Diplonemidae

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Diplonemidae
Diplonema papillatum SEM image.gif
Scanning electron micrograph of Diplonema papillatum
Scientific classification
Domain:
Eukaryota
(unranked):
Excavata
Phylum:
Euglenozoa
Class:
Diplonemea
Order:
Diplonemida
Family:
Diplonemidae

Cavalier-Smith 1993 emend. Adl et al. 2019
Genus
Synonyms
  • Rhynchopodaceae Skuja 1948 ex Cavalier-Smith 1993

Diplonemidae is a family of biflagellated unicellular protists that may be among the more diverse and common groups of planktonic organisms in the ocean. Although this family is currently made up of three named genera; Diplonema , Rhynchopus , and Hemistasia , there likely exist thousands of still unnamed genera. [1] Organisms are generally colourless and oblong in shape, with two flagella emerging from a subapical pocket. [2] They possess a large mitochondrial genome composed of fragmented linear DNA. [3] These non-coding sequences must be massively trans-spliced, making it one of the most complicated post-transcriptional editing process known to eukaryotes.

Contents

Etymology

The word “Diplonemidae” come from the Greek words ‘diplo’, meaning two, and ‘nemat’, meaning thread. Together, Diplonemidae roughly translates to ‘two threads’, likely referring to the characteristic two flagella of the organism.

History

Primary studies done in the 1900s by Griessmann and Skuja had initially grouped Diplonemidae (or more specifically, the Diplonema and Rhynchopus taxa) with the euglenids. This was due to the two groups sharing many morphological similarities with the euglenids, such as metaboly, locomotion and a microtubule-reinforced feeding apparatus. [4] However, this conclusion was met with some controversy, as diplonemids lacked characteristic features shared by all euglenids, such as possession of pellicle strips and paraxonemal rods on their flagella. [5] Instead, they were placed in the euglenozoan phylum and shared this taxon with the kinetoplastids and euglenids. [6] The inclusion of Rhynchopus and Diplonema in the family Diplonemidae was later confirmed through nuclear 18S rRNA analysis. [7] As of now, Rhynchopus and Diplonema are part of the ‘classical’ diplonemid subgroup, and Hemistasia is part of the ‘nonclassical’ diplonemid subgroup.

Recently, there had been debates as to whether Diplonemidae were more closely related to the euglenids or kinetoplastids. It was not until analysis of cytosolic heat shock proteins that a sister relationship between the diplonemids and kinetoplastids was proposed. [5] This was further supported through phylogenetic analysis, which discovered that Diplonemidae possess a functional splice leader RNA that is characteristic of the kinetoplastids. [8] Additionally, the amino acid tryptophan is encoded by codon TGA in kinetoplastids and diplonemids, whereas in euglenids, the regular codon is used instead. [5]

Nevertheless, despite the similarities between kinetoplastids and diplonemids, the two taxa are still distinct form each other. Diplonemidae still lack a kinetoplast, and have a unique bi-flagellated trophic phase not seen in kinetoplastids. Presently, the kinetoplastids are regarded as the sister group to the Diplonemidae.

Although there are only three named genera within the Diplonemidae, environmental sequencing performed by the recent TARA Ocean Expedition concluded there are potentially thousands of genera, [1] suggesting that pelagic Diplonemidae are the most diverse planktonic eukaryotes in the oceans.

Habitat and ecology

Although Diplonemidae are generally predators, some species display parasitic life strategies. [3] Diplonemidae display a rich diversity in marine and freshwater environments, with their relative abundance increasing with depth. [9] The diplonemids that exist in these different environments are genetically distinct, and exhibit slightly different lifestyles. The ‘classic’ diplonemids (i.e. Diplonema and Rhynchopus) are benthic, whereas the marine diplonemids, which include Hemistasia, are planktonic. [2]

There are potentially thousands of unknown marine Diplonemidae species, with this diversity highly stratified in accordance to depth. Although molecular sequencing confirms the existence of these unnamed marine Diplonemidae, information regarding their morphology and lifestyle is absent. [1] As marine Diplonemidae are the most abundant and genetically diverse protists (and potentially eukaryotes) in the sea, there are strong implications that they play a key role in aquatic ecosystems. As of now, this exact role is unknown.

