Fungi are an important and diverse component of soil communities, but these communities have proven difficult to study in conventional biotic surveys. We evaluated soil fungal diversity at two sites in a temperate forest using direct isolation of small-subunit and internal transcribed spacer (ITS) rRNA genes by PCR and high-throughput sequencing of cloned fragments. We identified 412 sequence types from 863 fungal ITS sequences, as well as 112 ITS sequences from other eukaryotic microorganisms. Equal proportions of Basidiomycota and Ascomycota sequences were present in both the ITS and small-subunit libraries, while members of other fungal phyla were recovered at much lower frequencies. Many sequences closely matched sequences from mycorrhizal, plant-pathogenic, and saprophytic fungi. Compositional differences were observed among samples from different soil depths, with mycorrhizal species predominating deeper in the soil profile and saprophytic species predominating in the litter layer. Richness was consistently lowest in the deepest soil horizon samples. Comparable levels of fungal richness have been observed following traditional specimen-based collecting and culturing surveys, but only after much more extensive sampling. The high rate at which new sequence types were recovered even after sampling 863 fungal ITS sequences and the dominance of fungi in our libraries relative to other eukaryotes suggest that the abundance and diversity of fungi in forest soils may be much higher than previously hypothesized.

Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples

Rhizoctonia solani Kuhn and other Rhizoctonia spp. are widespread in the world and in both cultivated and noncultivated soils. Rhizoctonia spp. are readily isolated from diseased plants and soils, with isolates differing in pathogenicity and morphology, as well as cultural and physiological charac­ teristics. Based on these differences, many species and intraspecific groups (ISGs) have been described; however, identification of species and ISGs is sometimes very difficult, owing to the absence of the authentic cultures, which hinders mycological and pathological studies. Fortunately, this situa­ tion has been put in order through the efforts of many researchers through characterization of the genus Rhizoctonia, the species R. solani, and other Rhizoctonia spp. The introduction of the concept of anastomosis groups (AGs) or intraspecific groups, as this paper introduces, has also aided species and subspecies identification. Ecologically, Rhizoctonia spp. are diversified; they may be pathogens on many hosts, saprophytes in soils, or mycorrhizae of orchidiaceous plants. This paper outlines the present status of our knowledge of ecology and pathology of Rhizoctonia solani, especially of anastomosis groups or in­ traspecific groups.

Ecology and pathogenicity of anastomosis and intraspecific groups of

Phylogenetic and population genetic methods that compare nucleic acid variation are being used to identify species and populations of pathogenic fungi and determine how they reproduce in nature. These studies show that asexual or sexual reproductive morphology does not necessarily correlate with clonal or recombining reproductive behavior, and that fungi with all types of reproductive morphologies and behaviors can be accommodated by a phylogenetic species concept. Although approximately one fifth of described fungi have been thought to be asexual and clonal, recent studies have shown that they are also recombining. Whether a particular pathogen reproduces clonally or by recombination depends on factors relating to its biology and its distribution in space and time. Knowing the identity of species and populations and their reproductive modes, while taking a broad view of pathogen behavior in space and time, should enhance the ability of pathologists to control pathogens and even predict their behavior.

THE EVOLUTION OF ASEXUAL FUNGI: Reproduction, Speciation and Classification

Flavonoids and their glycosides, including anthocyanins

▪ Abstract The spermosphere represents a short-lived, rapidly changing, and microbiologically dynamic zone of soil surrounding a germinating seed. It is analogous to the rhizosphere, being established largely by the carbon compounds released into the soil once the seed begins to hydrate. These seed exudations drive the microbial activities that take place in the spermosphere, many of which can have long-lasting impacts on plant growth and development as well as on plant health. In this review, I discuss the nature of the spermosphere habitat and the factors that give rise to its character, with emphasis on the types of microbial activities in the spermosphere that have important implications for disease development and biological disease control. This review, which represents the first comprehensive synthesis of the literature on spermosphere biology, is meant to illustrate the unique nature of the spermosphere and how studies of interactions in this habitat may serve as useful experimental models for tes...

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Microbial dynamics and interactions in the spermosphere.

Sequence analysis of the rDNA region containing the internal transcribed spacer (ITS) regions and the 5.8s rDNA coding sequence was used to evaluate the genetic diversity of 45 isolates within and between anastomosis groups (AGs) in Rhizoctonia solani. The 5.8s rDNA sequence was completely conserved across all the AGs examined, whereas the ITS rDNA sequence was found to be highly variable among isolates. The sequence homology in the ITS regions was above 96% for isolates of the same subgroup, 66-100% for isolates of different subgroups within an AG, and 55-96% for isolates of different AGs. In neighbor-joining trees based on distances derived from ITS-5.8s rDNA sequences, subgroups IA, IB and IC within AG-1 and subgroups HG-I and HG-II within AG-4 were placed on statistically significant branches as assessed by bootstrap analysis. These results suggest that sequence analysis of ITS rDNA regions of R. solani may be a valuable tool for identifying AG subgroups of biological significance.

