Bigyra
Aplanochytrium, SEM showing one vegetative cell and extended ectoplasmic network.
Aplanochytrium, SEM showing one vegetative cell and extended ectoplasmic network.
Scientific classification Edit this classification
Domain: Eukaryota
Clade: Diaphoretickes
Clade: SAR
Clade: Stramenopiles
Phylum: Bigyra
Cavalier-Smith 1998,[1] emend. 2006[2] emend. 2013[3]
Clades[4]

Bigyra (from Latin bi- 'twice', and gyrus 'circle')[1] is a phylum of microscopic eukaryotes that are found at the base of the Stramenopiles clade. It includes three well-known heterotrophic groups Bicosoecida, Opalinata and Labyrinthulomycetes, as well as several small clades initially discovered through environmental DNA samples: Nanomonadea, Placididea, Opalomonadea and Eogyrea. The classification of Bigyra has changed several times since its origin, and its monophyly remains unresolved.

Ecological diversity

Bigyra is a diverse group of heterotrophic, mainly phagotrophic stramenopiles that lack cell walls.[4] It contains three well-known important groups with widely different ecological functions and morphologies: labyrinthulomycetes, opalines and bicosoecids.[5]

Labyrinthulomycetes is a group of protists that absorb nutrients in an osmotrophic or phagotrophic manner. They can behave either as free-living amoebae or as mycelium-like networks of cytoplasmic threads. Some of them are saprotrophic decomposers of the detrital food web; as such, they play a role in making organic matter more accessible to other organisms. Others are parasitic, and others are predators of bacteria. They are cosmopolitan, ubiquitous in marine, freshwater and estuarine environments. They live in association with algae, marine plants and detritus.[5]

Opalinata is a diverse assemblage of modified parasitic protists known as 'opalines'. They inhabit the intestines of various animals, primarily amphibians. They are found on every continent. Among them, the opalinids are highly unusual protists: their large cells have numerous flagella and from two to hundreds of nuclei. Their cell surface is delicately folded, giving it an iridescent appearance (hence their name, a reference to the iridescent opal). Another important group of opalines is Blastocystis, a prevalent parasite of humans and other animals.[5]

Bicosoecida is a small group that contains free-living marine and freshwater nanoflagellates that feed on bacteria. They are present in every ecosystem, including extreme environments such as the deep sea or salt flats. They play a crucial role in the microbial food web by composing the link between bacteria and higher trophic levels. They are also important in biogeochemical cycles by remineralizing the nutrients. Their classification has changed multiple times over the years,[6] and is still an unresolved issue.[7]

Opalinid
Blastocystis from primate intestines
Labyrinthulid with cytoplasmic network
Bicosoecid with two heterokont flagella

Evolution and systematics

External

Bigyra contains many of the earliest-diverging clades of the Stramenopiles.[8] The Stramenopiles are a supergroup of eukaryotic organisms (protists) characterized by the presence of an anterior flagellum with tripartite hairs, called mastigonemes. Together with Rhizaria and Alveolata, the Stramenopiles compose the SAR supergroup.[4]

All of Bigyra are heterotrophic microorganisms evolved from the last common ancestor of Stramenopiles, which is thought to have been phototrophic. Following this hypothesis, the bigyran ancestor would have secondarily lost their photosynthetic plastids. Some characteristics of bigyran groups can be explained by their origin from ancestral plastids. For example, labyrinthulomycetes can produce omega-3 poly-unsaturated fatty acids through a desaturase usually present in chloroplasts.[9]

Internal

Bigyra is composed of two subphyla: Opalozoa and Sagenista. Opalozoa is further subdivided into two groups: Placidozoa, which contains the opalines and three clades discovered through the detection of environmental DNA (Nanomonadea, Opalomonadea and Placididea), and the bicosoecid flagellates. Sagenista contains the labyrinthulomycetes and two environmental clades grouped under the name Eogyrea.[10][11]

