Jakobida is an

order Order, ORDER or Orders may refer to: * A socio-political or established or existing order, e.g. World order, Ancien Regime, Pax Britannica * Categorization, the process in which ideas and objects are recognized, differentiated, and understood ...

(sole order in the

class Class, Classes, or The Class may refer to: Common uses not otherwise categorized * Class (biology), a taxonomic rank * Class (knowledge representation), a collection of individuals or objects * Class (philosophy), an analytical concept used d ...

Jakobea) of free-living,

heterotrophic A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...

, flagellar

eukaryote The eukaryotes ( ) constitute the Domain (biology), domain of Eukaryota or Eukarya, organisms whose Cell (biology), cells have a membrane-bound cell nucleus, nucleus. All animals, plants, Fungus, fungi, seaweeds, and many unicellular organisms ...

s in the

clade In biology, a clade (), also known as a Monophyly, monophyletic group or natural group, is a group of organisms that is composed of a common ancestor and all of its descendants. Clades are the fundamental unit of cladistics, a modern approach t ...

Discoba Excavata is an obsolete, extensive and diverse Paraphyly, paraphyletic group of unicellular Eukaryote, Eukaryota. The group was first suggested by Simpson and Patterson in 1999 and the name latinized and assigned a rank by Thomas Cavalier-Smit ...

. They are small (less than 15

μm The micrometre (Commonwealth English as used by the International Bureau of Weights and Measures; SI symbol: μm) or micrometer (American English), also commonly known by the non-SI term micron, is a unit of length in the International System ...

), and can be found in aerobic and anaerobic environments. The order Jakobida, believed to be

monophyletic In biological cladistics for the classification of organisms, monophyly is the condition of a taxonomic grouping being a clade – that is, a grouping of organisms which meets these criteria: # the grouping contains its own most recent co ...

, consists of only twenty species at present, and was classified as a group in 1993. There is ongoing research into the

mitochondrial genomes Mitochondrial DNA (mtDNA and mDNA) is the DNA located in the mitochondria organelles in a eukaryotic cell that converts chemical energy from food into adenosine triphosphate (ATP). Mitochondrial DNA is a small portion of the DNA contained in ...

of jakobids, which are unusually large and bacteria-like, evidence that jakobids may be important to the evolutionary history of eukaryotes. Molecular phylogenetic evidence suggests strongly that jakobids are most closely related to

Heterolobosea Heterolobosea are a class of Percolozoa. The only member of this class that is infectious to humans is '' Naegleria fowleri'', the causative agent of the often fatal disease amoebic meningitis. Typically, their life cycle alternates between fl ...

and

Euglenozoa 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, ...

Description

Jakobids have two flagella, inserted in the anterior end of the cell, and, like other members of order

Excavata Excavata is an obsolete, extensive and diverse paraphyletic group of unicellular Eukaryota. The group was first suggested by Simpson and Patterson in 1999 and the name latinized and assigned a rank by Thomas Cavalier-Smith in 2002. It contains ...

, have a ventral feeding groove and associated

cytoskeleton The cytoskeleton is a complex, dynamic network of interlinking protein filaments present in the cytoplasm of all cells, including those of bacteria and archaea. In eukaryotes, it extends from the cell nucleus to the cell membrane and is compos ...

support. The posterior flagella has a dorsal vane and is aligned within the ventral groove, where it generates a current that the cell uses for food intake. The

nucleus Nucleus (: nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA Nucleu ...

is generally in the anterior part of the cell and bears a

nucleolus The nucleolus (; : nucleoli ) is the largest structure in the cell nucleus, nucleus of eukaryote, eukaryotic cell (biology), cells. It is best known as the site of ribosome biogenesis. The nucleolus also participates in the formation of signa ...

. Most known jakobids have one

mitochondrion A mitochondrion () is an organelle found in the cell (biology), cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double lipid bilayer, membrane structure and use aerobic respiration to generate adenosine tri ...

