A Bryophyte Flora of Berkshire and Oxfordshire

Abstract

In temperate North American forests, collections were made of myxomycetes (plasmodial slime molds) for which bryophytes served as the primary substrate for fruiting. Most associations among the 52 myxomycete species and 55 bryophyte species, represented in these collections, appeared to be coincidental but two species of myxomycetes (Barbeyella minutissima and Lepidoderma tigrinum) were evidently bryophilous, preferring leafy hepatics on rotten coniferous logs. Bryophytes obviously provide exposed surfaces convenient for myxomycete sporulation. Whether bryophytes also sustain the feeding phases of the myxomycete life-cycle (swarm cells, myxamoebae, and plasmodia) is not yet known.     

In the shadow of Darwin: Anton de Bary’s origin of myxomycetology and a molecular phylogeny of the plasmodial slime molds

In his Origin of Species (John Murray, London, 1859), Charles Darwin described the theory of descent with modification by means of natural selection and postulated that all life may have evolved from one or a few simple kinds of organisms. However, Darwin’s concept of evolutionary change is entirely based on observations of populations of animals and plants. He briefly mentioned ‘lower algae’, but ignored amoebae, bacteria and other micro-organisms. In 1859, Anton de Bary, the founder of mycology and plant pathology, published a seminal paper on the biology and taxonomy of the plasmodial slime molds (myxomycetes). These heterotrophic protists are known primarily as a large composite mass, the plasmodium, in which single nuclei are suspended in a common ‘naked’ cytoplasm that is surrounded by a plasma membrane. Here we summarize the contents of de Bary’s 1859 publication and highlight the significance of this scientific classic with respect to the establishment of the kingdom Protoctista (protists such as amoebae), the development of the protoplasmic theory of the cell, the introduction of the concept of symbiosis and the rejection of the dogma of spontaneous generation. We describe the life cycle of the myxomycetes, present new observations on the myxamoebae and propose a higher-order phylogeny based on elongation factor-1 alpha gene sequences. Our results document the congruence between the morphology-based taxonomy of the myxomycetes and molecular data. In addition, we show that free-living amoebae, common protists in the soil, are among the closest living relatives of the myxomycetes and conclude that de Bary’s ‘Amoeba-hypothesis’ on the evolutionary origin of the plasmodial slime molds may have been correct.     

Chromosome numbers in representative myxomycetes: a cytogenetic study

Myxomycetes are also called plasmodial slime molds, due to one of their characteristic features, the occurrence of the plasmodium. However, most of the distinguishing characters of the five orders currently recognised are based on the morphology of fruiting bodies and spores. Although a few myxomycetes have become widely used model organisms for genetic and cytological studies, complete information relating to the number of chromosomes in haploid cells (n) is lacking thus far. Only two species of the order Physarales have been examined with respect to chromosome numbers. Here, we present a complete data set on the numbers of chromosomes in ten species of myxomycetes that are members of all five orders. Our analysis indicates that n?=?21 is the evolutionary ancient chromosome number that occurs in the morphologically simple orders Liceales and Ceratiomyxales. More derived taxa, such as the Physarales, have significantly higher chromosome numbers (n?=?30). These data shed light on the phylogenetic relationships within the myxomycetes.     

Myxomycete distribution varies among leaf litters of different vegetation in a local secondary forest of warm-temperate western Japan

Although many myxomycetes inhabit leaf litter on the forest floor and have feeding stages in litter layers, there has been little understanding regarding how the different types of leaf litter in a forest influence myxomycetes to distribute. In this study, I focused on the microhabitat distribution of foliicolous myxomycetes within a local secondary forest that consisted of various vegetation types in warm-temperate western Japan. Newly defoliated leaf litters were collected from the ground surfaces of seven different sites and then incubated in trays at a forested site throughout the entire fruiting seasons (in situ incubation method). Forty-eight species of myxomycetes (with varieties treated as species) were found in a total of 4042 samples. Leaf litters derived from different vegetation sites yielded diverse myxomycete assemblages, i.e. the Quercus glauca site yielded the richest myxomycete community (26 species), followed by Quercus variabilis site (24), Prunus verecunda site (22), Cinnamomum camphora site (21), Castanopsis cuspidata site (18), Pinus densiflora site (7) and bamboo site (7). Several myxomycete species were found to be preferentially distributed in deciduous broadleaf or evergreen leaf litter. The fraction of vegetative cover of deciduous and evergreen trees influenced the species richness and diversity of myxomycetes. Leaf litter heterogeneity derived from forest vegetation and defoliation season influenced the myxomycete distribution and species diversity. Research using in situ incubation method demonstrated that heterogeneous myxomycete microhabitats are distributed at a small spatial scale in a local forest.     

