Atribacterota

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Atribacterota
41467 2020 20149 Fig1f.jpg
Morphology and membrane structure in Atribacter laminatus (type strain RT761)
Scientific classification
Domain:
Superphylum:
Phylum:
Atribacterota

Katayama 2021 [1]
Synonyms
  • Candidate phylum OP9
  • Candidate phylum JS1
  • "Candidatus Atribacteria" Dodsworth et al. 2013
  • "Atribacterota" Katayama et al. 2020

Atribacterota is a phylum of bacteria, which are common in anoxic sediments rich in methane. They are distributed worldwide and in some cases abundant in anaerobic marine sediments, geothermal springs, and oil deposits. Genetic analyzes suggest a heterotrophic metabolism that gives rise to fermentation products such as acetate, ethanol, and CO2. These products in turn can support methanogens within the sediment microbial community and explain the frequent occurrence of Atribacterota in methane-rich anoxic sediments. [2] [3] According to phylogenetic analysis, Atribacterota appears to be related to several thermophilic phyla within Terrabacteria [4] or may be in the base of Gracilicutes. [5] According to research, Atribacterota shows patterns of gene expressions which consists of fermentative, acetogenic metabolism. These expressions let Atribacterota to be able to create catabolic and anabolic functions which are necessary to generate cellular reproduction, even when the energy levels are limited due to the depletion of dissolved oxygen in the areas of sea waters, fresh waters, or ground waters. [6]

Contents

Taxonomy

National Center for Biotechnology Information (NCBI) [7] taxonomy and List of Prokaryotic names with Standing in Nomenclature (LPSN) [8] were used as the primary taxonomic authority for establishing naming priorities. Also Annotree website, [9] which uses the GTDB release 06-RS202. [10] was consulted.

See also

Related Research Articles

<span class="mw-page-title-main">Actinomycetota</span> Phylum of bacteria

The Actinomycetota are a diverse phylum of Gram-positive bacteria with high GC content. They can be terrestrial or aquatic. They are of great importance to land flora because of their contributions to soil systems. In soil they help to decompose the organic matter of dead organisms so the molecules can be taken up anew by plants. While this role is also played by fungi, Actinomycetota are much smaller and likely do not occupy the same ecological niche. In this role the colonies often grow extensive mycelia, as fungi do, and the name of an important order of the phylum, Actinomycetales, reflects that they were long believed to be fungi. Some soil actinomycetota live symbiotically with the plants whose roots pervade the soil, fixing nitrogen for the plants in exchange for access to some of the plant's saccharides. Other species, such as many members of the genus Mycobacterium, are important pathogens.

<span class="mw-page-title-main">Euryarchaeota</span> Phylum of archaea

Euryarchaeota is a kingdom of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines; halobacteria, which survive extreme concentrations of salt; and some extremely thermophilic aerobes and anaerobes, which generally live at temperatures between 41 and 122 °C. They are separated from the other archaeans based mainly on rRNA sequences and their unique DNA polymerase.

<span class="mw-page-title-main">Desulfovibrionales</span> Order of bacteria

Desulfovibrionales are a taxonomic order of bacteria belonging to the phylum Thermodesulfobacteriota, with four families. They are Gram-negative. The majority are sulfate-reducing, with the exception of Lawsonia and Bilophila. All members of this order are obligately anaerobic. Most species are mesophilic, but some are moderate thermophiles.

<span class="mw-page-title-main">Desulfovibrionaceae</span> Family of bacteria

Desulfovibrionaceae is a family of bacteria belonging to the phylum Thermodesulfobacteriota.

<i>Chlorobium</i> Genus of bacteria

Chlorobium is a genus of green sulfur bacteria. They are photolithotrophic oxidizers of sulfur and most notably utilise a noncyclic electron transport chain to reduce NAD+. Photosynthesis is achieved using a Type 1 Reaction Centre using bacteriochlorophyll (BChl) a. Two photosynthetic antenna complexes aid in light absorption: the Fenna-Matthews-Olson complex, and the chlorosomes which employ mostly BChl c, d, or e. Hydrogen sulfide is used as an electron source and carbon dioxide its carbon source.

<span class="mw-page-title-main">Campylobacterota</span> Phylum of bacteria

Campylobacterota are a phylum of Gram-negative bacteria. Until the 2021 revision of bacterial taxonomy by the ICSP, the entire phylum was classified within the Proteobacteria as the Epsilonproteobacteria and the Desulfurellales. The separation of this phylum from "Proteobacteria" was originally proposed in 2017, using GTDB-based methods.

