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.

Systematic revision of the Tubifera casparyi-T. dictyoderma complex: Resurrection of the genus Siphoptychium and introduction of the new genus Thecotubifera.

The genus Siphoptychium is resurrected on the basis of comparative morphology and phylogeny of partial nuc 18S rDNA (18S) and translation elongation factor 1-alpha (EF1A) nucleotide sequences. The genus is characterized by the firm upper surface of the pseudoaethalium, accreted but easily separable sporothecae, a tubular or fibrous columella, and spores with a reticulate ornamentation consisting of 7-9 meshes across the diameter. In addition to the currently known single species S. casparyi (= Tubifera casparyi), two new members of Siphoptychium are described: S. violaceum from coniferous forests of Europe, east Asia, and southeast Asia, and S. reticulatum from temperate and subarctic regions of North America and alpine regions of Europe. A second genus, Thecotubifera, is described to accommodate Tubifera dictyoderma. The fruiting body of this species is transitional between a pseudoaethalium and a true aethalium. It is covered by a contiguous membranous cortex formed by the fused tips of the sporothecae, a feature typical for aethalia. However, the inner portions of sporothecae remain discernible, a feature more typical for pseudoaethalia. Columellae of Th. dictyoderma are formed by perforated plates, and the spores have a reticulate ornamentation consisting of 2-5 meshes across the diameter. For Th. dictyoderma, we could confirm records only for tropical regions and Japan, whereas all studied European specimens, including those mentioned in current monographs, represent species of Siphoptychium.

The Species Problem in Myxomycetes Revisited.

Species identification in the myxomycetes (plasmodial slime molds or myxogastrids) poses particular challenges to researchers as a result of their morphological plasticity and frequent alteration between sexual and asexual life strategies. Traditionally, myxomycete morphology has been used as the primary method of species delimitation. However, with the increasing availability of genetic information, traditional myxomycete taxonomy is being increasingly challenged, and new hypotheses continue to emerge. Due to conflicts that sometimes occur between traditional and more modern species concepts that are based largely on molecular data, there is a pressing need to revisit the discussion surrounding the species concept used for myxomycetes. Biological diversity is being increasingly studied with molecular methods and data accumulates at ever-faster rates, making resolution of this matter urgent. In this review, currently used and potentially useful species concepts (biological, morphological, phylogenetic and ecological) are reviewed, and an integrated approach to resolve the myxomycete species problem is discussed.

On chirality of slime mould.

Left-right patterning and lateralised behaviour is an ubiquitous aspect of plants and animals. The mechanisms linking cellular chirality to the large-scale asymmetry of multicellular structures are incompletely understood, and it has been suggested that the chirality of living cells is hardwired in their cytoskeleton. We examined the question of biased asymmetry in a unique organism: the slime mould Physarum polycephalum, which is unicellular yet possesses macroscopic, complex structure and behaviour. In laboratory experiment using a T-shape, we found that Physarum turns right in more than 74% of trials. The results are in agreement with previously published studies on asymmetric movement of muscle cells, neutrophils, liver cells and growing neural filaments, and for the first time reveal the presence of consistently-biased laterality in the fungi kingdom. Exact mechanisms of the slime mould's direction preference remain unknown.

Species-specific cell mobility of bacteria-feeding myxamoebae in plasmodial slime molds.

On decaying wood or litter in forests, plasmodial slime molds (myxomycetes) represent a large fraction of eukaryotic protists that feed on bacteria. In his seminal book Experimental Physiology of Plants (1865), Julius Sachs referred to the multinucleate plasmodium of myxomycetes, which were considered at that time as primitive plants (or fungi). Today it is well established that myxomycetes are members of the Amoebozoa (Protista). In this study we compare the mobility of myxamoebae of 3 European species, Lycogala epidendrum (order Liceales), Tubulifera arachnoidea, and Trichia decipiens (order Trichiales). Using agar plates, on which 3 separate bacterial species were cultivated as prey organisms (Methylobacterium mesophilicum, Escherichia coli, Agrobacterium tumefaciens), we document large differences in cell motility between the myxomycetes investigated. In addition, we show that the 3 species of myxamoebae can be distinguished based on their average cell size. These data shed light on the mode of co-occurrence via differential substrate utilization in these members of the Amoebozoa.

