Melainabacteria

Melainabacteria is a phylum related to Cyanobacteria. Organisms belonging to this phylum have been found in the human gut and various aquatic habitats such as groundwater. By analyzing genomes of Melainabacteria, predictions are possible about the cell structure and metabolic abilities. The bacterial cell is similar to cyanobacteria in being surrounded by two membranes.[2] It differs from cyanobacteria in its ability to move by flagella (like gram-negative flagella), though some members (e.g. Gastranaerophilales) lack flagella.[3] Melainabacteria are not able to perform photosynthesis, but obtain energy by fermentation.

Melainabacteria
SEM of Chlorella sorokiniana and attached Vampirovibrio chlorellavorus cells.

Scale bar, 5.0 μm.

Scientific classification
Domain: Bacteria
(unranked): Cyanobacteria-Melainabacteria group
Phylum: Melainabacteria
Di Rienzi et al. 2013[1]
Order
  • "Caenarcaniphilales"
  • "Gastranaerophilales"
  • "Obscuribacterales"
  • "Vampirovibrionales"

The genomes of Melainabacteria organisms isolated from ground water indicate that the organism has the capacity to fix nitrogen.

Melainabacteria lack linked electron transport chains but have multiple methods to generate a membrane potential which can then produce ATP via ATP synthase. They are able to use Fe hydrogenases for H
2 production that can be consumed by other microorganisms. Melainabacteria from the human gut also synthesize several B and K vitamins, which suggests that these bacteria are beneficial to their host because they are consumed along with plant fibers.[2][4]

The Great Oxygenation Event (GOE) that occurred 2.4 billion years ago altered the course of life on Earth forever by increasing the abundance of oxygen in the atmosphere. [5][6]Bacteria that existed before the GEO did not rely on the presence of oxygen as a source for metabolism, such as the billion-year-old Cyanobacteria. Melainabacteria is a close relative to Cyanobacteria, more commonly known as blue-green algae, though Melainabacteria diverged and do not photosynthesize[7]. These ancient photosynthesizing microbes producing atmospheric oxygen are what allowed the environment to be composed in a way that supported early plant cells.[8] Melainabacteria is a primitive microbe that thrived anaerobically prior to the GEO.

Melainabacteria are found today in some groundwater and mammalian guts. [8] It was discovered that the gut and environmental types of Melainabacteria fall under different subphyla.  

Phylogeny
16S rRNA based LTP_12_2021[9][10][11] GTDB 07-RS207 by Genome Taxonomy Database[12][13][14]
Terrabacteria
 

"Cyanobacteriota"

 
"Melainabacteria"

Vampirovibrio

 
 
Terrabacteria
 

"Margulisbacteria"

 
"Cyanobacteriota"
 

"Sericytochromatia"

 
 
 

Cyanobacteria

 
"Melainabacteria"
 
"Caenarcanales"

"Ca. Caenarcanum"

 
"Obscuribacterales"

"Ca. Obscuribacter"

 
 
 
"Vampirovibrionales"

Vampirovibrio

 
"Gastranaerophilales"
CAJFVJ01

"Ca. Adamsella"

 
 
RUG14156

"Ca. Galligastranaerophilus"

 
"Gastranaerophilaceae"
 
 

Ca. Avigastranaerophilus"

 
 
 

Ca. Limenecus"

 
 

Ca. Spyradomonas"

 
 
 
 
 

Ca. Gastranaerophilus"

 
 
 

Ca. Stercorousia"

 
 
 

Ca. Scatenecus"

 
 

Ca. Scatousia"

 
 
 
 
 
 
 
 
 
 
 
 

