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

Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora

"Kingdom-level" branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down.1,2,3,4 Some are completely new discoveries, whereas others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19th century but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted.2Meteora sporadica5 is a protist with a unique morphology; cells glide over substrates along a long axis of anterior and posterior projections while a pair of lateral "arms" swing back and forth, a motility system without any obvious parallels. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved.6 Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that both the anterior-posterior projections and the arms are supported by microtubules originating from a cluster of subnuclear microtubule organizing centers (MTOCs). Neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be among the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse "supergroup" and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.

Ciliary transition zone evolution and the root of the eukaryote tree: implications for opisthokont origin and classification of kingdoms Protozoa, Plantae, and Fungi

I thoroughly discuss ciliary transition zone (TZ) evolution, highlighting many overlooked evolutionarily significant ultrastructural details. I establish fundamental principles of TZ ultrastructure and evolution throughout eukaryotes, inferring unrecognised ancestral TZ patterns for Fungi, opisthokonts, and Corticata (i.e., kingdoms Plantae and Chromista). Typical TZs have a dense transitional plate (TP), with a previously overlooked complex lattice as skeleton. I show most eukaryotes have centriole/TZ junction acorn-V filaments (whose ancestral function was arguably supporting central pair microtubule-nucleating sites; I discuss their role in centriole growth). Uniquely simple malawimonad TZs (without TP, simpler acorn) pinpoint the eukaryote tree's root between them and TP-bearers, highlighting novel superclades. I integrate TZ/ciliary evolution with the best multiprotein trees, naming newly recognised major eukaryote clades and revise megaclassification of basal kingdom Protozoa. Recent discovery of non-photosynthetic phagotrophic flagellates with genome-free plastids (Rhodelphis), the sister group to phylum Rhodophyta (red algae), illuminates plant and chromist early evolution. I show previously overlooked marked similarities in cell ultrastructure between Rhodelphis and Picomonas, formerly considered an early diverging chromist. In both a nonagonal tube lies between their TP and an annular septum surrounding their 9+2 ciliary axoneme. Mitochondrial dense condensations and mitochondrion-linked smooth endomembrane cytoplasmic partitioning cisternae further support grouping Picomonadea and Rhodelphea as new plant phylum Pararhoda. As Pararhoda/Rhodophyta form a robust clade on site-heterogeneous multiprotein trees, I group Pararhoda and Rhodophyta as new infrakingdom Rhodaria of Plantae within subkingdom Biliphyta, which also includes Glaucophyta with fundamentally similar TZ, uniquely in eukaryotes. I explain how biliphyte TZs generated viridiplant stellate-structures.

The New Tree of Eukaryotes

For 15 years, the eukaryote Tree of Life (eToL) has been divided into five to eight major groupings, known as 'supergroups'. However, the tree has been profoundly rearranged during this time. The new eToL results from the widespread application of phylogenomics and numerous discoveries of major lineages of eukaryotes, mostly free-living heterotrophic protists. The evidence that supports the tree has transitioned from a synthesis of molecular phylogenetics and biological characters to purely molecular phylogenetics. Most current supergroups lack defining morphological or cell-biological characteristics, making the supergroup label even more arbitrary than before. Going forward, the combination of traditional culturing with maturing culture-free approaches and phylogenomics should accelerate the process of completing and resolving the eToL at its deepest levels.

Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes

Almost all eukaryote life forms have now been placed within one of five to eight supra-kingdom-level groups using molecular phylogenetics^1-4. The 'phylum' Hemimastigophora is probably the most distinctive morphologically defined lineage that still awaits such a phylogenetic assignment. First observed in the nineteenth century, hemimastigotes are free-living predatory protists with two rows of flagella and a unique cell architecture^5-7; to our knowledge, no molecular sequence data or cultures are currently available for this group. Here we report phylogenomic analyses based on high-coverage, cultivation-independent transcriptomics that place Hemimastigophora outside of all established eukaryote supergroups. They instead comprise an independent supra-kingdom-level lineage that most likely forms a sister clade to the 'Diaphoretickes' half of eukaryote diversity (that is, the 'stramenopiles, alveolates and Rhizaria' supergroup (Sar), Archaeplastida and Cryptista, as well as other major groups). The previous ranking of Hemimastigophora as a phylum understates the evolutionary distinctiveness of this group, which has considerable importance for investigations into the deep-level evolutionary history of eukaryotic life-ranging from understanding the origins of fundamental cell systems to placing the root of the tree. We have also established the first culture of a hemimastigote (Hemimastix kukwesjijk sp. nov.), which will facilitate future genomic and cell-biological investigations into eukaryote evolution and the last eukaryotic common ancestor.

