A revised six-kingdom system of life is presented, down to the level of infraphylum. As in my 1983 system Bacteria are treated as a single kingdom, and eukaryotes are divided into only five kingdoms: Protozoa, Animalia, Fungi, Plantae and Chromista. Intermediate high level categories (superkingdom, subkingdom, branch, infrakingdom, superphylum, subphylum and infraphylum) are extensively used to avoid splitting organisms into an excessive number of kingdoms and phyla (60 only being recognized). The two 'zoological' kingdoms, Protozoa and Animalia, are subject to the International Code of Zoological Nomenclature, the kingdom Bacteria to the International Code of Bacteriological Nomenclature, and the three 'botanical' kingdoms (Plantae, Fungi, Chromista) to the International Code of Botanical Nomenclature. Circumscriptions of the kingdoms Bacteria and Plantae remain unchanged since Cavalier-Smith (1981). The kingdom Fungi is expanded by adding Microsporidia, because of protein sequence evidence that these amitochondrial intracellular parasites are related to conventional Fungi, not Protozoa. Fungi are subdivided into four phyla and 20 classes; fungal classification at the rank of subclass and above is comprehensively revised. The kingdoms Protozoa and Animalia are modified in the light of molecular phylogenetic evidence that Myxozoa are actually Animalia, not Protozoa, and that mesozoans are related to bilaterian animals. Animalia are divided into four subkingdoms: Radiata (phyla Porifera, Cnidaria, Placozoa, Ctenophora), Myxozoa, Mesozoa and Bilateria (bilateral animals: all other phyla). Several new higher level groupings are made in the animal kingdom including three new phyla: Acanthognatha (rotifers, acanthocephalans, gastrotrichs, gnathostomulids), Brachiozoa (brachiopods and phoronids) and Lobopoda (onychophorans and tardigrades), so only 23 animal phyla are recognized. Archezoa, here restricted to the phyla Metamonada and Trichozoa, are treated as a subkingdom within Protozoa, as in my 1983 six-kingdom system, not as a separate kingdom. The recently revised phylum Rhizopoda is modified further by adding more flagellates and removing some 'rhizopods' and is therefore renamed Cercozoa. The number of protozoan phyla is reduced by grouping Mycetozoa and Archamoebae (both now infraphyla) as a new subphylum Conosa within the phylum Amoebozoa alongside the subphylum Lobosa, which now includes both the traditional aerobic lobosean amoebae and Multicilia. Haplosporidia and the (formerly microsporidian) metchnikovellids are now both placed within the phylum Sporozoa. These changes make a total of only 13 currently recognized protozoan phyla, which are grouped into two subkingdoms: Archezoa and Neozoa the latter is modified in circumscription by adding the Discicristata, a new infrakingdom comprising the phyla Percolozoa and Euglenozoa). These changes are discussed in relation to the principles of megasystematics, here defined as systematics that concentrates on the higher levels of classes, phyla, and kingdoms. These principles also make it desirable to rank Archaebacteria as an infrakingdom of the kingdom Bacteria, not as a separate kingdom. Archaebacteria are grouped with the infrakingdom Posibacteria to form a new subkingdom, Unibacteria, comprising all bacteria bounded by a single membrane. The bacterial subkingdom Negibacteria, with separate cytoplasmic and outer membranes, is subdivided into two infrakingdoms: Lipobacteria, which lack lipopolysaccharide and have only phospholipids in the outer membrane, and Glycobacteria, with lipopolysaccharides in the outer leaflet of the outer membrane and phospholipids in its inner leaflet. (ABSTRACT TRUNCATED)

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A revised six-kingdom system of life.

Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an alpha-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an alpha-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. I argue that the ancestral eukaryote was uniciliate with a single centriole (unikont) and a simple centrosomal cone of microtubules, as in the aerobic amoebozoan zooflagellate Phalansterium. I infer the root of the eukaryote tree at the divergence between opisthokonts (animals, Choanozoa, fungi) with a single posterior cilium and all other eukaryotes, designated 'anterokonts' because of the ancestral presence of an anterior cilium. Anterokonts comprise the Amoebozoa, which may be ancestrally unikont, and a vast ancestrally biciliate clade, named 'bikonts'. The apparently conflicting rRNA and protein trees can be reconciled with each other and this ultrastructural interpretation if long-branch distortions, some mechanistically explicable, are allowed for. Bikonts comprise two groups: corticoflagellates, with a younger anterior cilium, no centrosomal cone and ancestrally a semi-rigid cell cortex with a microtubular band on either side of the posterior mature centriole; and Rhizaria [a new infrakingdom comprising Cercozoa (now including Ascetosporea classis nov.), Retaria phylum nov., Heliozoa and Apusozoa phylum nov.], having a centrosomal cone or radiating microtubules and two microtubular roots and a soft surface, frequently with reticulopodia. Corticoflagellates comprise photokaryotes (Plantae and chromalveolates, both ancestrally with cortical alveoli) and Excavata (a new protozoan infrakingdom comprising Loukozoa, Discicristata and Archezoa, ancestrally with three microtubular roots). All basal eukaryotic radiations were of mitochondrial aerobes; hydrogenosomes evolved polyphyletically from mitochondria long afterwards, the persistence of their double envelope long after their genomes disappeared being a striking instance of membrane heredity. I discuss the relationship between the 13 protozoan phyla recognized here and revise higher protozoan classification by updating as subkingdoms Lankester's 1878 division of Protozoa into Corticata (Excavata, Alveolata; with prominent cortical microtubules and ancestrally localized cytostome--the Parabasalia probably secondarily internalized the cytoskeleton) and Gymnomyxa [infrakingdoms Sarcomastigota (Choanozoa, Amoebozoa) and Rhizaria; both ancestrally with a non-cortical cytoskeleton of radiating singlet microtubules and a relatively soft cell surface with diffused feeding]. As the eukaryote root almost certainly lies within Gymnomyxa, probably among the Sarcomastigota, Corticata are derived. Following the single symbiogenetic origin of chloroplasts in a corticoflagellate host with cortical alveoli, this ancestral plant radiated rapidly into glaucophytes, green plants and red algae. Secondary symbiogeneses subsequently transferred plastids laterally into different hosts, making yet more complex cell chimaeras--probably only thrice: from a red alga to the corticoflagellate ancestor of chromalveolates (Chromista plus Alveolata), from green algae to a secondarily uniciliate cercozoan to form chlorarachneans and independently to a biciliate excavate to yield photosynthetic euglenoids. Tertiary symbiogenesis involving eukaryotic algal symbionts replaced peridinin-containing plastids in two or three dinoflagellate lineages, but yielded no major novel groups. The origin and well-resolved primary bifurcation of eukaryotes probably occurred in the Cryogenian Period, about 850 million years ago, much more recently than suggested by unwarranted backward extrapolations of molecular 'clocks' or dubious interpretations as 'eukaryotic' of earlier large microbial fossils or still more ancient steranes. The origin of chloroplasts and the symbiogenetic incorporation of a red alga into a corticoflagellate to create chromalveolates may both have occurred in a big bang after the Varangerian snowball Earth melted about 580 million years ago, thereby stimulating the ensuing Cambrian explosion of animals and protists in the form of simultaneous, poorly resolved opisthokont and anterokont radiations.

The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.

Kingdom protozoa and its 18 phyla.

Placozoans are arguably the simplest free-living animals, possibly evoking an early stage in metazoan evolution, yet their biology is poorly understood. Here we report the sequencing and analysis of the {approx}98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome exhibits conserved gene content, gene structure, and synteny relative to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signaling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages.

https://digital.library.unt.edu/ark:/67531/metadc895108/m2/1/high_res_d/937506.pdf

The Trichoplax genome and the nature of placozoans

Ecology of protozoa

1.

Von Trichoplax adhaerens wurden zwei Klone gezuehtet. Der eine wurde 1969 (Klon I), der andere 1971 isoliert (Klon II).




2.

Bei einer bestimmten Populationsdichte setzt eine degenerative Phase ein, die aus einem reversiblen und einem irreversiblen Abschnitt besteht. Werden die Tiere nicht rechtzeitig in eine frische Kulturschale ubertragen, so gehen sic zugrunde.




3.

Der Ubergang in die degenerative Phase bildet die wesentliche Voraussetzung fur die Eibildung.




4.

Obwohl in einem der beiden Klone vereinzelt auch eine spontane Eibildung beobachtet wurde (Klon I), fand sic in groserem Umfang erst statt, wenn beide Klone miteinander vermischt wurden.




5.

Der klonale Unterschied entspricht keiner sexuellen Differenzierung; durch Vermischen beider Klone wurde auch in Klon II eine Eibildung induziert, indem sie bisher noch nicht spontan aufgetreten ist.




6.