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.

Photonic simulation method applied to the study of structural color in Myxomycetes.

We present a novel simulation method to investigate the multicolored effect of the Diachea leucopoda (Physarales order, Myxomycetes class), which is a microorganism that has a characteristic pointillistic iridescent appearance. It was shown that this appearance is of structural origin, and is produced within the peridium -protective layer that encloses the mass of spores-, which is basically a corrugated sheet of a transparent material. The main characteristics of the observed color were explained in terms of interference effects using a simple model of homogeneous planar slab. In this paper we apply a novel simulation method to investigate the electromagnetic response of such structure in more detail, i.e., taking into account the inhomogeneities of the biological material within the peridium and its curvature. We show that both features, which could not be considered within the simplified model, affect the observed color. The proposed method is of great potential for the study of biological structures, which present a high degree of complexity in the geometrical shapes as well as in the materials involved.

A new species of Trichia from Australia.

A new species of Trichia (myxomycetes) was collected during surveys for myxomycetes carried out in Nothofagus cunninghamii forests in western Tasmania in May 2008 and a similar survey carried out in a N. morrei forest in New South Wales in May 2009. This new species, T. brimsiorum, is described and illustrated. It resembles T. decipiens in overall shape and size of the sporocarps but has smaller spores and the ornamentation of the capillitium is different.

Spore to spore culture of Didymium operculatum, a new Myxomycete from the Atacama Desert of Chile.

A new species of Didymium (Myxomycetes), D. operculatum, is described in this paper, and details of its life cycle are provided. The new species was recorded during studies of the Atacama Desert in Chile. It has been collected directly in the field and isolated in moist chamber cultures prepared with material from an endemic cactus. The distinguishing characters of this species are its dehiscence by means of an apical operculum combined with a whitish calcareous stalk and the banded reticulate ornamentation of the spores. The morphology of this new myxomycete was examined with scanning electron microscopy and light microscopy, and micrographs of relevant details are included in this paper. Some comments are made on the patterns of distribution of Didymium species in arid lands and adaptive characters enabling this genus to colonize such extreme environments. It is proposed that a longer cycle and the ability to resort to resistant forms many times during their development reflect the response of these myxomycetes to the largely unfavorable conditions of their environment.

Rare or rarely collected? Comatricha mirabilis from the desert of Bahrain.

A rarely collected myxomycete, Comatricha mirabilis, developed on five collections of bark of large shrubs from the desert in the Kingdom of Bahrain. The distinctive morphology of this specimen is identical or very similar to that of specimens previously known from goat droppings in the USA (Illinois, Holotype), straw (England) and an unreported substrate in France. The spore and capillitium of the new specimens are compared to those from USA and England with light and scanning electron micrographs. The new collections are considered in the light of the previously known distribution of this taxon and other species. Comatricha mirabilis is suggested to be a myxomycete that is more common in certain arid habitats than previously recognized.

Microhabitat and niche separation in species of Ceratiomyxa.

The eumycetozoan genus Ceratiomyxa appears to have a cosmopolitan distribution, although two of the three macroscopic species within the genus have been reported only from tropical regions of the world. In theory these two tropical species might be expected to display more narrow niches than their cosmopolitan counterpart due to their specialization for tropical environments. However ecological data documenting niche separation in eumycetozoans are largely lacking. As part of several investigations carried out in the neotropics the ecology of the three macroscopic species of Ceratiomyxa was studied. The results from in situ measurements of environmental factors associated with their fructifications reveal a clear separation of niches between the two tropical species, which might be an indication of resource partitioning within the genus. As expected in theory the cosmopolitan C. fruticulosa shows the broadest niche of the three species. Moreover the niche overlap value between C. morchella and C. sphaerosperma along with results from a multivariate CDA analysis seem to indicate that these two species are more specialized than C. fruticulosa.

A new ballistosporous species of Protostelium.

