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The Actinomycetota are a diverse phylum of Gram-positive bacteria with high G+C content. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on 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, like a fungus would, 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.
Nanoarchaeota is a proposed phylum in the domain Archaea that currently has only one representative, Nanoarchaeum equitans, which was discovered in a submarine hydrothermal vent and first described in 2002.
The Korarchaeota is a proposed phylum within the Archaea. The name is derived from the Greek noun koros or kore, meaning young man or young woman, and the Greek adjective archaios which means ancient. They are also known as Xenarchaeota. The name is equivalent to Candidatus Korarchaeota, and they go by the name Xenarchaeota or Xenarchaea as well.
"Candidatus Pelagibacter", with the single species "Ca. P. communis", was isolated in 2002 and given a specific name, although it has not yet been described as required by the bacteriological code. It is an abundant member of the SAR11 clade in the phylum Alphaproteobacteria. SAR11 members are highly dominant organisms found in both salt and fresh water worldwide and were originally known only from their rRNA genes, first identified in the Sargasso Sea in 1990 by Stephen Giovannoni's laboratory at Oregon State University and later found in oceans worldwide. "Ca. P. communis" and its relatives may be the most abundant organisms in the ocean, and quite possibly the most abundant bacteria in the entire world. It can make up about 25% of all microbial plankton cells, and in the summer they may account for approximately half the cells present in temperate ocean surface water. The total abundance of "Ca. P. communis" and relatives is estimated to be about 2 × 1028 microbes.
Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) were first discovered in an extremely acidic mine located in northern California (Richmond Mine at Iron Mountain) by Brett Baker in Jill Banfield's laboratory at the University of California Berkeley. These novel groups of archaea named ARMAN-1, ARMAN-2 (Candidatus Micrarchaeum acidiphilum ARMAN-2), and ARMAN-3 were missed by previous PCR-based surveys of the mine community because the ARMANs have several mismatches with commonly used PCR primers for 16S rRNA genes. Baker et al. detected them in a later study using shotgun sequencing of the community. The three groups were originally thought to represent three unique lineages deeply branched within the Euryarchaeota, a subgroup of the Archaea. However, based on a more complete archaeal genomic tree, they were assigned to a new superphylum named DPANN. The ARMAN groups now comprise deeply divergent phyla named Micrarchaeota and Parvarchaeota. Their 16S rRNA genes differ by as much as 17% between the three groups. Prior to their discovery, all of the Archaea shown to be associated with Iron Mountain belonged to the order Thermoplasmatales (e.g., Ferroplasma acidarmanus).
The Nitrososphaerota are a phylum of the Archaea proposed in 2008 after the genome of Cenarchaeum symbiosum was sequenced and found to differ significantly from other members of the hyperthermophilic phylum Thermoproteota. Three described species in addition to C. symbiosum are Nitrosopumilus maritimus, Nitrososphaera viennensis, and Nitrososphaera gargensis. The phylum was proposed in 2008 based on phylogenetic data, such as the sequences of these organisms' ribosomal RNA genes, and the presence of a form of type I topoisomerase that was previously thought to be unique to the eukaryotes. This assignment was confirmed by further analysis published in 2010 that examined the genomes of the ammonia-oxidizing archaea Nitrosopumilus maritimus and Nitrososphaera gargensis, concluding that these species form a distinct lineage that includes Cenarchaeum symbiosum. The lipid crenarchaeol has been found only in Nitrososphaerota, making it a potential biomarker for the phylum. Most organisms of this lineage thus far identified are chemolithoautotrophic ammonia-oxidizers and may play important roles in biogeochemical cycles, such as the nitrogen cycle and the carbon cycle. Metagenomic sequencing indicates that they constitute ~1% of the sea surface metagenome across many sites.
Nitrospirota is a phylum of bacteria. It includes multiple genera, such as Nitrospira, the largest. The first member of this phylum, Nitrospira marina, was discovered in 1985. The second member, Nitrospira moscoviensis, was discovered in 1995.
