Arcyria similaris: A new myxomycete species from China.

A new myxomycete species, Arcyria similaris, was reported herein. The specimens were found and collected in the field on dead bark from Jingangtai National Geopark in Henan Province of China. This species has distinct and unique morphological characteristics, including dark grayish olive sporothecae that fade to smoke gray with age, shallow saucer-shaped cups with marked reticulations and thick papillae on the inner surface, a netted capillitium with many bulges, uniformly marked with low, dense, and irregular reticulations, and spores (8.0-)9.3-10.1(-10.9) µm in diameter, marked with sparse small warts and grouped prominent warts. Apart from a comprehensive morphological study, partial sequences of the nuclear 18S rDNA and elongation factor-1 alpha (EF-1α) genes were also provided in this study. This new species was described and illustrated morphologically. The specimens are deposited in the Herbarium of Fungi of Nanjing Normal University (HFNNU).

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.

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.

Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps.

We used direct DNA amplification from soil extracts to analyze microbial communities from an elevational transect in the German Alps by parallel metabarcoding of bacteria (16S rRNA), fungi (ITS2), and myxomycetes (18S rRNA). For the three microbial groups, 5710, 6133, and 261 operational taxonomic units (OTU) were found. For the latter group, we can relate OTUs to barcodes from fruit bodies sampled over a 4-year period. The alpha diversity of myxomycetes was positively correlated with that of bacteria. Vegetation type was found to be the main explanatory parameter for the community composition of all three groups and a substantial species turnover with elevation was observed. Bacteria and fungi display similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae show a more patchy distribution, though still clearly stratified between taxa, which seems to be a response to both structural properties of the habitat and interaction with specific bacterial and fungal taxa. Finally, we report a high number of myxomycete OTUs not represented in a reference database from fructifications, which might represent novel species.

What an Intron May Tell: Several Sexual Biospecies Coexist in Meriderma spp. (Myxomycetes).

Specimens of the snowbank myxomycete Meriderma atrosporum agg. from five European mountain ranges were sequenced for parts of the nuclear small subunit ribosomal RNA gene (SSU) and the protein elongation factor 1 alpha gene (EF1A). A phylogeny of the EF1A gene, including a very variable spliceosomal intron, resulted in seven phylogroups, and this topology was confirmed by SSU sequences. Two thirds of all specimens were heterozygous for the EF1A gene, and the two haplotypes of these specimens occurred always in the same phylogroup. Except for two cases in closely related phylogroups all ribotypes were as well limited to one phylogroup. This pattern is consistent with the assumption of reproductively isolated sexual biospecies. Numbers of EF1A-haplotypes shared between mountain ranges correlate with geographical distance, suggesting relative isolation but occasional long-distance dispersal by spores. Most subpopulations (divided by putative biospecies and mountain ranges) were in Hardy-Weinberg equilibrium. A simulation assuming panmixis within but not in between subpopulations suggested that similar numbers of shared genotypes can be created by chance through sexual reproduction alone. Our results support the biospecies concept, derived from experiments with cultivable members of the Physarales. We discuss the results on the background of possible reproductive options in myxomycetes.

First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs.

Decaying wood hosts a large diversity of seldom investigated protists. Environmental sequencing offers novel insights into communities, but has rarely been applied to saproxylic protists. We investigated the diversity of bright-spored wood-inhabiting Myxomycetes by environmental sequencing. Myxomycetes have a complex life cycle culminating in the formation of mainly macroscopic fruiting bodies, highly variable in shape and colour that are often found on decaying logs. Our hypothesis was that diversity of bright-spored Myxomycetes would increase with decay. DNA was extracted from wood chips collected from 17 beech logs of varying decay stages from the Hainich-Dün region in Central Germany. We obtained 260 partial small subunit ribosomal RNA gene sequences of bright-spored Myxomycetes that were assembled into 29 OTUs, of which 65% were less than 98% similar to those in the existing database. The OTU richness revealed by molecular analysis surpassed that of a parallel inventory of fruiting bodies. We tested several environmental variables and identified pH, rather than decay stage, as the main structuring factor of myxomycete distribution.