During surveys of the protostelids of the Hawaiian Islands and the South Island of New Zealand, an undescribed species of Protostelium was discovered fruiting on collections of substrates found in several sites on the southern and western parts of the island of Hawaii and from one site near Port Elizabeth, New Zealand. The new species, P. okumukumu, has a sporocarp with a bipartite stalk that supports a single, spherical spore. The basal portion of the stalk is straight and rigid. The upper part of the stalk is a nearly spherical apophysis. The junction between the stalk base and the apophysis is flexible such that the spore and apophysis swing back and forth as a unit. Spores are forcibly discharged from the stalk, and only the straight base of the stalk is left behind. Amoebae typical of the taxon Protostelium germinate from the spores, and when an amoeba differentiates into a prespore cell, it becomes lozenge shaped (nearly ellipsoid) in top view, as is typical for species of Protostelium. This represents the seventh species of protostelids described to have forcible spore discharge, and the possibility of forcible discharge needs to be examined in several other species.

A new interpretation of the Keller-Segel model based on multiphase modelling.

In this paper an alternative derivation and interpretation are presented of the classical Keller-Segel model of cell migration due to random motion and chemotaxis. A multiphase modelling approach is used to describe how a population of cells moves through a fluid containing a diffusible chemical to which the cells are attracted. The cells and fluid are viewed as distinct components of a two-phase mixture. The principles of mass and momentum balance are applied to each phase, and appropriate constitutive laws imposed to close the resulting equations. A key assumption here is that the stress in the cell phase is influenced by the concentration of the diffusible chemical. By restricting attention to one-dimensional cartesian geometry we show how the model reduces to a pair of nonlinear coupled partial differential equations for the cell density and the chemical concentration. These equations may be written in the form of the Patlak-Keller-Segel model, naturally including density-dependent nonlinearities in the cell motility coefficients. There is a direct relationship between the random motility and chemotaxis coefficients, both depending in an inter-related manner on the chemical concentration. We suggest that this may explain why many chemicals appear to stimulate both chemotactic and chemokinetic responses in cell populations. After specialising our model to describe slime mold we then show how the functional form of the chemical potential that drives cell locomotion influences the ability of the system to generate spatial patterns. The paper concludes with a summary of the key results and a discussion of avenues for future research.

Beyond input-output computings: error-driven emergence with parallel non-distributed slime mold computer.

The emergence derived from errors is the key importance for both novel computing and novel usage of the computer. In this paper, we propose an implementable experimental plan for the biological computing so as to elicit the emergent property of complex systems. An individual plasmodium of the true slime mold Physarum polycephalum acts in the slime mold computer. Modifying the Elementary Cellular Automaton as it entails the global synchronization problem upon the parallel computing provides the NP-complete problem solved by the slime mold computer. The possibility to solve the problem by giving neither all possible results nor explicit prescription of solution-seeking is discussed. In slime mold computing, the distributivity in the local computing logic can change dynamically, and its parallel non-distributed computing cannot be reduced into the spatial addition of multiple serial computings. The computing system based on exhaustive absence of the super-system may produce, something more than filling the vacancy.

Ecology. The advantages of togetherness.

What would be the advantage of unicellular organisms becoming multicellular? For organisms that feed on organic food (heterotrophs), the most efficient way to produce energy is to metabolize the food by aerobic respiration, but the fastest way is to metabolize it by fermentation. In their Perspective, Cox and Bonner discuss a mathematical model (Pfeiffer et al.), which shows that when these two kinds of organisms (respirators and fermenters) compete for a limited food source, the respirators manage best when they are grouped in clusters rather than remaining as separate cells. In this way, multicellularity could have originated.

Positional information and whorl morphogenesis in Polysphondylium.

Cellular slime molds of the genus Polysphondylium periodically release cell masses from the base of culminating fruiting bodies. These masses quickly undergo a change in symmetry from spherical to radial as they differentiate into distinctive arrays of secondary fruiting bodies arranged about a primary axis of stalk cells. Here we show that a major event in whorl morphogenesis is the activation of a prestalk-specific promoter early and globally in newly forming whorls. With time, transcript synthesis and amplification become restricted to the equator of the whorl and then to patches which define where secondary tip morphogenesis will occur. The localization of early prestalk message synthesis depends on positional information, in contrast to the establishment of early prestalk/prespore patterns in both Polysphondylium and Dictyostelium.