Pattern of Substrate Preferences of Free Living Protists (Myxomycetes) on Decaying Wood

We have studied the influence of the stage of decomposition and acidity of wood, as well as the illumination of the microhabitat on the species composition, abundance, and occurrence of slime molds (Myxomycetes) of the xylobiontic (inhabitants of the wood) substrate complex of forest communities in Siberia (Altai krai, Altai Republic, and Novosibirsk oblast). This work is based on a study of 1777 samples of fruit bodies (sporophores) of myxomycetes. In the analysis of data for communities of Myxomycetes of the xylobiontic substrate complex, we recognize a successional series which clearly correlates with the stage of wood decomposition. The study of the distribution of the species composition of the slime mold on wood of various stages of decomposition shows that the maximum number of species is observed on dead trunks where the wood is of medium density and the bark can easily be separated (W3). The lowest specificity and diversity of species composition is observed on the fallen trunks of trees with very dense wood and dense bark (W1). These dead trees have low water-retaining capacity, tight bark, and almost intact wood containing large amounts of lignin, preventing the invasion of plasmodia and myxamoebae of Myxomycetes into the trunk. A study of the location of slime-mold colonies in relation to the illumination level shows that the greatest number of species is found on the front, side, and bottom parts of dead trunks of woody plants. The least specificity and the least variety of Myxomycetes species are found on apical parts of dead tree trunks facing the sun. The exception are species with large fruit bodies such as Fuligo septica and Reticularia splendens, which are most often observed on the upper parts of the sun facing trunks of woody plants. In the research area, the complex of species typical for wood of coniferous trees is described. It is noted that acidophilic slime molds of the genera Comatricha and Cribraria can be traced in xylobiontic and epiphytic–corticuloid substrate complexes.     

Paramoeba aparasomata n. sp., a symbiont-free species,and its relative Paramoeba karteshi n. sp. (Amoebozoa,Dactylopodida)

Two brackish water amoebae have been isolated and studied from the benthic biotopes of the Chupa Inlet (Kandalaksha Bay, northwestern Russia). Both strains can be identified as new species of the genus Paramoeba (Amoebozoa, Dactylopodida, Paramoebidae) based on light microscopical characters, structure of microscales on the cell surface and molecular evidence based on the analyses of two genes, nuclear SSU rRNA and mitochondrial cytochrome c oxidase subunit 1 (COI). Paramoeba aparasomata n. sp. is of particular interest because this amoeba is permanently lacking a symbiotic Perkinsela-like organism (PLO) present in other species of Paramoeba and Neoparamoeba. The results obtained show that scaly dactylopodial amoebae lacking PLO are not necessarily members of Korotnevella. In particular, we suggest that Korotnevella nivo Smirnov, 1997, with microscales very similar to those of Paramoeba eilhardi and the species studied here in structure, may be in fact a member of Paramoeba. Molecular data on K. nivo have to be obtained and analysed to test this hypothesis. Based on our new results we emend the diagnosis of the genus Paramoeba to make it more fit to the current phylogenetic conception.     

Vannella primoblina n. sp. – an unusual species of the genus Vannella (Amoebozoa,Discosea, Vannellida) with pronounced dorsal ridges and folds

Amoebae of the order Vannellida (Amoebozoa, Discosea) have a fairly recognizable spatulate, fan-shaped or semi-circular outlines and a wide area of frontal hyaloplasm. They can be easily distinguished from the other groups of lobose amoebae even by light microscopy. The dorsal side of these amoebae is usually smooth and rarely bears ridges or folds, which are never numerous or regular. We have isolated an unusual species of vannellid amoebae, called Vannella primoblina n. sp. from a terrestrial substrate. It has well-developed dorsal relief consisting of regularly appearing folds and ridges. This amoeba superficially resembles members of the genus Thecamoeba. However, molecular analysis showed that this strain belongs to the genus Vannella. This finding indicates that dorsal folds may also be a characteristic of some species of vannellid amoebae and probably are a functional detail of the cell morphology rather than an apomorphy of Thecamoebida lineage. Overall outlines of the cell and the presence of the expanded frontal hyaline area remains the most reliable characters used to differentiate vannellid amoebae from other gymnamoebae lineages.     