The monophyly of Bigyra remains uncertain. The positions of the two bigyran clades (Opalozoa and Sagenista) are not consistent between the published studies, because they diverged from each other very early after the separation from the ancestor of all stramenopiles. This 'deep branching' makes it difficult to find the exact branching order of bigyran clades.[2] Additionally, not all clades are well-represented by molecular data in these studies.[10] Several studies support the monophyly of Bigyra.[10][11] Other studies support its paraphyly.[12][13]

Monophyletic Bigyra[10] Paraphyletic Bigyra[13]
Stramenopiles
Gyrista

Ochrophyta

Pseudofungi

plastid loss
Bigyra
Opalozoa

Placidozoa

Bicosoecida

Sagenista

Labyrinthulomycetes

Eogyrea

plastid loss

Platysulcea
Stramenopiles
Gyrista

Ochrophyta

Pseudofungi

Bigyromonada

Sagenista

Labyrinthulomycetes   

Eogyrea

Opalozoa 

Placidozoa

Bicosoecida

Platysulcea
Bigyra

History

Initial phylogeny of Bigyra (1997)[14]
Heterokonta
Bigyra

Pseudofungi

Bigyromonadea

Opalinata

Limnistia

Sarcinochrysia

Dictyochia

Fucistia

Diatomeae

Sagenista

Bigyra was first described in 1997 by the protozoologist Thomas Cavalier-Smith as a phylum within Heterokonta (synonym of Stramenopiles). Bigyra was defined as organisms with the synapomorphy of a ciliary transition region (i.e. a structure that controls protein transport at the base of the flagellum) with structures in the shape of two helices or rings, hence the name 'bigyra' meaning 'double helix'. It contained three subgroups:[1]

  1. Pseudofungi, saprotrophic protists with cell walls.
  2. Opalinata, non-phagotrophic gut-symbiotes found in animals.
  3. Bigyromonada, phagotrophic zooflagellates.

Their common ancestor was thought to have evolved from photosynthetic heterokonts, but would have secondarily lost its plastids, as opposed to the photosynthetic Ochrophyta which retain them. Bigyra was, at the time, postulated as a monophyletic group (or clade), evolved from a paraphyletic grade of ochrophyte classes.[1][14]

Posterior analyses completely changed the phylogeny of Stramenopiles. They revealed Pseudofungi and Bigyromonadea were more closely related to a monophyletic Ochrophyta than they were to Opalinata, meaning that the synapomorphy of a double helix could have been present in the common ancestor of all heterokonts. This rendered Bigyra paraphyletic. Consequently, Bigyra was revised and modified in 2006 to comprise a different set of three subphyla:

  1. Opalozoa, a previously polyphyletic diverse phylum that was modified to only include Opalinata and Nucleohelea;
  2. Bicoecea, containing the bicosoecids;
  3. Sagenista, containing the osmotrophic Labyrinthulea.

Bigyra was modified again in 2013 after the discovery of several environmental clades called MAST ('MArine STramenopiles’). The subphylum Opalozoa assimilated the bicosoecids and an array of new clades: Placididea, Nanomonadea (MAST-3) and Opalomonadea (MAST-12). The subphylum Sagenista, on the other hand, received a new class Eogyrea that was composed of several MAST lineages not yet described.[3] Later, one of the MAST clades within Eogyrea would be described as Pseudophyllomitus (MAST-6).[15]

