A facultative anaerobic organism is an organism that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation if oxygen is absent.
41-572: See text Asgard or Asgardarchaeota is a proposed superphylum belonging to the domain Archaea that contain eukaryotic signature proteins. It appears that the eukaryotes , the domain that contains the animals , plants , and fungi , emerged within the Asgard , in a branch containing the Heimdallarchaeota. This supports the two-domain system of classification over the three-domain system . In
82-569: A PKD domain S-layer . They also share the three-way ES39 expansion in LSU rRNA with eukaryotes. Gene clusters or operons encoding ribosomal proteins are often less conserved in their organization in the Asgard group than in other Archaea, suggesting that the order of ribosomal protein coding genes may follow the phylogeny. Asgard archaea are generally obligate anaerobes , though Kariarchaeota, Gerdarchaeota and Hodarchaeota may be facultative aerobes . They have
123-412: A Wood–Ljungdahl pathway and perform glycolysis . Members can be autotrophs , heterotrophs , or phototrophs using heliorhodopsin . One member, Candidatus Prometheoarchaeum syntrophicum , is syntrophic with a sulfur-reducing proteobacteria and a methanogenic archaea. The RuBisCO they have is not carbon-fixing, but likely used for nucleoside salvaging. Asgard are widely distributed around
164-688: A ubiquitin modifier system, and N-glycosylation pathway homologs. Asgard archaeons have a regulated actin cytoskeleton , and the profilins and gelsolins they use can interact with eukaryotic actins. In addition, Asgard archaea tubulin from hydrothermal-living Odinarchaeota ( OdinTubulin ) was identified as a genuine tubulin. OdinTubulin forms protomers and protofilaments most similar to eukaryotic microtubules, yet assembles into ring systems more similar to FtsZ , indicating that OdinTubulin may represent an evolution intermediate between FtsZ and microtubule -forming tubulins. They also seem to form vesicles under cryogenic electron microscopy . Some may have
205-447: A century earlier). The definition was posited because extinct organisms are hardest to classify: they can be offshoots that diverged from a phylum's line before the characters that define the modern phylum were all acquired. By Budd and Jensen's definition, a phylum is defined by a set of characters shared by all its living representatives. This approach brings some small problems—for instance, ancestral characters common to most members of
246-472: A defective DNA gyrase subunit A gene ( gyrA ), while obligate anaerobes were defective in topoisomerase I ( topI ). This indicates that topoisomerase I and its associated relaxation of chromosomal DNA is required for transcription of genes required for aerobic growth, while the opposite is true for DNA gyrase. Additionally, in Escherichia coli K-12 it has been noted that phosphofructokinase (PFK) exists as
287-615: A dimer under aerobic conditions and as a tetramer under anaerobic conditions. Given PFK’s role in glycolysis, this has implications for the effect of oxygen on the glucose metabolism of E. coli K-12 in relation to the mechanism of the Pasteur effect . There may exist a core network of transcription factors (TFs) that includes the major oxygen-responsive ArcA and FNR control the adaptation of Escherichia coli to changes in oxygen availability. Activities of these two regulators are indicative of spatial effects that may affect gene expression in
328-477: A level of the Linnean hierarchy without referring to (evolutionary) relatedness is unsatisfactory, but a phenetic definition is useful when addressing questions of a morphological nature—such as how successful different body plans were. The most important objective measure in the above definitions is the "certain degree" that defines how different organisms need to be members of different phyla. The minimal requirement
369-422: A phylum may have been lost by some members. Also, this definition is based on an arbitrary point of time: the present. However, as it is character based, it is easy to apply to the fossil record. A greater problem is that it relies on a subjective decision about which groups of organisms should be considered as phyla. The approach is useful because it makes it easy to classify extinct organisms as " stem groups " to
410-689: A phylum, other phylum-level ranks appear, such as the case of Bacillariophyta (diatoms) within Ochrophyta . These differences became irrelevant after the adoption of a cladistic approach by the ISP, where taxonomic ranks are excluded from the classifications after being considered superfluous and unstable. Many authors prefer this usage, which lead to the Chromista-Protozoa scheme becoming obsolete. Currently there are 40 bacterial phyla (not including " Cyanobacteria ") that have been validly published according to
