Higher-Order Phylogeny of Plasmodial Slime Molds (Myxogastria) Based on Elongation Factor 1-A and Small Subunit rRNA Gene Sequences

The Systematics and Phylogeny of Myxomycetes: Yesterday, Today, and Tomorrow

Abstract-Myxomycetes are amoeboid fungus-like organisms (Amoebozoa) with a unique life cycle characterized by a great morphological diversity of fruiting bodies. Due to the similarity of these structures to the fruiting bodies of some representatives of Ascomycota and Basidiomycota, myxomycetes have been classified as fungi since the first known scientific description in 1654. Only in the 19th century, when their life cycle was studied, did the difference of this group from fungi become clear. During the same period, microscopic structures of fruiting bodies, as well as ornamentation of the spore surface, began to be considered as diagnostic features. Due to this, in the period from the end of the 19th to the middle of the 20th century, a rather stable system was formed. However, as further studies have shown, both macro- and micromorphological characters are often quite variable, depend on environmental conditions, and often result from convergent evolution, which causes difficulties in defining species and taxonomic units of higher ranks. Since the first decade of the 21st century, due to the development of molecular genetic methods and the accumulation of data on nucleotide sequences of marker genes together with the improvement of microscopic studies, it has been possible to obtain data on the evolutionary relationships of different groups of myxomycetes. A milestone in this process was the publication of the first phylogenetic system of myxomycetes in 2019. This work was the starting point for a number of studies on the relationships between different groups of myxomycetes at a lower taxonomic level. Thus, there has been a surge in the number of studies that bring us closer to constructing a natural system.

Two New Species of the Genus Diderma (Physarales, Didymiaceae) in China with an Addition to the Distribution

Myxomycetes are an important component of terrestrial ecosystems, and in order to understand their diversity and phylogenetic relationships, taxonomic issues need to be addressed. In our 1985-2021 biodiversity investigations in Shaanxi Province, Jilin Province, the Inner Mongolia Autonomous Region, Hubei Province, and Henan Province, China, Diderma samples were observed on rotten leaves, rotten branches, and dead wood. The samples were studied, based on morphological features coupled with multigene phylogenetic analyses of nSSU, EF-1α, and COI sequence data, which revealed two new species (Diderma shaanxiense sp. nov. and D. clavatocolumellum sp. nov.) and two known species (D. radiatum and D. globosum). In addition, D. radiatum and D. globosum were newly recorded in Henan Province and the Inner Mongolia Autonomous Region, respectively. The paper includes comprehensive descriptions, detailed micrographs, and the outcomes of phylogenetic analyses for both the newly discovered and known species. Additionally, it offers morpho-logical comparisons between the new species and similar ones.

Thin film structural color is widespread in slime molds (Myxomycetes, Amoebozoa)

Brilliant colors in nature arise from the interference of light with periodic nanostructures resulting in structural color. While such biological photonic structures have long attracted interest in insects and plants, they are little known in other groups of organisms. Unexpected in the kingdom of Amoebozoa, which assembles unicellular organisms, structural colors were observed in myxomycetes, an evolutionary group of amoebae forming macroscopic, fungal-like structures. Previous work related the sparkling appearance of Diachea leucopodia to thin film interference. Using optical and ultrastructural characterization, we here investigated the occurrence of structural color across 22 species representing two major evolutionary clades of myxomycetes including 14 genera. All investigated species showed thin film interference at the peridium, producing colors with hues distributed throughout the visible range that were altered by pigmentary absorption. A white reflective layer of densely packed calcium-rich shells is observed in a compound peridium in Metatrichia vesparium, whose formation and function are still unknown. These results raise interesting questions on the biological relevance of thin film structural colors in myxomycetes, suggesting they may be a by-product of their reproductive cycle.

Genome size and GC content of myxomycetes

More than 1272 myxomycetes species have been described, accounting for more than half of all Amoebozoa species. However, the genome size of only three myxomycetes species has been reported. Therefore, we used flow cytometry to present an extensive survey and a phylogeny-based analysis of genome size and GC content evolution in 144 myxomycetes species. The genome size of myxomycetes ranged from 18.7 Mb to 470.3 Mb, and the GC content ranged from 38.7% to 70.1%. Bright-spored clade showed larger genome sizes and more intra-order genome size variations than the dark-spored clade. GC content and genome size were positively correlated in both bright-spored and dark-spored clades, and spore size was positively correlated with genome size and GC content in the bright-spored clade. We provided the first genome size data set in Myxomycetes, and our results will provide helpful information for future Myxomycetes studies, such as genome sequencing.

