potential which can then produce ATP via ATP synthase. They are thought to be able to use Fe hydrogenases for H
2 production that can be consumed by other microorganisms. Melainabacteria from the human gut also are thought to synthesize several B and K vitamins, which suggests that these bacteria are beneficial to their host because they are consumed along with plant fibers.[8][25]
Animal habitats
[edit]Melainabacteria may play a role in digesting fiber in the human gut,[8] and their nucleic acids are more commonly found in herbivorous mammals and those with plant-rich diets.[8] Because plant diets require more fiber break-down, melainabacteria may aid in this digestive function. However, scientists do not know why these microbes are in the gut and how they got there.[8] Ongoing studies such as, "The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria," are funded by various organizations such as the National Institutes of Health, the David and Lucile Packard Foundation, The Hartwell Foundation, the Arnold and Mabel Beckman Foundation, the U.S. Department of Energy, the European Molecular Biology Organization and the Wellcome Trust. [24]
See also
[edit]References
[edit]- ^ a b c Oren, Aharon; Göker, Markus (9 May 2023). "Candidatus List. Lists of names of prokaryotic Candidatus phyla". International Journal of Systematic and Evolutionary Microbiology. 73 (5). doi:10.1099/ijsem.0.005821.
- ^ a b Vampirovibrionophyceae in LPSN; Parte, Aidan C.; Sardà Carbasse, Joaquim; Meier-Kolthoff, Jan P.; Reimer, Lorenz C.; Göker, Markus (1 November 2020). "List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5607–5612. doi:10.1099/ijsem.0.004332.
- ^ Di Rienzi, Sara C; Sharon, Itai; Wrighton, Kelly C; Koren, Omry; Hug, Laura A; Thomas, Brian C; Goodrich, Julia K; Bell, Jordana T; Spector, Timothy D; Banfield, Jillian F; Ley, Ruth E (2013-10-01). Kolter, Roberto (ed.). "The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria". eLife. 2: e01102. doi:10.7554/eLife.01102. ISSN 2050-084X. PMC 3787301. PMID 24137540.
- ^ Soo, Rochelle M.; Skennerton, Connor T.; Sekiguchi, Yuji; Imelfort, Michael; Paech, Samuel J.; Dennis, Paul G.; Steen, Jason A.; Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip (2014-05-02). "An Expanded Genomic Representation of the Phylum Cyanobacteria". Genome Biology and Evolution. 6 (5): 1031–1045. doi:10.1093/gbe/evu073. ISSN 1759-6653. PMC 4040986. PMID 24709563.
- ^ Chuvochina, Maria; Mussig, Aaron J; Chaumeil, Pierre-Alain; Skarshewski, Adam; Rinke, Christian; Parks, Donovan H; Hugenholtz, Philip (2023-01-17). "Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes". FEMS Microbiology Letters. 370. doi:10.1093/femsle/fnad071. ISSN 1574-6968. PMC 10408702. PMID 37480240.
- ^ Strunecký, Otakar; Ivanova, Anna Pavlovna; Mareš, Jan (2023). "An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis". Journal of Phycology. 59 (1): 12–51. doi:10.1111/jpy.13304. ISSN 1529-8817.
- ^ a b c d e Hu, Chenlin; Rzymski, Piotr (2022-02-05). "Non-Photosynthetic Melainabacteria (Cyanobacteria) in Human Gut: Characteristics and Association with Health". Life. 12 (4): 476. Bibcode:2022Life...12..476H. doi:10.3390/life12040476. ISSN 2075-1729. PMC 9029806. PMID 35454968.
- ^ a b c d e f Di Rienzi, SC; Sharon, I; Wrighton, KC; Koren, O; Hug, LA; Thomas, BC; Goodrich, JK; Bell, JT; Spector, TD; Banfield, JF; Ley, RE (2013). "The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria". eLife. 2: e01102. doi:10.7554/eLife.01102. PMC 3787301. PMID 24137540.
