Protists Research Articles

Selenocysteyl-tRNAs recognize UGA in Betavulgaris, a higher plant, and in Gliocladium virens, a filamentous fungus

Selenocysteyl-tRNAs that decode UGA were previously identified in representatives of three of the five life kingdoms which were the monera, animal and protist kingdoms. In the present study, we show that these tRNAs also occur in representatives of the two remaining kingdoms, plants and fungi; i.e., selenocysteyl-tRNAs which code for UGA occur in Beta vulgaris, a higher plant, and in Gliocladium virens, a filamentous fungus. The fact that selenocysteyl-tRNAs are present in all five life kingdoms strongly suggests that UGA, in addition to dictating the cessation of protein synthesis, also codes for selenocysteine in the universal genetic code.

Genetic code and phylogenetic origin of oomycetous mitochondria.

We sequenced the 3'-terminal part of the COX3 gene encoding cytochrome c oxidase subunit 3 from mitochondria of Phytophthora parasitica (phylum Oomycota, kingdom Protoctista). Comparison of the sequence with known COX3 genes revealed that UGG is used as a tryptophan codon in contrast to UGA in the mitochondrial codes of most organisms other than green plants. A very high AT mutation pressure operates on the mitochondrial genome of Phytophthora, as revealed by codon usage and by A+T content of noncoding regions, which seems paradoxical because AT pressure causes tryptophan codon reassignment from UGG to UGA in mitochondria of most species. The genetic code and other data suggest that mitochondria of Oomycota share a direct common ancestor with mitochondria of plants and that mitochondria of the ancestor of Planta and Oomycota were acquired in a second endosymbiotic event, which occurred later than the acquisition of mitochondria by other eukaryotes.

Protoctists and polyphyly: comment on ‘The number of symbiotic… by T. Cavalier-Smith’

Protoctists and polyphyly: comment on ‘The number of symbiotic… by T. Cavalier-Smith’

The diversity and ecological significance of Protozoa

The unicellular eukaryotes are currently grouped in the kingdom Protista, together with their multicellular relatives. The inclusion of protozoa, algae and water moulds in a single taxon has resulted in nomenclatural problems, academic homelessness, and a reduction in their teaching. There are around 40 000 described protozoan protist species. Protozoa are principally grazers of bacteria, increasing mineralization and making nutrients more available to other organisms; most are aquatic, but they are also widespread animal parasites and symbionts. Their biomass, role in food chains, roles as mutualists and pathogens, and value as biomonitors are reviewed. To assess the role of protozoa in ecosystems more accurately, the current poor taxonomic standards in ecological work on protozoa must be improved. The manpower to respond to existing and new challenges in the field is declining as protozoology disappears from university courses and this problem needs to be addressed.

Should there be a separate code of nomenclature for the protists?

The present Botanical and Zoological Codes of Nomenclature are often inadequate for resolution of all the peculiar problems caused by the very nature of the numerous and diverse groups of the so-called ‘lower’ eukaryotic organisms known as protists. Whether or not a separate code should therefore be created for these species — many but not all of which are unicellular in structure and microscopic in size — is complicated by several factors. The principal one is related to the wide dispersal of protists throughout many taxonomic classes and phyla/divisions; sometimes even multiple kingdoms are involved. If recognition of a single kingdom Protista is no longer tenable, then even the concept of one code per kingdom is not applicable. Other difficulties arise primarily from long-standing differences in major provisions of present Botanical and Zoological Codes. Numerous ‘ambiregnal’ forms exist, species currently under dual code jurisdiction. The matter of names for suprafamilial taxa of protists, irrespective of their ultimate kingdom assignment, poses another set of concerns not yet resolved. A plea is made to recognize the legitimacy of having distinct high-level ranks for protist species that seem to be widely separated phylogenetically from fellow protists or from other eukaryotic assembleges.