Dehydration and self-cell cleaning by a single cell drives the formation of fruiting body of Lamproderma columbinum (Myxomycetes)

The noncellular complex structures of fruiting body produced by a multinucleate large plasmodium are the distinct character of Myxomycetes. Although the fruiting body distinguishes myxomycetes from other amoeboid single-cell organisms, it is unclear how such complex structures arise out of a single cell. The present study investigated the detailed process of fruiting body formation in Lamproderma columbinum, the type species of the genus Lamproderma, at the cellular level. A single cell excretes cellular waste and excess water during the formation of the fruiting body by controlling its shape, secreted materials, and organelle distribution. These excretion phenomena lead to the morphology of the mature fruiting body. The results of this study suggest that the structures of the L. columbinum fruiting body are involved not merely in spore dispersal but also in the process of dehydration and self-cell cleaning of the single cell for the next generation.

Revisiting the morphology of Lamproderma reveals incongruities among the taxonomic characteristics of higher classifications of Myxomycetes

Despite various attempts during the last few decades to establish a natural system for the Myxomycetes, researchers have not yet reached a consensus. One of the most drastic recent proposals is the movement of the genus Lamproderma, an almost a trans-subclass transfer. The traditional subclasses are not supported by current molecular phylogenies, and various higher classifications have been proposed during the last decade. However, the taxonomic characteristics on which the traditional higher classifications were based have not been reinvestigated. In the present study, the key species involved in this transfer, Lamproderma columbinum (the type species of the genus Lamproderma), was assessed using correlational morphological analysis of stereo, light, and electron microscopic images. Correlational analysis of the plasmodium, fruiting body formation, and the mature fruiting bodies revealed that several concepts of taxonomic characteristics that have been used to distinguish higher classifications are questionable. The results of this study indicate that caution is required when interpreting the evolution of morphological traits in Myxomycetes, as the current concepts are vague. The definitions of the taxonomic characteristics need a detailed research, and attention should be paid to the lifecycle timing of observations, before discussing a natural system for Myxomycetes.

Phylogeny and evolution of morphological structures in a highly diverse lineage of fruiting-body-forming amoebae, order Trichiales (Myxomycetes, Amoebozoa)

Early phylogenetic studies refuted most previous assumptions concerning the evolution of the morphological traits in the fruiting bodies of the order Trichiales and did not detect discernible evolutionary patterns, yet they were based on a limited number of species. We infer a new Trichiales phylogeny based on three independently inherited genetic regions (nuclear and mitochondrial), with a fair taxonomic sampling encompassing its broad diversity. Besides, we study the evolutionary history of some key morphological characters. According to the new phylogeny, most fruiting body traits in Trichiales systematics do not represent exclusive synapomorphies or autapomorphies for most monophyletic groups. Instead, the evolution of the features derived from the peridium, stalk, capillitium, and spores showed intricate patterns, and character state transitions occurred rather within- than between clades. Thus, we should consider other evolutionary scenarios instead of assuming the homology of some characters. According to these results, we propose a new classification of Trichiales, including the creation of a new genus, Gulielmina, the resurrection of the family Dictydiaethaliaceae and the genus Ophiotheca, and the proporsal of 13 new combinations for species of the genera Arcyria (1), Hemitrichia (2), Ophiotheca (2), Oligonema (4), Gulielmina (3), and Perichaena (1).

<i>Lamproderma vietnamense</i>: a new species of myxomycetes with reticulate spores from Phia Oắc - Phia Đén National Park (northern Vietnam) supported by molecular phylogeny and morphological analysis

A new species of Lamproderma (Myxomycetes), described herein as L. vietnamense, was recovered in the field on ground litter from mountain subtropical forests (Phia Oắc - Phia Đén National Park) of northern Vietnam. Morphological details were examined by light and scanning electron microscopy. The species is characterized by a distinct and unique combination of morphological features, including a bright blue, shiny and very thin membranous peridium, a small dome-shaped columella, rigid, straight, branched, brown capillitial threads which gradually become pale at the periphery and finally colorless at the tips and small-meshed, banded-reticulate spores with 9-12 meshes across the spore diameter and solid walls without perforations 0.3-0.5 µm high. The stability of the taxonomic characters of L. vietnamense is supported by two well-developed collections found in 2018 and 2019. Partial sequences of three molecular markers (SSU, EF1α, COI) for both collections are identical. A two-gene phylogeny of the first two markers displays the two known accessions as a well-separated entity and indicates affinity of the new species with L. columbinum (the type taxon of the genus), L. violaceum, and several nivicolous Lamproderma species.

