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| Planctomycetota | |
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| Brocadia anammoxidans | |
Scientific classification 
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| Domain: | Bacteria |
| Superphylum: | PVC superphylum |
| Phylum: | Planctomycetota Garrity and Holt 2021[1] |
| Classes and orders[2][3] | |
| Synonyms | |
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The Planctomycetota are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats.[5] 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.[5][6] Many Planctomycetota occur in relatively high abundance as biofilms,[7] often associating with other organisms such as macroalgae and marine sponges.[8]
Planctomycetota are included in the PVC superphylum along with Verrucomicrobiota, Chlamydiota, Lentisphaerota, Kiritimatiellaeota, and Candidatus Omnitrophica.[9][10] The phylum Planctomycetota is composed of the classes Planctomycetia and Phycisphaerae. First described in 1924, members of the Planctomycetota were identified as eukaryotes and were only later described as bacteria in 1972.[5] Early examination of members of the Planctomycetota suggested a cell plan differing considerably from other bacteria, although they are now confirmed as Gram-negative bacteria, but with many unique characteristics.
Bacteria in the Planctomycetota are often small, spherical cells, but a large amount of morphological variation is seen.[11] Members of the Planctomycetota also display distinct reproductive habits, with many species dividing by budding, in contrast to all other free-living bacteria, which divide by binary fission.[5][12][13]
Interest is growing in the Planctomycetota regarding biotechnology and human applications, mainly as a source of bioactive molecules.[14] In addition, some Planctomycetota were recently described as human pathogens.[8]
The species Gemmata obscuriglobus has been identified specifically as comprising bacteria with unique characteristics among the Planctomycetota,[15][16] such as their ability to synthesize sterols.[5][17][15]
Structure and morphology
Cell shape and appendages
The distinct morphological characteristics of bacteria in the Planctomycetota have been discussed extensively.[6] The common morphology is often spherical cells roughly 2 μm in diameter, as observed in the species Aquisphaera giovannonii. However, the diversity in cell shape often varies greatly in them. Ovoid and pear-shaped cells have been described in some species, and often occur in rosettes of three to 10 cells.[11] Gemmata obscuriglobus is a well studied species in the Planctomycetota with spherical cells. In contrast, bacteria in the species Planctopirus limnophila have ovoid cells.[15]
Many Planctomycetota species display structures and appendages on the outer surface of the cell. Flagella, common in most bacteria, have also been observed in the species P. limnophila.[5][11][18] Many Planctomycetota also have a holdfast, or stalk, which attaches the cell to a surface or substrate.[5][18] Members of some species, though, such as Isosphaera pallida lack a holdfast.[5]
Unique appendages known as crateriform structures have been observed[5][11][18] in species of Planctomycetota belonging to the class Planctomycetia.[13] The outer surface of cells in the species P. limnophila display both large and small crateriform structures. Large crateriform structures often cover the cell surface, while small crateriform structures are often only at the end of the cell. Light microscopy demonstrated fibers of both stalk and pili type in P. limnophila and G. obscuriglobus. The pili fibers in both these species were often associated with large crateriform structures; in contrast, the stalk fibers were associated with small crateriform structures.[18]
Cell wall composition
Early examination of the Planctomycetota suggested that their cell plan differed considerably from both Gram-positive and Gram-negative bacteria.[5] Until recently, bacteria in the Planctomycetota were thought to lack peptidoglycans in their cell walls, and were instead suggested to have proteinaceous cell walls. Peptidoglycan is an essential polymer of glycans, present in all free-living bacteria, and its rigidity helps maintain integrity of the cell. Peptidoglycan synthesis is also essential during cell division. Recently, those in the species G. obscuriglobus were found to have peptidoglycan in their cell walls.[5][18]
Internal cell composition
Planctomycetota were once thought to display distinct compartmentalization within the cytosol.[5][18] Three-dimensional electron tomography reconstruction of G. obscuriglobus displayed varying interpretations of this suggested compartmentalization.[16] The cytosol was suggested to be separated into compartments, both the paryphoplasm and pirellulosome, by an intracytoplasmic membrane. This interpretation has since been demonstrated to be incorrect. In fact, the intracytoplasmic membrane is well known to be the cytoplasmic membrane which displays unique invaginations, giving the appearance of compartmentalization within the cytosol.[5][16][18] Planctomycetota therefore display the two compartments typical of Gram-negative bacteria, the cytoplasm and periplasm.