- ^ Di Rienzi, Sara C; Sharon, Itai; Wrighton, Kelly C; Koren, Omry; Hug, Laura A; Thomas, Brian C; Goodrich, Julia K; Bell, Jordana T; Spector, Timothy D; Banfield, Jillian F; Ley, Ruth E (2013-10-01). Kolter, Roberto (ed.). "The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria". eLife. 2: e01102. doi:10.7554/eLife.01102. ISSN 2050-084X. PMC 3787301. PMID 24137540.
- ^ Soo, Rochelle M.; Skennerton, Connor T.; Sekiguchi, Yuji; Imelfort, Michael; Paech, Samuel J.; Dennis, Paul G.; Steen, Jason A.; Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip (2014-05-02). "An Expanded Genomic Representation of the Phylum Cyanobacteria". Genome Biology and Evolution. 6 (5): 1031–1045. doi:10.1093/gbe/evu073. ISSN 1759-6653. PMC 4040986. PMID 24709563.
- ^ Oren, Aharon; Göker, Markus (1 February 2024). "Validation List no. 215. Valid publication of new names and new combinations effectively published outside the IJSEM". International Journal of Systematic and Evolutionary Microbiology. 74 (1). doi:10.1099/ijsem.0.006173. PMID 38299482.
- ^ Soo, Rochelle M.; Woodcroft, Ben J.; Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip (21 May 2015). "Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus". PeerJ. 3: e968. doi:10.7717/peerj.968. PMID 26038723.
- ^ Oren, Aharon (8 January 2025). "Addition of Section 10, Rules 66–73 for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes". International Journal of Systematic and Evolutionary Microbiology. 75 (1). doi:10.1099/ijsem.0.006638. PMID 39786349.
- ^ Oren, Aharon; Mareš, Jan; Rippka†, Rosmarie (21 October 2022). "Validation of the names Cyanobacterium and Cyanobacterium stanieri, and proposal of Cyanobacteriota phyl. nov". International Journal of Systematic and Evolutionary Microbiology. 72 (10). doi:10.1099/ijsem.0.005528.
- ^ "The LTP". Retrieved 10 December 2024.
- ^ "LTP_all tree in newick format". Retrieved 10 December 2024.
- ^ "LTP_10_2024 Release Notes" (PDF). Retrieved 10 December 2024.
- ^ "GTDB release 09-RS220". Genome Taxonomy Database. Retrieved 10 May 2024.
- ^ "bac120_r220.sp_labels". Genome Taxonomy Database. Retrieved 10 May 2024.
- ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2024.
- ^ Olejarz, Jason; Iwasa, Yoh; Knoll, Andrew H.; Nowak, Martin A. (2021-06-28). "The Great Oxygenation Event as a consequence of ecological dynamics modulated by planetary change". Nature Communications. 12 (1): 3985. Bibcode:2021NatCo..12.3985O. doi:10.1038/s41467-021-23286-7. ISSN 2041-1723. PMC 8238953. PMID 34183660. S2CID 235673343.
- ^ Grettenberger, Christen; Sumner, Dawn Y.; Eisen, Jonathan A.; Jungblut, Anne D.; Mackey, Tyler J. (2021-06-18). "Phylogeny and Evolutionary History of Respiratory Complex I Proteins in Melainabacteria". Genes. 12 (6): 929. doi:10.3390/genes12060929. ISSN 2073-4425. PMC 8235220. PMID 34207155.
- ^ Biello, David. "The Origin of Oxygen in Earth's Atmosphere". Scientific American. Retrieved 2022-10-03.
- ^ a b "New bacteria found in human gut". Cornell Chronicle. Retrieved 2022-10-03.
- ^ Soo, RM; Skennerton, CT; Sekiguchi, Y; Imelfort, M; Paech, SJ; Dennis, PG; Steen, JA; Parks, DH; Tyson, GW; Hugenholtz, P (2014). "An expanded genomic representation of the phylum cyanobacteria". Genome Biol Evol. 6 (5): 1031–45. doi:10.1093/gbe/evu073. PMC 4040986. PMID 24709563.