Spore ultrastructural features and significance of their diverse ornamental elements in the evolutionary history of the order Trichiales (Myxomycetes, Amoebozoa)

Spores are the dispersal and reproductive units in Myxomycetes, and their ornamentation, usually at the light microscopy resolution limit, is taxonomically meaningful. Here, we analyze with scanning and transmission electron microscopy the spore ultrastructural features in Trichiales, one of the most morphologically diverse orders. In Trichiales, the spore wall consists of two layers, an outer one, including the ornamentation, and an inner layer subdivided into two sections. The diversity of ornamental elements includes verrucae, bacula, pila, muri, and cristae, the two latter creating reticulate patterns. Each of these elements defines a broadly recognized ornamentation type except cristae, from which we differentiate for the first time the cristate reticulate and patched subtypes. Besides, our results point out a previous incorrect classification of the spores of the species Trichia decipiens and T. scabra. Advances in Trichiales phylogeny showed that the capillitium ornamental elements, such as the spirals, do not reflect phylogenetic relationships among the species. The same seems to apply to some of spore ornamentation types, e.g., baculate. Consequently, we may consider the need to combine multiple characters, like the spore and capillitium ornamentation, so that Trichiales systematics better reflect the still cryptic phylogenetic affinities.

New Approach to the Ultrastructure of the Capillitium in the Order Trichiales (Myxomycetes, Amoebozoa) and its Phylogenetic Implications

Myxomycetes constitute one of the major lineages within the supergroup Amoebozoa. At the end of their life cycles, most myxomycetes produce spore-bearing fruiting bodies, in which additional structures develop, like the capillitium, a system of sterile filaments intermingled with the spores. The capillitium is a relevant structure in the taxonomy of the order Trichiales, the target group in this study. However, the introduction of molecular phylogenies in Myxomycetes systematics is challenging our comprehension of this structure. We studied the capillitium of 25 species representing nine Trichiales genera, with both scanning and transmission electron microscopy. In this order, the capillitium showed higher diversity than so far recognized. Thus, we distinguished and described five capillitium types and two subtypes based on the presence or absence of a lumen and the wall ultrastructure. These types followed the evolutionary history reported in recent phylogenies, although not all of them defined monophyletic groups. Besides, the spiral ornamentation, which most taxonomists considered to have appeared once, occurred in three different capillitium types. The ultrastructural approaches in Myxomycetes systematics enable the reconsideration of their morphological features in the new phylogenetic scenario.

Design of potentially universal SSU primers in myxomycetes using next-generation sequencing

Unlike fungi, which have a universally accepted barcode marker, universal primers still lack in myxomycetes. Typically, DNA barcode primers were designed based on comparing existing myxomycetes sequences and targeting the conserved regions. However, the extreme genetic diversity within major myxomycetes groups and the frequent occurrence of group I introns have made the development of universal DNA barcode a severe challenge. The emergence of next-generation sequencing provides an opportunity to address this problem. We sequenced the mixed genomic DNA of 81 myxomycetes and extracted the SSU gene's reads using next-generation sequencing. After alignment and assembly, we designed a set of SSU primers that matched all potential SNPs, avoided all known group I intron insertion sites, and were highly conserved between major myxomycetes orders. This set of SSU primers has the potential to become one of the universal primer combinations. Due to the high genetic divergence caused by long and complicated evolutionary histories, the lack of universal barcode primers is common in protists. Our research provides a new method to solve this problem.

