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24-818: 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 described Jakoba incarcerata has been renamed Andalucia incarcerata , and Jakoba bahamensis / Jakoba bahamiensis is not formally described.) Jakoba are small bacterivorous zooflagellates ( jakobids ) found in marine and hypersaline environments. They are free swimming trophic cells with two flagella and range between five and ten micrometers in length. Cells rotate along their longitudinal axis to allow for swimming in straight lines unless deformation and “squirming” occurs due to compression in debris. During feeding, bacteria are removed from
48-484: A monophyletic group. Phylogenetic analyses often do not place malawimonads on the same branch as the other Excavata. Excavates were thought to include multiple groups: Euglenozoa and Heterolobosea (Percolozoa) or Eozoa (as named by Cavalier-Smith ) appear to be particularly close relatives, and are united by the presence of discoid cristae within the mitochondria (Superphylum Discicristata ). A close relationship has been shown between Discicristata and Jakobida ,
72-451: A degree of variability). Consequently, they will generally respond in a more uniform and reproducible fashion, simplifying the interpretation of experiments . The axenic culture of some pathogens is complicated because they normally thrive within host tissues which exhibit properties that are difficult to replicate in vitro . This is especially true in the case of intracellular pathogens . However, careful replication of key features of
96-421: A mitochondrial organelle in greatly modified form (e.g. a hydrogenosome or mitosome ). Among those with mitochondria, the mitochondrial cristae may be tubular, discoidal , or in some cases, laminar. Most excavates have two, four, or more flagella . Many have a conspicuous ventral feeding groove with a characteristic ultrastructure , supported by microtubules —the "excavated" appearance of this groove giving
120-485: A narrow longitudinal groove down one side of the cell. The ancyromonad groove is not used for "suspension feeding", unlike in "typical excavates" (e.g. malawimonads, jakobids, Trimastix , Carpediemonas , Kiperferlia , etc). Ancyromonads instead capture prokaryotes attached to surfaces. The phylogenetic placement of ancyromonads is poorly understood (in 2020), however some phylogenetic analyses place them as close relatives of malawimonads. The conventional explanation for
144-773: A phylogenetic tree with the metamonad Parabasalia as basal Eukaryotes. Discoba and the rest of the Eukaryota appear to have emerged as sister taxon to the Preaxostyla, incorporating a single alphaproteobacterium as mitochondria by endosymbiosis. Thus the Fornicata are more closely related to e.g. animals than to Parabasalia. The rest of the Eukaryotes emerged within the Excavata as sister of the Discoba; as they are within
168-728: A relationship with other platicristate taxa. The mitochondria of Jakoba are of particular interest evolutionarily due to their unique bacterial -like mitochondrial genomes . It has been found that their mitochondrial genomes contain considerably more functional genes than those of other eukaryotic groups and it appears they have retained the ancestral eubacterial RNA polymerase , which has been replaced by viral type polymerase in all other mitochondriate eukaryotes. Overall, jakobid mitochondrial genomes are primitively complex in that they resemble their proteobacterial ancestors more than any other mitochondria . Jakoba reproduce asexually by binary fission . The sexual reproduction or
192-430: Is an extensive and diverse but 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 a variety of free-living and symbiotic protists, and includes some important parasites of humans such as Giardia and Trichomonas . Excavates were formerly considered to be included in
216-413: Is an important tool for the study of symbiotic and parasitic organisms in a controlled environment. Axenic cultures of microorganisms are typically prepared by subculture of an existing mixed culture. This may involve use of a dilution series , in which a culture is successively diluted to the point where subsamples of it contain only a few individual organisms, ideally only a single individual (in
240-720: Is used for translation . Encoded genes include those commonly found in mtDNA , including the protein-coding genes nad1,2,3,4,4L,5,6, cob, cox1,2,3, and atp6,8,9, as well as large subunit (rnl) and small subunit (rns) rRNA genes and >22 tRNA genes. Also present are a number of protein genes typical of protist but not animal or fungal mtDNAs . These include nad7,9,11, atp1, rpl2,5,6,14,16, and rps2-4,11-14,19. A number of unique ORFs are also encoded by J. libera mtDNA .” “A number of J. libera mitochondrial genes are rare or absent in other mitochondrial genomes but are present in bacteria . Among these rare or unique mtDNA -encoded genes are dpo, rpoB,C, rrn5, rnpB, tufA, yejU-W, and several of
264-429: The case of an asexual species ). These subcultures are allowed to grow until the identity of their constituent organisms can be ascertained. Selection of those cultures consisting solely of the desired organism produces the axenic culture. Subculture selection may also involve manually sampling the target organism from an uncontaminated growth front in an otherwise mixed culture, and using this as an inoculum source for
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#1732798703879288-459: The composition of the excavates is given below, indicating that the group is paraphyletic. Except for some Euglenozoa , all are non- photosynthetic . Most excavates are unicellular, heterotrophic flagellates. Only some Euglenozoa are photosynthetic. In some (particularly anaerobic intestinal parasites), the mitochondria have been greatly reduced. Some excavates lack "classical" mitochondria , and are called "amitochondriate", although most retain
