PVC superphylum

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PVC superphylum
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Chlamydia trachomatis
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(temporary)
Domain: Bacteria
Clade: Hydrobacteria
Superphylum: PVC superphylum
Phyla

Chlamydiota
Kiritimatiellota
Lentisphaerota
Planctomycetota
Verrucomicrobiota
"Ca. Hydrogenedentes"
"Ca. Aureabacteria"
"Ca. Omnitrophica"

Contents

Synonyms

Planctobacteria Cavalier-Smith, 1987 [1]

The PVC superphylum is a superphylum of bacteria named after its three important members, Planctomycetota, Verrucomicrobiota, and Chlamydiota. [2] [3] Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wall twice. [4] 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. [5] [6]

Cavalier-Smith calls the same group Planctobacteria and considers it a phylum. However, this is not followed by the larger scientific community. [7] In the Cavalier-Smith bacterial megaclassification, it is within the bacterial Gracilicutes infra-kingdom and comprises the phyla Chlamydiota, Lentisphaerota, Planctomycetota, Verrucomicrobiota. [4] [8]

PVC superphylum [9] [10] [2] [11]
PVC

Molecular signatures

Planctomycetota, Verrucomicrobiota, and Chlamydiota in the traditional molecular phylogeny view are considered as phyla and also cluster together in the PVC superphylum, along with the candidate phyla Omnitrophica [12] (previously OP3) and the Poribacteria. [13] An important molecular marker in the form of a conserved signature protein has been found to be consistently shared by PVC members, with the exception of Poribacteria. The conserved signature protein may be a marker that represents a synapomorphic quality and a means to distinguish this bacterial group. In 2014, studies have characterized this protein and it has been attributed to play an important housekeeping function in DNA/RNA binding. [14] This observation not only provides a means to demarcate the PVC superphylum, but it supports strongly supports an evolutionary relationship shared by this clade that is distinct from other bacteria. [15] [16]

Conserved signature indels (CSIs) have also been found specific for the Planctomycetota, Verrucomicrobiota, and Chlamydiota that distinguish each respective phylum from one another, and from other bacteria. [15] [17] A three-amino-acid insert in the RNA polymerase protein RpoB has been found that is shared by all sequenced Verrucomicrobia, Chlamydiae, and Lentisphaerae species. The CSI is absent from neighbouring Planctomycetes' and Poribacteria, suggesting common ancestry among the groups for which the CSI is specific. [15]

Additional lines of evidence for the existence of this clade have been found. [18] [19] These include the presence of membrane coat-like proteins, tubulin, sterol synthesis, and the presence of condensed DNA.

Notes

    Related Research Articles

    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">Bacteroidota</span> Phylum of Gram-negative bacteria

    The phylum Bacteroidota is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals.

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

    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. The verrucomicrobial bacterium Akkermansia muciniphila is a human intestinal symbiotic bacterium that is considered as a promising probiotic.

    <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.

    <span class="mw-page-title-main">Gracilicutes</span> Infrakingdom of bacteria

    Gracilicutes is a clade in bacterial phylogeny.

    <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.

    <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.

    There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.

    There are several models of the Branching order of bacterial phyla, the most cited of these was proposed in 1987 paper by Carl Woese. This cladogram was later expanded by Rappé and Giovanoni in 2003 to include newly discovered phyla. Clear names are added in parentheses, see list of bacterial phyla.

    Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. CSIs, brought about by rare genetic changes, provide useful phylogenetic markers that are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability. While indels can be arbitrary inserts or deletions, CSIs are defined as only those protein indels that are present within conserved regions of the protein.

    <i>Gemmata obscuriglobus</i> Species of bacteria

    Gemmata obscuriglobus is a species of Gram-negative, aerobic, heterotrophic bacteria of the phylum Planctomycetota. G. obscuriglobus occur in freshwater habitats and was first described in 1984, and is the only described species in its genus.

    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.

    Sneathia is a Gram-negative, rod-shaped, non-spore-forming and non-motile genus of bacteria from the family of Leptotrichiaceae. Species have been identified as pathogens associated with bacterial vaginosis.

    <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.

    Fucophilus is a fucoidan-utilizing genus of bacteria from the phylum Verrucomicrobiota with one known species. Fucophilus fucoidanolyticus has been isolated from the gut contend of a sea cucumber.

    The Opitutales is an order in the phylum Verrucomicrobiota.