Nivicolous Trichiales from the austral Andes: unexpected diversity including two new species

Nivicolous myxomycetes are a group of amoebozoan protists dependent on long-lasting snow cover worldwide. Recent fine-scale analysis of species diversity from the austral Andes revealed high intraspecific variability of most taxa, suggesting independent evolutionary processes and significant differences in species compositions between the Northern (NH) and Southern (SH) Hemispheres. The present study is the second part of this analysis based on representatives of Trichiales. A total of 173 South American collections were studied based on morphological and molecular data, and 15 taxa have been identified. Two of them, Hemitrichia crassifila and Perichaena patagonica, are proposed as new species confirmed by a phylogeny of Trichiales. However, their affinity to the genera in which they are proposed are not confirmed due to polyphyletic character of all genera of Trichiales. Four species, Dianema subretisporum, Trichia contorta var. karstenii, T. nivicola, and T. sordida, are reported for the first time from the Southern Hemisphere. One species, T. alpina, is new for Argentina. Additionally, we provide the first record of Perichaena megaspora from Chile. Specimen frequency and species diversity of Trichiales found at nivicolous localities in the austral Andes are unexpectedly high, exceeding those of Stemonitidales, the most numerous group in the Northern Hemisphere, where Trichiales play a marginal role. By contrast, Trichiales appear the main component of nivicolous assemblages in the Andes. Results of the present work, together with the earlier analysis of Stemonitidales, indicate that the Andes constitute an exceptionally important evolutionary hot spot for nivicolous myxomycetes characterized by an outstanding species diversity.

New protocol for successful isolation and amplification of DNA from exiguous fractions of specimens: a tool to overcome the basic obstacle in molecular analyses of myxomycetes

Herbarium collections provide an essential basis for a wide array of biological research and, with development of DNA-based methods, they have become an invaluable material for genetic analyses. Yet, the use of such material is hindered by technical limitations related to DNA degradation and to quantity of biological material. The latter is inherent for some biological groups, as best exemplified by myxomycetes which form minute sporophores. It is estimated that ca. two-thirds of myxomycete taxa are represented by extremely scanty material. As DNA isolation methods applied so far in myxomycete studies require destructive sampling of many sporophores, a large part of described diversity of the group remains unavailable for phylogenetic studies or barcoding. Here, we tested several procedures of DNA isolation and amplification to seek for an efficient and possibly non-destructive method of sampling. Tests were based on herbarium specimens of 19 species representing different taxonomic orders. We assayed several variants of isolation based on silica gel membrane columns, and a newly designed procedure using highly reduced amount of biological material (small portion of spores), based on fine disruption of spores and direct PCR. While the most frequently used column-based method led to PCR success in 89.5% of samples when a large amount of material was used, its performance dropped to 52% when based on single sporophores. Single sporophores provided amplicons in 89.5% of samples when using a kit dedicated to low-amount DNA samples. Our new procedure appeared the most effective (94.7%) while it used only a small fraction of spores, being nearly non-destructive; it was also the most cost-effective. We thus demonstrate that combination of adequate handling of spore micro-disruption coupled with application of direct PCR can be an efficient way to circumvent technical limitations for genetic studies in myxomycetes and thus can substantially improve taxon sampling for phylogeny and barcoding. Additionally, this approach gives a unique possibility to apply both molecular and morphological assays to the same structure (sporophore), which then can be further stored as documentation.

Morphological stasis in the first myxomycete from the Mesozoic, and the likely role of cryptobiosis

Myxomycetes constitute a group within the Amoebozoa well known for their motile plasmodia and morphologically complex fruiting bodies. One obstacle hindering studies of myxomycete evolution is that their fossils are exceedingly rare, so evolutionary analyses of this supposedly ancient lineage of amoebozoans are restricted to extant taxa. Molecular data have significantly advanced myxomycete systematics, but the evolutionary history of individual lineages and their ecological adaptations remain unknown. Here, we report exquisitely preserved myxomycete sporocarps in amber from Myanmar, ca. 100 million years old, one of the few fossil myxomycetes, and the only definitive Mesozoic one. Six densely-arranged stalked sporocarps were engulfed in tree resin while young, with almost the entire spore mass still inside the sporotheca. All morphological features are indistinguishable from those of the modern, cosmopolitan genus Stemonitis, demonstrating that sporocarp morphology has been static since at least the mid-Cretaceous. The ability of myxomycetes to develop into dormant stages, which can last years, may account for the phenotypic stasis between living Stemonitis species and this fossil one, similar to the situation found in other organisms that have cryptobiosis. We also interpret Stemonitis morphological stasis as evidence of strong environmental selection favouring the maintenance of adaptations that promote wind dispersal.