312-500: The formation of cysts have not been observed. “The circular mitochondrial genome of Jakoba libera strain ATCC 50422 is 96.6 kbp in size. Sequencing is nearly completed. At present, 77 genes have been identified, none of them including an intron. Intergenic regions account for ~ 30% of the genome and contain clusters of tandem repeats whose unit length is ~20 bp. Transcribed genes are found on both DNA strands . The standard genetic code
336-745: The latter having tubular cristae like most other protists, and hence were united under the taxon name Discoba , which was proposed for this supposedly monophyletic group. Metamonads are unusual in not having classical mitochondria—instead they have hydrogenosomes , mitosomes or uncharacterised organelles. The oxymonad Monocercomonoides is reported to have completely lost homologous organelles. There are competing explanations. The malawimonads have been proposed to be members of Excavata owing to their typical excavate morphology, and phylogenetic affinity to other excavate groups in some molecular phylogenies. However, their position among eukaryotes remains elusive. Ancyromonads are small free-living cells with
360-451: The now obsolete Protista kingdom. They were distinguished from other lineages based on electron-microscopic information about how the cells are arranged (they have a distinctive ultrastructural identity ). They are considered to be a basal flagellate lineage. On the basis of phylogenomic analyses, the group was shown to contain three widely separated eukaryote groups, the discobids, metamonads, and malawimonads. A current view of
384-496: The organisms their name. However, various groups that lack these traits are considered to be derived excavates based on genetic evidence (primarily phylogenetic trees of molecular sequences). The Acrasidae slime molds are the only excavates to exhibit limited multicellularity. Like other cellular slime molds , they live most of their life as single cells, but will sometimes assemble into larger clusters. Excavate relationships were always uncertain, suggesting that they are not
408-439: The origin of the Eukaryotes is that a heimdallarchaeian or another Archaea acquired an alphaproteobacterium as an endosymbiont , and that this became the mitochondrion , the organelle providing oxidative respiration to the eukaryotic cell. Caesar al Jewari and Sandra Baldauf argue instead that the Eukaryotes possibly started with an endosymbiosis event of a Deltaproteobacterium or Gammaproteobacterium , accounting for
432-575: The otherwise unexplained presence of anaerobic bacterial enzymes in Metamonada. The sister of the Preaxostyla within Metamonada represents the rest of the Eukaryotes which acquired an Alphaproteobacterium. In their scenario, the hydrogenosome and mitosome , both conventionally considered "mitochondrion-derived organelles", would predate the mitochondrion, and instead be derived from the earlier symbiotic bacterium. In 2023, using molecular phylogenetic analysis of 186 taxa, Al Jewari and Baldauf proposed
456-475: The plate during this period, identifying cultures that are no longer axenic. As axenic cultures are derived from very few organisms, or even a single individual, they are useful because the organisms present within them share a relatively narrow gene pool . In the case of an asexual species derived from a single individual, the resulting culture should consist of identical organisms (though processes such as mutation and horizontal gene transfer may introduce
480-780: The ribosomal protein genes.” “A comparison of gene order in the mtDNAs of J. libera …” show “clusters that are otherwise not found in bacteria but that evidently appeared during evolution of the mitochondrial genome after the divergence of the proto-mitochondrion from the bacterial lineage. Examples are the clusters sdh3 to nad5, (comprising 5 genes), atp8-[trn]-rps4-atp9 and nad11-nad1-cox11-cox3-tufA.” There are currently three strains of Jakoba libera available for culture. They can not be grown axenically , but are easily raised in minimal media with added bacteria ( Klebsiella aerogenes ) Jakobids ( Jakobida or Jakobea ) Malawimonas : 1 described species Retortamonads : Carpediemonas-like organisms : Excavata Excavata
504-508: The root of a tree is often difficult to pinpoint. Metakaryota Axenic In biology , axenic ( / eɪ ˈ z ɛ n ɪ k / , / eɪ ˈ z i n ɪ k / ) describes the state of a culture in which only a single species, variety, or strain of organism is present and entirely free of all other contaminating organisms. The earliest axenic cultures were of bacteria or unicellular eukaryotes , but axenic cultures of many multicellular organisms are also possible. Axenic culture
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#1732798703879528-425: The same clade but are not cladistically considered part of the Excavata yet, the Excavata are in this analysis highly paraphyletic. Hodarchaeales Parabasalia Fornicata Preaxostyla Jakobida Heterolobosea Euglenozoa and allies Amorphea (inc. animals, fungi) SAR Archaeplastida (inc. plants) The Anaeramoeba are associated with Parabasalia, but could turn out to be more basal as
552-402: The subculture. Axenic cultures are usually checked routinely to ensure that they remain axenic. One standard approach with microorganisms is to spread a sample of the culture onto an agar plate , and to incubate this for a fixed period of time. The agar should be an enriched medium that will support the growth of common "contaminating" organisms. Such "contaminating" organisms will grow on
576-441: The water column by a current created by the posterior flagellum . This current causes the bacteria to collect in the groove on the right ventral side of the cell – aiding in ingestion and the creation of food vacuoles . Cellular components for Jakoba are not particularly unique. They contain a single nucleus found close to the flagellar bases, a single Golgi body , and the mitochondrial cristae are flattened suggesting
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