Nivicolous Stemonitales from the Austral Andes: analysis of morphological variability, distribution and phenology as a first step toward testing the large-scale coherence of species and biogeographical properties.

Nivicolous myxomycetes occur at the edge of spring-melting snow in mountainous areas. They are mostly considered cosmopolitan species morphologically and ecologically uniform across their entire distribution ranges. Thus, long-distance dispersal has been suggested to be the main mechanism shaping their ranges and geographical variability patterns. To test this hypothesis we conducted the first detailed analysis of morphological variability, occurrence frequency and phenology of nivicolous myxomycetes collected in the hitherto unexplored Austral Andes of South America (southern hemisphere = SH) in the comparative context of data from the northern hemisphere (NH). We used Stemonitales, the most representative and numerous taxonomic order in nivicolous myxomycetes, as a model. A total of 131 South American collections represented 13 species or morphotypes. One of them, Lamproderma andinum, is new to science and described here. Several others, L. aeneum, L. album, L. pulveratum, "Meriderma aff. aggregatum ad. int.", M. carestiae and "M. spinulosporum ad. int.", were previously unknown from the SH. Lamproderma ovoideum is reported for the first time from South America and Collaria nigricapillitia is new for Argentina. The fine-scale morphological analysis of all species from the study area and reference NH material demonstrated a high intraspecific variability in most of them. This suggests isolation and independent evolutionary processes among remote populations. On the other hand, the uniform morphology of a few species indicates that long-distance dispersal is also an effective mechanism, although not as universal as usually assumed, in some nivicolous myxomycetes. Analysis of nivicolous species assemblages also showed significant differences among major geographic regions in that the Stemonitales were significantly less common in the SH than in the NH. Furthermore, the occurrence of nivicolous species in summer and autumn, out of the typical phenological season, is recognized as a possible distinctive phenomenon for the SH populations.

Didymium xerophilum, a new myxomycete from the tropical Andes.

A new species of Didymium (Myxomycetes), D. xerophilum, is described, and some details of its life cycle are provided. The new species was collected during studies of arid areas of Argentina and Peru. It can be distinguished by the persistent funnel-shaped invagination of the peridium, the top of which appears as a deep umbilicus in closed sporothecae, and the calcareous hypothallus shared among several sporocarps. This combination of characters, with a circumscissile dehiscence of the sporotheca and a cream stalk packed with rhombic lime crystals, is unknown in other described species. Morphology was examined with scanning electron microscopy and light microscopy, and micrographs of relevant details are included here. Phylogenetic analysis with 18S rDNA sequences of different species of Didymium supports the distinct identity of this new species. Some collections of this myxomycete were made at up to 4600 m, an altitude almost unknown for this group of microorganisms.

A new species of Alwisia (Myxomycetes) from New South Wales and Tasmania.

Based on a morphological investigation of a series of specimens collected in New South Wales and Tasmania and a phylogeny constructed with partial 18S ribosomal RNA gene sequences, we describe a new species Alwisia lloydiae; the fourth species within the recently revalidated genus Alwisia. This new species is characterized by short ovate sporothecae with mostly free stalks, morphologically resembling the recently described A. morula. However, the new species possesses a tubular capillitium that suggests an affinity with A. bombarda. The capillitium of the new species is ornamented with globular warts, and this feature separates it from all other members of the genus.

The genus Alwisia (Myxomycetes) revalidated, with two species new to science.

Based on morphological investigations and a phylogeny constructed with partial sequences of the SSU rDNA gene, we revalidate the genus Alwisia and propose the combination Alwisia bombarda Berk. & Broome to be used against Tubifera bombarda (Berk. & Broome) G.W. Martin. Two new species, Alwisia morula and A. repens, are described based on material collected respectively in Costa Rica and Australia. Both new species lack a capillitium and possess individually stalked subspherical sporothecae. Alwisia repens differs from A. morula by its procumbent stalks and iridescent peridium. A comparison of 83 sequences of species in the genera Lycogala, Reticularia and Tubifera with a recent two-gene phylogeny of the bright-spored myxomycetes resulted in a similar topology of both Bayesian and maximum likelihood trees and placed A. bombarda, A. morula and A. repens in one well delimited clade within Reticulariaceae.