The puzzle of protist organelles

The puzzle of protist organelles

Epulopiscium fishelsoni N. G., N. Sp., a Protist of Uncertain Taxonomic Affinities from the Gut of an Herbivorous Reef Fish1

ABSTRACTEpulopiscium fishelsoni n. g., n. sp., is described from the gut of Acanthurus nigrofuscus, an herbivorous surgeonfish (Acanthuridae: Teleostei) from the Red Sea, Israel. The symbiont is placed in the kingdom Protoctista (or Protista) but more specific taxonomic assignment is impossible at this time. The organism is of an elongate oval shape, round in cross‐section, and highly mobile, with the ability to reverse direction rapidly. It lacks a mouth or other external structures, with the exception of fine surface filaments of an undetermined nature. Internally, there is a complex of folded membranes or tubules and a nucleus. No other organelles are evident. Reproduction is characterized by doubling of nuclei within the parental cell and emergence of daughter cells from a perforation in the parental cortex. Symbionts appear to exhibit circadian cycles of growth, reproductive activity, and movement within the gut. Although the organism greatly reduces local gut pH when present in large numbers, we know nothing of interactions between host and symbiont.

Discocelis saleuta gen. nov. et sp. nov. (Protista incertae sedis) : — A new heterotrophic marine flagellate

The colourless flagellate Discocelis saleuta, a new genus from marine sediments, has been studied by light microscopy and single-cell sectioning for electron microscopy. The cell is discshaped and possesses an anterior velum and two anteriorly inserted unequal flagella. The cell body periphery and the velum are supported by ribbons of microtubules. Three flagellar roots, each of which comprises relatively few microtubules, arise from the flagellar basal bodies. Two of these roots run posteriorly under the ventral cell membrane, whereas the third root mainly runs along the posterior edge of the velum. The cell is further characterized by a microbody-like paranuclear organelle, and by a row of extrusomes bordering the cell periphery. Mitochondria have short tubular cristae. This minute flagellate adheres tightly to sand grains. The ultrastructure is unlike that of any well circumscribed higher order taxon, and the new genus is consequently placed incertae sedis in the kingdom Protista.

The hemimastigophora ( Hemimastix amphikineta nov. gen., nov. spec.), a new protistan phylum from gondwanian soils

The morphology, morphogenesis and ultrastructure of Hemimastix amphikineta nov. gen., nov. spec, are described. This species occurred in some Australian and in 1 Chilean soil, but was absent from more than 1000 soil samples from Laurasian localities. Thus, it has probably a restricted Gondwanian distribution. Hemimastix amphikineta is a small (14-20 × 7-10 μn), colourless organism that looks distinctly Ciliophora-like because of its posteriorly located contractile vacuole and its 2 longitudinal somatic kineties each composed of about 12 cilia-like flagella. These 2 kineties are interposed between 2 large plicated and microtubule-bearing pellicular plates which are arranged inversely mirror-image like ("diagonal symmetry"). Hemimastix amphikineta has saccular to tubular mitochondrial cristae and complex extrusomes. It has 2 microtubular systems and a membranous sac associated with each kinetid. The nucleolus persists throughout nuclear division. A permanent cytostome-cytopharyngeal complex, pharyngeal rods, striated fibres, mastigonemes, and a paraflagellar rod are absent. This unique combination of characters dictates a very separate position for H. amphikineta within the known protists. Thus, the phylum Hemimastigophora nov. phylum (Hemimastigea nov. cl. and Hemimastigida nov. ord.), is established to include H. amphikineta and possibly Spironema multiciliatum Klebs, 1892. The structure of the pellicle and the nuclear apparatus of H. amphikineta indicate some relationship with the Euglenophyta. However, clear evidence for a certain affinity is lacking. Thus, the Hemimastigophora are placed in an incertae sedis position within the kingdom Protista Haeckel, 1866.

Advances in studies on phylogeny and evolution of protists

J. O. Corliss explained that the original title given to the Workshop (namely, the phylogeny and evolution of the protozoa) seemed out of date, since today we clearly cannot persist in separating various protozoa from many of the algae and from certain zoosporic fungi by erection of formidable taxonomic barriers at the phylum (division) or kingdom level. All such forms, the species of which are being discovered to be inextricably comingled at various levels (for the latest extensive review, see Corliss, 1984), are perhaps better assigned to a single kingdom Protista or to several kingdoms predominantly containing these ‘lower’ eukaryotes (see subsequent sections of this report, below).