Evidence of Intra-individual SSU Polymorphisms in Dark-spored Myxomycetes (Amoebozoa)

The nuclear small subunit rRNA gene (SSU or 18S) is a marker frequently used in phylogenetic and barcoding studies in Amoebozoa, including Myxomycetes. Despite its common usage and the confirmed existence of divergent copies of ribosomal genes in other protists, the potential presence of intra-individual SSU variability in Myxomycetes has never been studied before. Here we investigated the pattern of nucleotide polymorphism in the 5' end fragment of SSU by cloning and sequencing a total of 238 variants from eight specimens, each representing a species of the dark-spored orders Stemonitidales and Physarales. After excluding singletons, a relatively low SSU intra-individual variability was found but our data indicate that this might be a widely distributed phenomenon in Myxomycetes as all samples analyzed possessed various ribotypes. To determine if the occurrence of multiple SSU variants within a single specimen has a negative effect on the circumscription of species boundaries, we conducted phylogenetic analyses that revealed that clone variation may be detrimental for inferring phylogenetic relationships among some of the specimens analyzed. Despite that intra-individual variability should be assessed in additional taxa, our results indicate that special care should be taken for species identification when working with closely related species.

Speciation in progress? A phylogeographic study among populations of Hemitrichia serpula (Myxomycetes)

Myxomycetes (plasmodial slime molds, Amoebozoa) are often perceived as widely distributed, confounding to the “everything is everywhere” hypothesis. To test if gene flow within these spore-dispersed protists is restricted by geographical barriers, we chose the widespread but morphologically unmistakable species Hemitrichia serpula for a phylogeographic study. Partial sequences from nuclear ribosomal RNA genes (SSU) revealed 40 ribotypes among 135 specimens, belonging to three major clades. Each clade is dominated by specimens from a certain region and by one of two morphological varieties which can be differentiated by SEM micrographs. Partial sequences of the protein elongation factor 1 alpha (EF1A) showed each clade to possess a unique combination of SSU and EF1A genotypes. This pattern is best explained assuming the existence of several putative biospecies dominating in a particular geographical region. However, occasional mismatches between molecular data and morphological characters, but as well heterogeneous SSU and heterozygous EF1A sequences, point to ongoing speciation. Environmental niche models suggest that the putative biospecies are rather restricted by geographical barriers than by macroecological conditions. Like other protists, myxomycetes seem to follow the moderate endemicity hypothesis and are in active speciation, which is most likely shaped by limited gene flow and reproductive isolation.

Two-gene phylogeny of bright-spored Myxomycetes (slime moulds, superorder Lucisporidia)

Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ∼10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one Licea.

The revised classification of eukaryotes

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

The Amoebozoa

The model organism Dictyostelium discoideum is a member of the Amoebozoa, one of the six major -divisions of eukaryotes. Amoebozoa comprise a wide variety of amoeboid and flagellate organisms with single cells measuring from 5 μm to several meters across. They have adopted many different life styles and sexual behaviors and can live in all but the most extreme environments. This chapter provides an overview of Amoebozoan diversity and compares roads towards multicellularity within the Amoebozoa with inventions of multicellularity in other protist divisions. The chapter closes with a scenario for the evolution of Dictyostelid multicellularity from an Amoebozoan stress response.

Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa

I discuss how different feeding modes and related cellular structures map onto the eukaryote evolutionary tree. Centrally important for understanding eukaryotic cell diversity are Loukozoa: ancestrally biciliate phagotrophic protozoa possessing a posterior cilium and ventral feeding groove into which ciliary currents direct prey. I revise their classification by including all anaerobic Metamonada as a subphylum and adding Tsukubamonas. Loukozoa, often with ciliary vanes, are probably ancestral to all protozoan phyla except Euglenozoa and Percolozoa and indirectly to kingdoms Animalia, Fungi, Plantae, and Chromista. I make a new protozoan phylum Sulcozoa comprising subphyla Apusozoa (Apusomonadida, Breviatea) and Varisulca (Diphyllatea; Planomonadida, Discocelida, Mantamonadida; Rigifilida). Understanding sulcozoan evolution clarifies the origins from them of opisthokonts (animals, fungi, Choanozoa) and Amoebozoa, and their evolutionary novelties; Sulcozoa and their descendants (collectively called podiates) arguably arose from Loukozoa by evolving posterior ciliary gliding and pseudopodia in their ventral groove. I explain subsequent independent cytoskeletal modifications, accompanying further shifts in feeding mode, that generated Amoebozoa, Choanozoa, and fungi. I revise classifications of Choanozoa, Conosa (Amoebozoa), and basal fungal phylum Archemycota. I use Choanozoa, Sulcozoa, Loukozoa, and Archemycota to emphasize the need for simply classifying ancestral (paraphyletic) groups and illustrate advantages of this for understanding step-wise phylogenetic advances.