Description

Morphology and Anatomy

Classical diplonemids (i.e. Diplonema and Rhynchopus), are colourless and oblong in shape. They are approximately 20 μm in length and possess a microtubule layer underneath their plasma membrane. [10] Adjacent to it is a mitochondrion with discoidal cristae. [6] They also possess two flagella of equal length, both of which lack paraxial rods. [2] The two basal bodies originate from a subapical pocket, which merges with an adjacent feeding apparatus. [4] This feeding apparatus is surrounded by many food vacuoles and reinforced by microtubules. [10]

Nonclassical Diplonemidae (i.e. Hemistasia) are diverse in size but share many morphological aspects with the classic diplonemids. However, a great majority of these marine Diplonemidae have never been seen, with their existence only confirmed through molecular analysis. [2]

Although Diplonemidae do not possess pellicular strips like euglenids, they still move via metaboly. [3]

Diplonemidae also exhibit the compartmentalization of glycolytic and gluconeogenic enzymes into peroxisomes. These organelles are referred to as glycosomes, and is a characteristic feature also shared with their sister taxon, the kinetoplastids . [11]

Life cycles

Diplonemidae are capable of sexual reproduction, as genes involved in meiosis have been found. [12] Although marine diplonemids appear to reproduce sexually, not much is known about diplonemid reproduction as Euglenozoans rarely demonstrate sexual processes. [5]

Genetics

Diplonemidae have a unique mitochondrial DNA arrangement. Although Diplonemidae possess a large mitochondrial genome, these do not contain any intact full-sized genes. Instead, their mitochondrial DNA consists of linear gene fragments of different sizes. Because each fragment is both full of repeats and incomplete, individually they are unable to code for a gene themselves. Instead, fragments are transcribed and spliced together using their own specialized trans splicing machinery. [3] Once spliced together, the transcript undergoes extensive editing to become recognizable RNA. This is accomplished by either Uracil-insertion, nucleotide deanimation, or substitution, which eventually generates a fully mature and translatable transcript. [13]

The Diplonemidae genome contains a spliced leader RNA gene, which confirms their use of mRNA spliceosome-dependent trans splicing during nuclear expression.

Diplonemids possess the gap3 gene which is specifically found in cyanobacteria and Pseudomonadota. This is likely due to lateral gene transfer following the divergence of diplonemids from the euglenoids. [14] As to date, this is one of the most-supported examples of lateral gene transfer from a bacterium to eukaryote and may have implications for diplonemid acquisition of biochemical abilities.

Taxonomy

Although presently made up of less than a dozen named species, the existence of thousands of unknown diplonemid taxa has been suggested through environmental sequencing analyses. [1]

Related Research Articles

<span class="mw-page-title-main">Euglenozoa</span> Phylum of protozoans

Euglenozoa are a large group of flagellate Discoba. They include a variety of common free-living species, as well as a few important parasites, some of which infect humans. Euglenozoa are represented by four major groups, i.e., Kinetoplastea, Diplonemea, Euglenida, and Symbiontida. Euglenozoa are unicellular, mostly around 15–40 μm (0.00059–0.00157 in) in size, although some euglenids get up to 500 μm (0.020 in) long.

<span class="mw-page-title-main">Euglenid</span> Class of protozoans

Euglenids or euglenoids are one of the best-known groups of flagellates. They are excavate eukaryotes of the phylum Euglenophyta, classified as class Euglenida or Euglenoidea. Euglenids are commonly found in freshwater, especially when it is rich in organic materials, with a few marine and endosymbiotic members. Many euglenids feed by phagocytosis, or strictly by diffusion. A monophyletic group known as Euglenophyceae have chloroplasts and produce their own food through photosynthesis. This group is known to contain the carbohydrate paramylon.

<span class="mw-page-title-main">Kinetoplastida</span> Flagellated protists belonging to the phylum Euglenozoa

Kinetoplastida is a group of flagellated protists belonging to the phylum Euglenozoa, and characterised by the presence of a distinctive organelle called the kinetoplast, a granule containing a large mass of DNA. The group includes a number of parasites responsible for serious diseases in humans and other animals, as well as various forms found in soil and aquatic environments. The organisms are commonly referred to as "kinetoplastids" or "kinetoplasts".

<span class="mw-page-title-main">Euglenophyceae</span> Unicellular algae

Euglenophyceae (ICBN) or Euglenea (ICZN) is a group of single-celled algae belonging to the phylum Euglenozoa. They have chloroplasts originated from an event of secondary endosymbiosis with a green alga. They are distinguished from other algae by the presence of paramylon as a storage product and three membranes surrounding each chloroplast.