Quantitative cytophotometric and autoradiographic analysis of the cell cycle kinetics during growth and development of the plasmodium in the myxomycete Didymium iridis.

Nuclear changes in basic protein, RNA, and DNA in plasmodia of Didymium iridia at 4, 8, and 12 days during their progression through the growth cycle prior to sporulation were analysed. Relative determinations of basic protein and RNA were made using naphthol yellow-S/azure B in conjunction with absorption microspectrophotometry. DNA was quantified by quantitative cytophotometric measurements of Feulgen-stained nuclei. Autoradiographic techniques provided information on periods of DNA synthesis. A net decrease in protein and RNA to a point of stabilization was shown which correlated with increased age of the organism and decreased nutrient supply in the plasmodia. The 4C DNA content of the 4 day plasmodia indicated rapid growth and high metabolic activity while in the 8 day plasmodia a 2C DNA was observed consistent with the presence of a G1 period of some duration.

Microtubule centers and the interphase microtubule cytoskeleton in amoebae of the cellular slime molds (Mycetozoans) Acytostelium leptosomum and Protostelium mycophaga.

We investigated the microtubule (MT) cytoskeleton and microtubule centers (MTC) in undifferentiated amoebae by indirect immunofluorescence with six monoclonal antitubulin antibodies, and by transmission electron microscopy and immunogold ultracytochemistry. Interphase amoebae of both species contain a distinct cytoplasmic complex of MTs, which is more elaborate in Protostelium mycophaga. In Acytostelium leptosomum amoebae a single MTC is attached to each interphase nucleus at its pointed end, as in the other dictyostelid cellular slime molds Dictyostelium discoideum and Polysphondylium violaceum. Ultrastructurally, MTCs of A. leptosomum also resemble those of these two species: They consist of an electron-opaque core shaped like a stout rod, which is embedded, together with nodules, in a fuzzy matrix. The nodules are the points of origin of the MTs. In most amoebae of P. mycophaga there are two MTCs on opposite sides of and close to the nucleus, but many amoebae also contain a variable number of MTCs that are remote from the nucleus. Nucleus-associated and "remote" MTCs are structurally identical. They consist of a ring-shaped core with inner and outer diameters of ca. 130 nm and 340 nm. A plug sits in the ring, and satellites are connected to the core by fine fibrils. The satellites are the points of origin of MTs. New MTCs are apparently formed during mitosis, the parent MTC probably serving as a template for the genesis of a new ring. The results support the notion that phylogenetically related organisms have similarly constructed MTCs and that these are dissimilar in less closely related organisms.

Establishment and maintenance of stable spatial patterns in lacZ fusion transformants of Polysphondylium pallidum.

Polysphondylium pallidum cells were transformed with a construct containing the Dictyostelium discoideum ecmA promoter fused to a lacZ reporter gene. Two stably transformed lines, one in which beta-galactosidase (beta-gal) is expressed in apical cells of the fruiting body (p63/2.1), and one in which it is expressed in basal cells (p63/D), have enabled us to infer how cells move during aggregation and culmination. Several types of cell movement proposed to occur during slime mold culmination, such as random cell mixing and global cell circulation, can be ruled out on the basis of our observations. Cells of the two transformant lines express beta-gal very early in development. In both cases, stained cells are randomly scattered in a starving population. By mid to late aggregation, characteristic spatial patterns emerge. Marked cells of p63/2.1 are found predominantly at tips of tight aggregates; those of p63/D accumulate at the periphery. These patterns are conserved throughout culmination, showing that marked cells maintain their relative positions within the multicellular mass following aggregation. Neither the apical nor the basal pattern appears to be regulated within the primary sorogen by de novo gene expression or by cell sorting as whorls are formed. However, marked cells within a whorl re-establish the original pattern in secondary sorogens. This must be achieved by cell migration, since beta-gal is not re-expressed.