451-502: A possible link between the simple prokaryotic microorganisms and the complex eukaryotic microorganisms occurring approximately two billion years ago. The phylogenetic relationships of the Asgard archaea have been studied by several teams in the 21st century. Varying results have been obtained, for instance using 53 marker proteins from the Genome Taxonomy Database . In 2023, Eme, Tamarit, Caceres and colleagues reported that
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#1732851091967492-425: A set of highly conserved protein-coding genes. The group was named for the shape-shifting Norse god Loki , in an allusion to the hydrothermal vent complex from which the first genome sample originated. The Loki of mythology has been described as "a staggeringly complex, confusing, and ambivalent figure who has been the catalyst of countless unresolved scholarly controversies", analogous to the role of Lokiarchaeota in
533-516: A superphylum they call "Eukaryomorpha" defined by "shared derived characters" (eukaryote signature proteins). Superphylum In biology , a phylum ( / ˈ f aɪ l əm / ; pl. : phyla ) is a level of classification or taxonomic rank below kingdom and above class . Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature for algae, fungi, and plants accepts
574-467: Is a paraphyletic taxon, which is less acceptable to present-day biologists than in the past. Proposals have been made to divide it among several new kingdoms, such as Protozoa and Chromista in the Cavalier-Smith system . Protist taxonomy has long been unstable, with different approaches and definitions resulting in many competing classification schemes. Many of the phyla listed below are used by
615-472: Is generally included in kingdom Fungi, though its exact relations remain uncertain, and it is considered a protozoan by the International Society of Protistologists (see Protista , below). Molecular analysis of Zygomycota has found it to be polyphyletic (its members do not share an immediate ancestor), which is considered undesirable by many biologists. Accordingly, there is a proposal to abolish
656-459: Is that all organisms in a phylum should be clearly more closely related to one another than to any other group. Even this is problematic because the requirement depends on knowledge of organisms' relationships: as more data become available, particularly from molecular studies, we are better able to determine the relationships between groups. So phyla can be merged or split if it becomes apparent that they are related to one another or not. For example,
697-983: The Bacteriological Code Currently there are 2 phyla that have been validly published according to the Bacteriological Code Other phyla that have been proposed, but not validly named, include: Facultative aerobes Some examples of facultatively anaerobic bacteria are Staphylococcus spp. , Escherichia coli , Salmonella , Listeria spp., Shewanella oneidensis and Yersinia pestis . Certain eukaryotes are also facultative anaerobes, including fungi such as Saccharomyces cerevisiae and many aquatic invertebrates such as nereid polychaetes . It has been observed that in mutants of Salmonella typhimurium that underwent mutations to be either obligate aerobes or anaerobes, there were varying levels of chromatin-remodeling proteins. The obligate aerobes were later found to have
738-552: The Catalogue of Life , and correspond to the Protozoa-Chromista scheme, with updates from the latest (2022) publication by Cavalier-Smith . Other phyla are used commonly by other authors, and are adapted from the system used by the International Society of Protistologists (ISP). Some of the descriptions are based on the 2019 revision of eukaryotes by the ISP. The number of protist phyla varies greatly from one classification to
779-740: The White Oak River estuary in the United States contained Odinarchaeota and Heimdallarchaeota; following the Norse deity naming convention, these groups were named for Odin and Heimdall respectively. Researchers therefore named the superphylum containing these microbes " Asgard ", after the home of the gods in Norse mythology. Two Lokiarchaeota specimens have been cultured, enabling a detailed insight into their morphology. Asgard members encode many eukaryotic signature proteins, including novel GTPases , membrane-remodelling proteins like ESCRT and SNF7 ,
820-459: The bearded worms were described as a new phylum (the Pogonophora) in the middle of the 20th century, but molecular work almost half a century later found them to be a group of annelids , so the phyla were merged (the bearded worms are now an annelid family ). On the other hand, the highly parasitic phylum Mesozoa was divided into two phyla ( Orthonectida and Rhombozoa ) when it was discovered