Phylogeny of Physarida (Amoebozoa,Myxogastria) Based on the Small‐Subunit Ribosomal RNA Gene,Redefinition of Physarum pusillum s. str. and Reinstatement of P. gravidum Morgan

Myxomycetes (also called Myxogastria or colloquially, slime molds) are worldwide occurring soil amoeboflagellates. Among Amoebozoa, they have the notable characteristic to form, during their life cycle, macroscopic fruiting bodies, that will ultimately release spores. Some 1,000 species have been described, based on the macroscopic and microscopic characteristics of their fruiting bodies. We were interested in Physarum pusillum (Berk. & M.A. Curtis) G. Lister, a very common species described with two variants, each bearing such morphological differences that they could represent two distinct species. In order to test this, we observed key characters in a large selection of specimens attributed to P.  pusillum, to its synonyms (in particular Physarum gravidum), and to related species. In addition, the small‐subunit ribosomal RNA gene was obtained from seven of these specimens. Based on these data, we provide a comprehensive phylogeny of the order Physarida (Eukaryota: Amoebozoa: Conosa: Macromycetozoa: Fuscisporidia). Morphology and phylogeny together support the reinstatement of P. gravidum Morgan 1896 with a neotype here designated, distinct from P. pusillum, here redefined.     

Control of N-acetylglucosaminidase specific activity in myxamoebae of Dictyostelium discoideum

Myxamoebae of Dictyostelium discoideum were grown with Aerobacter aerogenes as substrate, on nutrient agar plates or in shaken culture, with mean doubling times that varied between 3 and 6 hr. Growth in axenic culture was with mean doubling times of 5–6 or 8 hr. The specific activity of N-acetylglucosaminidase was three to four times higher in myxamoebae grown axenically than in myxamoebae grown with A. aerogenes and there was no correlation between enzyme specific activity and myxamoebal growth rate. High specific activities of N-acetylglucosaminidase were also found in myxamoebae grown with gram-positive bacteria (Bacillus megaterium, Staphylococcus lactis) as substrate while low specific activities were found in myxamoebae grown with the gram-negative bacteria Acinetobacter lwoffi and Pseudomonas aeruginosa as well as with A. aerogenes. A preparation of the cell envelope of A. aerogenes was nearly as effective as the intact bacteria at depressing myxamoebal N-acetylglucosaminidase specific activity. Lipopolysaccharide extracted from the cell envelope of gram-negative bacteria, or the lipid A component of the lipopolysaccharide, also depressed N-acetylglucosaminidase specific activity when added to axenic cultures of myxamoebae.     

Geographical distribution of myxomycetes living on Cryptomeria japonica bark in Japan

There is little available data on the biogeography of myxomycetes at the regional scale within any given climate zone. To investigate the geographical distribution of these protozoans, we focused on corticolous myxomycetes associated with the bark of Cryptomeria japonica trees, which we sampled extensively throughout Japan. Myxomycete sporophores developed in 73% of 2244 moist-chamber cultures of 188 bark samples from 24 regions, including 31 species. The most abundant species were Paradiacheopsis rigida and Cribraria confusa, which accounted for over 20% of all myxomycetes sampled. Non-metric multidimensional scaling was used to analyze the distribution of myxomycetes in relation to geographical variables and bark pH. The distribution of myxomycetes was influenced by altitude, temperature and bark pH. Temperature gradients and relative abundance of species were negatively correlated in P. rigida and Comatricha laxa and positively correlated in C. confusa, Macbrideora cornea, and Diderma chondrioderma. Bark pH was also positively correlated with the relative abundance of C. confusa, D. chondrioderma, and Physarum nutans and negatively correlated with that of P. rigida, P. cribrata, Enerthnema papillatum, and E. melanospermum. Geographical distribution of corticolous myxomycete communities was determined based on temperature and bark pH, which acted as local barriers in our study area.     