Species diversity of corticolous myxomycetes in Tianmu Mountain National Nature Reserve, China.

The species diversity of corticolous myxomycetes on 4 vegetation types in the Tianmu Mountain National Natural Reserve, eastern China, was examined from 2011 to 2012. A total of 1440 moist chamber cultures were prepared with bark samples, which yielded several hundred collections representing 42 species in 20 genera. It was found that 79% of cultures produced some evidence (either plasmodia or fruiting bodies) of myxomycetes. Eight species (Comatricha elegans, Cribraria confusa, Licea pusilla, Cribraria microcarpa, Collaria arcyrionema, Licea biforis, Arcyria cinerea, and Clastoderma debaryanum) were abundant (exceeding 3% of all records), but about a third of all species were classified as rare. Species richness (S = 33) and diversity (exp[H'] = 16.60, S/G = 1.74) of corticolous myxomycetes were the most diverse in the deciduous broadleaf forest. The species recorded from coniferous forest showed the lowest species richness (S = 21) but the highest evenness (J' = 0.91). The cluster analyses were based on the Bray-Curtis similarity matrix, and the results indicated that corticolous myxomycete assemblages were distributed by a seasonal and annual pattern. Canonical correspondence analysis showed that season and pH were key factors in determining species distribution.

Perichaena megaspora, a new nivicolous species of myxomycete from the Andes.

A new nivicolous species of Perichaena is described from the Andes in Argentina. The most conspicuous characteristics of Perichaena megaspora are the large spores and their ornamentation in the form of flattened warts. The 16-21 µm diam spores make the new species unique in the genus in which all other species have spores rarely reaching 15 µm diam. Twenty-two collections were found in the field during two consecutive years at 10 localities in Mendoza province Argentina, including one collection isolated from a moist chamber culture of ground litter. The new species was examined under stereomicroscope, light microscope and scanning electron microscope and micrographs of relevant details are included.

Exploring slime mould diversity in high-altitude forests and grasslands by environmental RNA analysis.

In spite of the ecological importance of protists, very little data is available on their distribution in soil. This investigation is the first of its kind on what could be the major components of the soil protistan community, the Myxomycetes, or plasmodial slime-moulds, a monophyletic class in the phylum Amoebozoa. Myxomycetes have a complex life cycle culminating in the formation of mainly macroscopic fruiting bodies, highly variable in shape and colour, which can be found in every terrestrial biome. Despite their prevalence, they are paradoxically absent from environmental DNA sampling studies. We obtained myxomycete SSU rRNA gene sequences from soil-extracted RNAs using specific primers. Soil samples were collected in three mountain ranges (France, Scotland and Japan). Our study revealed an unexpectedly high diversity of dark-spored Myxomycetes, with the recovery of 74 phylotypes. Of these, 74% had < 98% identity with known sequences, showing a hidden diversity; there was little overlap between localities, implying biogeographical patterns. Few phylotypes were dominant and many were unique, consistent with the 'rare biosphere' phenomenon. Our study provides the first detailed insight into the community composition of this ecologically important group of protists, establishing means for future studies of their distribution, abundance and ecology.

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.

Licea eremophila, a new myxomycete from arid areas of South America.

A new stipitate species of myxomycete of the genus Licea is described based on material from arid areas in Argentina and Chile. It was isolated from moist chamber cultures and found fruiting on field collections, usually on the same substrate, Puya sp. (Bromeliaceae). It differs from all described species in the genus in that it has stipitate sporocarps with dehiscence by defined preformed platelets and a smooth inner peridial surface. The new species has polyhedral, yellow spores with a uniform thick spore wall and dense warts except on irregularly dispersed raised bands with fewer warts, visible by SEM, an ornamentation not previously observed in the genus. Life-cycle events are described and illustrated, from germination to sporulation, based on moist chamber and agar cultures. The morphology of the myxomycete specimens was examined with scanning electron microscopy and light microscopy, and both light and SEM micrographs of relevant details are included.