861-886: The Eukaryota are deep within Asgard, as sister of Hodarchaeales within the Heimdallarchaeota. TACK Jordarchaeia Odinarchaeia Baldrarchaeia Lokiarchaeales Helarchaeales Thorarcheaia Hermodarcheaia Sifarchaeia Wukongarchaeia Njordarchaeales Gerdarchaeales Heimdallarchaeaceae Kariarchaeaceae Hodarchaeales [REDACTED] [REDACTED] [REDACTED] Thermoproteota ( TACK ) " Thorarchaeia " (MBG-B) " Njordarchaeia " " Odinarchaeia " "Freyrarchaeaceae" "Jordarchaeaceae" " Baldrarchaeia " " Hermodarchaeia " "Helarchaeales" "Sigynarchaeaceae" Promethearchaeaceae ["Lokiarchaeaceae"] "Sifarchaeales" "Borrarchaeales" " Wukongarchaeia " "Hodarchaeales" "Gerdarchaeales" (JABLTI01) "Kariarchaeales" "Heimdallarchaeales" In
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#1732851091967902-495: The Greek phylon ( φῦλον , "race, stock"), related to phyle ( φυλή , "tribe, clan"). Haeckel noted that species constantly evolved into new species that seemed to retain few consistent features among themselves and therefore few features that distinguished them as a group ("a self-contained unity"): "perhaps such a real and completely self-contained unity is the aggregate of all species which have gradually evolved from one and
943-510: The Orthonectida are probably deuterostomes and the Rhombozoa protostomes . This changeability of phyla has led some biologists to call for the concept of a phylum to be abandoned in favour of placing taxa in clades without any formal ranking of group size. A definition of a phylum based on body plan has been proposed by paleontologists Graham Budd and Sören Jensen (as Haeckel had done
984-491: The Zygomycota phylum. Its members would be divided between phylum Glomeromycota and four new subphyla incertae sedis (of uncertain placement): Entomophthoromycotina , Kickxellomycotina , Mucoromycotina , and Zoopagomycotina . Kingdom Protista (or Protoctista) is included in the traditional five- or six-kingdom model, where it can be defined as containing all eukaryotes that are not plants, animals, or fungi. Protista
1025-500: The absence of oxygen, E. coli can use fumarate , nitrate , nitrite , dimethyl sulfoxide , or trimethylamine oxide as an electron acceptor. This flexibility allows facultative anaerobes to survive in a number of environments, and in environments with frequently changing conditions. Several species of protists use a facultative anaerobic metabolism to enhance their ATP production, and some can produce dihydrogen through this process. Since facultative anaerobes can grow in both
1066-534: The debates about the origin of eukaryotes. In 2016, a University of Texas -led team discovered Thorarchaeota from samples taken from the White Oak River in North Carolina, named in reference to Thor , another Norse god. Samples from Loki's Castle, Yellowstone National Park , Aarhus Bay , an aquifer near the Colorado River , New Zealand's Radiata Pool , hydrothermal vents near Taketomi Island , Japan, and
1107-454: The depicted scenario, the Eukaryota are deep in the tree of Asgard. A favored scenario is syntrophy, where one organism depends on the feeding of the other. An α-proteobacterium was incorporated to become the mitochondrion . In culture, extant Asgard archaea form various syntrophic dependencies. Gregory Fournier and Anthony Poole have proposed that Asgard is part of "the Eukaryote tree", forming
1148-504: The first publication of the APG system in 1998, which proposed a classification of angiosperms up to the level of orders , many sources have preferred to treat ranks higher than orders as informal clades. Where formal ranks have been provided, the traditional divisions listed below have been reduced to a very much lower level, e.g. subclasses . Wolf plants Hepatophyta Liver plants Coniferophyta Cone-bearing plant Phylum Microsporidia
1189-468: The four embranchements of Georges Cuvier . Informally, phyla can be thought of as groupings of organisms based on general specialization of body plan . At its most basic, a phylum can be defined in two ways: as a group of organisms with a certain degree of morphological or developmental similarity (the phenetic definition), or a group of organisms with a certain degree of evolutionary relatedness (the phylogenetic definition). Attempting to define
1230-536: The idea that each of the phyla represents a distinct body plan. A classification using this definition may be strongly affected by the chance survival of rare groups, which can make a phylum much more diverse than it would be otherwise. Total numbers are estimates; figures from different authors vary wildly, not least because some are based on described species, some on extrapolations to numbers of undescribed species. For instance, around 25,000–27,000 species of nematodes have been described, while published estimates of