The excess membrane observed in G. obscuriglobus triples the surface area of the cell relative to its volume, which is suggested to be associated with sterol synthesis.[16]
Pigments
Many Planctomycetota species display pink or orange coloring, suggested to result from the production of carotenoid pigments. Carotenoids are produced by plants and fungi, and by some heterotrophic bacteria to protect against oxidative stress. Three different carotenoid pigments have been identified in two different strains of the Planctomycetota.[19]
In marine environments, Planctomycetota are often suspended in the water column or present as biofilms on the surface of macroalgae, and are often exposed to harmful ultraviolet radiation. More highly pigmented species of the Planctomycetota are more resistant to ultraviolet radiation, although this is not yet well understood.[20] It has since been shown that Planctomycetota synthesize C30 carotenoids from squalene and that this squalene route to C30 carotenoids is the most widespread in prokaryotes.[21]
Unique characteristics of anammox cells
Bacteria in the Planctomycetota that are anammox-capable form the order Brocadiales.[22] The cells of anammox bacteria are often coccoid with a diameter of about 0.8 μm,[7] and are suggested to contain three compartments, each surrounded by a membrane. The outer membrane encloses the cell and the protoplasm and the innermost membrane surrounds the anammoxosome, the central structure of anammox bacteria.[18][23] The anammoxosome membrane is largely composed of unusual ladderane-based lipids.[23]
Life history and reproduction
Growth
Planctomycetota species grow slowly, when compared to other bacteria,[5][10][7][24] often forming rosette structures of 3-5 cells.[5][24] The species P. limnophila is suggested to be relatively fast growing,[5][25] with a doubling time of roughly 6-14 days. In contrast, some other Planctomycetota have doubling times of around 30 days.[25] Their high abundance in many ecosystems is surprising, given their slow growth rates.[7][10]
_and_in_current_PVC_species_(Right).jpg)
Lifecycle
Planctomycetota often perform a lifestyle switch between both a sessile stalked stage and a free-swimming stage.[24] Members of the species P. limnophila perform a lifestyle switch that is often associated with cell division. The sessile mother cell produces a free-swimming daughter cell. The daughter cell must then attach to a surface before starting the cycle over again. However, not all of the Planctomycetota have a motile stage, and the lifestyle switch observed in many species may not be common among all Planctomycetota.[5]
.jpg)
Reproduction
The current understanding of bacterial cell division is based on model organisms such as Escherichia coli.[15] The dominant form of reproduction observed in almost all bacteria is cell division by binary fission, which involves the synthesis of both peptidoglycans and proteins known as FtsZ.[15][26] In contrast, many bacteria in the Planctomycetota divide by budding.[5][12][13]
FtsZ proteins are suggested to be similar in structure to that of tubulin, the protein present in eukaryotes,[27] and is essential for septal formation during cell division.[5][6] The lack of FtsZ proteins is often lethal.[5] Peptidoglycan also play a considerable role in cell division by binary fission.[26]
Planctomycetota is one of the only known phyla whose members lack FtsZ proteins.[5][26][27] Bacteria in the Chlamydiales, also a member of the PVC superphylum, also lack FtsZ.[27] Although bacteria in the Planctomycetota lack FtsZ, two distinct modes of cell division have been observed.[5] Most Planctomycetota divide by binary fission, mainly species of the class Phycisphaerae. In contrast, species of the class Planctomycetia divide by budding.[5][12][13]
The mechanisms involved in budding have been described extensively for yeast cells. However, bacterial budding observed in Planctomycetota is still poorly understood.[15] Budding has been observed in both radial symmetric cells, such as bacteria in the species P. limnophila, and axially symmetric cells.[13] During cell division in members of P. limnophila, the daughter cells originate from the region opposite to the pole with the holdfast or stalk.