Fine structure of Telonema subtilis Griessmann, 1913: a flagellate with a unique cytoskeletal structure among eukaryotes

Telonema is a genus of heterotrophic flagellates with two flagella that occurs in marine environments. Although some aspects of the morphology and ultrastructure of Telonema have been reported in previous studies, several characters have been described incompletely or not at all. In the present study, we identify and describe several of these characteristics, such as extrusomes, telonemosome, adhesive fibers and the intricate cytoskeleton structure of T. subtilis using serial ultra-thin sections in transmission electron-microscopy. The extrusomes are scattered throughout the cell. Their structure in transverse section is similar to those of several monadofilosan cercozoa, but are distinguished by a longitudinal element. The telonemosome is an enigmatic organelle surrounded by a single membrane. It contains many thin tubular structures and resembles the K-bodies found in oomycetes. The complex cytoskeletal structure is multilayered and unique among eukaryotes, although the posterior half resembles the penetrating/feeding apparatus found in apicomplexans, protoalveolates and kathablepharids. The proposed function and distribution pattern of the adhesive fibers in Telonema resemble those of the fibrous structures of Microheliella maris (Heliozoa). Our observations provide a more complete understanding of the characteristics of Telonema and support the conclusion from molecular studies that Telonema is a lineage without a clear sister group among the eukaryotes.

Rigifila ramosa n. gen., n. sp., a filose apusozoan with a distinctive pellicle, is related to Micronuclearia

We report the ultrastructure, 18S and 28S rDNA sequences, and phylogenetic position of a distinctive free-living heterotrophic filose protist, Rigifila ramosa n. gen., n. sp., from a freshwater paddyfield. Rigifila lacks cilia and has a semi-rigid, radially symmetric, well-rounded, partially microtubule-supported, dorsal pellicle, and flat mitochodrial cristae. From a central aperture in a ventral depression emerges a protoplasmic stem that branches into several branching filopodia that draw bacteria to it. Electron microscopy reveals a general cell structure similar to Micronuclearia, the only non-flagellate previously known in Apusozoa; the large basal vacuole is probably an unusual giant contractile vacuole. Phylogenetic analysis of concatenated rDNA sequences groups Rigifila and Micronuclearia as sisters with maximal statistical support. However, novel morphological differences unique to Rigifila, notably a double (not single) proteinaceous layer beneath the cell membrane, and cortical microtubules, lead us to place it in a new family Rigifilidae. Our morphological and molecular analyses show that Rigifila is the closest known relative of Micronuclearia. Therefore we group Micronucleariidae and Rigifilidae as a new order Rigifilida within the existing class Hilomonadea, which now excludes planomonads. Rigifilida groups weakly with Collodictyon (Diphyllatea). We discuss the possible relationships of Rigifilida to other Apusozoa and Diphyllatea.

A cytological study of Aulacomonas submarina Skuja 1939, a heterotrophic flagellate with a novel ultrastructural identity

Aulacomonas submarina is a free-living freshwater heterotrophic flagellate, the ultrastructure of which is described here. It has two long, nearly equal flagella that insert apically and beat asynchronously. It engulfs prey as large as itself via a ventral groove. The nucleus is anterior and surrounded by several dictyosomes. The two flagella are similar in structure. The most external part of the transition zone is marked by a constriction of the membrane, and distal to this the periaxonemal space expands for a short distance. The two basal bodies are inclined to each other and connected by roots, in a style reminiscent of some heterokont organisms. The basal body of the dorsal flagellum (Fl) is connected to a dorsal cytoskeletal root that is comprised of 5 superimposed microtubules and which sweeps from right to left in an incomplete loop near the cell apex. This loop is reinforced near its origin by an electron-dense rootlet. Material associated with the dorsal root gives rise to cortical microtubules which form a cape covering the apical region of the cell. The ventral basal body (of flagellum F2) is connected to two microtubular and microfibrillar fibres which support the lips of the ventral groove. More distally the lips of the groove are bordered only by a ridge supported by microfibrillar material. Mitochondria have bleb-shaped tubular cristae similar to those of actinophryid heliozoa. There is no cyst. The shape of the mitochondrial cristae, and the arrangement of basal bodies suggest that this genus is distantly related to the heterokont flagellates. However, most aspects of the ultrastructure are unlike those of other flagellates, such that Aulacomonas cannot be assigned to any familiar subgroup of heterokont organisms or other group of flagellates.

Eukaryotic systematics: a user's guide for cell biologists and parasitologists

Single-celled parasites like Entamoeba, Trypanosoma, Phytophthora and Plasmodium wreak untold havoc on human habitat and health. Understanding the position of the various protistan pathogens in the larger context of eukaryotic diversity informs our study of how these parasites operate on a cellular level, as well as how they have evolved. Here, we review the literature that has brought our understanding of eukaryotic relationships from an idea of parasites as primitive cells to a crystallized view of diversity that encompasses 6 major divisions, or supergroups, of eukaryotes. We provide an updated taxonomic scheme (for 2011), based on extensive genomic, ultrastructural and phylogenetic evidence, with three differing levels of taxonomic detail for ease of referencing and accessibility (see supplementary material at Cambridge Journals On-line). Two of the most pressing issues in cellular evolution, the root of the eukaryotic tree and the evolution of photosynthesis in complex algae, are also discussed along with ideas about what the new generation of genome sequencing technologies may contribute to the field of eukaryotic systematics. We hope that, armed with this user's guide, cell biologists and parasitologists will be encouraged about taking an increasingly evolutionary point of view in the battle against parasites representing real dangers to our livelihoods and lives.