Polyphyletic origin of the genus Physarum (Physarales, Myxomycetes) revealed by nuclear rDNA mini-chromosome analysis and group I intron synapomorphy

Background

Physarales represents the largest taxonomic order among the plasmodial slime molds (myxomycetes). Physarales is of particular interest since the two best-studied myxomycete species, Physarum polycephalum and Didymium iridis, belong to this order and are currently subjected to whole genome and transcriptome analyses. Here we report molecular phylogeny based on ribosomal DNA (rDNA) sequences that includes 57 Physarales isolates.

Results

The Physarales nuclear rDNA sequences were found to be loaded with 222 autocatalytic group I introns, which may complicate correct alignments and subsequent phylogenetic tree constructions. Phylogenetic analysis of rDNA sequences depleted of introns confirmed monophyly of the Physarales families Didymiaceae and Physaraceae. Whereas good correlation was noted between phylogeny and taxonomy among the Didymiaceae isolates, significant deviations were seen in Physaraceae. The largest genus, Physarum, was found to be polyphyletic consisting of at least three well supported clades. A synapomorphy, located at the highly conserved G-binding site of L2449 group I intron ribozymes further supported the Physarum clades.

Conclusions

Our results provide molecular relationship of Physarales genera, species, and isolates. This information is important in further interpretations of comparative genomics nd transcriptomics. In addition, the result supports a polyphyletic origin of the genus Physarum and calls for a reevaluation of current taxonomy.

Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.

Genetic structure of two protist species (Myxogastria, Amoebozoa) suggests asexual reproduction in sexual Amoebae

Plasmodial slime molds (Myxogastria or Myxomycetes) are common and widespread unicellular organisms that are commonly assumed to have a sexual life cycle culminating with the formation of often macroscopic fruiting bodies that efficiently disseminate spores. However, laboratory studies based on mating compatibility revealed the coexistence of asexual as well as sexual strains. To test this hypothesis in natural populations, we investigated the genetic variability of two species of the genus Lamproderma. Detailed ecological relevés were carried out in 2007 and 2009 in several deep ravines in the Elbsandsteingebirge (Saxony, south-eastern Germany). Morphological characters of 93 specimens of Lamproderma were recorded and genetic analyses, based on the small subunit ribosomal gene, the internal transcribed spacer 1 and partial elongation factor 1α sequences were carried out for 52 specimens. Genetic analyses showed the existence of two major clades, each composed of several discrete lineages. Most of these lineages were composed of several identical sequences (SSU, ITS 1 and EF-1α) which is explained best by an asexual mode of reproduction. Detrended Correspondence Analysis of morphological characters revealed two morphospecies that corresponded to the two major clades, except for one genotype (Lc6), thus challenging the morphospecies concept. Genetic patterns were not related to the geographical distribution: specimens belonging to the same genotype were found in distinct ravines, suggesting effective long-distance dispersal via spores, except for the Lc6 genotype which was found only in one ravine. Implications for the morphological and biological species concept are discussed.

Comprehensive phylogenetic reconstruction of amoebozoa based on concatenated analyses of SSU-rDNA and actin genes

Evolutionary relationships within Amoebozoa have been the subject of controversy for two reasons: 1) paucity of morphological characters in traditional surveys and 2) haphazard taxonomic sampling in modern molecular reconstructions. These along with other factors have prevented the erection of a definitive system that resolves confidently both higher and lower-level relationships. Additionally, the recent recognition that many protosteloid amoebae are in fact scattered throughout the Amoebozoa suggests that phylogenetic reconstructions have been excluding an extensive and integral group of organisms. Here we provide a comprehensive phylogenetic reconstruction based on 139 taxa using molecular information from both SSU-rDNA and actin genes. We provide molecular data for 13 of those taxa, 12 of which had not been previously characterized. We explored the dataset extensively by generating 18 alternative reconstructions that assess the effect of missing data, long-branched taxa, unstable taxa, fast evolving sites and inclusion of environmental sequences. We compared reconstructions with each other as well as against previously published phylogenies. Our analyses show that many of the morphologically established lower-level relationships (defined here as relationships roughly equivalent to Order level or below) are congruent with molecular data. However, the data are insufficient to corroborate or reject the large majority of proposed higher-level relationships (above the Order-level), with the exception of Tubulinea, Archamoebae and Myxogastrea, which are consistently recovered. Moreover, contrary to previous expectations, the inclusion of available environmental sequences does not significantly improve the Amoebozoa reconstruction. This is probably because key amoebozoan taxa are not easily amplified by environmental sequencing methodology due to high rates of molecular evolution and regular occurrence of large indels and introns. Finally, in an effort to facilitate future sampling of key amoebozoan taxa, we provide a novel methodology for genome amplification and cDNA extraction from single or a few cells, a method that is culture-independent and allows both photodocumentation and extraction of multiple genes from natural samples.