Classification
  • Class "Melainabacteria" Soo et al. 2014 ["Vampirovibrionia"] (ACD20)
    • Order "Caenarcanales" corrig. Soo et al. 2014 ["Caenarcaniphilales" Soo et al. 2014]
      • Family "Caenarcanaceae"
        • Genus "Ca. Caenarcanum" Soo et al. 2014
          • "Ca. C. bioreactoricola" Soo et al. 2014
    • Order "Obscuribacterales" Soo et al. 2014
      • Family "Obscuribacteraceae"
        • Genus "Ca. Obscuribacter" Soo et al. 2014
          • "Ca. O. phosphatis" Soo et al. 2014
    • Order "Vampirovibrionales" Soo et al. 2015
      • Family "Vampirovibrionaceae" Soo 2015
        • Genus Vampirovibrio Gromov & Mamkayeva 1972 ex Gromov & Mamkaeva 1980
    • Order "Gastranaerophilales" Soo et al. 2014
      • Family CAJFVJ01
        • Genus "Ca. Adamsella" Glendinning et al. 2020
          • "Ca. A. avium" Glendinning et al. 2020
      • 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
      • Family "Gastranaerophilaceae"
        • 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. 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. Scatousia" Gilroy et al. 2021
          • "Ca. S. excrementigallinarum" Gilroy et al. 2021
          • "Ca. S. excrementipullorum" Gilroy et al. 2021

Ecological Niche

Melainabacteria 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 is often found in natural environments such as groundwater aquifers and lake sediment, as well as soil and bioreactors.[15]

Human Body Habitat

Melainabacteria has been found to potentially play a role in digesting fiber in the human gut,[16] as it is more commonly present in herbivorous mammals and those with plant-rich diets[17]. Because plant diets require more fiber break-down, Melainabacteria may aid in this digestive function. However, scientists are unsure of why these microbes are in the gut and how they got there. [17] Ongoing studies such as, "The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria," 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. [17]

Groundwater Harbor

Melainabacteria are also found in the aphotic zone of aquatic environments such as lake sediment and aquifers. [18] Cyanobacteria is an intensely studied microbe in relationship to environmental impacts. This microbe blooms in freshwater systems as a result of excess nutrients and high temperatures, resulting in blue-green appearing algae. [18]Because Melainabacteria and Cyanobacteria are related, it has raised concern that Melainabacteria thrives in groundwater systems. Melainabacteria seem to be originally accustomed to anaerobic functioning, yet evolved to tolerate oxygen following the GOE. 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[18].

References
  1. Di Rienzi, S.C., Sharon, I., Wrighton, K.C., Koren, O., Hug, L.A., Thomas, B.C., Goodrich, J.K., Bell, J.T., Spector, T.D., Banfield, J.F., and Ley, R.E. "The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria." eLife (2013) 2:e01102.
  2. 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.
  3. Soo RM, Woodcroft BJ, Parks DH, Tyson GW, Hugenholtz P. (2015) Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus. PeerJ 3:e968 https://doi.org/10.7717/peerj.968
  4. 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.
  5. 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. doi:10.1038/s41467-021-23286-7. ISSN 2041-1723.
  6. 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.
  7. Biello, David. "The Origin of Oxygen in Earth's Atmosphere". Scientific American. Retrieved 2022-10-03.
  8. "New bacteria found in human gut". Cornell Chronicle. Retrieved 2022-10-03.
  9. "The LTP". Retrieved 23 February 2021.
  10. "LTP_all tree in newick format". Retrieved 23 February 2021.
  11. "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.
  12. "GTDB release 07-RS207". Genome Taxonomy Database. Retrieved 20 June 2022.
  13. "ar53_r207.sp_label". Genome Taxonomy Database. Retrieved 20 June 2022.
  14. "Taxon History". Genome Taxonomy Database. Retrieved 20 June 2022.
  15. Hu, Chenlin; Rzymski, Piotr (2022-02-05). "Non-Photosynthetic Melainabacteria (Cyanobacteria) in Human Gut: Characteristics and Association with Health". Life. 12 (4): 476. doi:10.3390/life12040476. ISSN 2075-1729.
  16. C, Di Rienzi, Sara (2013-10-01). The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eScholarship, University of California. OCLC 1287394967.
  17. "New bacteria found in human gut". Cornell Chronicle. Retrieved 2022-10-03.
  18. Hu, Chenlin; Rzymski, Piotr (2022-03-25). "Non-Photosynthetic Melainabacteria (Cyanobacteria) in Human Gut: Characteristics and Association with Health". Life. 12 (4): 476. doi:10.3390/life12040476. ISSN 2075-1729. PMC 9029806. PMID 35454968.
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