The Myxococcota are a phylum of bacteria known as the fruiting gliding bacteria. All species of this group are Gram-negative. They are predominantly aerobic genera that release myxospores in unfavorable environments.

The Gemmatimonadota are a phylum of bacteria established in 2003. The phylum contains two classes Gemmatimonadetes and Longimicrobia.

Chloracidobacterium is a genus of the Acidobacteriota. It is currently assigned to the family Acidobacteriaceae, but phylogenetic evidence suggests that it belongs in Blastocatellia.

<span class="mw-page-title-main">Bacterial phyla</span> Phyla or divisions of the domain Bacteria

Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.

The phylum Elusimicrobiota, previously known as "Termite Group 1", has been shown to be widespread in different ecosystems like marine environment, sewage sludge, contaminated sites and soils, and toxic wastes. The high abundance of Elusimicrobiota representatives is only seen for the lineage of symbionts found in termites and ants.

Nanohaloarchaea is a clade of diminutive archaea with small genomes and limited metabolic capabilities, belonging to the DPANN archaea. They are ubiquitous in hypersaline habitats, which they share with the extremely halophilic haloarchaea.

<span class="mw-page-title-main">Parvarchaeota</span> Phylum of archaea

Parvarchaeota is a phylum of archaea belonging to the DPANN archaea. They have been discovered in acid mine drainage waters and later in marine sediments. The cells of these organisms are extremely small consistent with small genomes. Metagenomic techniques allow obtaining genomic sequences from non-cultured organisms, which were applied to determine this phylum.

<span class="mw-page-title-main">DPANN</span> A superphylum of Archaea grouping taxa that display various environmental and metabolic features

DPANN is a superphylum of Archaea first proposed in 2013. Many members show novel signs of horizontal gene transfer from other domains of life. They are known as nanoarchaea or ultra-small archaea due to their smaller size (nanometric) compared to other archaea.

<span class="mw-page-title-main">Candidate phyla radiation</span> A large evolutionary radiation of bacterial candidate phyla and superphyla

The candidate phyla radiation is a large evolutionary radiation of bacterial lineages whose members are mostly uncultivated and only known from metagenomics and single cell sequencing. They have been described as nanobacteria or ultra-small bacteria due to their reduced size (nanometric) compared to other bacteria.

<span class="mw-page-title-main">NC10 phylum</span> Phylum of bacteria

NC10 is a bacterial phylum with candidate status, meaning its members remain uncultured to date. The difficulty in producing lab cultures may be linked to low growth rates and other limiting growth factors.

Nitrospinota is a bacterial phylum. Despite only few described species, members of this phylum are major nitrite-oxidizing bacteria in surface waters in oceans. By oxidation of nitrite to nitrate they are important in the process of nitrification in marine environments.

There are several models of the branching order of bacterial phyla, one of these is the Genome Taxonomy Database (GTDB).

Bdellovibrionota is a phylum of bacteria.

References

  1. Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi: 10.1099/ijsem.0.005056 . PMID   34694987. S2CID   239887308.
  2. Nobu, M. K., Dodsworth, J. A., Murugapiran, S. K., Rinke, C., Gies, E. A., Webster, G., ... & Jørgensen, B. B. (2016) Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics. The ISME journal, 10(2), 273-286.
  3. Carr, S. A., Orcutt, B. N., Mandernack, K. W., & Spear, J. R. (2015). Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica. Frontiers in microbiology, 6.
  4. Christian Rinke et al 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature Volume: 499, Pages: 431–437 doi:10.1038/nature12352
  5. Hug, L. A. et al. 2016, A new view of the tree of life. Nature Microbiology, 1, 16048.
  6. Vuillemin, Aurèle; Vargas, Sergio; Coskun, Ömer K.; Pockalny, Robert; Murray, Richard W.; Smith, David C.; D’Hondt, Steven; Orsi, William D. (2020-07-11). "Atribacteria reproducing over millions of years in the Atlantic abyssal subseafloor". mBio. 11 (5). bioRxiv   10.1101/2020.07.10.198200 . doi: 10.1128/mbio.01937-20 . PMC   7542362 . PMID   33024037.
  7. Sayers; et al. "Atribacterota". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  8. J.P. Euzéby. "Atribacterota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-06-27.
  9. Mendler, K; Chen, H; Parks, DH; Hug, LA; Doxey, AC (2019). "AnnoTree: visualization and exploration of a functionally annotated microbial tree of life". Nucleic Acids Research. 47 (9): 4442–4448. doi: 10.1093/nar/gkz246 . PMC   6511854 . PMID   31081040. Archived from the original on 2021-04-23. Retrieved 2021-07-15.
  10. "GTDB release 06-RS202". Genome Taxonomy Database .