, again located anteriorly, and different genera have flattened, tubular, or absent

cristae A crista (; : cristae) is a fold in the inner membrane of a mitochondrion. The name is from the Latin for ''crest'' or ''plume'', and it gives the inner membrane its characteristic wrinkled shape, providing a large amount of surface area for che ...

. Food

vacuoles A vacuole () is a membrane-bound organelle which is present in plant and fungal cells and some protist, animal, and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic mo ...

are mostly located on the cell posterior, and in most jakobids the

endoplasmic reticulum The endoplasmic reticulum (ER) is a part of a transportation system of the eukaryote, eukaryotic cell, and has many other important functions such as protein folding. The word endoplasmic means "within the cytoplasm", and reticulum is Latin for ...

is distributed throughout the cell. The

sessile Sessility, or sessile, may refer to: * Sessility (motility), organisms which are not able to move about * Sessility (botany), flowers or leaves that grow directly from the stem or peduncle of a plant * Sessility (medicine), tumors and polyps that ...

, loricate

Histionidae Jakobids Discoba families Histionidae is a family of Jakobid, Jakobids in the Paraphyly, paraphyletic Excavata group. References

{{Taxonbar, from=Q12626268 ...

and occasionally free-swimming ''

Jakoba libera ''Jakoba'' is a genus in the taxon Excavata, and currently has a single described species, '' Jakoba libera'' described by Patterson in 1990, and named in honour of Dutch botanist (Algology, Myology and Lichenology) Jakoba Ruinen. (Previously d ...

'' (

Jakobidae ''Jakoba'' is a genus in the taxon Excavata, and currently has a single described species, '' Jakoba libera'' described by Patterson in 1990, and named in honour of Dutch botanist (Algology, Myology and Lichenology) Jakoba Ruinen. (Previously d ...

) have

extrusomes Extrusomes are membrane-bound organelles found in eukaryotic cells that are capable of discharging material contained within to the exterior of the cell. Due to the diversity in structure and function, it is unlikely that different types of extruso ...

under the dorsal membrane that are theorized to be defensive structures. 2023 Jakobid

Ecology

Jakobids are widely dispersed, having been found in soil, freshwater, and marine habitats, but generally not common. However,

environmental DNA Environmental DNA or eDNA is DNA that is collected from a variety of environmental samples such as soil, seawater, snow or air, rather than directly sampled from an individual organism. As various organisms interact with the environment, DNA ...

surveys suggest that Stygiellidae are abundant in anoxic marine habitats. Some are capable of surviving hypersaline and anoxic environments, though the Histionids have only been found in freshwater ecosystems, where they attach themselves to algae or zooplankton. Outside of obligate sessile species, many species of jakobids can attach temporarily to surfaces, using either of the two flagella or the cell body itself. All known jakobids are heterotrophic suspension feeders. Their primary prey is generally considered to be bacteria, though one species has been observed eating extremely small (< 1 μm) eukaryotic cells. Jakobids are generally slow swimmers, with low clearance rates relative to similar organisms. No study has suggested jakobids might be pathogenic or toxic.

Mitochondrial DNA

Since jakobids have no current commercial use, most research into jakobids has focused on their evolutionary significance. The

mitochondrial DNA Mitochondrial DNA (mtDNA and mDNA) is the DNA located in the mitochondrion, mitochondria organelles in a eukaryotic cell that converts chemical energy from food into adenosine triphosphate (ATP). Mitochondrial DNA is a small portion of the D ...

of jakobids is the most bacteria-like of all known eukaryotic mitochondrial DNA, suggesting that jakobid mitochondrial genomes might approximate the ancestral mitochondrial genome. jakobid mitochondrial DNA is substantially different from most other eukaryotes, especially in terms of the number of genes (nearly 100 in some species) and bacteria-like elements within their genomes. Nine of the genes have never been found in eukaryotic mitochondrial DNA. Uniquely, jakobid mitochondrial genomes code for bacteria-type

RNA polymerase In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template. Using the e ...