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 "Aigarchaeota" are a proposed archaeal phylum of which the main representative is Caldiarchaeum subterraneum. It is not yet clear if this represents a new phylum or a Nitrososphaerota order, since the genome of Caldiarchaeum subterraneum encodes several Nitrososphaerota-like features. The name "Aigarchaeota" comes from the Greek αυγή, avgí, meaning "dawn" or "aurora", for the intermediate features of hyperthermophilic and mesophilic life during the evolution of its lineage.
Lokiarchaeota is a proposed phylum of the Archaea. The phylum includes all members of the group previously named Deep Sea Archaeal Group, also known as Marine Benthic Group B. Lokiarchaeota is part of the superphylum Asgard containing the phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota, and Helarchaeota. A phylogenetic analysis disclosed a monophyletic grouping of the Lokiarchaeota with the eukaryotes. The analysis revealed several genes with cell membrane-related functions. The presence of such genes support the hypothesis of an archaeal host for the emergence of the eukaryotes; the eocyte-like scenarios.
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.
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.
"Candidatus Thorarchaeota", or simply Thorarchaeota, is a phylum within the superphylum Asgard archaea. The Asgard superphylum represents the closest prokaryotic relatives of eukaryotes. Since there is such a close relation between the two different domains, it provides further evidence to the two-domain tree of life theory which states that eukaryotes branched from the archaeal domain. Asgard archaea are single cell marine microbes that contain branch like appendages and have genes that are similar to eukarya. The asgard archaea superphylum is composed of Thorarchaeota, Lokiarchaeota, Odinarchaeota, and Heimdallarchaeota. Thorarchaeota were first identified from the sulfate-methane transition zone in tidewater sediments. Thorarcheota are widely distributed in marine and freshwater sediments.
Asgard or Asgardarchaeota is a proposed superphylum consisting of a group of archaea that contain eukaryotic signature proteins. It appears that the eukaryotes, the domain that contains the animals, plants, and fungi, emerged within the Asgard, in a branch containing the Heimdallarchaeota. This supports the two-domain system of classification over the three-domain system.
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. According to phylogenetic analysis, Atribacterota appears to be related to several thermophilic phyla within Terrabacteria or may be in the base of Gracilicutes. 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.
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.
Modulibacteria(Moduliflexota) is a bacterial phylum formerly known as KS3B3 or GN06. It is a candidate phylum, meaning there are no cultured representatives of this group. Members of the Modulibacteria phylum are known to cause fatal filament overgrowth (bulking) in high-rate industrial anaerobic wastewater treatment bioreactors.
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.
References
- ↑ Narasingarao; et al. (2011). "De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities". ISME J. 6 (1): 81–93. doi:10.1038/ismej.2011.78. PMC 3246234 . PMID 21716304.
- ↑ Ghai, Rohit; Lejla Pašić; Ana Beatriz Fernandez; Ana-Belen Martin-Cuadrado; et al. (10 October 2011). "New Abundant Microbial Groups in Aquatic Hypersaline Environments". Scientific Reports. 1: 135. Bibcode:2011NatSR...1E.135G. doi:10.1038/srep00135. PMC 3216616 . PMID 22355652.
- ↑ Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T (July 25, 2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature. 499, 431–437 (2013) (7459): 431–437. Bibcode:2013Natur.499..431R. doi: 10.1038/nature12352 . hdl: 10453/27467 . PMID 23851394.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ↑ Petitjean, C.; Deschamps, P.; López-García, P.; Moreira, D. (2014). "Rooting the domain Archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota". Genome Biol. Evol. 7 (1): 191–204. doi:10.1093/gbe/evu274. PMC 4316627 . PMID 25527841.
- ↑ Cavalier-Smith, Thomas; Chao, Ema E-Yung (2020). "Multidomain ribosomal protein trees and the planctobacterial origin of neomura (Eukaryotes, archaebacteria)". Protoplasma. 257 (3): 621–753. doi:10.1007/s00709-019-01442-7. PMC 7203096 . PMID 31900730.