Genetic Analysis of Resistance to Benzimidazoles in Physarum: Differential Expression of β-Tubulin Genes

Physarum displays two vegetative cell types, uninucleate myxamoebae and multinucleate plasmodia. Mutant myxamoebae of Physarum resistant to the antitubulin drug methylbenzimidazole-2-yl-carbamate (MBC) were isolated. All mutants tested were cross-resistant to other benzimidazoles but not to cycloheximide or emetine. Genetic analysis showed that mutation to MBC resistance can occur at any one of four unlinked loci, benA, benB, benC or benD. MBC resistance of benB and benD mutants was expressed in plasmodia, but benA and benC mutant plasmodia were MBC sensitive, suggesting that benA and benC encode myxamoeba-specific products. Myxamoebae carrying the recessive benD210 mutation express a β-tubulin with noval electrophoretic mobility, in addition to a β-tubulin with wild-type mobility. This and other evidence indicates that benD is a structural gene for β-tubulin, and that at least two β-tubulin genes are expressed in myxamoebae. Comparisons of the β-tubulins of wildtype and benD210 strains by gel electrophoresis revealed that, of the three (or more) β-tubulin genes expressed in Physarum, one, benD, is expressed in both myxamoebae and plasmodia, one is expressed specifically in myxamoebae and one is expressed specifically in plasmodia. However, mutation in only one gene, benD, is sufficient to confer MBC resistance on both myxamoebae and plasmodia.     

Phylogenetic position of the enigmatic myxomycete genus Kelleromyxa revealed by SSU rDNA sequences

The coprophilous myxomycete Kelleromyxa fimicola (Dearn. & Bisby) Eliasson was first described in 1929 as Licea fimicola Dearn. & Bisby. Based on the superficial resemblance of its sporocarps to those of Licea biforis, the species was placed within the Liceales, an order assigned by molecular phylogenies to the bright-spored clade of myxomycetes. However, detailed studies of the morphology and life cycle of K. fimicola revealed several characters of the dark-spored order Physarales. To elucidate the systematic position of Kelleromyxa, we obtained three partial and one complete sequence of the SSU rDNA, which demonstrated a clear relationship of K. fimicola to the order Physarales. However, the obtained sequences are not closely related to any of the two known families of Physarales, supporting the erection of a monotypic family for this species. Along with morphological observations, our data support the exclusion of K. fimicola from the order Liceales and placement among the order Physarales within the dark-spored clade of myxomycetes.     

Polychaos centronucleolus n. sp. – a new terrestrial species of the genus Polychaos (Amoebozoa,Tubulinea) with nontypical nuclear structure

A new species of the “proteus-type” naked amoebae (large cells with discrete tubular pseudopodia) was isolated from tree bark sample of a birch tree in the surrounding of Kislovodsk town, Russia and named Polychaos centronucleolus n. sp. (Amoebozoa, Tubulinea). Amoebae of this species have a filamentous cell coat and a nucleus with a central compact nucleolus. This type of nucleolar organization has not been previously known for the genus Polychaos. A sequence of the 18S rRNA gene of this strain was obtained using whole genome amplification of DNA from the single amoeba cell, followed by NGS sequencing. The analysis of molecular data robustly groups this species with Polychaos annulatum within the family Hartmannellidae. Our results, together with the results of our previous studies, show that the taxonomic assignment of “proteus-type” amoebae species is becoming increasingly complex, and the taxonomic characters that can be used to classify these organisms are becoming more shadowed.     

