Verrucomicrobiota

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Verrucomicrobiota
TEM - Epixenosomes.jpg
Transmission electron micrograph of stage II epixenosomes.
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Bacteria
Superphylum: PVC superphylum
Phylum: Verrucomicrobiota
Hedlund 2021 [1]
Classes
Synonyms
  • "Verrucomicrobaeota" Oren et al. 2015
  • Verrucomicrobia Hedlund 2012
  • "Verrucomicrobiota" Whitman et al. 2018

Verrucomicrobiota is a phylum of Gram-negative bacteria that contains only a few described species. The species identified have been isolated from fresh water, marine and soil environments and human faeces. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protists and endosymbionts of nematodes from genus Xiphinema , residing in their gametes. [2] [3] The verrucomicrobial bacterium Akkermansia muciniphila is a human intestinal symbiotic bacterium that is considered as a promising probiotic. [4]

Contents

Verrucomicrobiota are abundant within the environment, though relatively inactive. [5] This phylum is considered to have two sister phyla: Chlamydiota (formerly Chlamydiae) and Lentisphaerota (formerly Lentisphaerae) within the PVC superphylum. [6] The Verrucomicrobiota phylum can be distinguished from neighbouring phyla within the PVC group by the presence of several conserved signature indels (CSIs). [7] These CSIs represent unique, synapomorphic characteristics that suggest common ancestry within Verrucomicrobiota and an independent lineage amidst other bacteria. [8] CSIs have also been found that are shared by Verrucomicrobiota and Chlamydiota exclusively of all other bacteria. [9] These CSIs provide evidence that Chlamydiota is the closest relative to Verrucomicrobiota, and that they are more closely related to one another than to the Planctomycetales .

Verrucomicrobiota might belong in the clade Planctobacteria in the larger clade Gracilicutes. [10]

In 2008, the whole genome of Methylacidiphilum infernorum (2.3 Mbp) was published. On the single circular chromosome, 2473 predicted proteins were found, 731 of which had no detectable homologs. These analyses also revealed many possible homologies with Pseudomonadota. [11] [12]

Phylogeny

16S rRNA based LTP_10_2024 [13] [14] [15] 120 marker proteins based GTDB 09-RS220 [16] [17] [18]
Kiritimatiellota
Kiritimatiellae
Lentisphaerota
Lentisphaeria
Lentisphaerales

Lentisphaeraceae

Oligosphaeria
Oligosphaerales

Oligosphaeraceae

Victivallales

Victivallaceae

Verrucomicrobiota
Opitutia
Opitutales

Opitutaceae

Puniceicoccales

Alterococcaceae

Pelagicoccaceae

Puniceicoccaceae (incl. Cerasicoccaceae, Coraliomargaritaceae, Oceanipulchritudinaceae)

Verrucomicrobiia
Methylacidiphilales

Methylacidiphilaceae

Terrimicrobiales

Terrimicrobiaceae

Verrucomicrobiales

Verrucomicrobiaceae

Akkermansiaceae (incl. Rubritaleaceae)

Verrucomicrobiota
Lentisphaeria
Victivallales

Victivallaceae

Oligosphaerales

Oligosphaeraceae

Lentisphaerales

Lentisphaeraceae

Kiritimatiellia
"Spyradenecales"

"Spyradenecaceae"

Kiritimatiellales
Verrucomicrobiia
Opitutales

"Merdousiaceae"

"Spyradosomataceae"

Cerasicoccaceae

"Moanibacteraceae"

Oceanipulchritudinaceae

Opitutaceae (incl. Pelagicoccaceae)

Limisphaerales
Methylacidiphilales

Methylacidiphilaceae

Terrimicrobiales

"Chthoniobacteraceae"

"Udaeobacteraceae"

Terrimicrobiaceae

"Xiphinematobacteraceae"

Verrucomicrobiales

Verrucomicrobiaceae

SLCJ01

Akkermansiaceae (incl. Rubritaleaceae)

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [19] and National Center for Biotechnology Information (NCBI) [20]

See also

Related Research Articles

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

A spirochaete or spirochete is a member of the phylum Spirochaetota, which contains distinctive diderm (double-membrane) Gram-negative bacteria, most of which have long, helically coiled cells. Spirochaetes are chemoheterotrophic in nature, with lengths between 3 and 500 μm and diameters around 0.09 to at least 3 μm.