Ultrastructure and molecular phylogeny of Calkinsia aureus: cellular identity of a novel clade of deep-sea euglenozoans with epibiotic bacteria

Background

The Euglenozoa is a large group of eukaryotic flagellates with diverse modes of nutrition. The group consists of three main subclades – euglenids, kinetoplastids and diplonemids – that have been confirmed with both molecular phylogenetic analyses and a combination of shared ultrastructural characteristics. Several poorly understood lineages of putative euglenozoans live in anoxic environments, such as Calkinsia aureus, and have yet to be characterized at the molecular and ultrastructural levels. Improved understanding of these lineages is expected to shed considerable light onto the ultrastructure of prokaryote-eukaryote symbioses and the associated cellular innovations found within the Euglenozoa and beyond.

Results

We collected Calkinsia aureus from core samples taken from the low-oxygen seafloor of the Santa Barbara Basin (580 – 592 m depth), California. These biflagellates were distinctively orange in color and covered with a dense array of elongated epibiotic bacteria. Serial TEM sections through individually prepared cells demonstrated that C. aureus shares derived ultrastructural features with other members of the Euglenozoa (e.g. the same paraxonemal rods, microtubular root system and extrusomes). However, C. aureus also possessed several novel ultrastructural systems, such as modified mitochondria (i.e. hydrogenosome-like), an "extrusomal pocket", a highly organized extracellular matrix beneath epibiotic bacteria and a complex flagellar transition zone. Molecular phylogenies inferred from SSU rDNA sequences demonstrated that C. aureus grouped strongly within the Euglenozoa and with several environmental sequences taken from low-oxygen sediments in various locations around the world.

Conclusion

Calkinsia aureus possesses all of the synapomorphies for the Euglenozoa, but lacks traits that are specific to any of the three previously recognized euglenozoan subgroups. Molecular phylogenetic analyses of C. aureus demonstrate that this lineage is a member of a novel euglenozoan subclade consisting of uncharacterized cells living in low-oxygen environments. Our ultrastructural description of C. aureus establishes the cellular identity of a fourth group of euglenozoans, referred to as the "Symbiontida".

Why the World Needs Protists!1

In this brief review, literature references are given to researches--involving diverse species of protists--that support the author's firm conviction that the biological world of today absolutely requires the presence of numerous of these generally small and unicelled organisms if it is to survive. Examples supplied come from areas within the field of protistology sensu lato as widely separated as basic phycological research on photosynthesis and protozoological/medical/biomedical investigations on malaria and other pathogens of human beings. Emphasis is primarily on the most relevant works of the past 10-15 years, although historically highly significant papers of older vintage require at least indirect--and occasionally direct--citation.

The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists

We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium "Thiodendron latens." By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This "earliest branching protist" that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa.

Somatic kinetics or paroral membrane: which came first in ciliate evolution?

The ciliate species which lack a distinctive oral ciliature are considered to represent an ancestral state in ciliate evolution. Consequently, the somatic kineties composed of kinetids (kinetosomes plus cilia and associated fibrillar systems) are thought to be the ancestral ciliature. Results on stomatogenesis in 'gymnostomial ciliates' have shown that these ciliates probably have evolved from ancestors already equipped with an oral ciliature. Thus instead of the somatic, the oral ciliature may be regarded an ancestral. Based on these ideas a hypothesis on the evolution of the ciliate kinetome (assembly of all kinetids covering the body of a given ciliate) is presented. The first step in the evolution of the kinetome was the formation of a paroral membrane, a compound ciliary organelle lying along the right side of the oral area which historically but falsely is termed membrane. It was composed of kinetosomal dyads (dikinetids), derived from the kinetid of a dinoflagellate-like ancestor. From the beginning the paroral membrane was responsible for locomotion, ingestion and for the formation of a cytopharyngeal tube which the first ciliate probably had inherited from its flagellate ancestor. In the second step a first somatic kinety was formed from the right row of kinetosomes of the paroral membrane as a result of a longitudinal splitting of the paroral membrane and a subsequent migration of the forming kinety to the right into the somatic cortex. To increase the number of somatic kineties this process was repeated until the kinety produced first reached the left border of the oral area. By this step the locomotive and the nutritional functions were differentiated between somatic and oral structures. In a third step the adoral organelles were formed from somatic kinetids left of the oral area. The primitive type of stomatogenesis was a buccokinetal one derived from the mode the flagellate ancestor used to distribute its replicated kinetosomes to the offspring cells (buccokinetal means that at least parts of the oral anlage for the posterior offspring cell has its origin in the parental oral apparatus). This hypothesis, based on comparative studies on ciliate morphogenesis, is corroborated by molecular data from other laboratories.

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 assemblages.