, as opposed to typical eukaryotic mitochondrial

, referred to as “phage-type”, which appears to be viral in origin. This does not necessarily mean that jakobids are basal to the phylogeny of eukaryotes. While jakobid mitochondria have genetic features that seem to have developed from bacteria, and apparently lack phage-type RNA, it is possible that other eukaryotic clades lost their bacterial features independently. Several proposed possibilities might explain the bacterial features of jakobid mitochondrial DNA. One is that jakobids diverged very early from the rest of the eukaryotes. This hypothesis depends on whether or not jakobids are indeed basal to all living eukaryotes, but there is no evidence yet to support that suggestion. Another hypothesis is that the phage-type RNA polymerase moved from one eukaryote group to another via

lateral gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the e ...

, replacing the bacteria-type enzyme, and simply did not reach the jakobids. This would not depend on jakobids being basal to eukaryotes as a whole, but has not been widely studied. A third possibility is the reverse of the others, suggesting that the phage-type RNA polymerase is the basal one. Under this scenario, jakobids acquired their bacteria-type RNA polymerase much more recently and that then spread via lateral gene transfer. However, the gene arrangement of jakobid mitochondrial DNA suggests an ancestral origin of bacteria-type RNA polymerase over a more-recent divergence. One of the proposed scenarios suggests that the common ancestor of eukaryotes had two mitochondrial RNA polymerases, both phage-type and bacteria-type, and jakobids lost their phage-type polymerase while the rest of the eukaryotes lost the bacteria-type, possibly several times. Such a model eliminates the need for jakobids to be truly basal. One study proposed that the phage-type and bacteria-type polymerases, when present in the same mitochondrion, served different functions, much in the way that the organelles of land plants have two different RNA polymerase enzymes that transcribe different genes.

Taxonomy

Jakobida contains five families consisting of mostly free-swimming genera:

, Moramonadidae, Andaluciidae, and

Stygiellidae Stygiellidae is a family of free-living marine flagellates belonging to the order Jakobida, a deep-branching lineage within the eukaryotic supergroup Discoba. They are unicellular organisms that commonly inhabit anoxic, sulfide-rich and ammoni ...

. The sixth family,

Histionidae Jakobids Discoba families Histionidae is a family of Jakobid, Jakobids in the Paraphyly, paraphyletic Excavata group. References

{{Taxonbar, from=Q12626268 ...

, is largely populated by

loricate genera, and includes the first jakobids ever described. Jakobida is a

group, and are most closely related to the

and

. * Class

Jakobea Jakobida is an order (sole order in the class Jakobea) of free-living, heterotrophic, flagellar eukaryotes in the clade Discoba. They are small (less than 15 μm), and can be found in aerobic and anaerobic environments. The order Jakobida, ...

Cavalier-Smith 1999 ** Order Jakobida Cavalier-Smith 1993 *** Suborder Ophirinina Yabuki et al. 2018 **** Family Agogoniidae Galindo et al. 2023 ***** Genus '' Agogonia'' Galindo et al. 2023 ****** Species ''A. voluta'' Galindo et al. 2023 **** Family Ophirinidae Yabuki et al. 2018 ***** Genus '' Ophirina'' Yabuki et al. 2018 ****** Species ''O. amphinema'' Yabuki et al. 2018 ****** Species ''O. chinija'' Galindo et al. 2023 *** Suborder

Andalucina Andalucina is a suborder of unicellular organisms in the order of Jakobida. Many species in Andalucina inhabit anaerobic environments. References Jakobids Taxa described in 2013 {{Excavata-stub ...

Cavalier-Smith 2013 **** Family Andaluciidae Cavalier-Smith 2013 ***** Genus ''

Andalucia Andalusia ( , ; , ) is the southernmost autonomous community in Peninsular Spain, located in the south of the Iberian Peninsula, in southwestern Europe. It is the most populous and the second-largest autonomous community in the country. It i ...