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.

Distribution and ecology of protostelids in Great Smoky Mountains National Park.

In Oct. 2000 and Nov. 2003 samples for isolation of protostelids were collected from throughout Great Smoky Mountains National Park. Collecting sites included examples of all major forest types found in the park along with a number of non-forest vegetation types at 460-1920 m above sea level. Most samples consisted of aerial litter (dead but still attached plant parts) and ground litter, but some samples of the bark from living trees and coarse woody debris also were collected. Twenty-six of the 32 described species of protostelids were recovered, along with five species that appear to be new to science. Of the 205 cultures analyzed, 177 (86.5%) yielded protostelid fruiting bodies with an average of 3.22 species per sample. Protostelium mycophaga was the most frequently observed species followed by Soliformovum irregularis and Schizoplasmodiopsis pseudoendospora. Differences in protostelid community diversity and species richness were found between the aerial litter and ground litter microhabitats of primary plant tissues, between primary tissues and bark of living trees, between bark from angiosperms and bark from gymnosperms, and between primary tissues and coarse woody debris.

Aerial reproductive structures of vascular plants as a microhabitat for myxomycetes.

This study explored the occurrence and distribution of myxomycete species on the aerial reproductive structures of vascular plants. Eight species of vascular plants representing five families were sampled. The doubled rope climbing method was used to collect bark and cones from the canopy of Pinus echinata. Bark and aerial seed pods were gathered from Cercis canadensis, follicles and stems from Asclepias syriaca, dried composite inflorescences and stems from Echinacea angustifolia, E. pallida, and E. paradoxa var. paradoxa, and capsules and stems from Yucca glauca and Y. smalliana. Reproductive structures and bark/stems for 202 host plants were separated and cultured in 541 moist chambers, resulting in 118 collections yielding 32 myxomycete species representing 11 genera, seven families and five orders. There was no significant difference in pH values of the reproductive structures and bark/stems of the host plants, however legume pods of C. canadensis (6.9 +/- 1.3) had higher pH than the bark (6.0 +/- 1.1) and had a different composition of myxomycete species. Myxomycete orders have optimal pH ranges. Nonmetric multidimensional scaling, multiresponse permutation procedure and indicator species analysis showed a significant difference in species richness of reproductive structures and bark/stems. The bark of trees had greater mean species richness of myxomycetes than the reproductive structures, but the reproductive structures of herbaceous plants had greater mean species richness of myxomycetes than the stems. A new term, herbicolous myxomycetes, is proposed for a group of myxomycetes frequently associated with herbaceous, perennial, grassland plants. An undescribed species of Arcyria occurred only on cones of P. echinata.

First records and microhabitat assessment of protostelids in the Aberdare Region, Central Kenya.

A rapid assessment survey on the occurrence and distribution of protosteloid amoebae was carried out in central Kenya. Samples of dead plant materials were collected from 46 study sites (each 20 x 20 m) situated along an elevation gradient (1,785-3,396 m) that encompassed five major land use/cover types. Twenty-four species and subspecific taxa were recovered and included 23 protostelids and one minute myxomycete, often included in surveys for protostelids. All of these were the first records for Kenya, and six were new for Africa. Numbers of taxa were highest in ground litter and aerial litter microhabitats (20 taxa each) and lowest on aerial bark (10) and ground bark (7). Relative species abundance was greatest in aerial litter, moderate in ground litter, and low on aerial and ground bark microhabitats. The most frequently occurring species on ground litter were Schizoplasmodiopsis pseudoendospora, Schizoplasmodiopsis amoeboidea, and Protostelium mycophaga var. mycophaga, whereas the most common species on aerial litter were P. mycophaga var. mycophaga and Soliformovum irregularis. Species richness and abundance decreased with increasing elevation.

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.