<i>Bodo saltans</i> Species of kinetoplastid flagellated phagotrophic protozoa

Bodo saltans is a free-living nonparasitic species of kinetoplastid flagellated phagotrophic protozoa that feed on bacteria. Bodo saltans cells have been reported in freshwater and marine environments.

<span class="mw-page-title-main">Euglenales</span> Order of flagellate eukaryotes

Euglenales is an order of flagellates in the phylum Euglenozoa. The family includes the most well-known euglenoid genus, Euglena, as well as other common genera like Phacus and Lepocinclis.

<span class="mw-page-title-main">Malawimonadidae</span> Family of protists

Malawimonadidae is a family of unicellular eukaryotes of outsize importance in understanding eukaryote phylogeny.

<span class="mw-page-title-main">Jakobid</span>

Jakobids are an order of free-living, heterotrophic, flagellar eukaryotes in the supergroup Excavata. They are small, and can be found in aerobic and anaerobic environments. The order Jakobida, believed to be monophyletic, consists of only twenty species at present, and was classified as a group in 1993. There is ongoing research into the mitochondrial genomes of jakobids, which are unusually large and bacteria-like, evidence that jakobids may be important to the evolutionary history of eukaryotes.

<span class="mw-page-title-main">Katablepharid</span> Group of algae

The kathablepharids or katablepharids are a group of heterotrophic flagellates closely related to cryptomonads. First described by Heinrich Leonhards Skuja in 1939, kathablepharids were named after the genus Kathablepharis. This genus is corrected to Katablepharis under botanical nomenclature, but the original spelling is maintained under zoological nomenclature. They are single-celled protists with two anteriorly directed flagella, an anterior cytostome for ingesting eukaryotic prey, and a sheath that covers the cell membrane. They have extrusomes known as ejectisomes, as well as tubular mitochondrial cristae.

<i>Peranema</i> Genus of protozoans

Peranema is a genus of free-living phagotrophic euglenids. There are more than 20 nominal species, varying in size between 8 and 200 micrometers. Peranema cells are gliding flagellates found in freshwater lakes, ponds and ditches, and are often abundant at the bottom of stagnant pools rich in decaying organic material. Although they belong to the class Euglenoidea, and are morphologically similar to the green Euglena, Peranema have no chloroplasts, and do not conduct autotrophy. Instead, they capture live prey, such as yeast, bacteria and other flagellates, consuming them with the help of a rigid feeding apparatus called a "rod-organ." Unlike the green euglenids, they lack both an eyespot (stigma), and the paraflagellar body (photoreceptor) that is normally coupled with that organelle. However, while Peranema lack a localized photoreceptor, they do possess the light-sensitive protein rhodopsin, and respond to changes in light with a characteristic "curling behaviour."

<i>Diplonema</i> (excavate) Genus of protist

Diplonema is a genus of free-living organisms in the Euglenozoa. They are distinguished from Rhynchopus in Class Diplonemea by the absence of a fully flagellate dispersive stage.

<i>Neobodo</i> Genus of protists

Neobodo are diverse protists belonging to the eukaryotic supergroup Excavata. They are Kinetoplastids in the subclass Bodonidae. They are small, free-living, heterotrophic flagellates with two flagella of unequal length used to create a propulsive current for feeding. As members of Kinetoplastids, they have an evident kinetoplast There was much confusion and debate within the class Kinetoplastid and subclass Bodonidae regarding the classification of the organism, but finally the new genera Neobodo was proposed by Keith Vickerman. Although they are one of the most common flagellates found in freshwater, they are also able to tolerate saltwater Their ability to alternate between both marine and freshwater environments in many parts of the world give them a “cosmopolitan” character. Due to their relatively microscopic size ranging between 4–12 microns, they are further distinguished as heterotrophic nanoflagellates. This small size ratio limits them as bacterivores that swim around feeding on bacteria attached to surfaces or in aggregates.

Postgaardia is a proposed basal clade of flagellate Euglenozoa, following Thomas Cavalier-Smith. As of April 2023, the Interim Register of Marine and Nonmarine Genera treats the group as a subphylum. A 2021 review of Euglenozoa places Cavalier-Smith's proposed members of Postgaardia in the class Symbiontida. As Euglenozoans may be basal eukaryotes, the Postgaardia may be key to studying the evolution of Eukaryotes, including the incorporation of eukaryotic traits such as the incorporation of alphaproteobacterial mitochondrial endosymbionts.