Sequence variation of the rDNA ITS regions within and between anastomosis groups in Rhizoctonia solani

Genetic diversity among 51 isolates of Rhizoctonia solani AG-3, representing potato and tobacco populations, was inferred from the sequences of the internal transcribed spacer (ITS) and 5.8S ribosomal RNA (rRNA) gene. The 5.8S rDNA sequence was completely conserved not only in AG-3, but across all the AG isolates examined, whereas the rDNA-ITS sequence was found to be variable among the isolates. The nucleotide sequence similarity in the ITS 1 region was high (96-100%) for isolates within each of the two populations, but was 91-92% for isolates from different populations. The AG-3 isolates had 56 to 91% sequence similarities in the ITS 1 region with R. solani isolates of the other AGs. Phylogenetic analysis based on the ITS-5.8S rDNA sequence data indicated that the different populations in AG-3 are distantly related to each other. Genetic divergence between the two populations was also supported by the results of DNA-DNA hybridization studies. This study suggests that AG-3 consists of two genetically isolated groups corresponding to separate subgroups: AG-3 PT (potato type) and AG-3 TB (tobacco type). Specific primer sets for the detection of the two AG-3 subgroups were developed from the aligned rDNA-ITS sequences.

Comparison of rDNA-ITS Sequences between Potato and Tobacco Strains in Rhizoctonia solani AG-3

DNA base sequence homology among AG-6 isolates of Rhizoctonia solani was determined by DNA-DNA reassociation kinetics. Five of 10 isolates examined shared high DNA homology ranging from 91.8 to 97.7%. This group was classified as AG-6 homogeneous group I (HG-I). DNA homology among the remaining 5 isolates was 55.4 to 66.2%. They showed only 47.5 to 62.9% DNA homology with AG-6 HG-I isolates. These isolates were designated AG-6 genotypic variation (GV) isolates. Each of them appeared to have gene structures that differed by nucleotide substitutions. The genetic divergence among AG-6 isolates was also clearly demonstrated by the electrophoretic patterns of proteins and appearances of the cultures. These results suggest that AG-6 consists of strains that are phylogenetically related but have significant genetic polymorphism.

DNA Base Sequence Homology in Rhizoctonia solani Kühn

DNA base sequence homology among AG-2 group isolates of Rhizoctonia solani was investigated on the basis of DNA-DNA reassociation kinetics, and the genetic relationship among pathological types was examined. DNA homology value among isolates within each single type was 100.3% with the winter crops type (II), 98.1% with the rush type (IIIB) and 100.1% with the root rot type (IV). Comparatively high values of DNA homology ranging from 68.6 to 71.5% were observed between rush type isolates and root rot type isolates, both belonging to AG-2-2. DNA homology values of winter crops type isolates of AG-2-1 with rush type isolates of AG-2-2 was 37.6 to 40.1%, and 43.5 to 49.4% with root rot type isolates of AG-2-2. These results suggested that each pathological type in AG-2 is genetically homogenous, and that between the rush type and the root rot type of AG-2-2 there is a small but significant partial heterogeneity. AG-2-1 and AG-2-2 may form genetically distinct groups.

https://www.jstage.jst.go.jp/article/jjphytopath1918/48/5/48_5_659/_pdf

DNA base sequence homology in Rhizoctonia solani Kuehn II. Genetic relatedness within anastomosis group 2.

Nineteen isoflavones were synthesized and their attracting activity to Aphanomyces euteiches zoospore were investigated. Isoflavones (1, 2, 4, 16 and 19) with an unsubstituted B ring were synthesized by the oxidation of corresponding 2'-hydroxychalcones with thallium (III) nitrate trihydrate in methanolic perchloric acid. A hydroxyl group at the C-5 position in isoflavones was necessary for strong attraction to A. euteiches zoospore. The introduction of an additional hydroxyl group at the C-7 or C-4' position strengthened the attracting activity. Moreover, the methylation of the C-7 hydroxyl group strengthened the attracting activity, but the methylation of the C-4' hydroxyl group slightly weakened it. The naturally occurring isoflavones (9 and 10), which were reported to possess estrogen activity, showed moderate attracting activity.

Ryozo Yokosawa

Papers

Sequence variation of the rDNA ITS regions within and between anastomosis groups in Rhizoctonia solani

Comparison of rDNA-ITS Sequences between Potato and Tobacco Strains in Rhizoctonia solani AG-3

DNA Base Sequence Homology in Rhizoctonia solani Kühn

DNA base sequence homology in Rhizoctonia solani Kuehn II. Genetic relatedness within anastomosis group 2.

Studies on Zoospore Attracting Activity. II. Synthesis of Isoflavones and Their Attracting Activity to Aphanomyces euteiches Zoospore