References

  1. 1 2 3 4 Cavalier-Smith T (1998). "A revised six-kingdom system of life". Biol Rev Camb Philos Soc. 73 (3): 203–66. doi:10.1111/j.1469-185X.1998.tb00030.x. PMID 9809012. S2CID 6557779.
  2. 1 2 Cavalier-Smith T, Chao EE (April 2006). "Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista)". J. Mol. Evol. 62 (4): 388–420. Bibcode:2006JMolE..62..388C. doi:10.1007/s00239-004-0353-8. PMID 16557340. S2CID 29567514.
  3. 1 2 Cavalier-Smith, Thomas; Scoble, Josephine Margaret (2013). "Phylogeny of Heterokonta: Incisomonas marina, a uniciliate gliding opalozoan related to Solenicola (Nanomonadea), and evidence that Actinophryida evolved from raphidophytes". European Journal of Protistology. 49 (3): 328–353. doi:10.1016/j.ejop.2012.09.002. PMID 23219323.
  4. 1 2 3 Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q (2019). "Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes". Journal of Eukaryotic Microbiology. 66 (1): 4–119. doi:10.1111/jeu.12691. PMC 6492006. PMID 30257078.
  5. 1 2 3 Bennett, Reuel M.; Honda, D.; Beakes, Gordon W.; Thines, Marco (2017). "Chapter 14. Labyrinthulomycota". In Archibald, John M.; Simpson, Alastair G.B.; Slamovits, Claudio H. (eds.). Handbook of the Protists. Springer. pp. 507–542. doi:10.1007/978-3-319-28149-0_25. ISBN 978-3-319-28147-6.
  6. ↑ Karpov SA, Sogin ML, Silberman JD (2001). "Rootlet homology, taxonomy, and phylogeny of bicosoecids based on 18S rRNA gene sequences". Protistology. 2 (1): 34–47.
  7. ↑ Schoenle A, Hohlfeld M, Rybarski A, Sachs M, Freches E, Wiechmann K, Nitsche F, Arndt H (2022). "Cafeteria in extreme environments: Investigations on C. burkhardae and three new species from the Atacama Desert and the deep ocean". European Journal of Protistology. 85: 125905. doi:10.1016/j.ejop.2022.125905. PMID 35868212. S2CID 249935619.
  8. ↑ Riisberg I, Orr RJ, Kluge R, et al. (May 2009). "Seven gene phylogeny of heterokonts". Protist. 160 (2): 191–204. doi:10.1016/j.protis.2008.11.004. PMID 19213601.
  9. ↑ Tsui, Clement K M; Marshall, Wyth; Yokoyama, Rinka; Honda, Daiske; Lippmeier, J Casey; Craven, Kelly D; Peterson, Paul D; Berbee, Mary L (January 2009). "Labyrinthulomycetes phylogeny and its implications for the evolutionary loss of chloroplasts and gain of ectoplasmic gliding". Molecular Phylogenetics and Evolution. 50 (1): 129–40. doi:10.1016/j.ympev.2008.09.027. PMID 18977305.
  10. 1 2 3 4 Thakur, Rabindra; Shiratori, Takashi; Ishida, Ken-ichiro (2019). "Taxon-rich Multigene Phylogenetic Analyses Resolve the Phylogenetic Relationship Among Deep-branching Stramenopiles". Protist. 170 (5): 125682. doi:10.1016/j.protis.2019.125682. ISSN 1434-4610. PMID 31568885. S2CID 202865459.
  11. 1 2 Cavalier-Smith, Thomas (2017). "Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences". Protoplasma. 255 (1): 297–357. doi:10.1007/s00709-017-1147-3. PMC 5756292. PMID 28875267.
  12. ↑ Tan MH, Loke S, Croft LJ, Gleason FH, Lange L, Pilgaard B, Trevathan-Tackett SM (2021). "First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation". Microbial Ecology. 82 (2): 498–511. doi:10.1007/s00248-020-01647-x. PMID 33410934. S2CID 230819360.
  13. 1 2 Cho A, Tikhonenkov DV, Hehenberger E, Karnkowska A, Mylnikov AP, Keeling PJ (2022). "Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles" (PDF). Molecular Phylogenetics and Evolution. 171 (107468): 107468. doi:10.1016/j.ympev.2022.107468. ISSN 1055-7903. PMID 35358688. S2CID 247815732.
  14. 1 2 Cavalier-Smith T (1998). "Sagenista and Bigyra, two phyla of heterotrophic heterokont chromists". Archiv für Protistenkunde. 148 (3): 253–267. doi:10.1016/S0003-9365(97)80006-1.
  15. ↑ Shiratori, Takashi; Thakur, Rabindra; Ishida, Ken-ichiro (2017). "Pseudophyllomitus vesiculosus (Larsen and Patterson 1990) Lee, 2002, a Poorly Studied Phagotrophic Biflagellate is the First Characterized Member of Stramenopile Environmental Clade MAST-6". Protist. 168 (4): 439–451. doi:10.1016/j.protis.2017.06.004. ISSN 1434-4610. PMID 28822908.
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