The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms

Amoebae are generally assumed to be asexual. We argue that this view is a relict of early classification schemes that lumped all amoebae together inside the 'lower' protozoa, separated from the 'higher' plants, animals and fungi. This artificial classification allowed microbial eukaryotes, including amoebae, to be dismissed as primitive, and implied that the biological rules and theories developed for macro-organisms need not apply to microbes. Eukaryotic diversity is made up of 70+ lineages, most of which are microbial. Plants, animals and fungi are nested among these microbial lineages. Thus, theories on the prevalence and maintenance of sex developed for macro-organisms should in fact apply to microbial eukaryotes, though the theories may need to be refined and generalized (e.g. to account for the variation in sexual strategies and prevalence of facultative sex in natural populations of many microbial eukaryotes). We use a revised phylogenetic framework to assess evidence for sex in several amoeboid lineages that are traditionally considered asexual, and we interpret this evidence in light of theories on the evolution of sex developed for macro-organisms. We emphasize that the limited data available for many lineages coupled with natural variation in microbial life cycles overestimate the extent of asexuality. Mapping sexuality onto the eukaryotic tree of life demonstrates that the majority of amoeboid lineages are, contrary to popular belief, anciently sexual, and that most asexual groups have probably arisen recently and independently. Additionally, several unusual genomic traits are prevalent in amoeboid lineages, including cyclic polyploidy, which may serve as alternative mechanisms to minimize the deleterious effects of asexuality.

The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms

Amoebae are generally assumed to be asexual. We argue that this view is a relict of early classification schemes that lumped all amoebae together inside the 'lower' protozoa, separated from the 'higher' plants, animals and fungi. This artificial classification allowed microbial eukaryotes, including amoebae, to be dismissed as primitive, and implied that the biological rules and theories developed for macro-organisms need not apply to microbes. Eukaryotic diversity is made up of 70+ lineages, most of which are microbial. Plants, animals and fungi are nested among these microbial lineages. Thus, theories on the prevalence and maintenance of sex developed for macro-organisms should in fact apply to microbial eukaryotes, though the theories may need to be refined and generalized (e.g. to account for the variation in sexual strategies and prevalence of facultative sex in natural populations of many microbial eukaryotes). We use a revised phylogenetic framework to assess evidence for sex in several amoeboid lineages that are traditionally considered asexual, and we interpret this evidence in light of theories on the evolution of sex developed for macro-organisms. We emphasize that the limited data available for many lineages coupled with natural variation in microbial life cycles overestimate the extent of asexuality. Mapping sexuality onto the eukaryotic tree of life demonstrates that the majority of amoeboid lineages are, contrary to popular belief, anciently sexual, and that most asexual groups have probably arisen recently and independently. Additionally, several unusual genomic traits are prevalent in amoeboid lineages, including cyclic polyploidy, which may serve as alternative mechanisms to minimize the deleterious effects of asexuality.

Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum

Background

The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum.

Results

We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict.

Conclusions

The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.

RNA editing of 10 Didymium iridis mitochondrial genes and comparison with the homologous genes in Physarum polycephalum

Regions of the Didymium iridis mitochondrial genome were identified with similarity to typical mitochondrial genes; however, these regions contained numerous stop codons. We used RT-PCR and DNA sequencing to determine whether, through RNA editing, these regions were transcribed into mRNAs that could encode functional proteins. Ten putative gene regions were examined: atp1, atp6, atp8, atp9, cox1, cox2, cytb, nad4L, nad6, and nad7. The cDNA sequences of each gene could encode a functional mitochondrial protein that was highly conserved compared with homologous genes. The type of editing events and editing sequence features were very similar to those observed in the homologous genes of Physarum polycephalum, though the actual editing locations showed a variable degree of conservation. Edited sites were compared with encoded sites in D. iridis and P. polycephalum for all 10 genes. Edited sequence for a portion of the cox1 gene was available for six myxomycetes, which, when compared, showed a high degree of conservation at the protein level. Different types of editing events showed varying degrees of site conservation with C-to-U base changes being the least conserved. Several aspects of single C insertion editing events led to the preferential creation of hydrophobic amino acid codons that may help to minimize adverse effects on the resulting protein structure.

