en Atribacterota

Atribacterota
	Morphology and membrane structure in Atribacter laminatus (type strain RT761)
Scientific classification
Domain:	Bacteria
Superphylum:	Terrabacteria
Phylum:	Atribacterota; Katayama et al. 2021
Classes
	Atribacteria; "Phoenicimicrobiia";
Synonyms
	"Ca. Atribacteria" Dodsworth et al. 2013; "Atribacterota" Katayama et al. 2020; "Caldatribacteriota" Hahn 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]

Classification

Phylogeny

120 marker proteins based GTDB 09-RS220^[7]^[8]^[9]

"Phoenicimicrobiia"

"Phoenicimicrobiales"

"Stramentimicrobiaceae"

	"Ca. Stramentimicrobium"

	"Ca. Oleincola"

"Phoenicimicrobiaceae"

"Ca. Immundihabitans"

	"Ca. Infernicultor"

	"Ca. Sediminicultor"

Atribacteria

Atribacterales

Atribacteraceae

	"Ca. Nitricultor"

	Atribacter

"Caldatribacteriaceae"

"Ca. Sordicultor"

	"Ca. Profundicultor"

	"Ca. Caldatribacterium"

Taxonomy

National Center for Biotechnology Information (NCBI)^[10] taxonomy and List of Prokaryotic names with Standing in Nomenclature (LPSN)^[11] were used as the primary taxonomic authority for establishing naming priorities. Also Annotree website,^[12] which uses the GTDB release 06-RS202.^[13] was consulted.

"Class Phoenicimicrobiia" Jiao et al. 2024 [JS1]
- Order "Phoenicimicrobiales" Jiao et al. 2024 [SB-45]
  - Family "Stramentimicrobiaceae" Jiao et al. 2024
    - Genus ?"Candidatus Oleihabitans" Jiao et al. 2024 [R3-B20]
    - Genus "Candidatus Oleincola" Jiao et al. 2024 [M55B131]
    - Genus "Candidatus Stramentimicrobium" Jiao et al. 2024 [JAAYOB01]
  - Family "Phoenicimicrobiaceae" Jiao et al. 2024 [34-128]
    - Genus "Candidatus Immundihabitans" Jiao et al. 2024 [UBA5772]
    - Genus "Candidatus Infernicultor" Jiao et al. 2024 [CG2-30-33-13]
    - Genus ?"Candidatus Phoenicimicrobium" Jiao et al. 2024
    - Genus "Candidatus Sediminicultor" Jiao et al. 2024 [UBA9311]
Class Atribacteria Katayama et al. 2021
- Order Atribacterales Katayama et al. 2021
  - Family Atrimonadaceae Kawamoto et al. 2024
    - Genus ?Atrimonas Kawamoto et al. 2024
  - Family Thermatribacteraceae Jiao et al. 2024
    - Genus ?Thermatribacter Jiao et al. 2024
  - Family Atribacteraceae Katayama et al. 2021 (OP9)
    - Genus Atribacter Katayama et al. 2021
    - Genus "Candidatus Nitricultor" Jiao et al. 2024 [SKXZ01]
  - Family "Caldatribacteriaceae"
    - Genus "Candidatus Caldatribacterium" Dodsworth et al. 2013
    - Genus "Candidatus Profundicultor" Jiao et al. 2024 [JABUEZ01]
    - Genus "Candidatus Sordicultor" Jiao et al. 2024 [UBA3950]

References

^ 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.
^ 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.
^ 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.
^ 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
^ Hug, L. A. et al. 2016, A new view of the tree of life. Nature Microbiology, 1, 16048.
^ 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.
^ "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.
^ Sayers; et al. "Atribacterota". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
^ J.P. Euzéby. "Atribacterota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-06-27.
^ 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.
^ "GTDB release 06-RS202". Genome Taxonomy Database.

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[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.

[about-7] "GTDB release 09-RS220". Genome Taxonomy Database. Retrieved 10 May 2024.

[tree-8] "bac120_r220.sp_labels". Genome Taxonomy Database. Retrieved 10 May 2024.

[taxon_history-9] "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2024.

[10] Sayers; et al. "Atribacterota". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.

[11] J.P. Euzéby. "Atribacterota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-06-27.

[Mendler-12] 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.

[GTDB-13] "GTDB release 06-RS202". Genome Taxonomy Database.

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Atribacterota

Classification

Phylogeny

Taxonomy

See also

References

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