Unraveling the distribution pattern and driving forces of soil microorganisms under geographic barriers.

The Altai Mountains (ALE) and the Greater Khingan Mountains (GKM) in northern China are forest regions dominated by coniferous trees. These geographically isolated regions provide an ideal setting for studying microbial biogeographic patterns. In this study, we employed high-throughput techniques to obtain DNA sequences of soil myxomycetes, bacteria, and fungi and explored the mechanisms underlying the assembly of both local and cross-regional microbial communities in relation to environmental factors. Our investigation revealed that the environmental heterogeneity in ALE and GKM significantly affected the succession and assembly of soil bacterial communities at cross-regional scales. Specifically, the optimal environmental factors affecting bacterial Bray-Curtis similarity were elevation and temperature seasonality. The spatial factors and climate change impact on bacterial communities under the geographical barriers surpassed that of local soil microenvironments. The assembly pattern of bacterial communities transitions from local drift to cross-regional heterogeneous selection. Environmental factors had a relatively weak influence on myxomycetes and fungi. Both soil myxomycetes and fungi faced considerable dispersal limitation at local and cross-regional scales, ultimately leading to weak geographical distribution patterns.IMPORTANCEThe impact of environmental selection and dispersal on the soil microbial spatial distribution is a key concern in microbial biogeography, particularly in large-scale geographical patterns. However, our current understanding remains limited. Our study found that soil bacteria displayed a distinct cross-regional geographical distribution pattern, primarily influenced by environmental selection. Conversely, the cross-regional geographical distribution patterns of soil myxomycetes and fungi were relatively weak. Their composition exhibited a weak association with the environment at local and cross-regional scales, with assembly primarily driven by dispersal limitation.

Morphological and phylogenetic analyses reveal four species of myxomycetes new to China.

Four species of myxomycetes (Arcyria pseudodenudata, Diderma europaeum, Lycogala irregulare, and Trichia armillata) new to China were observed via light microscope and scanning electron microscope, and detailed descriptions and illustrations are provided, along with comparisons with related species. Among them, A. pseudodenudata was discovered for the first time outside of the type locality, D. europaeum was discovered for the first time outside of Europe, and L. irregulare and T. armillata were reported again after being named. Phylogenetic analyses based on nuclear 18S rDNA and elongation factor-1 alpha sequences or nuclear 18S rDNA and cytochrome oxidase subunit I sequences was performed to provide a molecular basis for morphological identification. These specimens were deposited in the Herbarium of Fungi of Nanjing Normal University.

A Non-Flagellated Member of the Myxogastria and Expansion of the Echinosteliida.

Myxogastria (also called Myxomycetes or plasmodial slime-moulds) are mostly known through their usually conspicuous fruiting bodies. Another unifying trait is the presence of a facultative flagellate stage along with the obligate amoeboid stage. Here we show with two-gene phylogenies (SSU rRNA and EF-1alpha genes) that the incertae sedis, non-flagellate Echinosteliopsis oligospora belongs to the dark-spore clade (Fuscisporidia) of the Myxogastria. In addition, we confirm that Echinostelium bisporum, firstly described as a protostelid, belongs to the Echinosteliida, which are divided into three major clades and are paraphyletic to the remaining Fuscisporidia.

The Life Cycle of Didymium laxifilum and Physarum album on Oat Agar Culture.

The plasmodial slime molds is the largest group in the phylum Amoebozoa. Its life cycle includes the plasmodial trophic stage and the spore-bearing fruiting bodies. However, only a few species have their complete life cycle known in details so far. This study is the first reporting the morphogenesis of Didymium laxifilum and Physarum album. Spores, from field-collected sporangia, were incubated into hanging drop cultures for viewing germination and axenic oat agar plates for viewing plasmodial development and sporulation. The spores of D. laxifilum and P. album germinated by method of V-shape split and minute pore, respectively. The amoeboflagellates, released from spores, were observed in water film. The phaneroplasmodia of two species developed into a number of sporangia by subhypothallic type on oat agar culture. The main interspecific difference of morphogenesis was also discussed.

Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa).

Myxomycetes or plasmodial slime molds are widespread and very common soil amoebae with the ability to form macroscopic fruiting bodies. Even if their phylogenetic position as a monophyletic group in Amoebozoa is well established, their internal relationships are still not entirely resolved. At the base of the most intensively studied dark-spored clade lies the order Echinosteliales, whose highly divergent small subunit ribosomal (18S) RNA genes represent a challenge for phylogenetic reconstructions. This is because they are characterized by unusually long variable helices of unknown secondary structure and a high inter- and infraspecific divergence. Current classification recognizes two families: the monogeneric Echinosteliaceae and the Clastodermataceae with the genera Barbeyella and Clastoderma. To better resolve the phylogeny of the Echinosteliales, we obtained three new small subunit ribosomal (18S) RNA gene sequences of Clastoderma and Echinostelium corynophorum. Our phylogenetic analyses suggested the polyphyly of the family Clastodermataceae, as Barbeyella was more closely related to Echinostelium arboreum than to Clastoderma, while Clastoderma debaryanum was the earliest branching clade in Echinosteliales. We also found that E. corynophorum was the closest relative of the enigmatic Semimorula liquescens, a stalkless-modified Echinosteliales. We discuss possible evolutionary pathways in dark-spored Myxomycetes and propose a taxonomic update.

Perichaena longipes, a new myxomycete from the Neotropics.

