Planctobacteria

Last updated

PVC group
ChlamydiaTrachomatisEinschlusskorperchen.jpg
Chlamydia trachomatis
Scientific classification
(temporary)
Domain:
(unranked):
Superphylum:
PVC group
Phyla

Chlamydiae
Kiritimatiellaeota
Lentisphaerae
Planctomycetes
Verrucomicrobia
"Ca. Abyssubacteria"
"Ca. Aureabacteria"
"Ca. Omnitrophica"

Contents

Synonyms

Planctobacteria Cavalier-Smith, 1987 [1]

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

Cavalier-Smith calls the same group Planctobacteria and considers it a phylum. However, this is not followed by the larger scientific community. [6] In the Cavalier-Smith bacterial megaclassification, it is within the bacterial Gracilicutes infra-kingdom and comprises the phyla Chlamydiae, Lentisphaerae, Planctomycetes, Verrucomicrobia. [3] [7]

PVC superphylum [8] [9] [2] [10]
PVC

Aureabacteria

Planctomycetes

Omnitrophica

Chlamydiae

Kiritimatillaeota

Lentisphaerae

Verrucomicrobia

Molecular signatures

Planctomycetes, Verrucomicrobia, and Chlamydiae in the traditional molecular phylogeny view are considered as phyla and also cluster together in what is referred to as the PVC superphylum, along with the candidate phyla Omnitrophica [11] (previously OP3) and the Poribacteria. [12] 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. Recent studies have characterized this protein and it has been attributed to play an important housekeeping function in DNA/RNA binding. [13] 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. [14] [15]

Conserved signature indels (CSIs) have also been found specific for the Planctomycetes, Verrucomicrobia, and Chlamydiae that distinguish each respective phylum from one another, and from other bacteria. [14] [16] 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. [14]

Additional lines of evidence for the existence of this clade have been found. [17] [18] These include the presence of membrane coat-like proteins, tubulin, sterol synthesis, and the presence of condensed DNA.

Notes

    Related Research Articles

    Gram-positive bacteria Bacteria that give a positive result in the Gram stain test

    In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.

    Gram-negative bacteria Group of bacteria that do not retain the crystal violet stain used in the Gram-staining method of bacterial differentiation

    Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the gram-staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane.

    Bacteroidetes Phylum of Gram-negative bacteria

    The phylum Bacteroidetes 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.

    Verrucomicrobia Phylum of bacteria

    Verrucomicrobia 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 residing in their gametes.

    Chlamydiae Phylum of bacteria

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

    Planctomycetes Phylum of aquatic bacteria

    Planctomycetes 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 planctomycetes occur in relatively high abundance as biofilms, often associating with other organisms such as macroalgae and marine sponges.

    Anammox Anaerobic ammonium oxidation, a microbial process of the nitrogen cycle

    Anammox, an abbreviation for anaerobic ammonium oxidation, is a globally important microbial process of the nitrogen cycle that takes place in many natural environments. The bacteria mediating this process were identified in 1999, and were a great surprise for the scientific community. In the anammox reaction, nitrite and ammonium ions are converted directly into diatomic nitrogen and water.

    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.

    Fibrobacteres is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla. The genus Fibrobacter was removed from the genus Bacteroides in 1988.

    Gracilicutes

    Gracilicutes is a clade in bacterial phylogeny.

    The order Sphingobacteriales comprises four families of environmental bacteria.

    Sphingobacteria (phylum) Phylum of bacteria

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

    Bacterial phyla 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.

    Bacterial taxonomy is the taxonomy, i.e. the rank-based classification, of bacteria.

    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 bacterium

    Gemmata obscuriglobus is a Gram-negative, aerobic, heterotrophic, motile bacterium of the phylum Planctomycetes, first described in 1984 as the only described species in the genus Gemmata. It is exceptional for its unusual morphology and for the unusual features in its genome, often considered to represent large differences in internal organization compared with most prokaryotes. G. obscuriglobus has been described as "the platypus of microbiology".

    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.

    Ubiquitin bacterial

    Ubiquitin Bacterial (UBact) is a protein that is homologous to Prokaryotic ubiquitin-like protein (Pup). UBact was recently described by the group of Professor Aaron Ciechanover at the Technion, Israel.

    Candidate phyla radiation A large evolutionary radiation of bacterial candidate phyla and superphyla

    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. Originally, it has been suggested that CPR represents over 15% of all bacterial diversity and may consist of more than 70 different phyla. However, a recently proposed standardized bacterial taxonomy based on relative evolutionary divergence found that CPR represents a single phylum. CPR lineages are generally characterized as having small genomes and lacking several biosynthetic pathways and ribosomal proteins. This has led to the speculation that they are likely obligate symbionts.

    References

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