The Aquificota phylum is a diverse collection of bacteria that live in harsh environmental settings. The name Aquificota was given to this phylum based on an early genus identified within this group, Aquifex, which is able to produce water by oxidizing hydrogen. They have been found in springs, pools, and oceans. They are autotrophs, and are the primary carbon fixers in their environments. These bacteria are Gram-negative, non-spore-forming rods. They are true bacteria as opposed to the other inhabitants of extreme environments, the Archaea.

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

The Chlamydiota are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of the Chlamydiota that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all have hosts. Historically it was believed that all Chlamydiota had a peptidoglycan-free cell wall, but studies in the 2010s demonstrated a detectable presence of peptidoglycan, as well as other important proteins.

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

The Planctomycetota are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats. They play a considerable role in global carbon and nitrogen cycles, with many species of this phylum capable of anaerobic ammonium oxidation, also known as anammox. Many Planctomycetota occur in relatively high abundance as biofilms, often associating with other organisms such as macroalgae and marine sponges.

The Thermotogota are a phylum of the domain Bacteria. The phylum contains a single class, Thermotogae. The phylum Thermotogota is composed of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria. It is the sole phylum in the kingdom Thermotogati.

<span class="mw-page-title-main">PVC superphylum</span> Superphylum of bacteria

The PVC superphylum is a superphylum of bacteria named after its three important members, Planctomycetota, Verrucomicrobiota, and Chlamydiota. Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wall twice. It has been hypothesised that a member of the PVC clade might have been the host cell in the endosymbiotic event that gave rise to the first proto-eukaryotic cell.

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

The Acidobacteriaceae are a family of Acidobacteriota.

Lentisphaerota is a phylum of bacteria closely related to Chlamydiota and Verrucomicrobiota.

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

The FCB group is a superphylum of bacteria named after the main member phyla Fibrobacterota, Chlorobiota, and Bacteroidota. The members are considered to form a clade due to a number of conserved signature indels.

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.

Methylacidiphilum infernorum is an extremely acidophilic methanotrophic aerobic bacteria first isolated and described in 2007 growing on soil and sediment on Hell's Gate, New Zealand. Similar organisms have also been isolated from geothermal sites on Italy and Russia.

Singulisphaera is a moderately acidophilic and mesophilic genus of bacteria from the family of Planctomycetaceae.

The Ignavibacteriales are an order of obligately anaerobic, non-photosynthetic bacteria that are closely related to the green sulfur bacteria.

Cerasicoccus is a Gram-negative, non-motile, obligately aerobic and chemoheterotrophic bacterial genus from the family Puniceicoccaceae.

Pelagicoccus is a Gram-negative genus of bacteria from the family of Puniceicoccaceae.

The Opitutales is an order in the phylum Verrucomicrobiota.

The Opitutaceae are a Gram-negative and chemoheterotrophic order of the domain Bacteria. Opitutaceae bacteria were isolated from soil and coastal marine springs.

<span class="mw-page-title-main">Acidobacteriia</span> Class of bacteria

The "Acidobacteriia" is a class of Acidobacteriota.

Omnitrophica or Omnitrophota is a proposed candidate phylum of bacteria with chemolithoautotrophic nutrition. It was previously known as candidate phylum OP3. These bacteria appear to thrive in anoxic environments, such as deep marine sediments, hypersaline environments, freshwater lakes, aquifers, flooded soils, and methanogenic bioreactors. Genomic analyzes have found genes responsible for the construction of magnetosomes, which are also present in other phyla of bacteria. These organelles have magnetic properties, which causes bacteria to orient themselves magnetically in the environment. Omnitrophica is part of the PVC superphylum along with the phyla Planctomycetota, Verrucomicrobiota and Chlamydiota with which it shares a common ancestor.

References

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