Concept, Definition, Prevalence, and Host‐Interactions of Xenosomes (Cytoplasmic and Nuclear Endosymbionts)1,2

ABSTRACT.In this paper the concept of “xenosome” is greatly expanded from its current usage, which has been based on its application during the past 10 years by Soldo and co‐workers solely to certain bacterial invaders of the cytoplasm in species of a single genus of marine scuticociliales. The author proposes that the term now be considered to embrace all DNA‐containing, membrane‐bounded bodies or organelles—prokaryotic or eukaryotic in original nature—found within the cytoplasm or nucleus of eukaryotic cells of any or all kinds, whether the occupation (“colonization”) is temporary and transient or permanent and stable. Thus, virulent or pathogenically infectious organisms can be included as well as the commonly recognized cell endosymbionts sensu stricto, which are often mutualistic in nature. Of significance, such “normal” cell organelles as plastids, mitochondria, and even nuclei may also be embraced by this expanded definition of xenosome, based on the conjecture that these inclusions might have been “alien” or “foreign” extracellular, independent, free‐living organisms in their own past evolutionary histories. The author's enlarged concept and unifying principle allows more meaningful comparative consideration of the numerous and diverse kinds of xenosome‐host interrelationships, many of which involve species of protozoa and algae from a large number of the taxonomic groups comprising the kingdom Protista.

The kingdom PROTISTA and its 45 phyla

Because most recent treatments of the protists (‘lower’ eukaryotes comprising the kingdom PROTISTA Haeckel, 1866) have been preoccupied with either a ‘phylogenetic-tree’ approach or a discussion of the impact of possible endosymbiotic origins of major intracellular organelles, the overall systematics of the group, from taxonomic and nomenclatural points of view, has been almost totally neglected. As a result, confusion over contained phyla, their places in a classification scheme, and even their names (and authorships) is growing; the situation could become chaotic. The principal objective of the present paper is to recognize the taxonomic interrelationships among all protist groups; and it includes the specific proposal that some 45 phyla, defined and characterized, be assigned to 18 supraphyletic assemblages within the kingdom PROTISTA (itself redefined and contrasted with the other eukaryotic kingdoms recognized here: ANIMALIA, PLANTAE and FUNGI). Vernacular terms are employed for identification of the 18 assemblages, but defensible formal names are proposed at the level of phylum. None is presented as new: authorship-and-date credits are given to preceding workers on the taxonomy of the many groups involved. By presenting taxonomic characterizations as well as relevant nomenclatural data for each taxon described, a comprehensive scheme of overall higher-level classification within the kingdom emerges that may be considered to serve as a solid base or ‘taking-off point’ for future discussions. The 18 supraphyletic groups and their phyla (in parentheses and including authorships and dates of their formal names) are as follows: I. The rhizopods (phyla Karyoblastea Margulis, 1974; Amoebozoa Lühe, 1913; Acrasia Van Tieghem, 1880; Eumycetozoa Zopf, 1885; Plasmodiophorea Zopf, 1885; Granuloreticulosa De Saedeleer, 1934; incertae sedis Xenophyophora Schulze, 1904). II. The mastigomycetes ( Hypochytridiomycota Sparrow, 1959; Oomycota Winter, 1897; incert. sed. Chytridiomycota Sparrow, 1959). III. The chlorobionts ( Chlorophyta Pascher, 1914; Prasinophyta Christensen, 1962; Conjugatophyta Engler, 1892; Charophyta Rabenhorst, 1863; incert. sed. Glaucophyta Bohlin, 1901). IV. The euglenozoa ( Euglenophyta Pascher, 1931; Kinetoplastidea Honigberg, 1963; incert. sed. Pseudociliata Corliss & Lipscomb, 1982). V. The rhodophytes ( Rhodophyta Rabenhorst, 1863). VI. The cryptomonads ( Cryptophyta Pascher, 1914). VII. The choanoflagellates ( Choanoflagellata Kent, 1880). VIII. The chromobionts ( Chrysophyta Pascher, 1914; Haptophyta Christensen, 1962; Bacillariophyta Engler & Gild, 1924; Xanthophyta Allorge in Fritsch, 1935; Eustigmatophyta Hibberd & Leedale, 1970; Phaeophyta Kjellman, 1891; incert. sed. Proteromonadea Grassé in Grassé, 1952). IX. The labyrinthomorphs ( Labyrinthulea Cienkowski, 1867; Thraustochytriacea Sparrow, 1943 [possibly infraphyletic rank?]). X The polymastigotes ( Metamonadea Grassé in Grassé, 1952; Parabasalia Honigberg, 1973). XI. The paraflagellates ( Opalinata Wenyon, 1926). XII. The actinopods ( Heliozoa Haeckel, 1866; Taxopoda Fol, 1883; Acantharia Haeckel, 1879; Polycystina Ehrenberg, 1839; Phaeodaria Haeckel, 1879). XIII. The dinoflagellates ( Peridinea Ehrenberg, 1830; Syndinea Chatton, 1920). XIV. The ciliates ( Ciliophora Doflein, 1901). XV. The sporozoa ( Sporozoa Leuckart, 1879). XVI. The microsporidia ( Microsporidia Balbiani, 1882). XVII. The haplosporidia ( Haplosporidia Caullery & Mesnil, 1899). XVIII. The myxosporidia ( Myxosporidia Bütschli, 1881; incert. sed. Actinomyxidea Štolc, 1899 [perhaps not separate phylum?]).