- ↑ Monique Aouad, Najwa Taïb, Anne Oudart, Michel Lecocq, Manolo Gouy,Céline Brochier-Armanet (21 Apr 2018). "Extreme halophilic archaea derive from two distinct methanogen Class II lineages" (PDF). Molecular Phylogenetics and Evolution. Elsevier. 2018 (27): 46–54. doi:10.1016/j.ympev.2018.04.011. PMID 29684598. S2CID 25111200.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ↑ Karen Andrade, Jörn Logemann, Karla B Heidelberg, Joanne B Emerson, Luis R Comolli, Laura A Hug, Alexander J Probst, Angus Keillar, Brian C Thomas, Christopher S Miller, Eric E Allen, John W Moreau, Jochen J Brocks & Jillian F Banfield (28 April 2015). "Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem". ISME J. ISME J 9, 2697–2711 (2015) (12): 2697–2711. doi: 10.1038/ismej.2015.66 . PMC 4817636 . PMID 25918833.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ↑ Rohit Ghai, Lejla Pašić, Ana Beatriz Fernández, Ana-Belen Martin-Cuadrado, Carolina Megumi Mizuno, Katherine D. McMahon, R. Thane Papke, Ramunas Stepanauskas, Beltran Rodriguez-Brito, Forest Rohwer, Cristina Sánchez-Porro, Antonio Ventosa & Francisco Rodríguez-Valera (31 October 2011). "New Abundant Microbial Groups in Aquatic Hypersaline Environments". Scientific Reports. 1 (Sci Rep 1, 135 (2011)): 135. Bibcode:2011NatSR...1E.135G. doi: 10.1038/srep00135 . PMC 3216616 . PMID 22355652.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ↑ Vavourakis Charlotte D., Ghai Rohit, Rodriguez-Valera Francisco, Sorokin Dimitry Y., Tringe Susannah G., Hugenholtz Philip, Muyzer Gerard (25 February 2016). "Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines". Frontiers in Microbiology. 7: 211. doi: 10.3389/fmicb.2016.00211 . PMC 4766312 . PMID 26941731.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ↑ Olga Zhaxybayeva 1 , Ramunas Stepanauskas, Nikhil Ram Mohan, R Thane Papke (29 January 2013). "Cell sorting analysis of geographically separated hypersaline environments". Extremophiles. 17, 2 (2013) (2): 265–275. doi:10.1007/s00792-013-0514-z. PMID 23358730. S2CID 5933801 . Retrieved 2 March 2021.
{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: numeric names: authors list (link) - ↑ Alexander Crits‐Christoph Diego R. Gelsinger Bing Ma Jacek Wierzchos Jacques Ravel Alfonso Davila M. Cristina Casero Jocelyne DiRuggiero (21 March 2016). "Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community". Environmental Microbiology. 18 (2016 v.18 no.6): 2064–2077. doi:10.1111/1462-2920.13259. PMID 26914534 . Retrieved 2 March 2021.
- ↑ Gómez, Felipe; Cavalazzi, Barbara; Rodríguez, Nuria; Amils, Ricardo; Ori, Gian Gabriele; Olsson-Francis, Karen; Escudero, Cristina; Martínez, Jose M.; Miruts, Hagos (2019-05-27). "Ultra-small microorganisms in the polyextreme conditions of the Dallol volcano, Northern Afar, Ethiopia". Scientific Reports. 9 (1): 7907. Bibcode:2019NatSR...9.7907G. doi:10.1038/s41598-019-44440-8. ISSN 2045-2322. PMC 6536532 . PMID 31133675.
- ↑ J.P. Euzéby. "Phylum "Candidatus Nanohaloarchaeota"". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2011-11-17.
- ↑ Sayers; et al. "Nanohaloarchaea". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2011-06-05.
- ↑ "GTDB release 08-RS214". Genome Taxonomy Database . Retrieved 6 December 2021.
- ↑ "ar53_r214.sp_label". Genome Taxonomy Database . Retrieved 10 May 2023.
- ↑ "Taxon History". Genome Taxonomy Database . Retrieved 6 December 2021.
- ↑ La Cono; et al. (2020). "Symbiosis between nanohaloarchaeon and haloarchaeon is based on utilization of different polysaccharides". Proc Natl Acad Sci USA. 117 (33): 20223–20234. Bibcode:2020PNAS..11720223L. doi: 10.1073/pnas.2007232117 . PMC 7443923 . PMID 32759215.