黏菌个体发育特征及其与系统发育关联的研究进展

黏菌作为真核生物“树冠”中的原始类群,是研究真核生物演化模式的重要分支。本文通过对黏菌在生活史不同阶段的生物学特征、行为与相关发育机制综述,展现了黏菌多样的细胞发生模式。通过对黏菌与变形虫门其他类群的系统发育关系进行阐述,比较了各类群间的同源特征,进一步说明了黏菌的个体发育特征与系统发育关联,为黏菌类群的演化研究提供理论支持。     

Four years in the Caucasus – observations on the ecology of nivicolous myxomycetes

Abundance and habitat requirements of nivicolous myxomycetes were surveyed over 4 yr at the northwestern Greater Caucasus ridge (Russia). An elevational transect spanning 3.66 km from 1 700 to 3 000 m a.s.l. was established at the summit Malaya Khatipara situated within the Teberda State Biosphere reserve. Between 2010 and 2013 1177 fructifications of nivicolous myxomycetes were recorded, with 700 of these determined to 44 species, varieties, and forms. Virtually all fructifications developed near or at the margin of a snow field. Abundance of myxomycete fructifications varied extremely between years, ranging from near zero to hundreds of colonies. At sites with known myxomycete occurrences 16 data loggers were installed in the years 2011 and 2012, measuring relative humidity and temperature at the soil surface. Together with weather data recorded on the nearby Klukhor pass and experiments with myxamoebae cultured on agar, these data explain the observed extreme fluctuations in myxomycete abundance. A sudden frost (one night below −10 °C) occurring before the first lasting snow in Nov. 2011 was most likely the reason for the nearly complete absence of myxomycete fruiting in spring 2012. Culture experiments showed that amoebae survived a slow decrease in temperature, as occurs under a sheltering snow cover, but are killed by sudden freezing. Extreme temperature changes recorded at the margin of snow fields explain why nivicolous myxomycetes must fruit before snow melt is complete, and the different transmittance of snow packs for light of different wave lengths may be crucial for triggering the formation of fruiting bodies. The high abundance of fructifications in nivicolous myxomycetes suggests them to be important predators of microbial communities under snow.     

CYTOPHOTOMETRIC MEASUREMENT OF NUCLEAR DNA IN SEVEN HETEROTHALLIC ISOLATES OF DIDYMIUM IRIDIS,A MYXOMYCETE

Absorption cytophotometry was used to measure nuclear Feulgen-DNA content of myxamoebae and Plasmodia in seven heterothallic isolates of Didymium iridis. Measurements of myxamoebal nuclei from clones of four isolates (Hon 1, Pan 1, Pan 2, and CR 5) gave a mean DNA value of 0.34, whereas the nuclei of Plasmodia which develop from each of the four intraisolate crosses had a mean value of 0.63. These values correspond to the 2C haploid level in myxamoebae and the 4C diploid level in Plasmodia. DNA values in two additional isolates (Pan 3 and CR 2) are much higher than the mean for the other five. Accordingly, it is proposed that these may be polyploid. The question of polyploidy in D. iridis and in other myxomycetes is evaluated. The seventh isolate, Ky 1, is taxonomically very close to D. nigripes and was not included in calculations of mean values for D. iridis.     

几种黏菌黏变形体形态及运动特征

黏菌黏变形体结构对变形运动方式具有影响,在显微镜下观察了长期培养中的5种黏菌的黏变形体的形态及运动特征。结果表明:不同种类的黏菌黏变形体形态差别较大,主要是透明外质的有无、形态规则或不规则。运动特征上有滑动型、流动型和爬行运动方式,运动方式和透明外质结构有关,透明外质较厚很难形成典型的伪足,表现为滑动运动方式,移动速度较慢。     

Myxomycete diversity and distribution from the fossil record to the present

The myxomycetes (plasmodial slime molds or myxogastrids) are a group of eukaryotic microorganisms usually present and sometimes abundant in terrestrial ecosystems. Evidence from molecular studies suggests that the myxomycetes have a significant evolutionary history. However, due to the fragile nature of the fruiting body, fossil records of the group are exceedingly rare. Although most myxomycetes are thought to have very large distributional ranges and many species appear to be cosmopolitan or nearly so, results from recent studies have provided evidence that spatial distribution patterns of these organisms can be successfully related to (1) differences in climate and/or vegetation on a global scale and (2) the ecological differences that exist for particular habitats on a local scale. A detailed examination of the global distribution of four examples (Barbeyella minutissima, Ceratiomyxa morchella, Leocarpus fragilis and Protophysarum phloiogenum) demonstrates that these species have recognizable distribution patterns in spite of the theoretical ability of their spores to bridge continents. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.