A new species of myxomycete, Perichaena longipes, is described from 56 sporocarp specimens that appeared in moist chamber cultures prepared with samples of decaying plant materials collected in Panama, Costa Rica and Brazil. This new species is distinguished from the morphologically similar species P. pedata on the basis of the much longer stipe, lighter peridium and the unique ornamentation of the capillitium. The nuc 18S ribosomal DNA sequences obtained from four specimens of P. longipes support the distinction of this new taxon and its separation from P. pedata. Furthermore, maximum likelihood phylogeny supports earlier evidence that species currently within the genus Perichaena do not form a monophyletic clade. Instead they appear to form three separate branches within the bright-spored clade. The first clade includes P. longipes together with several species of Trichia and Metatrichia, the second includes P. pedata and P. chrysosperma, and the third clade is composed of P. corticalis, P. depressa and P. luteola.

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.

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.

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.

Taxonomy and phylogeny of three species in Perichaena sensu lato (Myxomycetes = Myxogastria) from China.

After Gulielmina was erected and Ophiotheca was resurrected based on some species originally included in Perichaena (Trichiaceae, Trichiales, Myxomyxetes), some specimens from the Herbarium of Fungi of Nanjing Normal University previously identified as Perichaena species were reexamined from morphological and two-gene (nuclear 18S rDNA and elongation factor-1 alpha) phylogenetic perspectives. In this study, two new myxomycete species, Gulielmina subreticulospora and Ophiotheca dictyospora, are described. Gulielmina subreticulospora shows the following character combination: branched plasmodiocarps, single peridium with circular protrusions in the inner surface, capillitium (2.4-)2.8-3.0(-3.4) µm in diameter, spores (7.4-)8.0-8.5(-9.0) µm in diameter and sub-reticulated. Ophiotheca dictyospora shows the following character combination: sessile sporocarps to short plasmodiocarps, single peridium with a densely irregular network and protrusions in the inner surface, capillitium (2.7-)3.5-5.0(-7.1) µm in diameter, uneven, decorated with spines of uneven size, spores (7.7-)8.2-8.6(-9.4) µm in diameter including obviously complete cristate reticulation with serrated edges, with deep and clear grids. Both new taxa were compared with related species and their genetic isolation was statistically tested. Moreover, a comprehensive morphological description and a detailed figure plate are provided for Perichaena verrucifera, and its phylogenetic position is determined.

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).

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.

Fifteen new species from the myxomycete genus Lycogala.

Based on a study of 255 collections from four continents and four floristic kingdoms, we describe 15 new species of the genus Lycogala. The new species, all morphologically close to L. epidendrum, L. exiguum, and L. confusum, differ from each other by the structure of the peridium and, in some cases, also by the color of the fresh spore mass and the ornamentation of the capillitium and spores. Species delimitation is confirmed by two independently inherited molecular markers, as well as previously performed tests of reproductive isolation and genetic distances. We studied authentic material of L. exiguum and L. confusum and found fresh specimens of these species, which allowed us to obtain molecular barcodes and substantiate the separation of new species from these taxa. We propose to retain the name L. epidendrum for the globally most abundant species, for which we provide a more precise description and a neotypification. Two formerly described species, L. leiosporum and L. fuscoviolaceum, we consider to be dubious. We do not recognize the species L. terrestre.

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.

Comparison of wood-inhabiting myxomycetes in subalpine and montane coniferous forests in the Yatsugatake Mountains of Central Japan.

To demonstrate altitudinal gradients (and resulting temperatures) that affect myxomycete biodiversity and species composition, we statistically compared myxomycete assemblages between a subalpine coniferous forest and a montane pine forest within the region of the Yatsugatake Mountains, Nagano Prefecture, Central Japan. In summer and autumn field surveys during 2003-2010, 53 myxomycete taxa (with varieties treated as species) were observed from 639 records of fruiting bodies in the subalpine forest and 32 taxa were detected from 613 records in the montane forest. There were 20 species in common between the assemblages and the percentage similarity index was 0.400. Myxomycete biodiversity was higher in the subalpine than in the montane forest. Nine myxomycete species were statistically frequent occurrences in the subalpine forest and appeared in autumn: Lamproderma columbinum, Cribraria macrocarpa, Trichia botrytis, Physarum newtonii, Diderma ochraceum, Enteridium splendens, Elaeomyxa cerifera, Trichia verrucosa, and Colloderma oculatum. Five species were restricted to appear in the subalpine forest: Cribraria purpurea, Cribraria rufa, Cribraria ferruginea, Cribraria piriformis, and Lepidoderma tigrinum. Dead wood in the subalpine forest provided a breeding habitat for specific myxomycetes that inhabit cold areas; that is those areas having geographical features of decreasing temperature and increasing elevation, such as the temperate area of Central Japan.

Description and life cycle of a new Physarum (Myxomycetes) from the Atacama Desert in Chile.

A new species of Physarum (Myxomycetes), Physarum atacamense is described in this paper, and details are provided on its life cycle as observed in spore-to-spore culture in agar. The new species was collected 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 combination of characters that make this species unique in the genus are its large fusiform nodes of the capillitium, its long, bicolored stalk and the very dark brown and densely warted angular spores. The morphology of specimens of this myxomycete was examined with scanning electron microscopy and light microscopy, and micrographs of relevant details and life cycle stages are included in this paper. The importance of resistant stages in the life cycle of this myxomycete is stressed, and the close association of this myxomycete with its plant substrates is discussed.

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.