1271-703: The influential (though contentious) Cavalier-Smith system in equating "Plantae" with Archaeplastida , a group containing Viridiplantae and the algal Rhodophyta and Glaucophyta divisions. The definition and classification of plants at the division level also varies from source to source, and has changed progressively in recent years. Thus some sources place horsetails in division Arthrophyta and ferns in division Monilophyta, while others place them both in Monilophyta, as shown below. The division Pinophyta may be used for all gymnosperms (i.e. including cycads, ginkgos and gnetophytes), or for conifers alone as below. Since
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1312-427: The microaerobic range. It has also been observed that these oxygen-sensitive proteins are protected within the cytoplasm by oxygen consumers within the cell membrane, known as terminal oxidases . Facultative anaerobes are able to grow in both the presence and absence of oxygen due to the expression of both aerobic and anaerobic respiratory chains using either oxygen or an alternative electron acceptor. For example, in
1353-411: The next. The Catalogue of Life includes Rhodophyta and Glaucophyta in kingdom Plantae, but other systems consider these phyla part of Protista. In addition, less popular classification schemes unite Ochrophyta and Pseudofungi under one phylum, Gyrista , and all alveolates except ciliates in one phylum Myzozoa , later lowered in rank and included in a paraphyletic phylum Miozoa . Even within
1394-436: The phyla with which they bear the most resemblance, based only on the taxonomically important similarities. However, proving that a fossil belongs to the crown group of a phylum is difficult, as it must display a character unique to a sub-set of the crown group. Furthermore, organisms in the stem group of a phylum can possess the "body plan" of the phylum without all the characteristics necessary to fall within it. This weakens
1435-435: The presence and absence of oxygen, they can survive in many different environments, adapt easily to changing conditions, and thus have a selective advantage over other bacteria. As a result, most life-threatening pathogens are facultative anaerobes. The ability of facultative anaerobic pathogens to survive without oxygen is important since their infection is shown to reduce oxygen levels in their host's gut tissue. Moreover,
1476-411: The same common original form, as, for example, all vertebrates. We name this aggregate [a] Stamm [i.e., stock] ( Phylon )." In plant taxonomy , August W. Eichler (1883) classified plants into five groups named divisions, a term that remains in use today for groups of plants, algae and fungi. The definitions of zoological phyla have changed from their origins in the six Linnaean classes and
1517-650: The summer of 2010, sediments were analysed from a gravity core taken in the rift valley on the Knipovich ridge in the Arctic Ocean, near the Loki's Castle hydrothermal vent site. Specific sediment horizons previously shown to contain high abundances of novel archaeal lineages were subjected to metagenomic analysis . In 2015, an Uppsala University -led team proposed the Lokiarchaeota phylum based on phylogenetic analyses using
1558-416: The terms as equivalent. Depending on definitions, the animal kingdom Animalia contains about 31 phyla, the plant kingdom Plantae contains about 14 phyla, and the fungus kingdom Fungi contains about 8 phyla. Current research in phylogenetics is uncovering the relationships among phyla within larger clades like Ecdysozoa and Embryophyta . The term phylum was coined in 1866 by Ernst Haeckel from
1599-420: The total number of nematode species include 10,000–20,000; 500,000; 10 million; and 100 million. The kingdom Plantae is defined in various ways by different biologists (see Current definitions of Plantae ). All definitions include the living embryophytes (land plants), to which may be added the two green algae divisions, Chlorophyta and Charophyta , to form the clade Viridiplantae . The table below follows
1640-503: The world, both geographically and by habitat. Many of the known clades are restricted to sediments, whereas Lokiarchaeota, Thorarchaeota and another clade occupy many different habitats. Salinity and depth are important ecological drivers for most Asgard archaea. Other habitats include the bodies of animals, the rhizosphere of plants, non-saline sediments and soils, the sea surface, and freshwater. In addition, Asgard are associated with several other microorganisms. The phylum Heimdallarchaeota
1681-501: Was found in 2017 to have N-terminal core histone tails , a feature previously thought to be exclusively eukaryotic. Two other archaeal phyla, both outside of Asgard, were found to also have tails in 2018. In January 2020, scientists found Candidatus Prometheoarchaeum syntrophicum , a member of the Lokiarcheota, engaging in cross-feeding with two bacterial species. Drawing an analogy to symbiogenesis , they consider this relationship