Descriptions of Acrasid Cellular Slime Molds: Pocheina Rosea and a New Species, Pocheina Flagellata

Numerous collections of the orange-colored Pocheina have been obtained in North Carolina and other areas of the United States, and in Australia and England. All but one were found on bark of live gymnosperm and frondose trees. A single collection from a dead Juniperus virginiana tree most closely resembles the type collection of P. rosea. Further studies may reveal that the majority of our collections of P. rosea represent a new variety. The new species, P. flagellata, found on the bark of live gymnosperm trees in Wisconsin and North Carolina, has sorocarps that resemble those of our common P. rosea collections but differs in having flagellate cells, spores with more abundant punctations, and nuclei that, during mitosis, lack divided nucleolar parts at the polar areas, which are present in the mitotic nuclei of P. rosea. Pocheina and Acrasis are considered related genera that are unrelated to other acrasid cellular slime molds. As previously noted by Loeblich and Tappan (1961), Guttulina Cienkowsky (1873), a cellular slime mold genus, was antedated by Guttulina d'Orbigny, a foraminiferan genus. Since we have considered both groups of organisms as members of the Kingdom Protista, reclassification of the cellular slime mold genus as Pocheina Loeblich & Tappan and the single known species as P. rosea (Cienk.) Loeblich & Tappan was accepted but retained in the Class Acrasea, Subphylum Mycetozoa, and Phylum Gymnomyxa of the Kingdom Protista (Olive, 1975). At the same time, the acrasid and dictyostelid cellular slime molds were classified separately because of a number of major differences among them. Also, as will be indicated later, Pocheina appears to be related to the genus Acrasis but to no other genus of cellular slime molds presently known. Cienkowsky discovered his cellular slime mold on dead wood containing lichens in a part of Russia that is now Poland, and he described the rose-colored sorocarp as having a round mass of spores at the top of a stalk composed of rows of wedge-shaped cells. In the presence of water the sorocarp cells germinated, yielding amoebae with lobose pseudopodia. The organism was not discovered and described again until it was found on bark of a live cypress tree sent to K. B. Raper from the Netherlands by Nannenga-Bremekamp. Raper (1973) found it to be very similar to the one described by Cienkowsky, although the spores failed to germinate. Our numerous collections of Pocheina in the past several years have turned out to comprise more than a single species. In the following discussion, we will describe what may be two varieties of P. rosea and a new species of the genus. Both species have been grown in culture.