Semimorula liquescens is a modified echinostelid myxomycete (Mycetozoa)

The enigmatic Semimorula liquescens E.F. Haskins, McGuin. & C.S. Berry has been isolated repeatedly from dried infructescences of Lythrum salicaria collected from Seattle and Kirkland, Washington. Detailed developmental, morphological and ultrastructural studies suggested that it represents a taxon within Mycetozoa, closely allied with Myxogastria (Myxomycetes) but with unique characteristics. Phylogeny based on two genes places it with confidence in family Echinosteliidae. This species differs from a typical Echinostelium in the way spores germinate and in the lack of a stalked sporophore, the latter being a secondary loss. Semimorula liquescens therefore might be a useful negative model to search for genes inducing stalk formation during sporulation.

Molecular diversity of myxomycetes associated with decaying wood and forest floor leaf litter

Denaturing gradient gel electrophoresis (DGGE) fingerprinting was used to assess the molecular diversity of myxomycetes from environmental samples (decaying wood and forest floor litter) collected at the Mushroom Research Centre in northern Thailand. Total genomic DNA was extracted directly from environmental samples on which myxomycetes were not apparent. Part of the small subunit ribosomal RNA gene (SSU rDNA) was amplified and DNA sequences analyzed. DGGE gels revealed up to 17 operational taxonomic units (OTU) from decaying wood and 10 OTU from forest floor litter samples, but only seven (wood) and six (litter) OTU could be re-amplified and/or sequenced. Based on results obtained with the BLAST analysis program, the species involved appeared to correspond most closely to Diderma saundersii, Didymium iridis, Stemonitis flavogenita and Hyperamoeba sp. strain W2i on decaying wood and to Diderma saundersii and Physarum didermoides on forest floor litter. Our results suggest that then PCR-DGGE can be used to obtain data on the presence of myxomycetes in their primary microhabitats without the need to observe the sporocarps of these organisms. As such the technique would seem to have considerable potential for contributing to a more complete understanding of myxomycete diversity and ecology in terrestrial ecosystems.

Eumycetozoa = Amoebozoa?: SSUrDNA phylogeny of protosteloid slime molds and its significance for the amoebozoan supergroup

Amoebae that make fruiting bodies consisting of a stalk and spores and classified as closely related to the myxogastrids have classically been placed in the taxon Eumycetozoa. Traditionally, there are three groups comprising Eumycetozoa: myxogastrids, dictyostelids, and the so-called protostelids. Dictyostelids and myxogastrids both make multicellular fruiting bodies that may contain hundreds of spores. Protostelids are those amoebae that make simple fruiting bodies consisting of a stalk and one or a few spores. Protostelid-like organisms have been suggested as the progenitors of the myxogastrids and dictyostelids, and they have been used to formulate hypotheses on the evolution of fruiting within the group. Molecular phylogenies have been published for both myxogastrids and dictyostelids, but little molecular phylogenetic work has been done on the protostelids. Here we provide phylogenetic trees based on the small subunit ribosomal RNA gene (SSU) that include 21 protostelids along with publicly available sequences from a wide variety of amoebae and other eukaryotes. SSU trees recover seven well supported clades that contain protostelids but do not appear to be specifically related to one another and are often interspersed among established groups of amoebae that have never been reported to fruit. In fact, we show that at least two taxa unambiguously belong to amoebozoan lineages where fruiting has never been reported. These analyses indicate that we can reject a monophyletic Eumycetozoa, s.l. For this reason, we will hereafter refer to those slime molds with simple fruiting as protosteloid amoebae and/or protosteloid slime molds, not as protostelids. These results add to our understanding of amoebozoan biodiversity, and demonstrate that the paradigms for understanding both nonfruiting and sporulating amoebae must be integrated. Finally, we suggest strategies for future research on protosteloid amoebae and nonfruiting amoebae, and discuss the impact of this work for taxonomists and phylogenomicists.