    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

    1. ↑ Cavalier-Smith, T (1987). "The origin of eukaryote and archaebacterial cells". Annals of the New York Academy of Sciences. 503 (1): 17–54. Bibcode:1987NYASA.503...17C. doi:10.1111/j.1749-6632.1987.tb40596.x. PMID   3113314. S2CID   38405158.
    2. 1 2 Wagner, M.; Horn, M. (2006). "The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance". Current Opinion in Biotechnology. 17 (3): 241–249. doi:10.1016/j.copbio.2006.05.005. PMID   16704931.
    3. ↑ Rivas-Marín, Elena; Devos, Damien P. (1 June 2018). "The Paradigms They Are a-Changin': past, present and future of PVC bacteria research". Antonie van Leeuwenhoek. 111 (6): 785–799. doi:10.1007/s10482-017-0962-z. PMC   5945725 . PMID   29058138.
    4. 1 2 Cavalier-Smith, T (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 1): 7–76. doi: 10.1099/00207713-52-1-7 . PMID   11837318.
    5. ↑ Forterre, Patrick (January 2011). "A new fusion hypothesis for the origin of Eukarya: better than previous ones, but probably also wrong". Research in Microbiology. 162 (1): 77–91. doi: 10.1016/j.resmic.2010.10.005 . PMID   21034817.
    6. ↑ Baum, David A; Baum, Buzz (28 October 2014). "An inside-out origin for the eukaryotic cell". BMC Biology. 12 (1): 76. doi: 10.1186/s12915-014-0076-2 . PMC   4210606 . PMID   25350791.
    7. ↑ Krieg, N.R.; Ludwig, W.; Whitman, W.B.; Hedlund, B.P.; Paster, B.J.; Staley, J.T.; Ward, N.; Brown, D.; Parte, A. (November 24, 2010) [1984(Williams & Wilkins)]. George M. Garrity (ed.). The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Bergey's Manual of Systematic Bacteriology. Vol. 4 (2nd ed.). New York: Springer. p. 908. ISBN   978-0-387-95042-6. British Library no. GBA561951.
    8. ↑ Cavalier-Smith T (2006). "Rooting the tree of life by transition analyses". Biol. Direct. 1 (1): 19. doi: 10.1186/1745-6150-1-19 . PMC   1586193 . PMID   16834776.
    9. ↑ Rappe, M. S.; Giovannoni, S. J. (2003). "The Uncultured Microbial Majority". Annual Review of Microbiology. 57: 369–394. doi:10.1146/annurev.micro.57.030502.090759. PMID   14527284.
    10. ↑ Woese, C. R. (1987). "Bacterial evolution". Microbiological Reviews. 51 (2): 221–271. doi:10.1128/MMBR.51.2.221-271.1987. PMC   373105 . PMID   2439888.
    11. ↑ Stefan Spring, Boyke Bunk, Cathrin Spröer, Peter Schumann, Manfred Rohde, Brian J Tindall & Hans-Peter Klenk, (2016). Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum. Nature.
    12. ↑ "Taxonomy - Candidatus Omnitrophica (PHYLUM)". UniProt.
    13. ↑ Wagner, M.; Horn, M. (2006). "The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance". Current Opinion in Biotechnology. 17 (3): 241–249. doi:10.1016/j.copbio.2006.05.005. PMID   16704931.
    14. ↑ Lagkouvardos I, Jehl MA, Rattei T, Horn M (2014). "Signature protein of the PVC superphylum". Appl Environ Microbiol. 80 (2): 440–445. Bibcode:2014ApEnM..80..440L. doi:10.1128/AEM.02655-13. PMC   3911108 . PMID   24185849.
    15. 1 2 3 Gupta RS, Bhandari V, Naushad HS (2012). "Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships". Front Microbiol. 3: 327. doi: 10.3389/fmicb.2012.00327 . PMC   3444138 . PMID   23060863.
    16. ↑ Gupta RS (2016). "Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification". FEMS Microbiol Rev. 40 (4): 520–53. doi: 10.1093/femsre/fuw011 . PMID   27279642.
    17. ↑ Gupta RS, Naushad S, Chokshi C, Griffiths E, Adeolu M (2015). "A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia". Antonie van Leeuwenhoek. 108 (3): 765–781. doi:10.1007/s10482-015-0532-1. PMID   26179278. S2CID   17099157.
    18. ↑ Wagner M, Horn M (2006). "The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance". Curr. Opin. Biotechnol. 17 (3): 241–9. doi:10.1016/j.copbio.2006.05.005. PMID   16704931.
    19. ↑ Kamneva OK, Liberles DA, Ward NL (2010). "Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method". Genome Biol Evol. 2: 870–86. doi:10.1093/gbe/evq071. PMC   3000692 . PMID   21048002.
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