Bihospites is a genus of symbiontid euglenozoans characterized by the presence of two species of epibiotic bacteria on the cell surface. Bihospites cells are clear, biflagellated, and uninucleated, that range between 40–120 μm long and 15–30 μm wide. Bihospites, as well as other members of the symbiontids, are found in semi-anoxic to anoxic sediments in benthic marine environments. Each cell surface is covered by both rod-shaped and spherical-shaped epibiotic bacteria that may share a commensalistic or mutualistic relationship with Bihospites host cells. Bihospites cells are highly contractile and contain several morphological synapomorphies which are present in euglenozoans, however they also contain several unique morphological traits including a unique C-shaped feeding apparatus.

<span class="mw-page-title-main">Peranemid</span> Group of flagellates

The peranemids are a group of phagotrophic flagellates, single-celled eukaryotes or protists. They belong to the Euglenida, a diverse lineage of flagellates that contains the closely related euglenophyte algae. Like these algae, peranemids have flexible cells capable of deformation or metaboly, and have one or two flagella in the anterior region of the cell. They are classified as family Peranemidae (ICZN) or Peranemataceae (ICBN) within the monotypic order Peranemida (ICZN) or Peranematales (ICBN).

<span class="mw-page-title-main">Spirocuta</span> Group of flagellates with flexible cells

Spirocuta is a clade of euglenids, single-celled eukaryotes or protists belonging to the phylum Euglenozoa. They are distinguished from other euglenids by active deformation of their cell shape, a process called euglenid motion or metaboly. This is made possible by a high number of spirally arranged protein strips that run below their cell membrane and confer the cell with flexibility. These strips compose the helicoidal pellicle, a trait referenced by the alternative name Helicales.

<span class="mw-page-title-main">Anisonemia</span> Group of flagellates

Anisonemia is a clade of single-celled protists belonging to the phylum Euglenozoa, relatives of the Euglenophyceae algae. They are flagellates, with two flagella for locomotion. Anisonemia includes various phagotrophic species and a group of primary osmotrophic protists known as Aphagea.

<i>Rapaza</i> Monospecific genus of predatory algae

Rapaza viridis is a species of single-celled flagellate within the Euglenophyceae, a group of algae. It is the only species within the genus Rapaza, family Rapazidae and order Rapazida. It was discovered in a tide pool in British Columbia and described in 2012.

Eutreptiaceae (ICN) or Eutreptiidae (ICZN) is a family of algae in the class Euglenophyceae. It is the only family within the monotypic order Eutreptiales (ICN) or Eutreptiida (ICZN). It contains predominantly marine single-celled flagellates with photosynthetic chloroplasts.

Neometanema is a genus of phagotrophic flagellates belonging to the Euglenida, a diverse group of flagellates in the phylum Euglenozoa. It is the sole genus within the monotypic family Neometanemidae and suborder Metanemina. It composes the order Natomonadida together with a closely related clade of osmotrophs known as Aphagea.