'' Lara et al. 2006 ****** Species ''A. godoyi'' Lara et al. 2006 **** Family

Pánek, Táborský & Čepička 2015 ***** Genus '' Velundella'' Pánek, Táborský & Čepička 2015 ****** Species ''V. nauta'' Pánek, Táborský & Čepička 2015 ****** Species ''V. trypanoides'' Pánek, Táborský & Čepička 2015 ***** Genus ''

Stygiella ''Stygiella'' /ˌstɪ.d͡ʒiˈɛ.lə/ is a genus of free-living marine flagellates belonging to the family Stygiellidae in the Jakobids (excavata). The genus currently includes four species, all of which are secondary obligate anaerobes. The s ...

'' Pánek, Táborský & Čepička 2015 non Bruand 1853 ****** Species '' S. incarcerata'' (Bernard, Simpson & Patterson 2000) Pánek, Táborský & Čepička 2015 'Jakoba incarcerata'' Bernard, Simpson & Patterson 2000; ''Andalucia incarcerata'' (Bernard, Simpson & Patterson 2000) Lara et al. 2006] ****** Species ''S. agilis'' Pánek, Táborský & Čepička 2015 ****** Species ''S. cryptica'' Pánek, Táborský & Čepička 2015 ****** Species ''S. adhaerens'' Pánek, Táborský & Čepička 2015 *** Suborder Histonina Cavalier-Smith 1993 **** Species ?'' Jakoba echidna'' O'Kelly 1991 **** Family Moramonadidae Strassert et al. 2016 ***** Genus '' Moramonas'' Strassert et al. 2016 ****** Species ''M. marocensis'' Strassert et al. 2016 ***** Genus '' Seculamonas'' Marx et al. 2003 nomen nudum ****** Species ''S. ecuadoriensis'' Marx et al. 2003 nomen nudum **** Family

Patterson 1990 ***** Genus ''

Jakoba ''Jakoba'' is a genus in the taxon Excavata, and currently has a single described species, ''Jakoba libera'' described by David_J._Patterson, Patterson in 1990, and named in honour of Dutch botanist (Algology, Myology and Lichenology) Jakoba Rui ...

'' Patterson 1990 ****** Species ''J. bahamiensis'' Burger & Lang (indeitum) ****** Species ''J. libera'' (Ruinen 1938) Patterson 1990 'Cryptobia libera'' Ruinen 1938**** Family

Histionidae Jakobids Discoba families Histionidae is a family of Jakobid, Jakobids in the Paraphyly, paraphyletic Excavata group. References

{{Taxonbar, from=Q12626268 ...

Flavin & Nerad 1993 ***** Genus ''

Histiona ''Histiona'' is a genus of Excavata containing four species. It has a worldwide distribution. It is a Jakobid Jakobida is an order (sole order in the class Jakobea) of free-living, heterotrophic, flagellar eukaryotes in the clade Discoba. The ...

'' Voigt 1902 'Zachariasia'' Voigt 1901 non Lemmermann 1895">Zachariasia.html" ;"title="'Zachariasia">'Zachariasia'' Voigt 1901 non Lemmermann 1895****** Species ?''H. planctonica'' Scourfield 1937 ****** Species ''H. aroides'' Pascher 1943 ****** Species ''H. velifera'' (Voigt 1901) Pascher 1943 [''Zachariasia velifera'' Voigt 1901; ''Histiona zachariasii'' Voigt 1901 nom. illeg.] ***** Genus ''Reclinomonas'' Flavin & Nerad 1993 ****** Species ''Reclinomonas americana, R. americana'' Flavin & Nerad 1993 ****** Species ''R. campanula'' (Penard 1921) Flavin & Nerad 1993 'Histiona campanula'' Penard 1921; ''Stenocodon campanula'' (Penard 1921) Pascher 1942***** Genus '' Stenocodon'' Pascher 1942 ****** Species ''S epiplankton'' Pascher 1942 ***** Genus '' Stomatochone'' Pascher 1942 ****** Species ''S. infundibuliformis'' Pascher 1942 ****** Species ''S. cochlear'' Pascher 1942 ****** Species ''S. excavata'' Pascher 1942 ****** Species ''S. epiplankton'' Pascher 1942

References

{{Taxonbar, from=Q1135350 Protists

Description

Ecology

Mitochondrial DNA

Taxonomy

See also

References