A Puddle of Protists

A Puddle of Protists

Consequences of Creating New Kingdoms of Organisms

Numerous taxonomic-nomenclatural problems arise when more than two kingdoms of eukaryotic organisms are recognized. The current international codes of botanical and zoological nomenclature are inadequate, especially for a kingdom Protista that embraces many groups of species conventionally considered (“mini”) plants or animals, but which definitely are not. Should the two codes be modified, united, or replaced by separate ones for every major kingdom proposed and accepted? Another problem discussed is the (unnecessary) proliferation of new names for redefined or reshuffled high-level taxa.

The paleobiology of plant protists

The paleobiology of plant protists

What are the taxonomic and evolutionary relationships of the protozoa to the protista?

In order to consider the problems of protist-protozoan interrelationships in proper perspective, a new “packaging” of phyla within the great kingdom Protista is proposed. Although it is based largely on historical groupings and is admittedly “unnatural” (nor are taxonomic names proposed for my five supraphyletic groupings), the arrangement may clarify some long-persisting problems, especially with regard to mixed algal-protozoan groups and/or phylogenies. Some three dozen phyla are recognized as comprising the kingdom, with the number that might be considered as “protozoan” ranging from 10 to 25, depending on one's viewpoint. No taxon should have the normal name “Protozoa”, “Phytoflagellate” and “zooflagellate” are also misleading categories. Taxonomic and evolutionary relationships of phyla containing protozoa (with small “p”) are inextricably intermeshed with those of other protist phyla, and thus no unified protozoan super-group exists.

Protist classification and the kingdoms of organisms

Traditional classification imposed a division into plant-like and animal-like forms on the unicellular eukaryotes, or protists; in a current view the protists are a diverse assemblage of plant-, animal- and fungus-like groups. Classification of these into phyla is difficult because of their relatively simple structure and limited geological record, but study of ultrastructure and other characteristics is providing new insight on protist classification. Possible classifications are discussed, and a summary classification of the living world into kingdoms (Monera, Protista, Fungi, Animalia, Plantae) and phyla is suggested. This classification also suggests groupings of phyla into superphyla and form-superphyla, and a broadened kingdom Protista (including green algae, oomycotes and slime molds but excluding red and brown algae). The classification thus seeks to offer a compromise between the protist and protoctist kingdoms of Whittaker and Margulis and to combine a full listing of phyla with grouping of these for synoptic treatment.

Genetic Data. (Book Reviews: Handbook of Genetics. Vol. 1, Bacteria, Bacteriophages, and Fungi; Handbook of Genetics. Vol. 2, Plants, Plant Viruses, and Protists)

Genetic Data. (Book Reviews: Handbook of Genetics. Vol. 1, Bacteria, Bacteriophages, and Fungi; Handbook of Genetics. Vol. 2, Plants, Plant Viruses, and Protists)

TIME FOR EVOLUTIONARY BIOLOGISTS TO TAKE MORE INTEREST IN PROTOZOAN PHYLOGENETICS?

SummaryStudies on the evolution and phylogeny of various groups of the Protozoa, a major taxon or portion of the eukaryotic kingdom Protista, have been proceeding apace, particularly in recent years, although they appear to have attracted little attention to date among students of evolutionary biology in general. In searching for the reasons for this apparent fact the “shortcomings” of the protozoa themselves, as objects of phylogenetic investigation, may be held responsible. Such difficulties are discussed under six broad headings: the very nature of the Protozoa (microscopic size, unicellularity, common absence of sexuality, ubiquity), the frequent lack of fossil material, the paucity of described species, the scarcity of morphological features, the even greater rareness of non‐morphological characteristics usable in comparative study, and the unevenness in both our specific and general knowledge of these microorganisms. At the same time, new approaches and recent research in progress mitigate the awesomeness of these challenges to a degree which should allow us to recognize that such work is not being carried out entirely in vain. Many examples, often from the ciliate literature, are cited in illustration of points made. If protozoologists interested in phylogenetic problems can more successfully avoid the pitfalls inherent in their research, apply approaches broader in nature yet technically as sophisticated as possible, take into account constructive criticism, whether from insiders or outsiders, and learn from the experiences of other evolutionary biologists, they and their works will then be predictably deserving of considerably wider respect and recognition than apparently they are presently accorded.