References

  1. 1 2 3 4 Flegontova, Olga; Flegontov, Pavel; Malviya, Shruti; Audic, Stephane; Wincker, Patrick; De Vargas, Colomban; Bowler, Chris; Lukeš, Julius; Horák, Aleš (2016). "Extreme Diversity of Diplonemid Eukaryotes in the Ocean". Current Biology. 26 (22): 3060–3065. doi: 10.1016/j.cub.2016.09.031 . PMID   27875689.
  2. 1 2 3 4 Gawryluk, Ryan M.R.; Del Campo, Javier; Okamoto, Noriko; Strassert, Jürgen F.H.; Lukeš, Julius; Richards, Thomas A.; Worden, Alexandra Z.; Santoro, Alyson E.; Keeling, Patrick J. (2016). "Morphological Identification and Single-Cell Genomics of Marine Diplonemids". Current Biology. 26 (22): 3053–3059. doi: 10.1016/j.cub.2016.09.013 . PMID   27875688.
  3. 1 2 3 4 Lukeš, Julius; Flegontova, Olga; Horák, Aleš (2015). "Diplonemids". Current Biology. 25 (16): R702–R704. doi: 10.1016/j.cub.2015.04.052 . PMID   26294177.
  4. 1 2 3 Roy, Joannie; Faktorová, Drahomíra; Benada, Oldřich; Lukeš, Julius; Burger, Gertraud (2007). "Description of Rhynchopus euleeides n. sp. (Diplonemea), a Free-Living Marine Euglenozoan". The Journal of Eukaryotic Microbiology. 54 (2): 137–145. doi:10.1111/j.1550-7408.2007.00244.x. PMID   17403154.
  5. 1 2 3 4 Heyden, Sophie; Chao, EMA E.; Vickerman, Keith; Cavalier-Smith, Thomas (2004). "Ribosomal RNA Phylogeny of Bodonid and Diplonemid Flagellates and the Evolution of Euglenozoa". The Journal of Eukaryotic Microbiology. 51 (4): 402–416. doi:10.1111/j.1550-7408.2004.tb00387.x.
  6. 1 2 Simpson, Alastair G.B. (1997). "The identity and composition of the Euglenozoa". Archiv für Protistenkunde. 148 (3): 318–328. doi:10.1016/s0003-9365(97)80012-7.
  7. ↑ Busse, I.; Preisfeld, Angelika (2002). "Phylogenetic position of Rhynchopus sp. and Diplonema ambulator as indicated by analyses of euglenozoan small subunit ribosomal DNA". Gene. 284 (1–2): 83–91. doi:10.1016/s0378-1119(02)00390-6. PMID   11891049.
  8. ↑ Sturm, Nancy R.; Maslov, Dmitri A.; Grisard, Edmundo C.; Campbell, David A. (2001). "Diplonema spp. Possess Spliced Leader RNA Genes Similar to the Kinetoplastida". The Journal of Eukaryotic Microbiology. 48 (3): 325–331. doi:10.1111/j.1550-7408.2001.tb00321.x.
  9. ↑ Debroas, Didier; Domaizon, Isabelle; Humbert, Jean-Francois; Jardillier, Ludwig; Lepère, Cécile; Oudart, Anne; Taïb, Najwa (2017). "Overview of freshwater microbial eukaryotes diversity: A first analysis of publicly available metabarcoding data". FEMS Microbiology Ecology. 93 (4). doi: 10.1093/femsec/fix023 . PMID   28334157.
  10. 1 2 3 4 Triemer, Richard E.; Ott, Donald W. (1990). "Ultrastructure of Diplonema ambulator larsen & patterson (euglenozoa) and its relationship to Isonema". European Journal of Protistology. 25 (4): 316–320. doi:10.1016/s0932-4739(11)80123-9. PMID   23196044.
  11. ↑ Gabaldón, Toni; Ginger, Michael L.; Michels, Paul A.M. (2016). "Peroxisomes in parasitic protists". Molecular and Biochemical Parasitology. 209 (1–2): 35–45. doi:10.1016/j.molbiopara.2016.02.005. PMID   26896770.
  12. ↑ Goodenough, U.; Heitman, J. (2014). "Origins of Eukaryotic Sexual Reproduction". Cold Spring Harbor Perspectives in Biology. 6 (3): a016154. doi:10.1101/cshperspect.a016154. PMC   3949356 . PMID   24591519.
  13. ↑ David, Vojtěch; Archibald, John M. (2016). "Evolution: Plumbing the Depths of Diplonemid Diversity". Current Biology. 26 (24): R1290–R1292. doi: 10.1016/j.cub.2016.10.050 . PMID   27997843.
  14. ↑ Qian, Q.; Keeling, P. J. (2001). "Diplonemid Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) and Prokaryote-to-Eukaryote Lateral Gene Transfer". Protist. 152 (3): 193–201. doi:10.1078/1434-4610-00059. PMID   11693658.
  15. 1 2 Tashyreva, Daria; Prokopchuk, Galina; Yabuki, Akinori; Kaur, Binnypreet; Faktorová, Drahomíra; Votýpka, Jan; Kusaka, Chiho; Fujikura, Katsunori; Shiratori, Takashi; Ishida, Ken-Ichiro; Horák, Aleš; Lukeš, Julius (2018). "Phylogeny and Morphology of New Diplonemids from Japan". Protist. 169 (2): 158–179. doi:10.1016/j.protis.2018.02.001. PMID   29604574.
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