Spermien konnten noch nicht eindeutig identifiziert werden. Far das Vorkommen einer Befruchtung spricht aber, das sich nur Eier weiterentwickeln konnen, die eine besondere Hulle (“Befruchtungsmembran”) ausgebildet haben.




7.

Die Furchung ist total-aqual. Unter den derzeitigen Kulturbedingungen sterben alle Furchungsstadien fruher oder spater ab. Das Ergebnis der Embryonalentwicklung ist daher noch unbekannt.

Eibildung und furchung von Trichoplax adhaerens F. E. Schulze (Placozoa)

1. Die Zellen des Ventralepithels bilden keine Mikrovilli, sondern ein schwammartiges Maschenwerk gefensterter Leisten und Falten, welches bei der Haftung des Tieres an der Unterlage und/oder bei der extrasomatischen Vorverdauung der Nahrung eine Rolle spielen durfte. 2. Wahrend der Zellteilungen treten typische Centriole an den Spindelpolen auf. 3. Die wachsenden Eizellen phagocytieren Fortsatze der Faserzellen, die als Trophocyten fungieren. 4. Unter den gleichen Bedingungen, die zur Eibildung fuhren, konnen sogen. S-Zellen auftreten. Einige ultrastrukturelle Befunde sprechen dafur, das es sich um Spermien handelt.

Ergänzende Untersuchungen zur Ultrastruktur von Trichoplax adhaerens F.E. Schulze (Placozoa)

1.

Cachon-Enjumet's (1961) attempt to interpret the nuclear division of the radiolarian, Aulacantha scolymantha, as a typical, though superficially modified mitosis is subject to criticism. There is no evidence for differences between the numerous chromosomes of this species. The identification of nucleolus organizing chromosomes is inconclusive since supposed nucleoli contain DNA and are obviously due to the disintegration of chromosomes. No evidence for the existence of true nucleoli was found. Instead, all chromosomes contain unusually great amounts of RNA. Evidence for chromosomal differences on the basis of arm length and kinetochore position is equally inconclusive. No localized points of spindle fiber attachment could be identified in the electron microscope. Attention was drawn to a number of artefacts in this connection. It is concluded that Cachon-Enjumet did not succeed in bringing forth any new and conclusive arguments against Grell's (1953) hypothesis that all chromosomes of Aulacantha are homologous and genetically equivalent.




2.

The basic ultrastructural component of the chromosomes of this radiolarian is a fibril about 80 A in thickness.




3.

A new ultrastructural component, consisting of an axial complex demonstrable after treatment of the sections with both uranyl and lead ions, is described. So far, it is unknown if this represents a special feature of Aulacantha chromosomes which may have some bearing on cytogenetic peculiarities of this species.




4.

Within a specialized „spindle plasma“ excluding formed elements like Golgi vesicles and mitochondria, tubular spindle fibers have been identified. Their attachment to the chromosomes is not confined to localized kinetochores. It seems to conform to a type of „diffuse“ spindle fiber attachment as described from various insect orders by technique of light microscopy.

Über die Karyologie des Radiolars Aulacantha scolymantha und die Feinstruktur seiner Chromosomen

The ultrastructure of Reticulosphaera socialis grell (Heterokontophyta).

1.

Es wird der Feinbau des Tentakels bei dem Suktor Acineta tuberosa beschrieben.




2.

Die an der Membran des Tentakelkopfchens verankerten Organellen, welche bisher als “missile-like bodies” beschrieben wurden, bezeichnen wir als Haptocysten. Sie stellen den ersten Kontakt zwischen dem Tentakelkopfchen und dem Beutetier her.




3.

Auf Grund einiger Befunde, die die Ergebnisse anderer Autoren erganzen, wird eine neue Auffassung uber den Saugvorgang entwickelt. Erst durch die Auskleidung des „Tentakelinnenrohrs“ mit einer feinen Membran wird es zu einem funktionsfahigen Rohr.

Karl G. Grell

Papers

Eibildung und furchung von Trichoplax adhaerens F. E. Schulze (Placozoa)

Ergänzende Untersuchungen zur Ultrastruktur von Trichoplax adhaerens F.E. Schulze (Placozoa)

Über die Karyologie des Radiolars Aulacantha scolymantha und die Feinstruktur seiner Chromosomen

The ultrastructure of Reticulosphaera socialis grell (Heterokontophyta).

Elektronenmikroskopische Beobachtungen zur Nahrungsaufnahme bei dem Suktor Acineta tuberosa Ehrenberg