Considerable diversity has been observed in cell division among bacteria in the Planctomycetota.[12][13] During cell division in Fuerstia marisgermanicae, a tubular structure is connected from the bud to the mother cell.[5][22] The species Kolteria novifilia forms a distinct clade of Planctomycetota, and is the only known species to divide by lateral budding at the middle of the cell. Lastly, members of the clade Saltatorellus are capable of switching between both binary fission and budding.[12][13]
Genetic characteristics
Molecular signatures
Planctomycetota are known for their unusual cellular characteristics, and their distinctness from all other bacteria is additionally supported by the shared presence of two conserved signature indels (CSIs).[28] These CSIs demarcate the group from neighboring phyla within the PVC group.[29] An additional CSI has been found that is shared by all Planctomycetota species, with the exception of Kuenenia stuttgartiensis. This supports the idea that K. stuttgartiensis forms a deep branch within the Planctomycetota phylum.
A CSI has also been found to be shared by the entire PVC superphylum, including the Planctomycetota.[28][29] Planctomycetota also contain an important conserved signature protein that has been characterized to play an important housekeeping function that is exclusive to members belonging to the PVC superphylum.[30]
General characteristics
The genome size of Rhodopirellula baltica has been estimated to be over 7 million bases, making it one of the largest prokaryotic genomes sequenced. Extensive genome duplication takes up about 25% of the genome sequence.[6] This may be a way for the organism to adapt to mutations, allowing for redundancy if a part of the genome is damaged. The polymerase chain reaction primer used often mismatches with the genes, creating difficulty when sequencing the genome.[9]
When comparing under a microscope, a defining characteristic for some Planctomycetota is that a single unlinked rRNA operon can be identified near the origin. The changes of genetic material is through internal chromosomal inversion, and not through lateral gene transfer. This creates a way of diversification in the Planctomycetota variants as multiple transposon genes in these regions have reverse orientation that transfers to rearrangements.
Some Planctomycetota thrive in regions containing highly concentrated nitrate,[6] and have genes that are required for heterotactic acid fermentation. The enzyme lactate dehydrogenase plays a key role in this process. The genetic process also has ultraviolet radiation protection response, and is associated with the genes recA, lexA, uvrA, uvrB, and uvrC, in addition to a photolyase gene that is expressed when the environment offers excessive ultraviolet radiation stress. Other stress responses include the decomposition of hydrogen peroxide and oxidation.
Many Planctomycetota also express sulfatase genes. The genome of Pirellula sp. strain 1 incorporates 110 genes that contribute to encoding proteins that produce sulfatase enzymes. In comparison with a different species of prokaryotic, Pseudomonas aeruginosa, only 6 sulfatases occur and the genes that express these proteins are contained as two to five pairs, usually clustered in 22 groups.[6]
Molecular evolution
Planctomycetota originate from within the Bacteria and these similarities between proteins in Planctomycetales and eukaryotes reflect convergent evolution. Gained protein families in Gemmataceae, a subgroup within Planctomycetota, have low sequence similarity to eukaryotic proteins; however, they show highest sequence similarity to other Gemmataceae protein families.[31]
There is massive emergence of novel protein families within the Gemmataceae. More than one thousand protein families were acquired by duplications and domain rearrangements. The new paralogs function in signal transduction, regulatory systems, and protein interaction pathways. They are related to the functional organisation of the cell, which can be interpreted as an adaptation to a more complex lifestyle.[31] The protein length is longer in the Gemmataceae than in most other bacteria and the genes have linkers. There is an overlap between the longest proteins in Planctomycetales and the shortest proteins in eukaryotes. In the terms of gene paralogy, protein length, and protein domain structures, prokaryotes and eukaryotes do not have sharp boundaries.[31]
Phylogeny
Originally classified as a eukaryote due to morphology, the advent of genetic sequencing allowed researchers to agree that the Planctomycetota belong to the domain Bacteria.[5] Within that domain, Planctomycetota are classified as their own phylum, however, other researchers have argued they could also be categorized as part of a larger superphylum entitled PVC, which would encompass the phyla Verrucomicrobia, Chlamydiae and Lentisphaerae, and the candidate phylum "Candidatus Omnitrophica".[9] Within this superphylum, its members have been found to be closely related through the creation of 16S rRNA trees. Both the Planctomycetota and Chlamydiota encode proteins for nucleotide transporters, and the Verrucomicrobiota have also been found to have features common among eukaryotic cells. Thus, a common ancestor of this superphylum may have been the start of the eukaryotic lineage.[9] While this is one possible explanation, because PVC is not the start of the bacterial tree,[32] the existence of eukaryotic traits and genes is more likely explained through lateral gene transfer, and not a more recent eukaryotic ancestor.[9]